diff --git a/CHANGELOG b/CHANGELOG
index a3c6006bcad3bed452dbccf929402840e5e71658..cd0d0115d5a4e3194d4ab7b13624c823249e5508 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,5 +1,6 @@
minerva (15.0.0~alpha.0) stable; urgency=medium
* Improvement: logs provided for validation data model are structurized (#325)
+ * Improvement: import/export of GPML implemented
* Small improvement: compartments in not layouted SBML file are more
scattered (#326)
* Small improvement: when downloading a map results in too big file (>1MB)
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Pair.java b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
index 0b486d1627ef7c2492a67e48729dd46f3323c1f7..5f26aa5def5390822e6c69e125b85c268a5a5f19 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Pair.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
@@ -78,7 +78,9 @@ public class Pair<L, R> implements Serializable {
@Override
public String toString() {
- return "Pair: " + getLeft().toString() + ", " + getRight().toString();
+ String left = getLeft() == null ? "null" : getLeft().toString();
+ String right = getRight() == null ? "null" : getRight().toString();
+ return "Pair: " + left + ", " + right;
}
}
\ No newline at end of file
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/AbstractComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/AbstractComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..f3215e5a92793a567ae95c948669f0ca04228c60
--- /dev/null
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/AbstractComparator.java
@@ -0,0 +1,18 @@
+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+public abstract class AbstractComparator<T> implements Comparator<T> {
+ private Logger logger = LogManager.getLogger();
+
+ public int compare(T o1, T o2, String objectName) {
+ int result = compare(o1, o2);
+ if (result != 0) {
+ logger.debug(objectName + " different: " + o1 + "\t" + o2);
+ }
+ return result;
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java
index a788fe958a5fa3604df900607ee637544f4cfe4f..a077704aa2d78d0af79c181dec939a5476606598 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.common.comparator;
-import java.awt.*;
-import java.util.Comparator;
+import java.awt.Color;
/**
* Comparator implementation for {@link Color} class.
@@ -9,7 +8,7 @@ import java.util.Comparator;
* @author Piotr Gawron
*
*/
-public class ColorComparator implements Comparator<Color> {
+public class ColorComparator extends AbstractComparator<Color> {
@Override
public int compare(Color arg0, Color arg1) {
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java
index d5ee693a0f281550991fb32bfc336d9d08e3a0b9..434ca24d0bbd42c2535f7a54df7366c01d626b90 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java
@@ -1,7 +1,5 @@
package lcsb.mapviewer.common.comparator;
-import java.util.Comparator;
-
import lcsb.mapviewer.common.Configuration;
/**
@@ -10,7 +8,7 @@ import lcsb.mapviewer.common.Configuration;
* @author Piotr Gawron
*
*/
-public class DoubleComparator implements Comparator<Double> {
+public class DoubleComparator extends AbstractComparator<Double> {
/**
* Epsilon value used for comparison of doubles.
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java
index 793a591aa4dbd60979578b98ffcaa352e9ec1b3a..5a7408b7a1715d9e8d9161c039e5d947edfd43e6 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java
@@ -1,14 +1,12 @@
package lcsb.mapviewer.common.comparator;
-import java.util.Comparator;
-
/**
* Comparator implemented for {@link Integer} class.
*
* @author Piotr Gawron
*
*/
-public class IntegerComparator implements Comparator<Integer> {
+public class IntegerComparator extends AbstractComparator<Integer> {
@Override
public int compare(Integer arg0, Integer arg1) {
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java
index 737c4cde770fc01ee7b809ba0bf8dc7bfea7dcae..c2447f0d935071e6428d3327f530359ad70e3164 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java
@@ -1,7 +1,5 @@
package lcsb.mapviewer.common.comparator;
-import java.util.Comparator;
-
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -12,7 +10,7 @@ import org.apache.logging.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class StringComparator implements Comparator<String> {
+public class StringComparator extends AbstractComparator<String> {
/**
* Default class logger.
*/
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 6c63f5a7683f4c19af8f8fb9acfa4e26babc9de4..733ba83e10bec191fdc6cf03a7ec210759d02976 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -67,6 +67,13 @@
<scope>compile</scope>
</dependency>
+ <!-- https://mvnrepository.com/artifact/org.springframework/spring-context -->
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-context</artifactId>
+ <version>${springframework.version}</version>
+ </dependency>
+
</dependencies>
</project>
\ No newline at end of file
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index c6386575d66324c51057c8837de764cddd3d11d8..34aaa538dc4da97460c25497de82897e2efa8379 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -11,6 +11,7 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
import org.apache.xerces.parsers.DOMParser;
+import org.springframework.stereotype.Component;
import org.w3c.dom.*;
import lcsb.mapviewer.common.*;
@@ -55,6 +56,7 @@ import lcsb.mapviewer.model.map.species.Element;
* @author Piotr Gawron
*
*/
+@Component
public class CellDesignerXmlParser extends Converter {
/**
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
index 95ed20c1231cbc99cecb006e58f324b4cc3c8d0d..892dab8549a8c6bb5900b0b5ef8a12a2bf776702 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
@@ -9,12 +9,14 @@ import org.apache.commons.text.StringEscapeUtils;
import org.apache.logging.log4j.core.LogEvent;
import org.sbgn.SbgnUtil;
import org.sbgn.bindings.Sbgn;
+import org.springframework.stereotype.Component;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.model.map.model.Model;
+@Component
public class SbgnmlXmlConverter extends Converter {
@Override
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index 0c2f6c3abb411e3bbdafd857983bebeccbbac9b7..11f6e6a78549e26a4d1f0a76fc9af4f1acce8667 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -420,8 +420,8 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
public void drawText(final T species, final Graphics2D graphics, final ConverterParams params) {
String text = getText(species);
Font oldFont = graphics.getFont();
- Font font = getFont(species, params);
Color oldColor = graphics.getColor();
+ Font font = getFont(species, params);
graphics.setColor(species.getFontColor());
graphics.setFont(font);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 1e47dc8e3b0763adfa23f41bf262a4d664eece88..9e0bd55f28c1da9496b0669925471697d91c29ea 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -13,6 +13,7 @@ import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
+import org.springframework.stereotype.Component;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
@@ -33,6 +34,7 @@ import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+@Component
public class SbmlParser extends Converter {
/**
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java b/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java
index 4bbbf8235473913319a911a565a89bf879104935..318375fbe3372a1f2b60ef1f6fe4c449785fe750 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java
@@ -40,7 +40,6 @@ public class ZIndexPopulator {
int maxZIndex = 0;
List<Drawable> bioEntities = new ArrayList<>();
- bioEntities.addAll(model.getBioEntities());
for (Layer layer : model.getLayers()) {
bioEntities.addAll(layer.getOvals());
bioEntities.addAll(layer.getRectangles());
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
index 78926645503b9bef1fcd11abe3ff8df9ebbdc37d..94770529cf87fba15e69f6381d3b41deb0775a50 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
@@ -260,15 +260,17 @@ public class PolylineData implements Serializable, Drawable {
* @param distToTrim
* distance by which end of line should be trimmed
*/
- public void trimEnd(double distToTrim) {
+ public double trimEnd(double distToTrim) {
Point2D last = points.get(points.size() - 1);
Point2D last2 = points.get(points.size() - 2);
double oldDist = last.distance(last2);
if (distToTrim < 0 && oldDist <= Configuration.EPSILON) {
logger.debug("Cannot extend empty line");
last.setLocation(last2);
+ return 0;
} else if (oldDist <= distToTrim) {
last.setLocation(last2);
+ return oldDist;
} else {
double newDistr = oldDist - distToTrim;
double ratio = newDistr / oldDist;
@@ -277,6 +279,7 @@ public class PolylineData implements Serializable, Drawable {
dx *= ratio;
dy *= ratio;
last.setLocation(last2.getX() + dx, last2.getY() + dy);
+ return distToTrim;
}
}
@@ -286,12 +289,13 @@ public class PolylineData implements Serializable, Drawable {
* @param distToTrim
* distance by which beginning of line should be trimmed
*/
- public void trimBegin(double distToTrim) {
+ public double trimBegin(double distToTrim) {
Point2D last = points.get(0);
Point2D last2 = points.get(1);
double oldDist = last.distance(last2);
if (oldDist <= distToTrim) {
last.setLocation(last2);
+ return oldDist;
} else {
double newDistr = oldDist - distToTrim;
double ratio = newDistr / oldDist;
@@ -300,6 +304,7 @@ public class PolylineData implements Serializable, Drawable {
dx *= ratio;
dy *= ratio;
last.setLocation(last2.getX() + dx, last2.getY() + dy);
+ return distToTrim;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
index 887bef49548405663899777bbc663e9dde6113c7..74400f56281d0b9ae949fa0bc437285d6a8c0539 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
@@ -50,7 +50,7 @@ public class Compartment extends Element {
/**
* Default thickness of compartment border.
*/
- private static final int DEFAULT_COMPARTMENT_THICKNESS = 12;
+ public static final int DEFAULT_COMPARTMENT_THICKNESS = 12;
/**
* Default class logger.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
index fd61a1c447f789a5b32c1f8a4539ace01243fea2..53ed7c7276d403ca8b7ebe2935970d2761b86280 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
@@ -6,6 +6,7 @@ import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.*;
+import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.graphics.PolylineDataComparator;
/**
@@ -88,40 +89,32 @@ public class LayerComparator extends Comparator<Layer> {
return integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size());
}
- LayerTextComparator textComparator = new LayerTextComparator(epsilon);
- for (int i = 0; i < arg0.getTexts().size(); i++) {
- int status = textComparator.compare(arg0.getTexts().get(i), arg1.getTexts().get(i));
- if (status != 0) {
- logger.debug("layer texts different");
- return status;
- }
+ ListComparator<LayerText> textComparator = new ListComparator<>(new LayerTextComparator(epsilon));
+ int status = textComparator.compare(arg0.getTexts(), arg1.getTexts());
+ if (status != 0) {
+ logger.debug("layer texts different");
+ return status;
}
- LayerOvalComparator ovalComparator = new LayerOvalComparator(epsilon);
- for (int i = 0; i < arg0.getOvals().size(); i++) {
- int status = ovalComparator.compare(arg0.getOvals().get(i), arg1.getOvals().get(i));
- if (status != 0) {
- logger.debug("layer ovals different");
- return status;
- }
+ ListComparator<LayerOval> ovalComparator = new ListComparator<>(new LayerOvalComparator(epsilon));
+ status = ovalComparator.compare(arg0.getOvals(), arg1.getOvals());
+ if (status != 0) {
+ logger.debug("layer ovals different");
+ return status;
}
- LayerRectComparator rectComparator = new LayerRectComparator(epsilon);
- for (int i = 0; i < arg0.getRectangles().size(); i++) {
- int status = rectComparator.compare(arg0.getRectangles().get(i), arg1.getRectangles().get(i));
- if (status != 0) {
- logger.debug("layer rectangles different ");
- return status;
- }
+ ListComparator<LayerRect> rectComparator = new ListComparator<>(new LayerRectComparator(epsilon));
+ status = rectComparator.compare(arg0.getRectangles(), arg1.getRectangles());
+ if (status != 0) {
+ logger.debug("layer rectangles different ");
+ return status;
}
- PolylineDataComparator lineComparator = new PolylineDataComparator(epsilon);
- for (int i = 0; i < arg0.getLines().size(); i++) {
- int status = lineComparator.compare(arg0.getLines().get(i), arg1.getLines().get(i));
- if (status != 0) {
- logger.debug("layer lines different ");
- return status;
- }
+ ListComparator<PolylineData> lineComparator = new ListComparator<>(new PolylineDataComparator(epsilon));
+ status = lineComparator.compare(arg0.getLines(), arg1.getLines());
+ if (status != 0) {
+ logger.debug("layer lines different ");
+ return status;
}
return 0;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
index e656f63c47b6ba0fd0a43cbc592b5d4847ddc790..82ffeb69a3491f3b6dd50bd7ffd24a13b9368ecc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
@@ -1,5 +1,8 @@
package lcsb.mapviewer.model.map.layout.graphics;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.*;
@@ -13,6 +16,8 @@ import lcsb.mapviewer.common.comparator.*;
*/
public class LayerTextComparator extends Comparator<LayerText> {
+ private Logger logger = LogManager.getLogger();
+
/**
* Epsilon value used for comparison of doubles.
*/
@@ -44,35 +49,35 @@ public class LayerTextComparator extends Comparator<LayerText> {
IntegerComparator integerComparator = new IntegerComparator();
if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth(), "width");
}
if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight(), "height");
}
if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- return doubleComparator.compare(arg0.getX(), arg1.getX());
+ return doubleComparator.compare(arg0.getX(), arg1.getX(), "x");
}
if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- return doubleComparator.compare(arg0.getY(), arg1.getY());
+ return doubleComparator.compare(arg0.getY(), arg1.getY(), "y");
}
if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ return colorComparator.compare(arg0.getColor(), arg1.getColor(), "color");
}
if (stringComparator.compare(arg0.getNotes(), arg1.getNotes()) != 0) {
- return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
+ return stringComparator.compare(arg0.getNotes(), arg1.getNotes(), "notes");
}
if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
- return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
+ return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize(), "fontSize");
}
if (integerComparator.compare(arg0.getZ(), arg1.getZ()) != 0) {
- return integerComparator.compare(arg0.getZ(), arg1.getZ());
+ return integerComparator.compare(arg0.getZ(), arg1.getZ(), "z");
}
return 0;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index 52bef262b9c4bc71a4c5f74ea4459ca3b94cae06..18d836f3136ac3014bbea7bdba6517b7e1b8856b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -117,7 +117,7 @@ public class ElementComparator extends Comparator<Element> {
}
if (colorComparator.compare(arg0.getFontColor(), arg1.getFontColor()) != 0) {
- logger.debug("Border Font different: " + arg0.getFontColor() + ", " + arg1.getFontColor());
+ logger.debug("Font color different: " + arg0.getFontColor() + ", " + arg1.getFontColor());
return colorComparator.compare(arg0.getFontColor(), arg1.getFontColor());
}
diff --git a/pathvisio/.project b/pathvisio/.project
index 7edba154eee624dd2b07c88fb90dd823e8f38d6e..7c27b022d33f191f441d65a7d69e7934f674ee84 100644
--- a/pathvisio/.project
+++ b/pathvisio/.project
@@ -5,6 +5,11 @@
<projects>
</projects>
<buildSpec>
+ <buildCommand>
+ <name>org.eclipse.wst.common.project.facet.core.builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
@@ -15,6 +20,11 @@
<arguments>
</arguments>
</buildCommand>
+ <buildCommand>
+ <name>org.eclipse.wst.validation.validationbuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
@@ -22,8 +32,11 @@
</buildCommand>
</buildSpec>
<natures>
+ <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+ <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>net.sf.eclipsecs.core.CheckstyleNature</nature>
+ <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml
index 9eac37f38a086b402840afb81feb6930ebec46ce..30ee0f01455a80296445bc7ed63ace99ae147b74 100644
--- a/pathvisio/pom.xml
+++ b/pathvisio/pom.xml
@@ -8,7 +8,7 @@
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
- <packaging>bundle</packaging>
+<!-- <packaging>bundle</packaging>
<build>
<plugins>
@@ -128,7 +128,7 @@
</plugin>
</plugins>
</build>
-
+-->
<repositories>
<repository>
<id>repo</id>
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..796d4a006eb3dff90a82508037b8d1b981ca0143
--- /dev/null
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java
@@ -0,0 +1,57 @@
+package lcsb.mapviewer.wikipathway;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Component;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.*;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+import lcsb.mapviewer.wikipathway.XML.ModelToGPML;
+
+@Component
+public class GpmlParser extends Converter {
+ Logger logger = LogManager.getLogger();
+
+ @Override
+ public Model createModel(ConverterParams params) throws InvalidInputDataExecption, ConverterException {
+ GPMLToModel gpmlToModel = new GPMLToModel();
+ File inputFile = null;
+ try {
+ Model result = gpmlToModel.getModel(params.getInputStream());
+ return result;
+
+ } catch (IOException e) {
+ throw new ConverterException("Failed to convert input stream to file.", e);
+ } finally {
+ assert inputFile == null || inputFile.delete();
+ }
+ }
+
+ @Override
+ public String model2String(Model model) throws InconsistentModelException, ConverterException {
+ ModelToGPML modelToGPML = new ModelToGPML();
+ return modelToGPML.getGPML(model);
+ }
+
+ @Override
+ public String getCommonName() {
+ return "GPML";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.XML;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "gpml";
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
index 0296f8a1e1d69546133b3bb71c1678c2b08f9747..e1a3725b8d2e926e4da1ccfb2d798f3dbfcaa704 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
@@ -8,8 +8,8 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.wikipathway.model.biopax.*;
/**
@@ -36,11 +36,11 @@ public class BiopaxParser {
private Map<MiriamData, String> miriamHash = new HashMap<>();
/**
- * Creates data structure from biopax xml node.
+ * Creates data structure from BioPax xml node.
*
* @param biopax
* xml node
- * @return {@link BiopaxData} structure containing biopax data
+ * @return {@link BiopaxData} structure containing BioPax data
*/
public BiopaxData parse(Node biopax) {
BiopaxData result = new BiopaxData();
@@ -150,12 +150,12 @@ public class BiopaxParser {
/**
* Returns unique hash for the {@link MiriamData} that can be used as a key in
- * Biopax xml.
+ * BioPax xml.
*
* @param md
* {@link MiriamData} for which we want to have unique hash value
* @return unique hash for the {@link MiriamData} that can be used as a key in
- * Biopax xml
+ * BioPax xml
*/
private String getHash(MiriamData md) {
if (miriamHash.get(md) == null) {
@@ -167,11 +167,11 @@ public class BiopaxParser {
/**
* Converts collection of {@link MiriamData} into an xml {@link String}
- * representing this collection as a biopax data.
+ * representing this collection as a BioPax data.
*
* @param miriamData
* collection of {@link MiriamData}
- * @return xml {@link String} representing this collection as a biopax data
+ * @return xml {@link String} representing this collection as a BioPax data
*/
public String toXml(Collection<MiriamData> miriamData) {
StringBuilder sb = new StringBuilder("");
@@ -187,11 +187,11 @@ public class BiopaxParser {
}
/**
- * Converts {@link MiriamData} into xml string in biopax format.
+ * Converts {@link MiriamData} into xml string in BioPax format.
*
* @param md
* {@link MiriamData} to transform
- * @return xml string in biopax format representing {@link MiriamData}
+ * @return xml string in BioPax format representing {@link MiriamData}
*/
public String toXml(MiriamData md) {
StringBuilder sb = new StringBuilder();
@@ -203,54 +203,4 @@ public class BiopaxParser {
sb.append("</bp:PublicationXref>\n");
return sb.toString();
}
-
- /**
- * Creates {@link MiriamData annotation} from {@link BiopaxPublication}.
- *
- * @param publication
- * input biopax structure
- * @return {@link MiriamData annotation}
- */
- protected MiriamData createMiriamData(BiopaxPublication publication) {
- if ("PubMed".equals(publication.getDb())) {
- if (publication.getId() == null || publication.getId().equals("")) {
- return null;
- } else {
- return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, publication.getId());
- }
- } else {
- throw new InvalidArgumentException("Unknown biopax database: " + publication.getDb());
- }
- }
-
- /**
- * Returns list of {@link MiriamData} that are refernced in {@link BiopaxData}
- * with identifier given in biopaxReference.
- *
- * @param biopaxData
- * {@link BiopaxData} where annotations are stored
- * @param biopaxReference
- * list of refrences (to data in {@link BiopaxData}) that we want to
- * convert into {@link MiriamData}
- * @return list of {@link MiriamData} that are refernced in {@link BiopaxData}
- * with identifier given in biopaxReference.
- */
- public Collection<MiriamData> getMiriamData(BiopaxData biopaxData, List<String> biopaxReference) {
- List<MiriamData> result = new ArrayList<>();
- for (String string : biopaxReference) {
- BiopaxPublication bp = biopaxData.getPublicationByReference(string);
- if (bp != null) {
- MiriamData md = createMiriamData(bp);
- if (md != null) {
- result.add(md);
- } else {
- logger.warn("[" + string + "]\tBiopax publication is invalid.");
- }
- } else {
- logger.warn("[" + string + "]\tBiopax publication doesn't exist.");
- }
- }
- return result;
- }
-
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
index d1d4c91cb6a66e42556cbdd6f29da81845f7d12e..fe9739662e138fa4532dba0e273eff324e196ca1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
@@ -152,8 +152,8 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
* thrown when data for the edge is invalid
*/
protected void parseGraphics(Edge edge, Element graphicsNode) throws ConverterException {
- List<Element> points = new ArrayList<Element>();
- List<Element> anchors = new ArrayList<Element>();
+ List<Element> points = new ArrayList<>();
+ List<Element> anchors = new ArrayList<>();
GpmlLineConnectorType connectorType = GpmlLineConnectorType.STRAIGHT;
@@ -163,7 +163,6 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
connectorType = GpmlLineConnectorType.getByGpmlName(entry.getRight());
break;
case ("LineThickness"):
- // line thicknes
edge.getLine().setWidth(entry.getRight());
break;
case ("LineStyle"):
@@ -175,7 +174,6 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
edge.setzOrder(Integer.valueOf(entry.getRight()));
break;
case ("Color"):
- // graphics color
edge.setColor(hexStringToColor(entry.getRight()));
break;
default:
@@ -184,8 +182,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
}
}
- NodeList nodes;
- nodes = graphicsNode.getChildNodes();
+ NodeList nodes = graphicsNode.getChildNodes();
for (int i = 0; i < nodes.getLength(); i++) {
Node node = nodes.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
@@ -217,6 +214,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
edge.setType(pointData.getType());
}
+ edge.setReversibleReaction(pointDataList.get(0).getType() == GpmlInteractionType.ARROW);
edge.getLine().setPoints(getPoints(edge.getWarningPrefix(), pointDataList, connectorType));
if (edge.getLine().getPoints().size() < 2) {
@@ -252,16 +250,16 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
}
/**
- * This method transforms list of {@link PointData points} from gpml xml into
+ * This method transforms list of {@link PointData points} from GPML xml into
* list of standard {@link Point2D points}.
*
* @param warningPrefix
* prefix that should be used for warnings
* @param pointDataList
- * list of points from gpml format
+ * list of points from GPML format
* @param connectorType
* {@link GpmlLineConnectorType type} defining how points are connected
- * in gpml format
+ * in GPML format
* @return list of standard {@link Point2D points} obtained from input data
* @throws UnknownGpmlLineConnectorTypeException
* thrown when {@link GpmlLineConnectorType type} is unknown
@@ -270,7 +268,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
* @throws UnknownTypeException
* throw when connector type is invalid
*/
- private List<Point2D> getPoints(String warningPrefix, List<PointData> pointDataList,
+ List<Point2D> getPoints(String warningPrefix, List<PointData> pointDataList,
GpmlLineConnectorType connectorType)
throws InvalidElbowConnectorException, UnknownTypeException {
List<Point2D> result = new ArrayList<>();
@@ -286,11 +284,17 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
if (to == null) {
to = Direction.EAST;
}
+ if (from == Direction.NONE) {
+ from = to.nextClockwiseDirection().nextClockwiseDirection();
+ for (int i = 0; i < pointDataList.size() - 1; i++) {
+ from = from.nextClockwiseDirection();
+ }
+ }
// how many segments do we have
int lines = computeNumberOfPerpendicularSegments(warningPrefix, pointDataList.get(0),
pointDataList.get(pointDataList.size() - 1));
- // now we know how many segments should be i the line
+ // now we know how many segments should be in the line
// if segments are defined in the input the it's easy
if (lines == pointDataList.size()) {
@@ -310,11 +314,11 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
// add middle point
points.add(1, computeDefaultPoint(from, points.get(0)));
// CHECKSTYLE:OFF
- // if something is still missing then add defult beginning line
+ // if something is still missing then add default beginning line
if (lines > 3) {
points.add(2, computeDefaultPoint(to, points.get(2)));
}
- // if something is still missing then add defult end line
+ // if something is still missing then add default end line
if (lines > 4) {
double x = (points.get(1).getX() + points.get(2).getX()) / 2;
double y = (points.get(1).getY() + points.get(2).getY()) / 2;
@@ -331,9 +335,9 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
// and now transform the points into perpendicular segments
result = preparePerpendicularLines(from, points);
- // if number of expectred segments is lower than number of defined
+ // if number of expected segments is lower than number of defined
// segments then we probably missed something, let's assume that in
- // gpml file the data is correct and parse it
+ // GPML file the data is correct and parse it
} else if (pointDataList.size() > lines) {
List<Point2D> points = new ArrayList<>();
for (PointData pd : pointDataList) {
@@ -341,7 +345,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
}
result = preparePerpendicularLines(from, points);
- // if number of expectred segments is different than number of defined
+ // if number of expected segments is different than number of defined
// segments then something is wrong
} else {
throw new InvalidElbowConnectorException(
@@ -407,10 +411,14 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
to = Direction.EAST;
}
- // result (2 is the minimu)
+ if (from == Direction.NONE || to == Direction.NONE) {
+ return 2;
+ }
+
+ // result (2 is the minimum)
int lines = 2;
- // if line starts and ends i nthe same axis then number of segments
+ // if line starts and ends in the same axis then number of segments
// should be at least3
if (from.getAxis().equals(to.getAxis())) {
lines++;
@@ -421,7 +429,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
// then check if some addition lines are needed
if (!from.equals(to)) {
int addition = 0;
- // check if begining requires additional lines because the end is
+ // check if beginning requires additional lines because the end is
// overlapping the beginning
switch (from) {
case EAST:
@@ -447,7 +455,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
default:
throw new InvalidElbowConnectorException(warningPrefix + "Unknown direction: " + from);
}
- // check if emdrequires additional lines because the beginning is
+ // check if end requires additional lines because the beginning is
// overlapping end part
switch (to) {
case EAST:
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
index 4563d839db45485adbe910539edb40b25dce8bae..43be3375771c9693b150f15205de2b7df1f839ed 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
@@ -71,7 +71,7 @@ public class GpmlParser {
/**
* This function returns parent interaction for edge that has anchor at one end.
- *
+ *
* @param graph
* model where data is stored
* @param edge
@@ -107,7 +107,7 @@ public class GpmlParser {
/**
* This function sets width and height in given graph.
- *
+ *
* @param node
* xml node where data is stored
* @param graph
@@ -121,62 +121,66 @@ public class GpmlParser {
graph.setBoardHeight(Math.ceil(Double.parseDouble(boardHeight)));
}
- /**
- * This function adds groups to graph and nest them.
- *
- * @param groups
- * xml nodes
- * @param graph
- * object where data is stored
- * @throws UnknownAttributeValueException
- * thrown when there is a problem with xml attributes
- */
- protected void addGroups(List<Node> groups, Graph graph) throws UnknownAttributeValueException {
- // Adding Groups to graph
- for (Node nNode : groups) {
- if (nNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eElement = (Element) nNode;
- String graphId = eElement.getAttribute("GraphId");
- String groupId = eElement.getAttribute("GroupId");
- if (graphId.equals("") || graphId == null) {
- graphId = groupId;
- }
- String style = eElement.getAttribute("Style");
- if ("".equals(style)) {
- style = null;
- }
- if (style != null &&
- !"Complex".equalsIgnoreCase(style) &&
- !"Group".equalsIgnoreCase(style)) {
- throw new UnknownAttributeValueException(
- "Unknown value of \"style\" attribute for group node: " + style
- + ". Only null, Complex, Group are supported.");
- }
- Group group = new Group(graphId, groupId);
- group.setStyle(style);
- graph.addGroup(group);
- }
- }
- // Handling nested groups
- Group gr1, gr2;
- for (Node nNode : groups) {
- if (nNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eElement = (Element) nNode;
- String groupRef = eElement.getAttribute("GroupRef");
- String groupId = eElement.getAttribute("GroupId");
- if (groupRef != null && !groupRef.equals("")) {
- gr1 = graph.getGroupByGroupId(groupRef);
- gr2 = graph.getGroupByGroupId(groupId);
- gr1.addNode(gr2);
- }
- }
- }
- }
+ /**
+ * This function adds groups to graph and nest them.
+ *
+ * @param groups
+ * xml nodes
+ * @param graph
+ * object where data is stored
+ * @throws UnknownAttributeValueException
+ * thrown when there is a problem with xml attributes
+ */
+ protected void addGroups(List<Node> groups, Graph graph) throws UnknownAttributeValueException {
+ // Adding Groups to graph
+ for (Node nNode : groups) {
+ if (nNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eElement = (Element) nNode;
+ String graphId = eElement.getAttribute("GraphId");
+ String groupId = eElement.getAttribute("GroupId");
+ if (graphId.equals("") || graphId == null) {
+ graphId = groupId;
+ }
+ String style = eElement.getAttribute("Style");
+ if ("".equals(style)) {
+ style = null;
+ }
+ if (style != null &&
+ !"Complex".equalsIgnoreCase(style) &&
+ !"Group".equalsIgnoreCase(style)) {
+ throw new UnknownAttributeValueException(
+ "Unknown value of \"style\" attribute for group node: " + style + ". Only null, Complex, Group are supported.");
+ }
+ Group group = new Group(graphId, groupId);
+ group.setStyle(style);
+
+ String zIndex = eElement.getAttribute("ZOrder");
+ if (zIndex!=null && !zIndex.isEmpty()) {
+ group.setzOrder(Integer.valueOf(zIndex));
+ }
+ graph.addGroup(group);
+ }
+ }
+ // Handling nested groups
+ Group gr1, gr2;
+ for (Node nNode : groups) {
+ if (nNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eElement = (Element) nNode;
+ String groupRef = eElement.getAttribute("GroupRef");
+ String groupId = eElement.getAttribute("GroupId");
+ if (groupRef != null && !groupRef.equals("")) {
+ gr1 = graph.getGroupByGroupId(groupRef);
+ gr2 = graph.getGroupByGroupId(groupId);
+ gr1.addNode(gr2);
+ }
+ }
+ }
+ }
/**
* This function adds edges to graph. It ignores edges that have no connection
* at one end and edges that connects to shapes or labels.
- *
+ *
* @param nodes
* xml nodes
* @param graph
@@ -224,31 +228,16 @@ public class GpmlParser {
* NodeToNode connection are transformed into Interactions. Second: Edges with
* AnchorToNode connection are added to right interaction. Edges with
* AnchorToAnchor connection are ignored.
- *
+ *
* @param graph
- * object where data is sotred
+ * object where data is sorted
* @throws InvalidXmlSchemaException
* thrown when the data in input file is invalid
*/
protected void addInteractions(Graph graph) throws InvalidXmlSchemaException {
for (Edge edge : graph.getEdges()) {
if (graph.getNodeByGraphId(edge.getEnd()) != null && graph.getNodeByGraphId(edge.getStart()) != null) {
- if (graph.getNodeByGraphId(edge.getEnd()) instanceof Label) {
- Label label = (Label) graph.getNodeByGraphId(edge.getEnd());
- label.setTreatAsNode(true);
- }
- if (graph.getNodeByGraphId(edge.getStart()) instanceof Label) {
- Label label = (Label) graph.getNodeByGraphId(edge.getStart());
- label.setTreatAsNode(true);
- }
- if (graph.getShapeByGraphId(edge.getEnd()) instanceof Shape) {
- Shape shape = (Shape) graph.getShapeByGraphId(edge.getEnd());
- shape.setTreatAsNode(true);
- }
- if (graph.getShapeByGraphId(edge.getStart()) instanceof Shape) {
- Shape shape = (Shape) graph.getShapeByGraphId(edge.getStart());
- shape.setTreatAsNode(true);
- }
+ markLabelsAndShapesToBecomeSpeciesForEdge(graph, edge);
Interaction interaction = new Interaction(edge);
graph.addInteraction(interaction);
@@ -287,6 +276,7 @@ public class GpmlParser {
throw new InvalidStateException(
"Unknown internal model type: " + mapping.getModelInputReactionNodeType());
}
+ markLabelsAndShapesToBecomeSpeciesForEdge(graph, edge);
} else {
throw new InvalidXmlSchemaException("Unknown interaction type: " + edge.getType());
}
@@ -301,7 +291,7 @@ public class GpmlParser {
if (mapping != null) {
if (mapping.isOutputWarning()) {
logger.warn(edge.getWarningPrefix() + "Invalid interaction type \"" + edge.getType()
- + "\" as an input to reaction.");
+ + "\" as an output from reaction.");
}
if (Modifier.class.isAssignableFrom(mapping.getModelOutputReactionNodeType())) {
tmp.addModifier(edge);
@@ -313,6 +303,7 @@ public class GpmlParser {
throw new InvalidStateException(
"Unknown internal model type: " + mapping.getModelOutputReactionNodeType());
}
+ markLabelsAndShapesToBecomeSpeciesForEdge(graph, edge);
} else {
throw new InvalidXmlSchemaException("Unknown interaction type: " + edge.getType());
}
@@ -328,9 +319,28 @@ public class GpmlParser {
}
}
+ private void markLabelsAndShapesToBecomeSpeciesForEdge(Graph graph, Edge edge) {
+ if (graph.getNodeByGraphId(edge.getEnd()) instanceof Label) {
+ Label label = (Label) graph.getNodeByGraphId(edge.getEnd());
+ label.setTreatAsNode(true);
+ }
+ if (graph.getNodeByGraphId(edge.getStart()) instanceof Label) {
+ Label label = (Label) graph.getNodeByGraphId(edge.getStart());
+ label.setTreatAsNode(true);
+ }
+ if (graph.getShapeByGraphId(edge.getEnd()) instanceof Shape) {
+ Shape shape = (Shape) graph.getShapeByGraphId(edge.getEnd());
+ shape.setTreatAsNode(true);
+ }
+ if (graph.getShapeByGraphId(edge.getStart()) instanceof Shape) {
+ Shape shape = (Shape) graph.getShapeByGraphId(edge.getStart());
+ shape.setTreatAsNode(true);
+ }
+ }
+
/**
* Creates gpml {@link Graph} model from gpml input stream.
- *
+ *
* @param stream
* input stream with gpml model
* @return {@link Graph} model
@@ -447,7 +457,7 @@ public class GpmlParser {
/**
* This method merge edges that should be merged into single line.
- *
+ *
* @param graph
* model where edges are stored
*/
@@ -518,7 +528,7 @@ public class GpmlParser {
/**
* Method that merge two {@link Edge edges}.
- *
+ *
* @param edge1
* first edge to merge
* @param edge2
@@ -572,7 +582,7 @@ public class GpmlParser {
/**
* Creates edges from lines when it's possible.
- *
+ *
* @param lines
* xml nodes with lines
* @return list of edges that could be created from xml nodes
@@ -595,7 +605,7 @@ public class GpmlParser {
/**
* Creates lines from the list of gpml xml nodes.
- *
+ *
* @param lines
* list of xml nodes
* @return list of {@link PolylineData lines}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
index c3c91d277e21792e2163a1e769c5345fa5a4272d..383d5a3718c70f9cc009c5b7fbcc0b8425d37940 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
@@ -11,6 +11,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.wikipathway.model.Label;
import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
@@ -26,7 +27,9 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
/**
* Default class logger.
*/
- private final Logger logger = LogManager.getLogger(LabelParser.class);
+ private final Logger logger = LogManager.getLogger();
+
+ private ReferenceParser referenceParser = new ReferenceParser();
@Override
public Label parse(Element eElement) throws UnknownTypeException {
@@ -42,6 +45,14 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
case ("TextLabel"):
label.setTextLabel(entry.getRight());
break;
+ case ("Href"):
+ MiriamData md = referenceParser.hrefToMiriamData(entry.getRight());
+ if (md == null) {
+ label.addComment(entry.getRight());
+ } else {
+ label.addReference(md);
+ }
+ break;
case ("GroupRef"):
label.setGroupRef(entry.getRight());
break;
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index c4065bc2c070119eef68f9ad9ba62b00262ae879..b464424687cb37690b025e0cce8339ff67ee7836 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -1,7 +1,8 @@
package lcsb.mapviewer.wikipathway.XML;
import java.awt.Color;
-import java.awt.geom.*;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
import java.util.*;
import org.apache.commons.text.StringEscapeUtils;
@@ -9,17 +10,15 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.*;
import lcsb.mapviewer.model.map.layout.graphics.*;
@@ -31,8 +30,7 @@ import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.wikipathway.model.*;
-import lcsb.mapviewer.wikipathway.model.biopax.BiopaxPublication;
-import lcsb.mapviewer.wikipathway.utils.Geo;
+import lcsb.mapviewer.wikipathway.model.biopax.BiopaxFactory;
/**
* Class contains methods for GraphToModel conversion.
@@ -46,14 +44,7 @@ public class ModelContructor {
* Default color used by complexes.
*/
private static final Color DEFAULT_COMPLEX_ALIAS_COLOR = new Color(102, 255, 255);
- /**
- * How much of central line is used by and operator that joins reactants.
- */
- private static final int AND_OPERATOR_CENTRAL_LINE_RATIO = 10;
- /**
- * How much of central line is used by split operator that split products.
- */
- private static final int SPLIT_OPERATOR_CENTRAL_LINE_RATIO = 10;
+
/**
* Epsilon used for double comparison.
*/
@@ -90,83 +81,7 @@ public class ModelContructor {
/**
* Parser used for extracting {@link MiriamData references} from GPML model.
*/
- private BiopaxParser biopaxParser = new BiopaxParser();
- private PointTransformation pt = new PointTransformation();
-
- /**
- * This function splits {@link PolylineData} into two parts. It also assumes
- * that last segment on the left part is equal to the length of the first
- * segment on the right side.
- *
- * @param pd
- * line to split
- * @return pair of lines into which parameter was split to
- */
- protected Pair<PolylineData, PolylineData> splitPolyline(PolylineData pd) {
- PolylineData p1 = new PolylineData();
- PolylineData p2 = new PolylineData();
- p1.setColor(pd.getColor());
- p2.setColor(pd.getColor());
-
- List<Line2D> lines = pd.getLines();
- double lenght = 0.0;
- for (Line2D line : lines) {
- lenght += Geo.lineLen(line);
- }
- if (lenght > Configuration.EPSILON) {
- double tmp = 0.0;
- boolean first = true;
- for (Line2D line : lines) {
- if (tmp + Geo.lineLen(line) > lenght / 2) {
- if (first) {
- double a = (lenght / 2 - tmp) / Geo.lineLen(line);
- double x = line.getX1() + a * (line.getX2() - line.getX1());
- double y = line.getY1() + a * (line.getY2() - line.getY1());
- p1.addPoint((Point2D) line.getP1().clone());
- p1.addPoint(new Point2D.Double(x, y));
- p2.addPoint(new Point2D.Double(x, y));
- first = false;
- }
- p2.addPoint((Point2D) line.getP2().clone());
- tmp += Geo.lineLen(line);
- } else {
- p1.addPoint((Point2D) line.getP1().clone());
- tmp += Geo.lineLen(line);
- }
- }
- } else { // we have line with empty length
- p1.addPoint((Point2D) pd.getBeginPoint().clone());
- p1.addPoint((Point2D) pd.getBeginPoint().clone());
- p2.addPoint((Point2D) pd.getBeginPoint().clone());
- p2.addPoint((Point2D) pd.getBeginPoint().clone());
- }
-
- // and now make sure that we have equal distances from left and right
- double leftDist = p1.getEndPoint().distance(p1.getPoints().get(p1.getPoints().size() - 2));
- double rightDist = p2.getEndPoint().distance(p2.getPoints().get(p2.getPoints().size() - 2));
- if (Math.abs(leftDist - rightDist) > Configuration.EPSILON) {
- if (leftDist > rightDist) {
- double ratio = rightDist / leftDist;
- double dx = p1.getPoints().get(p1.getPoints().size() - 1).getX()
- - p1.getPoints().get(p1.getPoints().size() - 2).getX();
- double dy = p1.getPoints().get(p1.getPoints().size() - 1).getY()
- - p1.getPoints().get(p1.getPoints().size() - 2).getY();
- double x = p1.getPoints().get(p1.getPoints().size() - 2).getX() + dx * ratio;
- double y = p1.getPoints().get(p1.getPoints().size() - 2).getY() + dy * ratio;
- Point2D newPoint = new Point2D.Double(x, y);
- p1.addPoint(p1.getPoints().size() - 1, newPoint);
- } else {
- double ratio = leftDist / rightDist;
- double dx = p2.getPoints().get(0).getX() - p2.getPoints().get(1).getX();
- double dy = p2.getPoints().get(0).getY() - p2.getPoints().get(1).getY();
- double x = p2.getPoints().get(1).getX() + dx * ratio;
- double y = p2.getPoints().get(1).getY() + dy * ratio;
- Point2D newPoint = new Point2D.Double(x, y);
- p2.addPoint(1, newPoint);
- }
- }
- return new Pair<PolylineData, PolylineData>(p1, p2);
- }
+ private BiopaxFactory biopaxFactory = new BiopaxFactory();
/**
* This function creates Species from DataNode.
@@ -177,7 +92,7 @@ public class ModelContructor {
* ...
* @return {@link Species} created from input {@link DataNode}
*/
- protected Species createAlias(DataNode dataNode, Data data) {
+ protected Species createSpecies(DataNode dataNode, Data data) {
Species res = null;
String type = dataNode.getType();
if (type == null || type.equals("")) {
@@ -204,14 +119,18 @@ public class ModelContructor {
}
res.addMiriamData(dataNode.getReferences());
- res.setZ(dataNode.getzOrder());
res.setName(dataNode.getName());
+ StringBuilder notes = new StringBuilder();
+ for (String comment : dataNode.getComments()) {
+ notes.append(comment + "\n\n");
+ }
+ res.setNotes(notes.toString());
return res;
}
/**
- * This function adds ComplexSpecies to model from graph. ComplexName is set as
- * groupId from .gpml
+ * This function adds {@link Complex} to model from graph. ComplexName is set as
+ * groupId from GPML
*
* @param model
* to this model complexes will be added
@@ -220,28 +139,29 @@ public class ModelContructor {
* @param data
* ...
*/
- protected void addComplexSpecies(Model model, Graph graph, Data data) {
+ protected void addComplex(Model model, Graph graph, Data data) {
for (Group group : graph.getGroups()) {
- Complex alias = new Complex(group.getGraphId());
- alias.setName(group.getGraphId());
+ Complex complex = new Complex(group.getGraphId());
+ complex.setName(group.getGraphId());
if ("Complex".equalsIgnoreCase(group.getStyle())) {
- alias.setHypothetical(false);
+ complex.setHypothetical(false);
} else {
- alias.setHypothetical(true);
+ complex.setHypothetical(true);
}
Rectangle2D rec = group.getRectangle();
if (rec == null) {
rec = new Rectangle2D.Double(0, 0, 0, 0);
}
- alias.setX(rec.getX());
- alias.setY(rec.getY());
- alias.setWidth((int) rec.getWidth());
- alias.setHeight((int) rec.getHeight());
- alias.setFillColor(DEFAULT_COMPLEX_ALIAS_COLOR);
-
- data.id2alias.put(group.getGraphId(), alias);
- model.addElement(alias);
+ complex.setX(rec.getX());
+ complex.setY(rec.getY());
+ complex.setWidth((int) rec.getWidth());
+ complex.setHeight((int) rec.getHeight());
+ complex.setZ(group.getzOrder());
+ complex.setFillColor(DEFAULT_COMPLEX_ALIAS_COLOR);
+
+ data.id2alias.put(group.getGraphId(), complex);
+ model.addElement(complex);
}
}
@@ -251,14 +171,14 @@ public class ModelContructor {
* @param model
* model to which species will be added
* @param graph
- * gpml data model
+ * GPML data model
* @param data
* ...
*/
protected void addElement(Model model, Graph graph, Data data) {
for (DataNode dataNode : graph.getDataNodes()) {
- Species species = createAlias(dataNode, data);
- species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReference()));
+ Species species = createSpecies(dataNode, data);
+ species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReference()));
Element alias = updateAlias(dataNode, species);
@@ -268,13 +188,13 @@ public class ModelContructor {
for (Label label : graph.getLabels()) {
if (label.isTreatAsNode()) {
Species species = createSpecies(label);
- species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), label.getBiopaxReference()));
+ species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), label.getBiopaxReference()));
Element alias = updateAlias(label, species);
data.id2alias.put(label.getGraphId(), alias);
model.addElement(alias);
- } else {
+ } else if (label.getGroupRef() == null || label.getGroupRef().isEmpty()) {
LayerText text = createText(label);
data.layer.addLayerText(text);
}
@@ -282,7 +202,7 @@ public class ModelContructor {
for (Shape shape : graph.getShapes()) {
if (shape.isTreatAsNode()) {
Species species = createSpecies(shape);
- species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), shape.getBiopaxReference()));
+ species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), shape.getBiopaxReference()));
Element alias = updateAlias(shape, species);
@@ -294,6 +214,8 @@ public class ModelContructor {
if (shape.getShape().equalsIgnoreCase("oval")) {
LayerOval oval = createOval(shape);
data.layer.addLayerOval(oval);
+ } else if (shape.getComments().size() > 0 || shape.getTextLabel() != null) {
+ data.shapeLabelLayer.addLayerText(createText(shape));
} else {
LayerRect rect = createRectangle(shape);
data.layer.addLayerRect(rect);
@@ -393,12 +315,17 @@ public class ModelContructor {
* Creates {@link LayerRect} object from {@link Shape}.
*
* @param shape
- * source gpml object to be transformed
+ * source GPML object to be transformed
* @return {@link LayerRect} obtained from {@link Shape} object
*/
public LayerRect createRectangle(Shape shape) {
LayerRect rect = new LayerRect();
- Rectangle2D rec = shape.getRectangle();
+ Rectangle2D rec;
+ if (shouldRotate90degrees(shape.getRotation())) {
+ rec = rotate90degrees(shape.getRectangle());
+ } else {
+ rec = shape.getRectangle();
+ }
rect.setX(rec.getX());
rect.setY(rec.getY());
rect.setHeight(rec.getHeight());
@@ -407,11 +334,39 @@ public class ModelContructor {
return rect;
}
+ Rectangle2D rotate90degrees(Rectangle2D rectangle) {
+ return new Rectangle2D.Double(rectangle.getCenterX() - rectangle.getHeight() / 2,
+ rectangle.getCenterY() - rectangle.getWidth() / 2, rectangle.getHeight(), rectangle.getWidth());
+ }
+
+ boolean shouldRotate90degrees(Double rot) {
+ if (rot == null) {
+ return false;
+ }
+ double rotation = rot;
+ while (rotation > Math.PI / 2) {
+ rotation -= Math.PI;
+ }
+ while (rotation < -Math.PI / 2) {
+ rotation += Math.PI;
+ }
+ if (Math.abs(rotation) < Math.PI / 4) {
+ if (Math.abs(rotation) > Configuration.EPSILON) {
+ logger.warn("Rotation of objects is not supported. Rotation=" + rot);
+ }
+ return false;
+ }
+ if ((Math.PI / 2 - Math.abs(rotation)) > Configuration.EPSILON) {
+ logger.warn("Rotation of objects is not supported. Rotation=" + rot);
+ }
+ return true;
+ }
+
/**
* Creates {@link LayerOval} object from {@link Shape}.
*
* @param shape
- * source gpml object to be transformed
+ * source GPML object to be transformed
* @return {@link LayerOval} obtained from {@link Shape} object
*/
public LayerOval createOval(Shape shape) {
@@ -444,7 +399,38 @@ public class ModelContructor {
if (text.getColor().equals(Color.WHITE)) {
text.setColor(Color.BLACK);
}
- text.setNotes(label.getName());
+ StringBuilder notes = new StringBuilder(label.getName());
+ for (String comment : label.getComments()) {
+ notes.append(comment + "\n\n");
+ }
+ text.setNotes(notes.toString());
+ return text;
+ }
+
+ public LayerText createText(Shape shape) {
+ Rectangle2D rec = shape.getRectangle();
+
+ LayerText text = new LayerText();
+ text.setX(rec.getX());
+ text.setY(rec.getY());
+ text.setHeight(rec.getHeight());
+ text.setWidth(rec.getWidth());
+ text.setColor(shape.getColor());
+ if (text.getColor().equals(Color.WHITE)) {
+ text.setColor(Color.BLACK);
+ }
+
+ String name = shape.getTextLabel();
+ if (name == null) {
+ name = "";
+ }
+
+ StringBuilder notes = new StringBuilder(name);
+ for (String comment : shape.getComments()) {
+ notes.append(comment + "\n\n");
+ }
+ text.setNotes(notes.toString());
+
return text;
}
@@ -481,6 +467,11 @@ public class ModelContructor {
if (element instanceof Compartment && !Objects.equals(Color.WHITE, gpmlElement.getFillColor())) {
element.setBorderColor(gpmlElement.getFillColor());
}
+ element.setZ(gpmlElement.getzOrder());
+ element.setFontColor(gpmlElement.getColor());
+ if (gpmlElement.getFontSize() != null) {
+ element.setFontSize(gpmlElement.getFontSize());
+ }
return element;
}
@@ -495,7 +486,13 @@ public class ModelContructor {
logger.warn(label.getWarningPrefix() + " Label cannot be part of reaction. Tranforming to Unknown");
Species res = new Unknown(label.getGraphId());
+ res.addMiriamData(label.getReferences());
res.setName(label.getName());
+ StringBuilder notes = new StringBuilder();
+ for (String comment : label.getComments()) {
+ notes.append(comment + "\n\n");
+ }
+ res.setNotes(notes.toString());
return res;
}
@@ -510,6 +507,11 @@ public class ModelContructor {
logger.warn(shape.getWarningPrefix() + " Shape can not be part of reaction. Tranforming to Unknown");
Species res = new Unknown(shape.getGraphId());
+ StringBuilder notes = new StringBuilder();
+ for (String comment : shape.getComments()) {
+ notes.append(comment + "\n\n");
+ }
+ res.setNotes(notes.toString());
res.setName(shape.getName());
return res;
}
@@ -518,7 +520,7 @@ public class ModelContructor {
* This function add Species to right Complexes.
*
* @param graph
- * gpml data model
+ * GPML data model
* @param data
* ...
* @throws UnknownChildClassException
@@ -527,25 +529,23 @@ public class ModelContructor {
protected void putSpeciesIntoComplexes(Graph graph, Data data) throws UnknownChildClassException {
for (Group group : graph.getGroups()) {
- Complex complexSpecies = (Complex) data.id2alias.get(group.getGraphId());
+ Complex complex = (Complex) data.id2alias.get(group.getGraphId());
for (PathwayElement pe : group.getNodes()) {
- Element species = data.id2alias.get(pe.getGraphId());
- if (species != null) {
- if (species instanceof Species) {
-
- Species speciesAlias = (Species) species;
- speciesAlias.setComplex(complexSpecies);
- complexSpecies.addSpecies(speciesAlias);
+ Element element = data.id2alias.get(pe.getGraphId());
+ if (element != null) {
+ if (element instanceof Species) {
+ Species species = (Species) element;
+ complex.addSpecies(species);
}
// we have label
} else if (graph.getLabelByGraphId(pe.getGraphId()) != null) {
Label label = graph.getLabelByGraphId(pe.getGraphId());
// if complex has generic name then change it into label
- if (complexSpecies.getName().equals(group.getGraphId())) {
- complexSpecies.setName(label.getTextLabel());
+ if (complex.getName().equals(group.getGraphId())) {
+ complex.setName(label.getTextLabel());
} else {
// if there are more labels than one then merge labels
- complexSpecies.setName(complexSpecies.getName() + "\n" + label.getTextLabel());
+ complex.setName(complex.getName() + "\n" + label.getTextLabel());
}
} else if (graph.getShapeByGraphId(pe.getGraphId()) != null) {
Shape shape = graph.getShapeByGraphId(pe.getGraphId());
@@ -567,12 +567,12 @@ public class ModelContructor {
* This function creates {@link Reaction} from {@link Interaction} from graph.
*
* @param interaction
- * gpml interaction
+ * GPML interaction
* @param graph
- * gpml data model
+ * GPML data model
* @param data
* ...
- * @return reaction created from gpml {@link Interaction}
+ * @return reaction created from GPML {@link Interaction}
*/
protected Reaction createReactionFromInteraction(Interaction interaction, Graph graph, Data data) {
InteractionMapping mapping = InteractionMapping.getInteractionMapping(interaction.getType(),
@@ -582,32 +582,25 @@ public class ModelContructor {
}
Reaction reaction = createReactionByType(mapping.getModelReactionType());
reaction.setIdReaction(interaction.getGraphId());
- reaction.setReversible(mapping.isReversible());
+ reaction.setReversible(mapping.isReversible() || interaction.isReversible());
reaction.addMiriamData(interaction.getReferences());
reaction.setZ(interaction.getzOrder());
- for (String ref : interaction.getBiopaxReferences()) {
- BiopaxPublication publication = graph.getBiopaxData().getPublicationByReference(ref);
- MiriamData md = biopaxParser.createMiriamData(publication);
- if (md != null) {
- reaction.addMiriamData(md);
- }
- }
-
- PolylineData pd = interaction.getLine();
+ reaction.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), interaction.getBiopaxReferences()));
- Pair<PolylineData, PolylineData> pair = splitPolyline(pd);
- PolylineData pdfirstpart = pair.getLeft();
- PolylineData pdsecondpart = pair.getRight();
+ ReactionLayoutFinder layoutFinder = new ReactionLayoutFinder();
+ Map<Class<?>, PolylineData> lines = layoutFinder.getNodeLines(interaction);
+ PolylineData reactantLine = lines.get(Reactant.class);
+ PolylineData productLine = lines.get(Product.class);
Reactant reactant = new Reactant();
reactant.setElement(data.id2alias.get(interaction.getStart()));
- reactant.setLine(pdfirstpart);
+ reactant.setLine(reactantLine);
reaction.addReactant(reactant);
Product product = new Product();
product.setElement(data.id2alias.get(interaction.getEnd()));
- product.setLine(pdsecondpart);
+ product.setLine(productLine);
reaction.addProduct(product);
for (Edge e : interaction.getReactants()) {
@@ -620,16 +613,8 @@ public class ModelContructor {
reaction.addProduct(pro);
}
- double centralLength = pdfirstpart.getPoints().get(pdfirstpart.getPoints().size() - 2)
- .distance(pdfirstpart.getEndPoint()) * 2;
-
if (reaction.getReactants().size() > 1) {
- PolylineData operatorLine = new PolylineData();
- operatorLine.setColor(pdfirstpart.getColor());
- operatorLine.addPoint((Point2D) pdfirstpart.getEndPoint().clone());
- operatorLine.addPoint((Point2D) pdfirstpart.getEndPoint().clone());
- pdfirstpart.trimEnd(centralLength / AND_OPERATOR_CENTRAL_LINE_RATIO);
- operatorLine.setStartPoint((Point2D) pdfirstpart.getEndPoint().clone());
+ PolylineData operatorLine = lines.get(AndOperator.class);
NodeOperator andOperator;
// heterodimer association use association operator
if (reaction instanceof HeterodimerAssociationReaction) {
@@ -642,28 +627,36 @@ public class ModelContructor {
andOperator.setLine(operatorLine);
for (int i = 1; i < reaction.getReactants().size(); i++) {
Reactant r = reaction.getReactants().get(i);
- r.getLine().addPoint((Point2D) pdfirstpart.getEndPoint().clone());
+ r.getLine().getEndPoint().setLocation(operatorLine.getBeginPoint());
andOperator.addInput(r);
}
reaction.addNode(andOperator);
+ } else {
+ PolylineData operatorLine = lines.get(AndOperator.class);
+ for (int i = 1; i < operatorLine.getPoints().size(); i++) {
+ reactantLine.addPoint(operatorLine.getPoints().get(i));
+ }
+ reactant.setLine(PolylineDataFactory.removeCollinearPoints(reactantLine));
}
if (reaction.getProducts().size() > 1) {
- PolylineData operatorLine = new PolylineData();
- operatorLine.setColor(pdsecondpart.getColor());
+ PolylineData operatorLine = lines.get(SplitOperator.class);
- operatorLine.addPoint((Point2D) pdsecondpart.getBeginPoint().clone());
- pdsecondpart.trimBegin(centralLength / SPLIT_OPERATOR_CENTRAL_LINE_RATIO);
- operatorLine.addPoint((Point2D) pdsecondpart.getBeginPoint().clone());
SplitOperator splitOperator = new SplitOperator();
splitOperator.addOutput(product);
- splitOperator.setLine(operatorLine);
+ splitOperator.setLine(operatorLine.reverse());
for (int i = 1; i < reaction.getProducts().size(); i++) {
Product r = reaction.getProducts().get(i);
- r.getLine().addPoint(0, (Point2D) pdsecondpart.getBeginPoint().clone());
+ r.getLine().getBeginPoint().setLocation(operatorLine.getEndPoint());
splitOperator.addOutput(r);
}
reaction.addNode(splitOperator);
+ } else {
+ PolylineData operatorLine = lines.get(SplitOperator.class);
+ for (int i = 0; i < operatorLine.getPoints().size()-1; i++) {
+ productLine.addPoint(i, operatorLine.getPoints().get(i));
+ }
+ product.setLine(PolylineDataFactory.removeCollinearPoints(productLine));
}
for (Edge e : interaction.getModifiers()) {
@@ -704,7 +697,9 @@ public class ModelContructor {
}
}
- createReactionCenterLine(reaction);
+ PolylineData modifierLine = lines.get(Modifier.class);
+ modifierLine.setType(rld.getLineType());
+ reaction.setLine(modifierLine);
ModifierTypeUtils mtu = new ModifierTypeUtils();
for (Modifier m : reaction.getModifiers()) {
@@ -715,36 +710,8 @@ public class ModelContructor {
return reaction;
}
- private void createReactionCenterLine(Reaction reaction) {
- AbstractNode input = reaction.getReactants().get(0);
- AbstractNode output = reaction.getProducts().get(0);
-
- for (NodeOperator operator : reaction.getOperators()) {
- if (operator.isReactantOperator()) {
- input = operator;
- } else if (operator.isProductOperator()) {
- output = operator;
- }
- }
- PolylineData line = new PolylineData();
-
- input.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
- line.addPoint(pt.copyPoint(input.getLine().getEndPoint()));
-
- if (output instanceof NodeOperator) {
- output.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
- line.addPoint(pt.copyPoint(output.getLine().getEndPoint()));
- } else {
- output.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
- line.addPoint(pt.copyPoint(output.getLine().getBeginPoint()));
- }
- line.setType(input.getLine().getType());
- line.setColor(input.getLine().getColor());
- reaction.setLine(line);
- }
-
/**
- * Creates {@link Reactant} from gpml edge.
+ * Creates {@link Reactant} from GPML edge.
*
* @param data
* ...
@@ -777,13 +744,13 @@ public class ModelContructor {
}
/**
- * Creates {@link Product} from gpml edge.
+ * Creates {@link Product} from GPML edge.
*
* @param data
* ...
* @param e
* edge
- * @return {@link Product} from gpml edge
+ * @return {@link Product} from GPML edge
*/
protected Product createProductFromEdge(Data data, Edge e) {
String id = null;
@@ -793,7 +760,7 @@ public class ModelContructor {
id = e.getEnd();
}
if (id == null) {
- throw new InvalidStateException("This product is invalid");
+ throw new InvalidStateException("[" + e.getGraphId() + "]\tThis product is invalid");
}
Product pro = new Product();
pro.setElement(data.id2alias.get(id));
@@ -896,7 +863,7 @@ public class ModelContructor {
model.setWidth(graph.getBoardWidth());
model.setHeight(graph.getBoardHeight());
- addComplexSpecies(model, graph, data);
+ addComplex(model, graph, data);
addElement(model, graph, data);
putSpeciesIntoComplexes(graph, data);
@@ -924,31 +891,68 @@ public class ModelContructor {
notes = StringEscapeUtils.unescapeHtml4(notes);
}
model.setNotes(notes);
- StringBuilder references = new StringBuilder("");
- for (String string : graph.getBiopaxReferences()) {
- references.append(string + ", ");
- }
- if (references.length() > 0) {
- logger.warn("[Biopax, " + references.toString() + "]\tModel annotations are not supported.");
- }
+ model.addMiriamData(new BiopaxFactory().getMiriamData(graph.getBiopaxData(), graph.getBiopaxReferences()));
data.layer.addLayerLines(createLines(graph));
if (!data.layer.isEmpty()) {
model.getLayers().add(data.layer);
}
+ if (!data.shapeLabelLayer.isEmpty()) {
+ model.getLayers().add(data.shapeLabelLayer);
+ }
assignNamesToComplexes(model);
assignNamesToCompartments(model);
putAliasesIntoCompartments(model);
+ putMissingZIndexes(model.getDrawables());
+
return model;
} catch (UnknownChildClassException e) {
throw new ConverterException(e);
}
}
+ private void putMissingZIndexes(Collection<Drawable> bioEntities) {
+ int maxZIndex = 0;
+ for (Drawable bioEntity : bioEntities) {
+ if (bioEntity.getZ() != null) {
+ maxZIndex = Math.max(maxZIndex, bioEntity.getZ());
+ }
+ }
+
+ for (Drawable bioEntity : bioEntities) {
+ if (bioEntity.getZ() == null) {
+ Integer index = null;
+ if (bioEntity instanceof Complex) {
+ index = getMinZIndex(((Complex) bioEntity).getAllChildren());
+ }
+
+ if (index == null) {
+ index = ++maxZIndex;
+ } else {
+ index--;
+ }
+ bioEntity.setZ(index);
+ }
+ }
+
+ }
+
+ private Integer getMinZIndex(List<Species> allChildren) {
+ Integer result = null;
+ for (Species species : allChildren) {
+ if (species.getZ() != null) {
+ if (result == null)
+ result = species.getZ();
+ result = Math.min(result, species.getZ());
+ }
+ }
+ return result;
+ }
+
/**
* Method that put {@link Species aliases} that are not assigned into any
* {@link Compartment} into a proper compartment.
@@ -1024,18 +1028,20 @@ public class ModelContructor {
if (alias instanceof Complex) {
if (alias.getName() == null || (alias.getName().isEmpty())) {
for (Layer layer : model.getLayers()) {
- LayerText toRemove = null;
- for (LayerText lt : layer.getTexts()) {
- if (alias.contains(lt)) {
- alias.setName(lt.getNotes());
- toRemove = lt;
+ if (layer.getName().equals("defaultLayer")) {
+ LayerText toRemove = null;
+ for (LayerText lt : layer.getTexts()) {
+ if (alias.contains(lt)) {
+ alias.setName(lt.getNotes());
+ toRemove = lt;
+ break;
+ }
+ }
+ if (toRemove != null) {
+ layer.removeLayerText(toRemove);
break;
}
}
- if (toRemove != null) {
- layer.removeLayerText(toRemove);
- break;
- }
}
}
}
@@ -1043,21 +1049,22 @@ public class ModelContructor {
}
/**
- * Tries to find a name to assign to compartments if comparments don't contain
+ * Tries to find a name to assign to compartments if compartments don't contain
* them.
*
* @param model
* model where compartments are placed
*/
private void assignNamesToCompartments(Model model) {
- for (Element alias : model.getElements()) {
- if (alias instanceof Compartment) {
- if (alias.getName() == null || alias.getName().isEmpty()) {
- for (Layer layer : model.getLayers()) {
+ for (Compartment compartment : model.getCompartments()) {
+ if (compartment.getName() == null || compartment.getName().isEmpty()) {
+ for (Layer layer : model.getLayers()) {
+ if (layer.getName().equals("defaultLayer")) {
LayerText toRemove = null;
for (LayerText lt : layer.getTexts()) {
- if (alias.contains(lt)) {
- alias.setName(lt.getNotes());
+ if (compartment.contains(lt)) {
+ compartment.setName(lt.getNotes());
+ compartment.setNamePoint(new Point2D.Double(lt.getX(), lt.getY()));
toRemove = lt;
break;
}
@@ -1141,6 +1148,11 @@ public class ModelContructor {
*/
private Layer layer;
+ /**
+ * Default layer.
+ */
+ private Layer shapeLabelLayer;
+
/**
* Default constructor.
*/
@@ -1150,6 +1162,10 @@ public class ModelContructor {
layer.setVisible(true);
layer.setLayerId("1");
layer.setName("defaultLayer");
+ shapeLabelLayer = new Layer();
+ shapeLabelLayer.setVisible(true);
+ shapeLabelLayer.setLayerId("2");
+ shapeLabelLayer.setName("shapeLabelLayer");
}
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index af1a751a67e6e49fa5fd1f2dca63e3f845258874..ffc86624258d3625c019e9c343faf3f08215cce0 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.wikipathway.XML;
+import java.awt.Color;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.util.HashSet;
@@ -9,6 +10,7 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.BioEntity;
@@ -66,6 +68,8 @@ public class ModelToGPML {
*/
private BiopaxParser biopaxParser = new BiopaxParser();
+ private ColorParser colorParser = new ColorParser();
+
/**
* Returns new unique identifier for the model.
*
@@ -198,7 +202,7 @@ public class ModelToGPML {
* This function calculates PolylineData based on ReactionNode.
*
* @param rn
- * rection node for which polyline is calculated
+ * reaction node for which polyline is calculated
* @param mainLine
* main line to which polyline is attached
* @return polyline for {@link ReactionNode}
@@ -265,11 +269,11 @@ public class ModelToGPML {
/**
* This function transform Compartments into Shapes (Oval or Rectangle) from
- * PathVisio. LineThickness=3.0 and Color=ffcc66. It can be easily changed.
+ * PathVisio.
*
* @param model
* model where compartments are placed
- * @return String that encodes all compartments in gpml format
+ * @return String that encodes all compartments in GPML format
*/
private String getComparments(Model model) {
StringBuilder comparments = new StringBuilder("");
@@ -288,9 +292,17 @@ public class ModelToGPML {
comparments.append(" <Attribute Key=\"org.pathvisio.CellularComponentProperty\" Value=\"Cell\" />\n");
comparments.append(" <Attribute Key=\"org.pathvisio.DoubleLineProperty\" Value=\"Double\" />\n");
comparments.append(
- " <Graphics CenterX=\"" + x + "\" CenterY=\"" + y + "\" Width=\"" + w + "\" Height=\"" + h
- + "\" ZOrder=\"" + ca.getZ() + "\" FontSize=\"20\" Valign=\"Bottom\" ShapeType=\"" + shape
- + "\" LineThickness=\"3.0\" Color=\"ffcc66\" Rotation=\"0.0\" />\n");
+ " <Graphics CenterX=\"" + x + "\" "
+ + "CenterY=\"" + y + "\" "
+ + "Width=\"" + w + "\" "
+ + "Height=\"" + h + "\" "
+ + "ZOrder=\"" + ca.getZ() + "\" "
+ + "FontSize=\"" + ca.getFontSize() + "\" "
+ + "Valign=\"Bottom\" "
+ + "ShapeType=\"" + shape + "\" "
+ + "LineThickness=\"3.0\" "
+ + "Color=\"" + colorToString(ca.getFillColor()) + "\" "
+ + "Rotation=\"0.0\" />\n");
comparments.append(" </Shape>\n");
}
return comparments.toString();
@@ -302,7 +314,7 @@ public class ModelToGPML {
* model).
*
* @param rn
- * object representing rectanat/product/modifier
+ * object representing reactant/product/modifier
* @param anchId
* identifier of the anchor where it will be connected
* @param anchors
@@ -326,7 +338,10 @@ public class ModelToGPML {
interaction.append(" <Interaction GraphId=\"" + getNewId() + "\">\n");
interaction.append(" <Attribute Key=\"org.pathvisio.core.ds\" Value=\"\"/>\n");
interaction.append(" <Attribute Key=\"org.pathvisio.core.id\" Value=\"\"/>\n");
- interaction.append(" <Graphics ConnectorType=\"Segmented\" ZOrder=\"32827\" LineThickness=\"1.0\">\n");
+ interaction.append(" <Graphics "
+ + "ConnectorType=\"Segmented\" "
+ + "ZOrder=\"" + rn.getReaction().getZ() + "\" "
+ + "LineThickness=\"" + rn.getLine().getWidth() + "\">\n");
if (rn instanceof Reactant) {
for (Point2D p2d : line.getPoints()) {
@@ -385,7 +400,7 @@ public class ModelToGPML {
}
/**
- * This function encode SpeciesAliases into DataNodes from .gpml format. Empty
+ * This function encode SpeciesAliases into DataNodes from GPML format. Empty
* complexes are also transformed into DataNodes.
*
* @param model
@@ -398,45 +413,33 @@ public class ModelToGPML {
protected String getDataNodes(Model model) throws ConverterException {
StringBuilder dataNodes = new StringBuilder("");
- for (Species sa : model.getNotComplexSpeciesList()) {
- if (!(sa instanceof Complex)) {
- dataNodes.append(" <DataNode TextLabel=\"" + sa.getName() + "\" GraphId=\"" + sa.getElementId() + "\" Type=\""
- + getType(sa) + "\"");
- if (sa.getComplex() != null) {
- dataNodes.append(" GroupRef=\"" + sa.getComplex().getElementId() + "\"");
+ for (Species species : model.getNotComplexSpeciesList()) {
+ if (!(species instanceof Complex)) {
+ dataNodes.append(
+ " <DataNode TextLabel=\"" + species.getName() + "\" GraphId=\"" + species.getElementId() + "\" Type=\""
+ + getType(species) + "\"");
+ if (species.getComplex() != null) {
+ dataNodes.append(" GroupRef=\"" + species.getComplex().getElementId() + "\"");
}
dataNodes.append(">\n");
- dataNodes.append(" <Comment>" + sa.getNotes() + "</Comment>\n");
- dataNodes.append(biopaxParser.toReferenceXml(sa.getMiriamData()));
+ dataNodes.append(" <Comment>" + species.getNotes() + "</Comment>\n");
+ dataNodes.append(biopaxParser.toReferenceXml(species.getMiriamData()));
- String red = Integer.toHexString(sa.getFillColor().getRed());
- String green = Integer.toHexString(sa.getFillColor().getGreen());
- String blue = Integer.toHexString(sa.getFillColor().getBlue());
- if (red.length() == 1) {
- red = "0" + red;
- }
- if (green.length() == 1) {
- green = "0" + green;
- }
- if (blue.length() == 1) {
- blue = "0" + blue;
- }
- String color = red + green + blue;
- Rectangle2D rec = sa.getBorder();
+ Rectangle2D rec = species.getBorder();
dataNodes.append(
- " <Graphics CenterX=\"" + rec.getCenterX() +
- "\" CenterY=\"" + rec.getCenterY() +
- "\" Width=\"" + rec.getWidth() +
- "\" Height=\"" + rec.getHeight() +
- "\" ZOrder=\"" + sa.getZ() +
- "\" FontSize=\"10\"" +
- " Valign=\"Middle\" "
- + "Color=\"" + "0000ff"
- + "\" FillColor=\"" + color + "\"/>\n");
-
- dataNodes.append(referenceParser.toXml(sa.getMiriamData()));
+ " <Graphics CenterX=\"" + rec.getCenterX() + "\" " +
+ "CenterY=\"" + rec.getCenterY() + "\" " +
+ "Width=\"" + rec.getWidth() + "\" " +
+ "Height=\"" + rec.getHeight() + "\" " +
+ "ZOrder=\"" + species.getZ() + "\" " +
+ "FontSize=\"" + species.getFontSize() + "\" " +
+ "Valign=\"Middle\" " +
+ "Color=\"" + colorToString(species.getFontColor()) + "\" " +
+ "FillColor=\"" + colorToString(species.getFillColor()) + "\"/>\n");
+
+ dataNodes.append(referenceParser.toXml(species.getMiriamData()));
dataNodes.append(" </DataNode>\n");
}
}
@@ -455,16 +458,16 @@ public class ModelToGPML {
Rectangle2D rec = ca.getBorder();
dataNodes.append(
- " <Graphics CenterX=\"" + rec.getCenterX() +
- "\" CenterY=\"" + rec.getCenterY() +
- "\" Width=\"" + rec.getWidth() +
- "\" Height=\"" + rec.getHeight() +
- "\" ZOrder=\"" + ca.getZ() +
- "\" FontSize=\"10\"" +
- " Valign=\"Middle\" " +
- "Color=\"0000ff\" " +
- "FillColor=\"ffffcc\"" +
- " LineStyle=\"Broken\"/>\n");
+ " <Graphics CenterX=\"" + rec.getCenterX() + "\" " +
+ "CenterY=\"" + rec.getCenterY() + "\" " +
+ "Width=\"" + rec.getWidth() + "\" " +
+ "Height=\"" + rec.getHeight() + "\" " +
+ "ZOrder=\"" + ca.getZ() + "\" " +
+ "FontSize=\"" + ca.getFontSize() + "\" " +
+ "Valign=\"Middle\" " +
+ "Color=\"" + colorToString(ca.getFontColor()) + "\" " +
+ "FillColor=\"" + colorToString(ca.getFillColor()) + "\" " +
+ "LineStyle=\"Broken\"/>\n");
dataNodes.append(referenceParser.toXml(ca.getMiriamData()));
dataNodes.append(" </DataNode>\n");
@@ -475,11 +478,11 @@ public class ModelToGPML {
}
/**
- * This function encode ComplexAliases into Groups from .gpml format.
+ * This function encode ComplexAliases into Groups from GPML format.
*
* @param model
* model where aliases are placed
- * @return string representing groups in gpml format
+ * @return string representing groups in GPML format
*/
protected String getGroups(Model model) {
StringBuilder groups = new StringBuilder("");
@@ -497,11 +500,11 @@ public class ModelToGPML {
}
/**
- * This function encode Reactions into Interactions from .gpml format.
+ * This function encode Reactions into Interactions from GPML format.
*
* @param model
* model where reactions are placed
- * @return string with interactions in gpml format
+ * @return string with interactions in GPML format
* @throws ConverterException
* thrown when there is a problem with conversion
*/
@@ -514,11 +517,10 @@ public class ModelToGPML {
interactions.append(" <Interaction GraphId=\"" + reaction.getIdReaction() + "\">\n");
interactions.append(biopaxParser.toReferenceXml(reaction.getMiriamData()));
- // interactions.append(" <Attribute Key=\"org.pathvisio.core.ds\"
- // Value=\"\"/>\n");
- // interactions.append(" <Attribute Key=\"org.pathvisio.core.id\"
- // Value=\"\"/>\n");
- interactions.append(" <Graphics ConnectorType=\"Segmented\" ZOrder=\"32827\" LineThickness=\"1.0\">\n");
+ interactions.append(" <Graphics "
+ + "ConnectorType=\"Segmented\" "
+ + "ZOrder=\"" + reaction.getZ() + "\" "
+ + "LineThickness=\"" + reaction.getLine().getWidth() + "\">\n");
/** Start and End **/
Reactant start = reaction.getReactants().get(0);
@@ -575,11 +577,11 @@ public class ModelToGPML {
}
/**
- * This function returns Model in .gpml format.
+ * This function returns Model in GPML format.
*
* @param model
* model to transform
- * @return string in gpml format representing model
+ * @return string in GPML format representing model
* @throws ConverterException
* thrown when there is a problem with conversion
*/
@@ -608,4 +610,8 @@ public class ModelToGPML {
return gpml.toString();
}
+
+ private String colorToString(Color color) {
+ return colorParser.colorToHtml(color).substring(1);
+ }
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinder.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinder.java
new file mode 100644
index 0000000000000000000000000000000000000000..0e07207c462112f8465d11f1e860930874373d13
--- /dev/null
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinder.java
@@ -0,0 +1,315 @@
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.wikipathway.model.Edge;
+import lcsb.mapviewer.wikipathway.model.Interaction;
+import lcsb.mapviewer.wikipathway.utils.Geo;
+
+class ReactionLayoutFinder {
+
+ @SuppressWarnings("unused")
+ private Logger logger = LogManager.getLogger();
+
+ private LineTransformation lt = new LineTransformation();
+ private PointTransformation pt = new PointTransformation();
+
+ private Interaction interaction;
+
+ /**
+ * Return coordinates where all {@link Reactant} should end, all
+ * {@link Modifier} should end, and all {@link Product} should start.
+ *
+ * @param interaction
+ * GPML {@link Interaction}
+ * @return map consisted of three entries for classes: {@link Product},
+ * {@link Reactant}, {@link Modifier}
+ */
+ public Map<Class<?>, Point2D> getNodeStartPoints(Interaction interaction) {
+ this.interaction = interaction;
+ List<Pair<Class<?>, Point2D>> possiblePoints = getPointsInOrder(interaction);
+ Point2D modifierPoint = getModifierPoint(possiblePoints);
+ Point2D reactantPoint = getReactantPoint(possiblePoints, modifierPoint);
+ Point2D productPoint = getProductPoint(possiblePoints, modifierPoint);
+
+ Map<Class<?>, Point2D> result = new HashMap<>();
+ result.put(Reactant.class, reactantPoint);
+ result.put(Product.class, productPoint);
+ result.put(Modifier.class, modifierPoint);
+
+ return result;
+ }
+
+ public Map<Class<?>, PolylineData> getNodeLines(Interaction interaction) {
+ Map<Class<?>, Point2D> points = getNodeStartPoints(interaction);
+
+
+ Map<Class<?>, PolylineData> result = new HashMap<>();
+ PolylineData reactantLine = getSubline(interaction.getLine(), interaction.getLine().getBeginPoint(),
+ points.get(Reactant.class));
+ PolylineData inputReactionLine = getSubline(interaction.getLine(), points.get(Reactant.class),
+ points.get(Modifier.class));
+ inputReactionLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2);
+
+ PolylineData outputReactionLine = getSubline(interaction.getLine(),
+ points.get(Modifier.class), points.get(Product.class));
+
+ outputReactionLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2);
+ PolylineData productLine = getSubline(interaction.getLine(),
+ points.get(Product.class), interaction.getLine().getEndPoint());
+ PolylineData modifierLine = new PolylineData(pt.copyPoint(inputReactionLine.getEndPoint()),
+ pt.copyPoint(outputReactionLine.getBeginPoint()));
+ modifierLine.setColor(interaction.getColor());
+ modifierLine.setWidth(productLine.getWidth());
+
+ result.put(Reactant.class, reactantLine);
+ result.put(Product.class, productLine);
+ result.put(Modifier.class, modifierLine);
+ result.put(AndOperator.class, inputReactionLine);
+ result.put(SplitOperator.class, outputReactionLine);
+
+ return result;
+ }
+
+ private List<Pair<Class<?>, Point2D>> getPointsInOrder(Interaction interaction) {
+ PolylineData pd = interaction.getLine();
+ List<Pair<Class<?>, Point2D>> possiblePoints = new ArrayList<>();
+ for (Edge e : interaction.getReactants()) {
+ if (pointOnPolyline(pd, e.getLine().getEndPoint())) {
+ possiblePoints.add(new Pair<>(Reactant.class, e.getLine().getEndPoint()));
+ } else if (pointOnPolyline(pd, e.getLine().getBeginPoint())) {
+ possiblePoints.add(new Pair<>(Reactant.class, e.getLine().getBeginPoint()));
+ }
+ }
+ for (Edge e : interaction.getProducts()) {
+ if (pointOnPolyline(pd, e.getLine().getEndPoint())) {
+ possiblePoints.add(new Pair<>(Product.class, e.getLine().getEndPoint()));
+ } else if (pointOnPolyline(pd, e.getLine().getBeginPoint())) {
+ possiblePoints.add(new Pair<>(Product.class, e.getLine().getBeginPoint()));
+ }
+ }
+ for (Edge e : interaction.getModifiers()) {
+ if (pointOnPolyline(pd, e.getLine().getEndPoint())) {
+ possiblePoints.add(new Pair<>(Modifier.class, e.getLine().getEndPoint()));
+ } else if (pointOnPolyline(pd, e.getLine().getBeginPoint())) {
+ possiblePoints.add(new Pair<>(Modifier.class, e.getLine().getBeginPoint()));
+ }
+ }
+ Comparator<Pair<Class<?>, Point2D>> comparator = new Comparator<Pair<Class<?>, Point2D>>() {
+
+ @Override
+ public int compare(Pair<Class<?>, Point2D> o1, Pair<Class<?>, Point2D> o2) {
+ double dist1 = distanceFromPolylineStart(pd, o1.getRight());
+ double dist2 = distanceFromPolylineStart(pd, o2.getRight());
+ return new DoubleComparator(Configuration.EPSILON).compare(dist1, dist2);
+ }
+ };
+
+ Collections.sort(possiblePoints, comparator);
+ return possiblePoints;
+ }
+
+ private Point2D getProductPoint(List<Pair<Class<?>, Point2D>> possiblePoints, Point2D modifierPoint) {
+ Point2D result = null;
+ for (Pair<Class<?>, Point2D> pair : possiblePoints) {
+ if (pair.getLeft().equals(Product.class)) {
+ if (distanceFromPolylineStart(interaction.getLine(),
+ modifierPoint) < distanceFromPolylineStart(interaction.getLine(), pair.getRight())) {
+ result = pair.getRight();
+ break;
+ }
+ }
+ }
+ if (result == null) {
+ for (Point2D point : interaction.getLine().getPoints()) {
+ if (distanceFromPolylineStart(interaction.getLine(),
+ modifierPoint) < distanceFromPolylineStart(interaction.getLine(), point)) {
+ double x = modifierPoint.getX() + (point.getX() - modifierPoint.getX()) / 2;
+ double y = modifierPoint.getY() + (point.getY() - modifierPoint.getY()) / 2;
+ result = new Point2D.Double(x, y);
+ break;
+ }
+ }
+ }
+ return result;
+ }
+
+ private Point2D getReactantPoint(List<Pair<Class<?>, Point2D>> possiblePoints, Point2D modifierPoint) {
+ Point2D result = null;
+ for (Pair<Class<?>, Point2D> pair : possiblePoints) {
+ if (pair.getLeft().equals(Reactant.class)) {
+ if (distanceFromPolylineStart(interaction.getLine(),
+ modifierPoint) > distanceFromPolylineStart(interaction.getLine(), pair.getRight())) {
+ result = pair.getRight();
+ }
+ }
+ }
+ if (result == null) {
+ for (Point2D point : interaction.getLine().getPoints()) {
+ if (distanceFromPolylineStart(interaction.getLine(),
+ modifierPoint) > distanceFromPolylineStart(interaction.getLine(), point)) {
+ double x = modifierPoint.getX() + (point.getX() - modifierPoint.getX()) / 2;
+ double y = modifierPoint.getY() + (point.getY() - modifierPoint.getY()) / 2;
+ result = new Point2D.Double(x, y);
+ }
+ }
+ }
+ return result;
+ }
+
+ private Point2D getModifierPoint(List<Pair<Class<?>, Point2D>> points) {
+ List<Pair<Class<?>, Point2D>> possiblePoints = new ArrayList<>(points);
+ int productPoints = 0;
+ int reactantPoints = 0;
+ for (Pair<Class<?>, Point2D> pair : possiblePoints) {
+ if (pair.getLeft().equals(Product.class)) {
+ productPoints++;
+ } else if (pair.getLeft().equals(Reactant.class)) {
+ reactantPoints++;
+ }
+ }
+ int countedReactants = 0;
+ int countedProducts = 0;
+ int score = Integer.MIN_VALUE;
+ Point2D point = null;
+ for (Pair<Class<?>, Point2D> pair : possiblePoints) {
+ if (pair.getLeft().equals(Product.class)) {
+ countedProducts++;
+ } else if (pair.getLeft().equals(Reactant.class)) {
+ countedReactants++;
+ } else if (pair.getLeft().equals(Modifier.class)) {
+ int currentScore = countedReactants + (productPoints - countedProducts);
+ if (point == null || score < currentScore) {
+ score = currentScore;
+ point = pair.getRight();
+ }
+ }
+ }
+
+ if (point == null) {
+ possiblePoints.add(0, new Pair<Class<?>, Point2D>(null, interaction.getLine().getBeginPoint()));
+ possiblePoints.add(new Pair<Class<?>, Point2D>(null, interaction.getLine().getEndPoint()));
+ countedReactants = 0;
+ countedProducts = 0;
+
+ Point2D previousPoint = null;
+ for (Pair<Class<?>, Point2D> pair : possiblePoints) {
+ if (previousPoint != null) {
+ int currentScore = countedReactants + (productPoints - countedProducts);
+ if (point == null || score < currentScore) {
+ score = currentScore;
+ if (reactantPoints == 0) { // shift to most right possible line when there are no other reactants
+ point = getRightCenterPoint(interaction.getLine(), previousPoint, pair.getRight());
+ } else if (productPoints == 0) {
+ point = getLeftCenterPoint(interaction.getLine(), previousPoint, pair.getRight());
+ } else {
+ point = getCenterPoint(interaction.getLine(), previousPoint, pair.getRight());
+ }
+ }
+ }
+ if (pair.getLeft() == Product.class) {
+ countedProducts++;
+ } else if (pair.getLeft() == Reactant.class) {
+ countedReactants++;
+ }
+ previousPoint = pair.getRight();
+ }
+ }
+ return point;
+ }
+
+ private Point2D getCenterPoint(PolylineData originalPolylineData, Point2D startPoint, Point2D endPoint) {
+ PolylineData pd = getSubline(originalPolylineData, startPoint, endPoint);
+ return getCenterPoint(pd);
+ }
+
+ private Point2D getLeftCenterPoint(PolylineData originalPolylineData, Point2D startPoint, Point2D endPoint) {
+ PolylineData pd = getSubline(originalPolylineData, startPoint, endPoint);
+ double x = pd.getPoints().get(0).getX() + (pd.getPoints().get(1).getX() - pd.getPoints().get(0).getX()) / 2;
+ double y = pd.getPoints().get(0).getY() + (pd.getPoints().get(1).getY() - pd.getPoints().get(0).getY()) / 2;
+ return new Point2D.Double(x, y);
+ }
+
+ private Point2D getRightCenterPoint(PolylineData originalPolylineData, Point2D startPoint, Point2D endPoint) {
+ PolylineData pd = getSubline(originalPolylineData, startPoint, endPoint);
+ int points = pd.getPoints().size();
+ double x = pd.getPoints().get(points - 2).getX()
+ + (pd.getPoints().get(points - 1).getX() - pd.getPoints().get(points - 2).getX()) / 2;
+ double y = pd.getPoints().get(points - 2).getY()
+ + (pd.getPoints().get(points - 1).getY() - pd.getPoints().get(points - 2).getY()) / 2;
+ return new Point2D.Double(x, y);
+ }
+
+ private PolylineData getSubline(PolylineData originalPolylineData, Point2D startPoint, Point2D endPoint) {
+ int start = 0;
+ int end = originalPolylineData.getPoints().size() - 1;
+ for (int i = 0; i < originalPolylineData.getPoints().size(); i++) {
+ if (distanceFromPolylineStart(originalPolylineData, startPoint) > distanceFromPolylineStart(originalPolylineData,
+ originalPolylineData.getPoints().get(i))) {
+ start = i;
+ }
+ if (distanceFromPolylineStart(originalPolylineData, endPoint) < distanceFromPolylineStart(originalPolylineData,
+ originalPolylineData.getPoints().get(i))) {
+ end = Math.min(end, i);
+ }
+ }
+ PolylineData result = originalPolylineData.getSubline(start, end + 1);
+ result.setStartPoint(pt.copyPoint(startPoint));
+ result.setEndPoint(pt.copyPoint(endPoint));
+ return PolylineDataFactory.removeCollinearPoints(result);
+ }
+
+ private Point2D getCenterPoint(PolylineData pd) {
+ List<Line2D> lines = pd.getLines();
+ double lenght = 0.0;
+ for (Line2D line : lines) {
+ lenght += Geo.lineLen(line);
+ }
+ double tmp = 0.0;
+ for (Line2D line : lines) {
+ if (tmp + Geo.lineLen(line) > lenght / 2) {
+ double x = line.getX1() + (line.getX2() - line.getX1()) / 2;
+ double y = line.getY1() + (line.getY2() - line.getY1()) / 2;
+ return new Point2D.Double(x, y);
+ } else {
+ tmp += Geo.lineLen(line);
+ }
+ }
+ return pt.copyPoint(pd.getEndPoint());
+ }
+
+ double distanceFromPolylineStart(PolylineData line, Point2D point) {
+ double distance = 0;
+ for (Line2D l : line.getLines()) {
+ if (lt.distBetweenPointAndLineSegment(l, point) <= Configuration.EPSILON) {
+ return distance + point.distance(l.getP1());
+ }
+ distance += l.getP1().distance(l.getP2());
+ }
+ throw new InvalidArgumentException("Point doesn't lay on the line");
+ }
+
+ private boolean pointOnPolyline(PolylineData line, Point2D point) {
+ for (Line2D l : line.getLines()) {
+ if (lt.distBetweenPointAndLineSegment(l, point) <= Configuration.EPSILON) {
+ return true;
+ }
+ }
+ return false;
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
index f2efd4e5da3c5707f0cafbb68e8fcc1232ae4a37..3439c7fd94af2f96f509d2be4fb996f1ecac68de 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
@@ -15,7 +15,7 @@ import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.wikipathway.model.ReferenceMapping;
/**
- * Parser used to extract {@link MiriamData refernces} in miriam format from
+ * Parser used to extract {@link MiriamData references} in miriam format from
* GPML data.
*
* @author Piotr Gawron
@@ -35,7 +35,7 @@ public class ReferenceParser extends ElementGpmlParser<MiriamData> {
* - resource identifier
* @param db
* -database type
- * @return {@link MiriamData} object referenceing to the resource
+ * @return {@link MiriamData} object referencing to the resource
*/
protected MiriamData createMiriamData(String id, String db) {
if (db == null || db.equals("")) {
@@ -67,6 +67,26 @@ public class ReferenceParser extends ElementGpmlParser<MiriamData> {
}
}
+ public MiriamData hrefToMiriamData(String href) {
+ if (href == null) {
+ return null;
+ }
+ if (href.startsWith("https://omim.org/entry/")) {
+ return new MiriamData(MiriamType.OMIM, href.replaceAll("https://omim.org/entry/", ""));
+ }
+ if (href.startsWith("http://omim.org/entry/")) {
+ return new MiriamData(MiriamType.OMIM, href.replaceAll("http://omim.org/entry/", ""));
+ }
+ if (href.startsWith("https://omim.org/")) {
+ return new MiriamData(MiriamType.OMIM, href.replaceAll("https://omim.org/", ""));
+ }
+ if (href.startsWith("http://omim.org/")) {
+ return new MiriamData(MiriamType.OMIM, href.replaceAll("http://omim.org/", ""));
+ }
+ logger.warn("Don't know how to process href: " + href);
+ return null;
+ }
+
@Override
public MiriamData parse(Element node) {
String id = null;
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
index 532fdd97c23c7eb379bf3e8c90d68b11bdd5925b..cd1834340f271c4eb07094a2c2b4de658193e6fe 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
@@ -108,6 +108,7 @@ public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
switch (value) {
case ("Double"):
shape.setLineType(LineType.DOUBLE);
+ shape.setCompartment(true);
break;
default:
logger.warn(shape.getWarningPrefix() + "Unknown line type: " + value);
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
index 480dfef4fec3c4374d8d183ff5c67948b9e003bb..e3262048f1d0cc409965b29382c4f296152de8ff 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
@@ -7,7 +7,7 @@ import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.MiriamData;
/**
- * Class used to store data from DataNode from .gpml.
+ * Class used to store data from DataNode from GPML.
*
* @author Jan Badura
*
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
index 2fddb3e568501e598d8f53504740de1a984b4ef3..f808f3ad8e5a81b2c7a96c3ef064bc7ebbef6ed2 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
@@ -27,7 +27,13 @@ public enum Direction {
/**
* West.
*/
- WEST(Axis.EAST_WEST);
+ WEST(Axis.EAST_WEST),
+
+ /**
+ * None.
+ */
+ NONE(null),
+ ;
/**
* Defines axis in which direction lies (either {@link Axis#NORTH_SOUTH} or
@@ -36,7 +42,7 @@ public enum Direction {
private Axis axis;
/**
- * Default cosntructor.
+ * Default constructor.
*
* @param axis
* {@link #axis}
@@ -59,7 +65,11 @@ public enum Direction {
* @return next direction (by 90 degrees) in clockwise order
*/
public Direction nextClockwiseDirection() {
- return values()[(this.ordinal() + 1) % values().length];
+ Direction result = values()[(this.ordinal() + 1) % values().length];
+ if (result == NONE) {
+ result = values()[(this.ordinal() + 2) % values().length];
+ }
+ return result;
}
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
index 7baa8a54aaee6be32cf4da62743596f5147b0444..7b9d4d2f11d897d61265afce38ae96254c1bf4f0 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
@@ -29,7 +29,7 @@ public class Edge implements Serializable {
private static final long serialVersionUID = 1L;
/**
- * Epsilon valu used for comparison of doubles.
+ * Epsilon value used for comparison of doubles.
*/
private static final Double EPSILON = 1e-6;
@@ -39,7 +39,7 @@ public class Edge implements Serializable {
private final transient Logger logger = LogManager.getLogger(Edge.class);
/**
- * Identifier in gpml model.
+ * Identifier in GPML model.
*/
private String graphId;
@@ -69,9 +69,11 @@ public class Edge implements Serializable {
private PolylineData line = new PolylineData();
/**
- * Gpml interaction type (arrow).
+ * GPML interaction type (arrow).
*/
private GpmlInteractionType type = GpmlInteractionType.LINE;
+
+ private boolean reversibleReaction = false;
/**
* References for given edge.
@@ -89,7 +91,7 @@ public class Edge implements Serializable {
private List<String> comments = new ArrayList<>();
/**
- * List of identifiers used by biopax nodes that are inside gpml. These biopax
+ * List of identifiers used by BioPax nodes that are inside GPML. These BioPax
* nodes contain annotations.
*/
private List<String> biopaxReferences = new ArrayList<String>();
@@ -124,6 +126,7 @@ public class Edge implements Serializable {
this.comments.addAll(original.getComments());
this.biopaxReferences.addAll(original.getBiopaxReferences());
this.zOrder = original.getzOrder();
+ this.reversibleReaction = original.isReversibleReaction();
}
/**
@@ -467,4 +470,12 @@ public class Edge implements Serializable {
this.groupRef = groupRef;
}
+ public boolean isReversibleReaction() {
+ return reversibleReaction;
+ }
+
+ public void setReversibleReaction(boolean reversibleReaction) {
+ this.reversibleReaction = reversibleReaction;
+ }
+
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
index e789c9debc84a97275a71df7007dacbbca90556d..69efb26c026e0bc9b0e100bb524689d2db250303 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
@@ -45,7 +45,7 @@ public class Graph implements Serializable {
private double boardHeight;
/**
- * Information about biopax data in the gpml file.
+ * Information about BioPax data in the GPML file.
*/
private BiopaxData biopaxData;
@@ -171,7 +171,11 @@ public class Graph implements Serializable {
dataNodes.put(node.getGraphId(), node);
nodes.put(node.getGraphId(), node);
if (node.getGroupRef() != null && !node.getGroupRef().equals("")) {
- groupsByGroupId.get(node.getGroupRef()).addNode(node);
+ if (groupsByGroupId.get(node.getGroupRef()) == null) {
+ logger.warn(node.getWarningPrefix() + "Missing group: " + node.getGroupRef());
+ } else {
+ groupsByGroupId.get(node.getGroupRef()).addNode(node);
+ }
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
index 2bb2c2bd468fb48c4e5d618bd6a9d98490b4f601..76174f80a8b0b4023b599d6b07d7b149671e4ee0 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
@@ -10,7 +10,7 @@ import lcsb.mapviewer.common.geometry.TextAlignment;
import lcsb.mapviewer.model.graphics.LineType;
/**
- * Class with common data for all Gpml elements that have a graphical
+ * Class with common data for all GPML elements that have a graphical
* representation on the map.
*
* @author Piotr Gawron
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java
index 563536b9f0ed99fb1c720797903e603b1331bad6..0c70c936581c3746772a858415d81b6287fd3918 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java
@@ -1,20 +1,23 @@
package lcsb.mapviewer.wikipathway.model;
-import java.awt.*;
+import java.awt.Color;
import java.io.Serializable;
import java.util.*;
-import java.util.List;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
/**
- * Class used to store data from Interaction from .gpml.
+ * Class used to store data from Interaction from GPML.
*
* @author Jan Badura
*
*/
public class Interaction implements Serializable {
+ static Logger logger = LogManager.getLogger();
/**
*
@@ -22,7 +25,7 @@ public class Interaction implements Serializable {
private static final long serialVersionUID = 1L;
/**
- * Identifier in gpml model.
+ * Identifier in GPML model.
*/
private String graphId;
@@ -67,28 +70,30 @@ public class Interaction implements Serializable {
/**
* List of edges representing reactants in interaction.
*/
- private Set<Edge> reactants = new HashSet<Edge>();
+ private Set<Edge> reactants = new HashSet<>();
/**
* List of edges representing products in interaction.
*/
- private Set<Edge> products = new HashSet<Edge>();
+ private Set<Edge> products = new HashSet<>();
/**
* List of edges representing modifiers in interaction.
*/
- private Set<Edge> modifiers = new HashSet<Edge>();
+ private Set<Edge> modifiers = new HashSet<>();
/**
- * Identifiers of biopax references.
+ * Identifiers of BioPax references.
*/
- private Set<String> biopaxReferences = new HashSet<String>();
+ private Set<String> biopaxReferences = new HashSet<>();
/**
* References for given edge.
*/
private List<MiriamData> references = new ArrayList<>();
+ private boolean reversible = false;
+
/**
* Default constructor.
*
@@ -108,13 +113,14 @@ public class Interaction implements Serializable {
setColor(edge.getColor());
this.comments.addAll(edge.getComments());
biopaxReferences.addAll(edge.getBiopaxReferences());
+ reversible = edge.isReversibleReaction();
}
/**
* Empty constructor that should be used only by serialization tools and
* subclasses.
*/
- protected Interaction() {
+ Interaction() {
}
/**
@@ -385,4 +391,12 @@ public class Interaction implements Serializable {
this.zOrder = zOrder;
}
+ public boolean isReversible() {
+ return reversible;
+ }
+
+ public void setReversible(boolean reversible) {
+ this.reversible = reversible;
+ }
+
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
index d6ba71d23cc78adc7652af090d386ecd27289168..9a59e192093576db4004662ebea56770d1d1d840 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
@@ -1,13 +1,23 @@
package lcsb.mapviewer.wikipathway.model;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import lcsb.mapviewer.model.map.MiriamData;
+
/**
- * Class used to store data from Label from .gpml.
+ * Class used to store data from Label from GPML.
*
* @author Jan Badura
*
*/
public class Label extends GraphicalPathwayElement {
+ static Logger logger = LogManager.getLogger();
+
/**
*
*/
@@ -38,6 +48,8 @@ public class Label extends GraphicalPathwayElement {
*/
private String groupRef;
+ private Set<MiriamData> references = new HashSet<>();
+
/**
* Sometimes {@link Label labels} are connected to reactions. This field
*/
@@ -169,4 +181,15 @@ public class Label extends GraphicalPathwayElement {
this.shape = shape;
}
+ public Set<MiriamData> getReferences() {
+ return references;
+ }
+
+ public void setReferences(Set<MiriamData> references) {
+ this.references = references;
+ }
+
+ public void addReference(MiriamData md) {
+ this.references.add(md);
+ }
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
index 4b0a7263e85e47154e805dfa4fe3d3a9900665e2..ad817852bfa0ba1bc8a4a68043ca8105376c6715 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
@@ -9,7 +9,7 @@ import java.util.List;
* Abstract class for pathway elements. It defines common functionalities for
* all elements in the model. There are two known subclasses:
* <ul>
- * <li>{@link GraphicalPathwayElement}, representing elemnts with some graphical
+ * <li>{@link GraphicalPathwayElement}, representing elements with some graphical
* representation</li>
* <li>{@link Group}, representing just groups of elements</li>
* </ul>
@@ -41,7 +41,7 @@ public abstract class PathwayElement implements Serializable {
/**
*
- * Reference to biopax node with references about this element.
+ * Reference to BioPax node with references about this element.
*/
private List<String> biopaxReferences = new ArrayList<>();
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
index a651e4af3e98a96233c4bcca32afe340593631a6..bff65363b8b948998d165a48faf8826744b669a4 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
@@ -7,7 +7,7 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
/**
- * Class that defines infgomration about point stored in gpml structures.
+ * Class that defines information about point stored in GPML structures.
*
* @author Piotr Gawron
*
@@ -20,7 +20,7 @@ public class PointData implements Serializable {
private static final long serialVersionUID = 1L;
/**
- * Defdault clas logger.
+ * Default class logger.
*/
private final transient Logger logger = LogManager.getLogger(PointData.class);
@@ -35,7 +35,7 @@ public class PointData implements Serializable {
private Double y;
/**
- * String identifing anchor point on the map.
+ * String identifying anchor point on the map.
*/
private String graphRef;
@@ -52,7 +52,7 @@ public class PointData implements Serializable {
private String relY;
/**
- * Type of line asociated with line that ends in this point.
+ * Type of line associated with line that ends in this point.
*/
private GpmlInteractionType type;
@@ -180,8 +180,10 @@ public class PointData implements Serializable {
return Direction.SOUTH;
} else if (relY.equals("-1.0")) {
return Direction.NORTH;
+ } else if (relX.equals("0.0") && relY.equals("0.0")) {
+ return Direction.NONE;
} else {
- logger.warn(
+ logger.warn("[" + graphRef + "]\t" +
"Cannot determine connection direction from values: relX=" + relX + "; relY=" + relY + ". Estimating...");
double xVal = Double.valueOf(relX);
double yVal = Double.valueOf(relY);
@@ -200,4 +202,10 @@ public class PointData implements Serializable {
}
}
}
+
+ @Override
+ public String toString() {
+ return "[" + this.getClass().getSimpleName() + " x=" + x + "; y=" + y + "; graphRef=" + graphRef + "; relX=" + relX
+ + "; relY=" + relY + "; type=" + type + "]";
+ }
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
index 8755fc2ebc6ed28f4916d039bf29f876d3a9a91d..4f5c2a2e490482e2b0ce2017efd8ca1e2abced72 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
@@ -1,7 +1,9 @@
package lcsb.mapviewer.wikipathway.model;
+import java.awt.Color;
+
/**
- * Class used to store data from Shape from .gpml.
+ * Class used to store data from Shape from GPML.
*
* @author Jan Badura
*
@@ -66,6 +68,7 @@ public class Shape extends GraphicalPathwayElement {
setTextLabel(null);
setGroupRef(null);
setCompartment(false);
+ setFillColor(Color.GRAY);
}
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxData.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxData.java
index 48b8c782c244708bcabb4fbed7128bfecaff6d09..60422b26e2b2ba444a15d7e1da3b0c2d4e5f795d 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxData.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxData.java
@@ -9,7 +9,7 @@ import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
/**
- * Element containg all biopax information parsed from gpml file.
+ * Element containing all BioPax information parsed from GPML file.
*
* @author Piotr Gawron
*
@@ -30,12 +30,12 @@ public class BiopaxData implements Serializable {
/**
* List of {@link BiopaxPublication publications}.
*/
- private Map<String, BiopaxPublication> publications = new HashMap<String, BiopaxPublication>();
+ private Map<String, BiopaxPublication> publications = new HashMap<>();
/**
- * List of {@link BiopaxOpenControlledVocabulary biopax vocabulary}.
+ * List of {@link BiopaxOpenControlledVocabulary BioPax vocabulary}.
*/
- private List<BiopaxOpenControlledVocabulary> openControlledVocabularies = new ArrayList<BiopaxOpenControlledVocabulary>();
+ private List<BiopaxOpenControlledVocabulary> openControlledVocabularies = new ArrayList<>();
/**
* @return the publications
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..ac63f06475c24a885664eb3b058fd75b6dd80655
--- /dev/null
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java
@@ -0,0 +1,66 @@
+package lcsb.mapviewer.wikipathway.model.biopax;
+
+import java.util.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.*;
+
+public class BiopaxFactory {
+ private Logger logger = LogManager.getLogger();
+
+ /**
+ * Creates {@link MiriamData annotation} from {@link BiopaxPublication}.
+ *
+ * @param publication
+ * input BioPax structure
+ * @return {@link MiriamData annotation}
+ */
+ public MiriamData createMiriamData(BiopaxPublication publication) {
+ if ("PubMed".equals(publication.getDb())) {
+ if (publication.getId() == null || publication.getId().equals("")) {
+ return null;
+ } else {
+ return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, publication.getId());
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown biopax database: " + publication.getDb());
+ }
+ }
+
+ /**
+ * Returns list of {@link MiriamData} that are referenced in {@link BiopaxData}
+ * with identifier given in biopaxReference.
+ *
+ * @param biopaxData
+ * {@link BiopaxData} where annotations are stored
+ * @param biopaxReference
+ * list of references (to data in {@link BiopaxData}) that we want to
+ * convert into {@link MiriamData}
+ * @return list of {@link MiriamData} that are referenced in {@link BiopaxData}
+ * with identifier given in biopaxReference.
+ */
+ public Collection<MiriamData> getMiriamData(BiopaxData biopaxData, Collection<String> biopaxReference) {
+ List<MiriamData> result = new ArrayList<>();
+ for (String string : biopaxReference) {
+ if (biopaxData != null) {
+ BiopaxPublication bp = biopaxData.getPublicationByReference(string);
+ if (bp != null) {
+ MiriamData md = createMiriamData(bp);
+ if (md != null) {
+ result.add(md);
+ } else {
+ logger.warn("[" + string + "]\tBiopax publication is invalid.");
+ }
+ } else {
+ logger.warn("[" + string + "]\tBiopax publication doesn't exist.");
+ }
+ } else {
+ logger.warn("[Biopax, " + string + "]\tInvalid BioPax reference.");
+ }
+ }
+ return result;
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublication.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublication.java
index 7960830511f434a586757bc65a4637b26ca3b91a..27bb5a00f658bfdf43b261a7c0dacfd64c2c73f7 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublication.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublication.java
@@ -3,7 +3,7 @@ package lcsb.mapviewer.wikipathway.model.biopax;
import java.io.Serializable;
/**
- * Describes biopax node with publication.
+ * Describes BioPax node with publication.
*
* @author Piotr Gawron
*
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java
index 71d92007b1965eaa3341a2774a44634f94025a16..dc9fa236c55a08f5f954a2f1fd6462fed6e01e0b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java
@@ -15,12 +15,12 @@ import lcsb.mapviewer.model.graphics.PolylineData;
public final class Geo {
/**
- * Max distance betwen point and line that still allows to match intersection.
+ * Max distance between point and line that still allows to match intersection.
*/
private static final int DISTANCE_PROXIMITY = 10;
/**
- * Default class constructor. Prevents instatiation.
+ * Default class constructor. Prevents instantiation.
*/
private Geo() {
@@ -134,55 +134,11 @@ public final class Geo {
return res;
}
- /**
- * This function returns point on the middle of rectangle side, that is closest
- * to the given point.
- *
- * @param rect
- * rectangle on which we look for a point
- * @param point
- * point to which result should be as close as possible
- * @return point on the middle of rectangle side that is as close as possible to
- * the input point
- */
- public static Point2D pointOnRectangle(Rectangle2D rect, Point2D point) {
-
- Point2D p1 = new Point2D.Double(rect.getX(), rect.getY());
- Point2D p2 = new Point2D.Double(rect.getX(), rect.getY() + rect.getHeight());
- Point2D p3 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY() + rect.getHeight());
- Point2D p4 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY());
-
- Point2D p12 = new Point2D.Double((p1.getX() + p2.getX()) / 2, (p1.getY() + p2.getY()) / 2);
- Point2D p23 = new Point2D.Double((p2.getX() + p3.getX()) / 2, (p2.getY() + p3.getY()) / 2);
- Point2D p34 = new Point2D.Double((p3.getX() + p4.getX()) / 2, (p3.getY() + p4.getY()) / 2);
- Point2D p41 = new Point2D.Double((p4.getX() + p1.getX()) / 2, (p4.getY() + p1.getY()) / 2);
-
- double dis1, dis2, dis3, dis4, min;
- dis1 = point.distance(p12);
- dis2 = point.distance(p23);
- dis3 = point.distance(p34);
- dis4 = point.distance(p41);
-
- min = Math.min(dis1, dis2);
- min = Math.min(min, dis3);
- min = Math.min(min, dis4);
-
- if (min == dis1) {
- return p12;
- } else if (min == dis2) {
- return p23;
- } else if (min == dis3) {
- return p34;
- } else {
- return p41;
- }
- }
-
/**
* This function returns point on rectangle that is closest to given point.
*
* @param rect
- * rectangle on which the result poiint will be placed
+ * rectangle on which the result point will be placed
* @param point
* point for which we look the closest reference on rectangle
* @return the closest possible point on rectangle
@@ -213,47 +169,6 @@ public final class Geo {
}
}
- /**
- * Returns point that is outside given rectangle, but still close to the given
- * point. If the given point is inside rec then the given point is returned.
- *
- * @param rec
- * rectangle
- * @param point
- * point
- * @return point that is outside given rectangle, but still close to the given
- * point
- */
- public static Point2D pointRightOutsideRec(Rectangle2D rec, Point2D point) {
- if (!rec.contains(point)) {
- return (Point2D) point.clone();
- } else {
- double lx = rec.getX();
- double rx = lx + rec.getWidth();
- double uy = rec.getY();
- double dy = uy + rec.getHeight();
-
- double dis1 = Math.abs(point.getX() - lx);
- double dis2 = Math.abs(point.getX() - rx);
- double dis3 = Math.abs(point.getY() - uy);
- double dis4 = Math.abs(point.getY() - dy);
-
- double min = Math.min(dis1, dis2);
- min = Math.min(min, dis3);
- min = Math.min(min, dis4);
-
- if (min == dis1) {
- return new Point2D.Double(lx - 1.0, point.getY());
- } else if (min == dis2) {
- return new Point2D.Double(rx + 1.0, point.getY());
- } else if (min == dis3) {
- return new Point2D.Double(point.getX(), uy - 1.0);
- } else {
- return new Point2D.Double(point.getX(), uy + 1.0);
- }
- }
- }
-
/**
* Creates a {@link PolylineData} that is identical to parameter line, but
* doesn't contain duplicate points.
@@ -293,13 +208,13 @@ public final class Geo {
}
/**
- * Returns point on line that is as closse as possible to point.
+ * Returns point on line that is as close as possible to point.
*
* @param point
* point
* @param mainLine
* line
- * @return point on line that is as closse as possible to point
+ * @return point on line that is as close as possible to point
*/
public static Point2D closestPointOnPolyline(PolylineData mainLine, Point2D point) {
Point2D res = null;
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
index 6ca53968c42ad10c8f1745bed83f9e7df115a490..5c0944c51e4bc6ae5357a1eb8ff326b1aafd2f9f 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.wikipathway;
import static org.junit.Assert.*;
-import java.awt.*;
+import java.awt.Color;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -48,7 +48,7 @@ public class ComplexReactionToModelTest extends WikipathwaysTestFunctions {
assertEquals(2, reaction.getReactants().size());
assertEquals(1, reaction.getProducts().size());
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
}
@Test
@@ -107,7 +107,7 @@ public class ComplexReactionToModelTest extends WikipathwaysTestFunctions {
assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
- assertEquals(5, getWarnings().size());
+ assertEquals(4, getWarnings().size());
}
@Test
@@ -126,7 +126,7 @@ public class ComplexReactionToModelTest extends WikipathwaysTestFunctions {
assertFalse(Color.BLACK.equals(redAlias.getFillColor()));
assertTrue(Color.WHITE.equals(blackAlias.getFillColor()));
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
}
@Test
@@ -141,9 +141,9 @@ public class ComplexReactionToModelTest extends WikipathwaysTestFunctions {
lineCount += node.getLine().getLines().size();
}
- assertEquals(4, lineCount);
+ assertEquals(3, lineCount);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
}
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 3d7e5bab20526882f1efbb274272ec131cc5fd85..5431444858d8ac29f31004022adf3bab3c6cba7f 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -10,6 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
+import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -19,7 +20,7 @@ import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
public class GPMLToModelTest extends WikipathwaysTestFunctions {
- static Logger logger = LogManager.getLogger(GPMLToModelTest.class);
+ static Logger logger = LogManager.getLogger();
private ModelComparator mc = new ModelComparator(1.0);
@@ -29,17 +30,31 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
public void DopamineTest() throws Exception {
Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/Dopamine.gpml");
- assertEquals(22, getWarnings().size());
+ assertEquals(20, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
}
+ @Test
+ public void testZIndex() throws Exception {
+ try {
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/Dopamine.gpml");
+
+ for (Drawable bioEntity : model1.getDrawables()) {
+ assertNotNull(bioEntity.getElementId() + " has null z-index", bioEntity.getZ());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void WP1403_75220Test() throws Exception {
Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP1403_75220.gpml");
- assertEquals(22, getWarnings().size());
+ assertEquals(20, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
@@ -49,7 +64,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
public void WP528_76269Test() throws Exception {
Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP528_76269.gpml");
- assertEquals(15, getWarnings().size());
+ assertEquals(12, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
@@ -59,7 +74,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
public void WP550_73391Test() throws Exception {
Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP550_73391.gpml");
- assertEquals(16, getWarnings().size());
+ assertEquals(12, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -70,7 +85,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
public void WP197_69902Test() throws Exception {
Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP197_69902.gpml");
- assertEquals(3, getWarnings().size());
+ assertEquals(9, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -92,7 +107,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
public void WP306_71714Test() throws Exception {
Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP306_71714.gpml");
- assertEquals(41, getWarnings().size());
+ assertEquals(40, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -103,7 +118,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
public void WP481_72080Test() throws Exception {
Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP481_72080.gpml");
- assertEquals(22, getWarnings().size());
+ assertEquals(19, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -145,17 +160,6 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(0, mc.compare(model1, model2));
}
- @Test
- public void testGstp() throws Exception {
- Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/gstp.gpml");
-
- assertEquals(3, getWarnings().size());
-
- Model model2 = serializeModelOverCellDesignerParser(model1);
-
- assertEquals(0, mc.compare(model1, model2));
- }
-
@Test
public void testMissingAliasesInCompartment() throws Exception {
Model model1 = new GPMLToModel().getModel("testFiles/small/missing_aliases_in_compartment.gpml");
@@ -197,8 +201,11 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
public void testNonHypotheticlaComplex() throws Exception {
String fileName = "testFiles/complex/nonhypothetical_complex.gpml";
Model model = new GPMLToModel().getModel(fileName);
- for (Complex species : model.getComplexList()) {
- assertFalse("Complex parsed from gpml should be hypothetical", species.isHypothetical());
+ for (Complex complex : model.getComplexList()) {
+ assertFalse("Complex parsed from gpml should be hypothetical", complex.isHypothetical());
+ for (Species species : complex.getElements()) {
+ assertTrue("Complex z index should be lower than children x index", species.getZ() > complex.getZ());
+ }
}
assertEquals(0, getWarnings().size());
}
@@ -214,7 +221,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
}
}
assertTrue("Complex parsed from gpml should have a valid name", nameFound);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
}
@Test
@@ -312,7 +319,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertTrue("Modifier is too far from center point: " + distance,
distance < ReactionCellDesignerConverter.RECT_SIZE);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
}
@Test
@@ -354,4 +361,78 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertNotNull(protein.getStructuralState());
}
+ @Test
+ public void parseModelAnnotation() throws Exception {
+ String fileName = "testFiles/small/model_annotation.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ assertEquals(1, model.getMiriamData().size());
+ assertEquals(0, getWarnings().size());
+ }
+
+ @Test
+ public void parseInvalidModelAnnotation() throws Exception {
+ String fileName = "testFiles/small/model_invalid_annotation.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ assertEquals(0, model.getMiriamData().size());
+ assertEquals(2, getWarnings().size());
+ }
+
+ @Test
+ public void parseElementWithComment() throws Exception {
+ String fileName = "testFiles/small/element_with_comment.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ Element element = model.getElementByElementId("a12");
+ assertTrue(element.getNotes().length() > 0);
+ }
+
+ @Test
+ public void parseReversibleReaction() throws Exception {
+ String fileName = "testFiles/small/reversible_reaction.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ Reaction reaction = model.getReactionByReactionId("e5d42");
+ assertTrue(reaction.isReversible());
+ }
+
+ @Test
+ public void parseReactionWithLabelAsSideProduct() throws Exception {
+ String fileName = "testFiles/small/reaction_with_label_as_side_product.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ Reaction reaction = model.getReactionByReactionId("id6f2bfa37");
+ assertEquals(2, reaction.getProducts().size());
+ }
+
+ @Test
+ public void parseNodeWithMissingGroup() throws Exception {
+ String fileName = "testFiles/small/node_with_missing_group.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ assertEquals(1, getWarnings().size());
+ assertEquals(1, model.getElements().size());
+ }
+
+ @Test
+ public void parseMoleculeWithColor() throws Exception {
+ String fileName = "testFiles/small/molecule_with_color.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ Element element = model.getElementByElementId("d9620");
+ logger.debug(element.getFontColor());
+ }
+
+ @Test
+ public void parseComplexName() throws Exception {
+ String fileName = "testFiles/small/compartment_without_name_and_with_complex_with_name.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ Complex complex = model.getElementByElementId("b33da");
+ assertFalse(complex.getName().isEmpty());
+ Compartment compartment = model.getElementByElementId("a3e41");
+ assertTrue(compartment.getName().isEmpty());
+ }
+
+ @Test
+ public void parseCompartmentFromShape() throws Exception {
+ String fileName = "testFiles/small/compartment_from_shape.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ Compartment compartment = model.getElementByElementId("d5695");
+ assertFalse(compartment.getName().isEmpty());
+ assertTrue(compartment.contains(compartment.getNamePoint()));
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
index 4e9b4a2cd58f9d642a9e6c89215ab52a870f7da0..47bac7caa84620fb41e5c180e49eaaf41ce79932 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
@@ -43,9 +43,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(5, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -70,9 +70,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(6, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -97,9 +97,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(4, lines);
+ assertEquals(3, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -124,9 +124,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(7, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -151,9 +151,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(6, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -178,9 +178,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(4, lines);
+ assertEquals(3, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -205,9 +205,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(4, lines);
+ assertEquals(3, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -232,9 +232,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(6, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -259,9 +259,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(5, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -286,9 +286,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(6, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -313,9 +313,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(4, lines);
+ assertEquals(3, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -340,9 +340,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(5, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -367,9 +367,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(5, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -394,9 +394,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(6, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -421,9 +421,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(4, lines);
+ assertEquals(3, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -448,9 +448,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(5, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -475,9 +475,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(4, lines);
+ assertEquals(3, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -502,9 +502,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(6, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -529,9 +529,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(6, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -556,9 +556,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(4, lines);
+ assertEquals(3, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -583,9 +583,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(7, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -610,9 +610,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(6, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -637,9 +637,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(4, lines);
+ assertEquals(3, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -664,9 +664,9 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions {
}
}
- assertEquals(5, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(0, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
index b0cafb8f6bb0bb44870d0bff5b662ee190f38762..4f27be00af8391a07cf081a72844e27c68aba6d0 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
@@ -2,6 +2,10 @@ package lcsb.mapviewer.wikipathway;
import static org.junit.Assert.*;
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.util.List;
+
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Test;
@@ -1137,4 +1141,18 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
assertEquals(0, mc.compare(model1, model2));
}
+
+ @Test
+ public void testProblematicInhibition() throws Exception {
+ String fileName = "testFiles/reactions/inhibition_with_problematic_line.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+ Reaction r = model1.getReactionByReactionId("eff08");
+ r.getLine().setColor(Color.BLUE);
+
+ List<Point2D> points = r.getProducts().get(0).getLine().getPoints();
+ assertTrue("End points shouldn't be too close",
+ points.get(points.size() - 1).distance(points.get(points.size() - 2)) > 0);
+ }
+
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
index 81430606958253c7871315d36b2cc4147b45f43c..c263cc8a5dabcf43a1a001e125cf02256a4007f6 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.wikipathway;
+import java.awt.Color;
import java.io.*;
import java.net.URL;
import java.net.URLConnection;
@@ -24,8 +25,10 @@ import lcsb.mapviewer.common.*;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
public abstract class WikipathwaysTestFunctions {
@@ -218,8 +221,17 @@ public abstract class WikipathwaysTestFunctions {
protected Model serializeModelOverCellDesignerParser(Model model1)
throws InconsistentModelException, InvalidInputDataExecption {
- for (BioEntity bioEntity : model1.getBioEntities()) {
- bioEntity.setZ(null);
+ for (Drawable bioEntity : model1.getDrawables()) {
+ if (!(bioEntity instanceof PolylineData)) {
+ bioEntity.setZ(null);
+ }
+ }
+ for (lcsb.mapviewer.model.map.species.Element bioEntity : model1.getElements()) {
+ bioEntity.setFontColor(Color.BLACK);
+ }
+ //CellDesigner doesn't allow to store compartment font size
+ for (Compartment bioEntity : model1.getCompartments()) {
+ bioEntity.setFontSize(Compartment.DEFAULT_COMPARTMENT_THICKNESS);
}
new ZIndexPopulator().populateZIndex(model1);
CellDesignerXmlParser parser = new CellDesignerXmlParser();
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
index f52b49dddb85a54e886ff437c1cf89f87af47d41..b58aafc3d297662f10bff109cec124dd411eee8e 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
@@ -9,11 +9,13 @@ import org.junit.runners.Suite.SuiteClasses;
DataNodeParserTest.class,
BugTest.class,
EdgeLineParserTest.class,
+ EdgeParserTest.class,
GpmlParserTest.class,
LabelParserTest.class,
- ReferenceParserTest.class,
ModelToGPMLTest.class,
ModelContructorTest.class,
+ ReactionLayoutFinderTest.class,
+ ReferenceParserTest.class,
ShapeParserTest.class,
StateParserTest.class,
})
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..e59195edd55a88e15401db9d874ad768d3256a44
--- /dev/null
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeParserTest.java
@@ -0,0 +1,103 @@
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.wikipathway.model.*;
+
+public class EdgeParserTest {
+
+ Logger logger = LogManager.getLogger();
+
+ EdgeParser parser = new EdgeParser();
+
+ @Test
+ public void testGetPointsWithoutTargetDirection() throws Exception {
+ List<PointData> gpmlPoints = new ArrayList<>();
+ PointData pointData = new PointData();
+ pointData.setX(370.0);
+ pointData.setY(506.9845153753351);
+ pointData.setRelX("0.0");
+ pointData.setRelY("1.0");
+ pointData.setGraphRef("db29a");
+ gpmlPoints.add(pointData);
+
+ pointData = new PointData();
+ pointData.setX(337.9360555506242);
+ pointData.setY(558.2089552238806);
+ gpmlPoints.add(pointData);
+
+ pointData = new PointData();
+ pointData.setX(305.8721111012484);
+ pointData.setY(587.6687409348253);
+ pointData.setRelX("0.0");
+ pointData.setRelY("0.0");
+ pointData.setGraphRef("ba36a");
+ pointData.setType(GpmlInteractionType.CONVERSION);
+ gpmlPoints.add(pointData);
+
+ GpmlLineConnectorType type = GpmlLineConnectorType.ELBOW;
+
+ List<Point2D> result = parser.getPoints(null, gpmlPoints, type);
+
+ assertEquals(0.0, result.get(0).distance(new Point2D.Double(370.0, 506.9845153753351)), Configuration.EPSILON);
+ assertEquals(0.0, result.get(1).distance(new Point2D.Double(370.0, 558.2089552238806)), Configuration.EPSILON);
+ assertEquals(0.0, result.get(2).distance(new Point2D.Double(305.8721111012484, 558.2089552238806)),
+ Configuration.EPSILON);
+ assertEquals(0.0, result.get(3).distance(new Point2D.Double(305.8721111012484, 587.6687409348253)),
+ Configuration.EPSILON);
+ }
+
+ @Test
+ public void testGetPointsWithoutSourceDirection() throws Exception {
+ List<PointData> gpmlPoints = new ArrayList<>();
+ PointData pointData = new PointData();
+ pointData.setX(418.1490729057133);
+ pointData.setY(421.3813636363637);
+ pointData.setRelX("0.0");
+ pointData.setRelY("0.0");
+ pointData.setGraphRef("f78da");
+ gpmlPoints.add(pointData);
+
+ pointData = new PointData();
+ pointData.setX(506.83491062039946);
+ pointData.setY(396.35686597839583);
+ gpmlPoints.add(pointData);
+
+ pointData = new PointData();
+ pointData.setX(506.83491062039946);
+ pointData.setY(369.3819137749735);
+ gpmlPoints.add(pointData);
+
+ pointData = new PointData();
+ pointData.setX(718.8015247108307);
+ pointData.setY(343.0727655099894);
+ pointData.setRelX("0.0");
+ pointData.setRelY("1.0");
+ pointData.setGraphRef("ca8");
+ pointData.setType(GpmlInteractionType.ARROW);
+ gpmlPoints.add(pointData);
+
+ GpmlLineConnectorType type = GpmlLineConnectorType.ELBOW;
+
+ List<Point2D> result = parser.getPoints(null, gpmlPoints, type);
+
+ assertEquals(0.0, result.get(0).distance(new Point2D.Double(418.1490729057133, 421.3813636363637)), Configuration.EPSILON);
+ assertEquals(0.0, result.get(1).distance(new Point2D.Double(506.83491062039946, 421.3813636363637)), Configuration.EPSILON);
+ assertEquals(0.0, result.get(2).distance(new Point2D.Double(506.83491062039946, 369.3819137749735)),
+ Configuration.EPSILON);
+ assertEquals(0.0, result.get(3).distance(new Point2D.Double(718.8015247108307, 369.3819137749735)),
+ Configuration.EPSILON);
+ assertEquals(0.0, result.get(4).distance(new Point2D.Double(718.8015247108307, 343.0727655099894)),
+ Configuration.EPSILON);
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
index 14f6aeb0f9341a7099559b80e95088af923fc580..aa346f17ef07767653f3a8f4312c37269aea867e 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.wikipathway.XML;
import static org.junit.Assert.*;
-import java.awt.*;
+import java.awt.Color;
import org.junit.*;
import org.w3c.dom.Element;
@@ -42,6 +42,17 @@ public class LabelParserTest extends WikipathwaysTestFunctions {
assertEquals(0, getWarnings().size());
}
+ @Test
+ public void testParseLabeHrefl() throws Exception {
+ Element node = fileToNode("testFiles/elements/label_href.xml");
+ Label label = parser.parse(node);
+ assertNotNull(label);
+
+ assertEquals(1, label.getReferences().size());
+
+ assertEquals(0, getWarnings().size());
+ }
+
@Test
public void testParseGraphics() throws Exception {
Element node = fileToNode("testFiles/elements/label_graphics.xml");
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
index 2d960c9302a4dba1fb8cb97d8dfdc02ab875ec65..acb69da6375af10472e03df7a029ac0652ed50ec 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.wikipathway.XML;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.*;
-import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
import java.io.ByteArrayInputStream;
import java.nio.charset.StandardCharsets;
@@ -11,8 +10,7 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.*;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
@@ -32,21 +30,6 @@ public class ModelContructorTest extends WikipathwaysTestFunctions {
public void tearDown() throws Exception {
}
- @Test
- public void testSplitPolyline() {
- Point2D p1 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
- Point2D p2 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
- PolylineData pd = new PolylineData(p1, p2);
-
- ModelContructor mc = new ModelContructor();
- Pair<PolylineData, PolylineData> result = mc.splitPolyline(pd);
- assertNotNull(result);
- assertNotNull(result.getLeft());
- assertNotNull(result.getRight());
- assertEquals(2, result.getLeft().getPoints().size());
- assertEquals(2, result.getRight().getPoints().size());
- }
-
@Test
public void testZIndexForElement() throws Exception {
ModelToGPML parser = new ModelToGPML();
@@ -76,4 +59,51 @@ public class ModelContructorTest extends WikipathwaysTestFunctions {
return result;
}
+ @Test
+ public void testShouldRotate90degreesWithNoAsAnswer() {
+ ModelContructor mc = new ModelContructor();
+ assertFalse(mc.shouldRotate90degrees(0.0));
+ assertFalse(mc.shouldRotate90degrees(Math.PI));
+ assertFalse(mc.shouldRotate90degrees(15 * Math.PI));
+ assertFalse(mc.shouldRotate90degrees(-Math.PI));
+ assertFalse(mc.shouldRotate90degrees(null));
+ }
+
+ @Test
+ public void testShouldRotate90degrees() {
+ ModelContructor mc = new ModelContructor();
+ assertTrue(mc.shouldRotate90degrees(Math.PI / 2));
+ assertTrue(mc.shouldRotate90degrees(15 * Math.PI / 2));
+ assertTrue(mc.shouldRotate90degrees(-Math.PI / 2));
+ }
+
+ @Test
+ public void testShouldRotate90degreesWithWarnings() {
+ ModelContructor mc = new ModelContructor();
+ assertFalse(mc.shouldRotate90degrees(0.0 + 0.5));
+ assertEquals(1, super.getWarnings().size());
+ assertFalse(mc.shouldRotate90degrees(Math.PI + 0.5));
+ assertEquals(2, super.getWarnings().size());
+ assertFalse(mc.shouldRotate90degrees(15 * Math.PI + 0.5));
+ assertEquals(3, super.getWarnings().size());
+ assertFalse(mc.shouldRotate90degrees(-Math.PI + 0.5));
+ assertEquals(4, super.getWarnings().size());
+ assertTrue(mc.shouldRotate90degrees(Math.PI / 2 + 0.5));
+ assertEquals(5, super.getWarnings().size());
+ assertTrue(mc.shouldRotate90degrees(15 * Math.PI / 2 + 0.5));
+ assertEquals(6, super.getWarnings().size());
+ assertTrue(mc.shouldRotate90degrees(-Math.PI / 2 + 0.5));
+ assertEquals(7, super.getWarnings().size());
+ }
+
+ @Test
+ public void testRotate90degrees() {
+ ModelContructor mc = new ModelContructor();
+ Rectangle2D result = mc.rotate90degrees(new Rectangle2D.Double(10, 20, 30, 40));
+ assertEquals(5, result.getX(), Configuration.EPSILON);
+ assertEquals(25, result.getY(), Configuration.EPSILON);
+ assertEquals(40, result.getWidth(), Configuration.EPSILON);
+ assertEquals(30, result.getHeight(), Configuration.EPSILON);
+ }
+
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinderTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinderTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..0dc4747db50c4a46497978b09be33d9c4053c452
--- /dev/null
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinderTest.java
@@ -0,0 +1,270 @@
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.*;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.Arrays;
+import java.util.Map;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+import lcsb.mapviewer.wikipathway.model.Edge;
+import lcsb.mapviewer.wikipathway.model.Interaction;
+
+public class ReactionLayoutFinderTest extends WikipathwaysTestFunctions {
+
+ Logger logger = LogManager.getLogger();
+
+ LineTransformation lt = new LineTransformation();
+
+ ReactionLayoutFinder finder;
+
+ @Before
+ public void setUp() {
+ finder = new ReactionLayoutFinder();
+ }
+
+ @Test
+ public void testNodePointsInteractionWithoutAnything() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+ Map<Class<?>, Point2D> result = finder.getNodeStartPoints(interaction);
+ validatePointsResult(interaction, result);
+ }
+
+ @Test
+ public void testNodePointsInteractionWithAdditionalReactant() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+
+ interaction.addReactant(createEdge("react1", new Point2D.Double(10, 0), new Point2D.Double(200, 200)));
+
+ Map<Class<?>, Point2D> result = finder.getNodeStartPoints(interaction);
+ validatePointsResult(interaction, result);
+ assertEquals(0, result.get(Reactant.class).distance(new Point2D.Double(10, 0)), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testNodePointsInteractionWithShiftedReactant() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+
+ interaction.addReactant(createEdge("react1", new Point2D.Double(60, 0), new Point2D.Double(200, 200)));
+
+ Map<Class<?>, Point2D> result = finder.getNodeStartPoints(interaction);
+ validatePointsResult(interaction, result);
+ assertEquals(0, result.get(Reactant.class).distance(new Point2D.Double(60, 0)), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testNodePointsInteractionWithAdditionalProduct() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+
+ interaction.addProduct(createEdge("prod", new Point2D.Double(80, 0), new Point2D.Double(200, 200)));
+
+ Map<Class<?>, Point2D> result = finder.getNodeStartPoints(interaction);
+ validatePointsResult(interaction, result);
+ assertEquals(0, result.get(Product.class).distance(new Point2D.Double(80, 0)), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testNodePointsInteractionWithAdditionalModifier() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+
+ interaction.addModifier(createEdge("modifier", new Point2D.Double(80, 0), new Point2D.Double(200, 200)));
+
+ Map<Class<?>, Point2D> result = finder.getNodeStartPoints(interaction);
+ validatePointsResult(interaction, result);
+ assertEquals(0, result.get(Modifier.class).distance(new Point2D.Double(80, 0)), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testNodePointsInteractionWithMultiNodes() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+
+ interaction.addReactant(createEdge("react1", new Point2D.Double(10, 0), new Point2D.Double(200, 200)));
+ interaction.addReactant(createEdge("react2", new Point2D.Double(20, 0), new Point2D.Double(200, 200)));
+ interaction.addReactant(createEdge("react3", new Point2D.Double(30, 0), new Point2D.Double(200, 200)));
+ interaction.addModifier(createEdge("modifier", new Point2D.Double(40, 0), new Point2D.Double(200, 200)));
+ interaction.addProduct(createEdge("prod1", new Point2D.Double(50, 0), new Point2D.Double(200, 200)));
+ interaction.addProduct(createEdge("prod2", new Point2D.Double(60, 0), new Point2D.Double(200, 200)));
+ interaction.addProduct(createEdge("prod3", new Point2D.Double(70, 0), new Point2D.Double(200, 200)));
+
+ Map<Class<?>, Point2D> result = finder.getNodeStartPoints(interaction);
+ validatePointsResult(interaction, result);
+ assertEquals(0, result.get(Modifier.class).distance(new Point2D.Double(40, 0)), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testNodePointsInteractionWithMultiModifiers() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+
+ interaction.addReactant(createEdge("react1", new Point2D.Double(10, 0), new Point2D.Double(200, 200)));
+ interaction.addReactant(createEdge("react2", new Point2D.Double(20, 0), new Point2D.Double(200, 200)));
+ interaction.addReactant(createEdge("react3", new Point2D.Double(30, 0), new Point2D.Double(200, 200)));
+ interaction.addModifier(createEdge("modifier", new Point2D.Double(40, 0), new Point2D.Double(200, 200)));
+ interaction.addProduct(createEdge("prod1", new Point2D.Double(50, 0), new Point2D.Double(200, 200)));
+ interaction.addModifier(createEdge("modifier2", new Point2D.Double(60, 0), new Point2D.Double(200, 200)));
+ interaction.addProduct(createEdge("prod3", new Point2D.Double(70, 0), new Point2D.Double(200, 200)));
+
+ Map<Class<?>, Point2D> result = finder.getNodeStartPoints(interaction);
+ validatePointsResult(interaction, result);
+ assertEquals(0, result.get(Modifier.class).distance(new Point2D.Double(40, 0)), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testNodePointsInteractionWithMultiModifiers2() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+
+ interaction.addReactant(createEdge("react1", new Point2D.Double(10, 0), new Point2D.Double(200, 200)));
+ interaction.addModifier(createEdge("modifier2", new Point2D.Double(20, 0), new Point2D.Double(200, 200)));
+ interaction.addReactant(createEdge("react3", new Point2D.Double(30, 0), new Point2D.Double(200, 200)));
+ interaction.addModifier(createEdge("modifier", new Point2D.Double(40, 0), new Point2D.Double(200, 200)));
+ interaction.addProduct(createEdge("prod1", new Point2D.Double(50, 0), new Point2D.Double(200, 200)));
+ interaction.addProduct(createEdge("prod3", new Point2D.Double(70, 0), new Point2D.Double(200, 200)));
+
+ Map<Class<?>, Point2D> result = finder.getNodeStartPoints(interaction);
+ validatePointsResult(interaction, result);
+ assertEquals(0, result.get(Modifier.class).distance(new Point2D.Double(40, 0)), Configuration.EPSILON);
+ }
+
+ private Edge createEdge(String id, Point2D p1, Point2D p2) {
+ Edge modifierEdge = new Edge(id);
+ modifierEdge.setLine(new PolylineData(p1, p2));
+ return modifierEdge;
+ }
+
+ private void validatePointsResult(Interaction interaction, Map<Class<?>, Point2D> result) {
+ PolylineData pd = interaction.getLine();
+ Point2D reactantPoint = result.get(Reactant.class);
+ Point2D productPoint = result.get(Product.class);
+ Point2D modifierPoint = result.get(Modifier.class);
+ assertNotNull(reactantPoint);
+ assertNotNull(productPoint);
+ assertNotNull(modifierPoint);
+
+// logger.debug(reactantPoint);
+// logger.debug(modifierPoint);
+// logger.debug(productPoint);
+//
+ assertEquals(0, distanceFromLine(pd, reactantPoint), Configuration.EPSILON);
+ assertEquals(0, distanceFromLine(pd, productPoint), Configuration.EPSILON);
+ assertEquals(0, distanceFromLine(pd, modifierPoint), Configuration.EPSILON);
+
+ assertTrue(
+ finder.distanceFromPolylineStart(pd, reactantPoint) < finder.distanceFromPolylineStart(pd, modifierPoint));
+ assertTrue(
+ finder.distanceFromPolylineStart(pd, modifierPoint) < finder.distanceFromPolylineStart(pd, productPoint));
+ }
+
+ private double distanceFromLine(PolylineData pd, Point2D point) {
+ double distance = Double.MAX_VALUE;
+ for (Line2D line : pd.getLines()) {
+ distance = Math.min(distance, lt.distBetweenPointAndLineSegment(line, point));
+ }
+ return distance;
+ }
+
+ @Test
+ public void testDistanceFromPolylineStartSimple() {
+ PolylineData line = new PolylineData(new Point2D.Double(10, 20), new Point2D.Double(40, 60));
+ assertEquals(0, finder.distanceFromPolylineStart(line, new Point2D.Double(10, 20)), Configuration.EPSILON);
+ assertEquals(50, finder.distanceFromPolylineStart(line, new Point2D.Double(40, 60)), Configuration.EPSILON);
+ assertEquals(25, finder.distanceFromPolylineStart(line, new Point2D.Double(25, 40)), Configuration.EPSILON);
+ }
+
+ @Test(expected = InvalidArgumentException.class)
+ public void testDistanceFromPolylineStartInvalid() {
+ PolylineData line = new PolylineData(new Point2D.Double(10, 20), new Point2D.Double(40, 60));
+ finder.distanceFromPolylineStart(line, new Point2D.Double(1, 2));
+ }
+
+ @Test
+ public void testDistanceFromPolylineStartComplex() {
+ PolylineData line = new PolylineData(new Point2D.Double(10, 20), new Point2D.Double(40, 60));
+ line.addPoint(new Point2D.Double(60, 60));
+ assertEquals(50, finder.distanceFromPolylineStart(line, new Point2D.Double(40, 60)), Configuration.EPSILON);
+ assertEquals(60, finder.distanceFromPolylineStart(line, new Point2D.Double(50, 60)), Configuration.EPSILON);
+ assertEquals(70, finder.distanceFromPolylineStart(line, new Point2D.Double(60, 60)), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testNodeLinesInteractionWithoutAnything() {
+ Interaction interaction = new Interaction(createEdge("id", new Point2D.Double(0, 0), new Point2D.Double(100, 0)));
+ Map<Class<?>, PolylineData> result = finder.getNodeLines(interaction);
+ validateLinesResult(interaction, result);
+ }
+
+ @Test
+ public void testNodeLinesInteractionWithTwoReactants() {
+ Edge edge = new Edge("id");
+ PolylineData line = new PolylineData(Arrays.asList(
+ new Point2D.Double(0, 0),
+ new Point2D.Double(100, 0),
+ new Point2D.Double(100, 100)
+ ));
+ edge.setLine(line);
+ Interaction interaction = new Interaction(edge);
+ interaction.addReactant(createEdge("reactant", new Point2D.Double(200, 0), new Point2D.Double(100, 0)));
+
+ Map<Class<?>, PolylineData> result = finder.getNodeLines(interaction);
+ validateLinesResult(interaction, result);
+ }
+
+ @Test
+ public void testNodeLinesInteractionWithTwoProducts() {
+ Edge edge = new Edge("id");
+ PolylineData line = new PolylineData(Arrays.asList(
+ new Point2D.Double(0, 0),
+ new Point2D.Double(100, 0),
+ new Point2D.Double(100, 100)
+ ));
+ edge.setLine(line);
+ Interaction interaction = new Interaction(edge);
+ interaction.addProduct(createEdge("product", new Point2D.Double(200, 0), new Point2D.Double(100, 0)));
+
+ Map<Class<?>, PolylineData> result = finder.getNodeLines(interaction);
+ validateLinesResult(interaction, result);
+ }
+
+ private void validateLinesResult(Interaction interaction, Map<Class<?>, PolylineData> result) {
+ PolylineData pd = interaction.getLine();
+ PolylineData reactantLine = result.get(Reactant.class);
+ PolylineData inputOperatorLine = result.get(AndOperator.class);
+ PolylineData outputOperatorLine = result.get(SplitOperator.class);
+ PolylineData productLine = result.get(Product.class);
+ PolylineData modifierLine = result.get(Modifier.class);
+
+// logger.debug(reactantLine);
+// logger.debug(inputOperatorLine);
+// logger.debug(modifierLine);
+// logger.debug(outputOperatorLine);
+// logger.debug(productLine);
+//
+ assertNotNull(reactantLine);
+ assertTrue(reactantLine.length() > Configuration.EPSILON);
+ assertNotNull(productLine);
+ assertTrue(productLine.length() > Configuration.EPSILON);
+ assertNotNull(modifierLine);
+ assertTrue("Modifier line length must be > 0", modifierLine.length() > Configuration.EPSILON);
+ assertNotNull(inputOperatorLine);
+ assertTrue(inputOperatorLine.length() > Configuration.EPSILON);
+ assertNotNull(outputOperatorLine);
+ assertTrue(outputOperatorLine.length() > Configuration.EPSILON);
+
+ assertEquals(0, pd.getBeginPoint().distance(reactantLine.getBeginPoint()), Configuration.EPSILON);
+ assertEquals(0, reactantLine.getEndPoint().distance(inputOperatorLine.getBeginPoint()), Configuration.EPSILON);
+ assertEquals(0, inputOperatorLine.getEndPoint().distance(modifierLine.getBeginPoint()), Configuration.EPSILON);
+ assertEquals(0, modifierLine.getEndPoint().distance(outputOperatorLine.getBeginPoint()), Configuration.EPSILON);
+ assertEquals(0, outputOperatorLine.getEndPoint().distance(productLine.getBeginPoint()), Configuration.EPSILON);
+ assertEquals(0, productLine.getEndPoint().distance(pd.getEndPoint()), Configuration.EPSILON);
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/AllBiopaxTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/AllBiopaxTests.java
index 7962c204a2a79b43529de5715793376f586d0bbd..cd54c21984a90a08bd8510fa2ec07391b753ebcd 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/AllBiopaxTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/AllBiopaxTests.java
@@ -5,7 +5,9 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ BiopaxDataTest.class, BiopaxOpenControlledVocabularyTest.class, BiopaxPublicationTest.class })
+@SuiteClasses({ BiopaxDataTest.class,
+ BiopaxOpenControlledVocabularyTest.class,
+ BiopaxPublicationTest.class })
public class AllBiopaxTests {
}
diff --git a/pathvisio/testFiles/elements/label_href.xml b/pathvisio/testFiles/elements/label_href.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4c10b05272a1122e596dda5bcd160cf51ae6e839
--- /dev/null
+++ b/pathvisio/testFiles/elements/label_href.xml
@@ -0,0 +1,3 @@
+<Label
+ TextLabel="Phosphoribosylpyrophosphate synthetase 1 defects"
+ GraphId="cfbda" Href="http://omim.org/311850"></Label>
diff --git a/pathvisio/testFiles/reactions/inhibition_with_problematic_line.gpml b/pathvisio/testFiles/reactions/inhibition_with_problematic_line.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..955ba3e923f02d522af4e58c83fe1bf427176470
--- /dev/null
+++ b/pathvisio/testFiles/reactions/inhibition_with_problematic_line.gpml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="MAPK Signaling Pathway" Organism="Homo sapiens" License="CC BY 2.0">
+ <Graphics BoardWidth="1824.945655991181" BoardHeight="1510.0" />
+ <DataNode TextLabel="PPP5C" GraphId="e19" Type="GeneProduct" GroupRef="cd419">
+ <Attribute Key="org.pathvisio.model.BackpageHead" Value="PPP5C | protein phosphatase 5 catalytic subuni..." />
+ <Graphics CenterX="541.9543147208124" CenterY="1108.7648054145516" Width="40.0" Height="20.0" ZOrder="32932" FontSize="10" Valign="Middle" />
+ <Xref Database="Entrez Gene" ID="5536" />
+ </DataNode>
+ <DataNode TextLabel="MAP3K5" GraphId="d1a" Type="GeneProduct">
+ <Attribute Key="org.pathvisio.model.BackpageHead" Value="MAP3K5 | mitogen-activated protein kinase kinas..." />
+ <Graphics CenterX="590.5104765583576" CenterY="1082.6835871404394" Width="60.0" Height="20.0" ZOrder="33214" FontSize="10" Valign="Middle" />
+ <Xref Database="Entrez Gene" ID="4217" />
+ </DataNode>
+ <DataNode TextLabel="PPP5D1" GraphId="c908a" Type="GeneProduct" GroupRef="cd419">
+ <Attribute Key="org.pathvisio.model.BackpageHead" Value="PPP5C | protein phosphatase 5 catalytic subuni..." />
+ <Graphics CenterX="541.9543147208121" CenterY="1128.764805414554" Width="40.0" Height="20.0" ZOrder="33227" FontSize="10" Valign="Middle" />
+ <Xref Database="Ensembl" ID="ENSG00000230510" />
+ </DataNode>
+ <Interaction GraphId="eff08">
+ <Graphics ConnectorType="Elbow" ZOrder="12348" LineThickness="1.0" Color="ff0000">
+ <Point X="569.9543147208124" Y="1118.764805414553" GraphRef="efe70" RelX="1.0" RelY="0.0" />
+ <Point X="590.5104765583576" Y="1092.6835871404394" GraphRef="d1a" RelX="0.0" RelY="1.0" ArrowHead="mim-inhibition" />
+ </Graphics>
+ <Xref Database="" ID="" />
+ </Interaction>
+ <Group GroupId="cd419" GraphId="efe70" Style="Group" />
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/compartment_from_shape.gpml b/pathvisio/testFiles/small/compartment_from_shape.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..3f146f8843d3d12fe22645f294b93e123fd5b8ba
--- /dev/null
+++ b/pathvisio/testFiles/small/compartment_from_shape.gpml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="ACE Inhibitor Pathway" Organism="Homo sapiens">
+ <Label TextLabel="Zona glomerulosa of the adrenal gland" GraphId="a49c5">
+ <Graphics CenterX="400.0" CenterY="585.5" Width="184.0" Height="35.0" ZOrder="28672" FillColor="ffffff" FontWeight="Bold" FontSize="14" Valign="Middle" Color="999999"/>
+ </Label>
+ <Label TextLabel="EDHF" GraphId="b2aa3">
+ <Graphics CenterX="808.0" CenterY="475.0" Width="42.0" Height="20.0" ZOrder="28672" FillColor="ffffff" FontWeight="Bold" FontSize="10" Valign="Middle"/>
+ </Label>
+ <Label TextLabel="Blood vessels" GraphId="d3e2b">
+ <Graphics CenterX="749.0" CenterY="579.5" Width="184.0" Height="35.0" ZOrder="28672" FillColor="ffffff" FontWeight="Bold" FontSize="14" Valign="Middle" Color="999999"/>
+ </Label>
+ <Label TextLabel="Mesangial cells around blood vessels in the kidneys" GraphId="e166c">
+ <Graphics CenterX="139.0" CenterY="583.5" Width="222.0" Height="35.0" ZOrder="28672" FillColor="ffffff" FontWeight="Bold" FontSize="14" Valign="Middle" Color="999999"/>
+ </Label>
+ <Shape GraphId="c2049">
+ <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double"/>
+ <Graphics CenterX="748.0" CenterY="502.5" Width="232.0" Height="235.0" ZOrder="16384" FontSize="10" Valign="Middle" ShapeType="RoundedRectangle" LineThickness="3.0" Color="c0c0c0" Rotation="0.0"/>
+ </Shape>
+ <Shape GraphId="d5695">
+ <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double"/>
+ <Graphics CenterX="450.0" CenterY="503.5" Width="344.0" Height="235.0" ZOrder="16384" FontSize="10" Valign="Middle" ShapeType="RoundedRectangle" LineThickness="3.0" Color="c0c0c0" Rotation="0.0"/>
+ </Shape>
+ <Shape GraphId="f975e">
+ <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double"/>
+ <Graphics CenterX="140.0" CenterY="504.0" Width="254.0" Height="232.0" ZOrder="16384" FontSize="10" Valign="Middle" ShapeType="RoundedRectangle" LineThickness="3.0" Color="c0c0c0" Rotation="0.0"/>
+ </Shape>
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/compartment_without_name_and_with_complex_with_name.gpml b/pathvisio/testFiles/small/compartment_without_name_and_with_complex_with_name.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..b83e297d1dca930fa18ccd305046073f4eb72417
--- /dev/null
+++ b/pathvisio/testFiles/small/compartment_without_name_and_with_complex_with_name.gpml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="MAPK Signaling Pathway" Organism="Homo sapiens" License="CC BY 2.0">
+ <DataNode TextLabel="Apoptosis" GraphId="d8cd7" Type="Pathway" GroupRef="bbb58">
+ <Graphics CenterX="1411.756345177664" CenterY="989.730964467005" Width="80.0" Height="20.0" ZOrder="32991" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
+ <Xref Database="WikiPathways" ID="WP254" />
+ </DataNode>
+ <Label TextLabel="Proliferation, differentiation,
inflammation" GraphId="e66" GroupRef="bbb58">
+ <Graphics CenterX="1408.4230118443306" CenterY="969.230964467005" Width="138.66666666666666" Height="29.0" ZOrder="28688" FillColor="ffffff" FontWeight="Bold" FontSize="10" Valign="Middle" />
+ </Label>
+ <Group GroupId="bbb58" GraphId="b33da" Style="Group" />
+ <Shape GraphId="a3e41">
+ <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
+ <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double" />
+ <Graphics CenterX="861.0" CenterY="778.0" Width="1382.0" Height="1404.0" ZOrder="16384" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" LineThickness="3.0" Color="c0c0c0" Rotation="0.0" />
+ </Shape>
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/element_with_comment.gpml b/pathvisio/testFiles/small/element_with_comment.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..741131f2686c2c3ef5968d28f4dd5c20d78f08ef
--- /dev/null
+++ b/pathvisio/testFiles/small/element_with_comment.gpml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Cholesterol Biosynthesis Pathway" Last-Modified="2/22/2013" Organism="Homo sapiens">
+ <Graphics BoardWidth="709.6540434669985" BoardHeight="679.0097543709028" />
+ <DataNode TextLabel="NSDHL" GraphId="a12" Type="GeneProduct">
+ <Comment Source="GenMAPP remarks">NAD(P) dependent steroid dehydrogenase-like</Comment>
+ <Attribute Key="org.pathvisio.model.BackpageHead" Value="NSDHL | NAD(P) dependent steroid dehydrogenase-..." />
+ <Graphics CenterX="646.3207101336652" CenterY="261.70514694126564" Width="66.66666666666667" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
+ <Xref Database="Entrez Gene" ID="50814" />
+ </DataNode>
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/model_annotation.gpml b/pathvisio/testFiles/small/model_annotation.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..7195854a170005a14d59b4b68696299fac86a818
--- /dev/null
+++ b/pathvisio/testFiles/small/model_annotation.gpml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Purine metabolism" Version="20161102" Organism="Homo sapiens">
+ <BiopaxRef>de6</BiopaxRef>
+ <Graphics BoardWidth="2357.1066152108338" BoardHeight="1006.1828435291823"/>
+ <Biopax>
+ <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
+ <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">classic metabolic pathway</bp:TERM>
+ <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0000002</bp:ID>
+ <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
+ </bp:openControlledVocabulary>
+ <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="de6">
+ <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12235098</bp:ID>
+ <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
+ <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Malformation syndromes due to inborn errors of cholesterol synthesis.</bp:TITLE>
+ <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">J Clin Invest</bp:SOURCE>
+ <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2002</bp:YEAR>
+ <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Porter FD</bp:AUTHORS>
+ </bp:PublicationXref>
+ </Biopax>
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/model_invalid_annotation.gpml b/pathvisio/testFiles/small/model_invalid_annotation.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..ae791f773a8a1446dfa7f4fefcb90cdfe6872026
--- /dev/null
+++ b/pathvisio/testFiles/small/model_invalid_annotation.gpml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Purine metabolism" Version="20161102" Organism="Homo sapiens">
+ <BiopaxRef>de6</BiopaxRef>
+ <BiopaxRef>unknown</BiopaxRef>
+ <Graphics BoardWidth="2357.1066152108338" BoardHeight="1006.1828435291823"/>
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/molecule_with_color.gpml b/pathvisio/testFiles/small/molecule_with_color.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..fd6e1c9eee9083c1019e38f486682b271dbb03f3
--- /dev/null
+++ b/pathvisio/testFiles/small/molecule_with_color.gpml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="ACE Inhibitor Pathway" Organism="Homo sapiens">
+ <DataNode TextLabel="ACE Inhibitor" GraphId="d9620" Type="Metabolite">
+ <Graphics CenterX="467.5" CenterY="40.66666666666666" Width="91.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="cc0000"/>
+ <Xref Database="ChEBI" ID="CHEBI:35457"/>
+ </DataNode>
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/node_with_missing_group.gpml b/pathvisio/testFiles/small/node_with_missing_group.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..1617b316ad6e60deb49d78277ce42885808038dc
--- /dev/null
+++ b/pathvisio/testFiles/small/node_with_missing_group.gpml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Purine metabolism" Version="20161102" Organism="Homo sapiens">
+ <DataNode TextLabel="AO" GraphId="a7af3" Type="Protein" GroupRef="d0eb9">
+ <Graphics CenterX="1772.9349290844132" CenterY="61.849749175651525" Width="46.16009280742433" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle"/>
+ </DataNode>
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/reaction_with_label_as_side_product.gpml b/pathvisio/testFiles/small/reaction_with_label_as_side_product.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..0022c589e9292a4efea8d64a9f7e071238fa41e9
--- /dev/null
+++ b/pathvisio/testFiles/small/reaction_with_label_as_side_product.gpml
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Purine metabolism" Version="20161102" Organism="Homo sapiens">
+ <Graphics BoardWidth="2357.1066152108338" BoardHeight="1006.1828435291823"/>
+ <DataNode TextLabel="Hypoxanthine" GraphId="ce7d3" Type="Metabolite">
+ <Graphics CenterX="825.4195292898956" CenterY="771.2721891544751" Width="90.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" LineThickness="2.0" Color="ff6666"/>
+ <Xref Database="ChEBI" ID="CHEBI:17368"/>
+ </DataNode>
+ <DataNode TextLabel="2'-deoxyinosine" GraphId="dc77e" Type="Metabolite">
+ <Graphics CenterX="158.50507786644994" CenterY="873.9515387851391" Width="123.41614420062683" Height="25.0" ZOrder="32769" FontSize="12" Valign="Middle" LineThickness="2.0" Color="ff6666"/>
+ <Xref Database="ChEBI" ID="CHEBI:28997"/>
+ </DataNode>
+ <DataNode TextLabel="PNP" GraphId="e42f7" Type="Protein">
+ <Graphics CenterX="311.24362390084195" CenterY="868.6948483311019" Width="43.60542582228957" Height="25.0" ZOrder="32774" FontSize="12" Valign="Middle"/>
+ <Xref Database="Uniprot-TrEMBL" ID="P00491"/>
+ </DataNode>
+ <Interaction GraphId="id6f2bfa37">
+ <Graphics ConnectorType="Elbow" ZOrder="12288" LineThickness="1.0">
+ <Point X="189.35911391660665" Y="886.4515387851391" GraphRef="dc77e" RelX="0.5" RelY="1.0"/>
+ <Point X="802.9195292898956" Y="783.7721891544751" GraphRef="ce7d3" RelX="-0.5" RelY="1.0" ArrowHead="mim-conversion"/>
+ <Anchor Position="0.18744319428080264" Shape="None" GraphId="b5668"/>
+ </Graphics>
+ <Xref Database="Rhea" ID="27751"/>
+ </Interaction>
+
+ <Interaction GraphId="id63eeb6f">
+ <Graphics ZOrder="12288" LineThickness="1.0">
+ <Point X="311.24362390084195" Y="881.1948483311019" GraphRef="e42f7" RelX="0.0" RelY="1.0"/>
+ <Point X="311.11111111111114" Y="906.4515387851391" GraphRef="b5668" RelX="0.0" RelY="0.0" ArrowHead="mim-catalysis"/>
+ </Graphics>
+ <Xref Database="" ID=""/>
+ </Interaction>
+
+ <GraphicalLine GraphId="e8aae">
+ <Graphics ConnectorType="Elbow" ZOrder="12288" LineStyle="Broken" LineThickness="1.0">
+ <Point X="311.11111111111114" Y="906.4515387851391" GraphRef="b5668" RelX="0.0" RelY="0.0"/>
+ <Point X="337.42384957454703" Y="892.9824561403509"/>
+ <Point X="363.736588037983" Y="789.0918747157914" GraphRef="cd255" RelX="0.5" RelY="1.0" ArrowHead="Arrow"/>
+ </Graphics>
+ </GraphicalLine>
+
+ <Label TextLabel="Purine nucleoside phosphorylase deficiency" GraphId="cd255" Href="https://omim.org/entry/613179">
+ <Comment>DISEASE</Comment>
+ <Graphics CenterX="332.03769301035845" CenterY="765.6464158267954" Width="126.79558011049801" Height="46.890917777992016" ZOrder="32906" FillColor="ffcccc" FontSize="12" Valign="Middle" ShapeType="RoundedRectangle" Color="0000ff"/>
+ </Label>
+ <InfoBox CenterX="0.0" CenterY="0.0"/>
+
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/small/reversible_reaction.gpml b/pathvisio/testFiles/small/reversible_reaction.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..67ae2b86d2f00e2ee9afcefc148453565aaef852
--- /dev/null
+++ b/pathvisio/testFiles/small/reversible_reaction.gpml
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Cholesterol Biosynthesis Pathway" Last-Modified="2/22/2013" Organism="Homo sapiens">
+ <Graphics BoardWidth="709.6540434669985" BoardHeight="679.0097543709028" />
+ <DataNode TextLabel="IDI1" GraphId="c3b" Type="GeneProduct">
+ <Attribute Key="org.pathvisio.model.BackpageHead" Value="IDI1 | isopentenyl-diphosphate delta isomerase" />
+ <Graphics CenterX="263.62037134806815" CenterY="533.9075111234577" Width="66.66666666666667" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
+ <Xref Database="Entrez Gene" ID="3422" />
+ </DataNode>
+ <DataNode TextLabel="isopentenyl pyrophosphate" GraphId="db29a" Type="Metabolite">
+ <Graphics CenterX="370.0" CenterY="496.9845153753351" Width="141.71445929526124" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
+ <Xref Database="CAS" ID="358-71-4" />
+ </DataNode>
+ <DataNode TextLabel="Dimethylallyl pyrophosphate" GraphId="fce72" Type="Metabolite">
+ <Graphics CenterX="151.27502573612358" CenterY="496.9845153753352" Width="151.88176471647557" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
+ <Xref Database="CAS" ID="358-72-5" />
+ </DataNode>
+ <Interaction GraphId="e5d42">
+ <Graphics ZOrder="12288" LineThickness="1.0">
+ <Point X="227.21590809436137" Y="496.9845153753352" GraphRef="fce72" RelX="1.0" RelY="0.0" ArrowHead="Arrow" />
+ <Point X="299.1427703523694" Y="496.9845153753351" GraphRef="db29a" RelX="-1.0" RelY="0.0" ArrowHead="mim-conversion" />
+ <Anchor Position="0.504761824415362" Shape="None" GraphId="fd8da" />
+ </Graphics>
+ <Xref Database="" ID="" />
+ </Interaction>
+ <Interaction GraphId="id6b5f2131">
+ <Graphics ZOrder="12288" LineThickness="1.0">
+ <Point X="263.62037134806815" Y="523.9075111234577" GraphRef="c3b" RelX="0.0" RelY="-1.0" />
+ <Point X="263.5218423121859" Y="496.98451537533515" GraphRef="fd8da" RelX="0.0" RelY="0.0" ArrowHead="mim-catalysis" />
+ </Graphics>
+ <Xref Database="" ID="" />
+ </Interaction>
+</Pathway>
\ No newline at end of file
diff --git a/pathvisio/testFiles/wikipathways/gstp.gpml b/pathvisio/testFiles/wikipathways/gstp.gpml
deleted file mode 100644
index 304c78148cd059bee594c4320d2d8f33bdf6439f..0000000000000000000000000000000000000000
--- a/pathvisio/testFiles/wikipathways/gstp.gpml
+++ /dev/null
@@ -1,2629 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Generated">
- <Graphics BoardWidth="10030.0" BoardHeight="6030.0" />
- <DataNode TextLabel="GSTP1" GraphId="sa312" Type="Rna">
- <Comment></Comment>
- <Graphics CenterX="1161.0" CenterY="973.0" Width="90.0" Height="25.0" ZOrder="32883" FillColor="66ff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="electrophile-SG" GraphId="sa326" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="4601.5" CenterY="2106.5" Width="109.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="pyruvate" GraphId="sa374" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="1492.0" CenterY="2471.0" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="GLRX2" GraphId="sa397" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1381.0" CenterY="1994.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="PSMA5" GraphId="sa404" Type="Protein" GroupRef="csa14">
- <Comment></Comment>
- <Graphics CenterX="1127.0" CenterY="1130.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="GCLC" GraphId="sa257" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1470.518796992481" CenterY="1315.6447368421052" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="glucose" GraphId="sa373" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="3606.0" CenterY="2472.0" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="CAPN1" GraphId="sa379" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="480.0" CenterY="1298.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="GSTP1" GraphId="sa394" Type="Protein" GroupRef="csa12">
- <Comment></Comment>
- <Graphics CenterX="343.66666666666674" CenterY="1558.5" Width="80.0" Height="40.0" ZOrder="32883" FillColor="00ccff" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Paraquat-SG" GraphId="sa295" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="2189.5882352941176" CenterY="2037.6176470588236" Width="90.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="MTPT" GraphId="sa274" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="3966.0" CenterY="1524.0882352941176" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="pubchem.compound" ID="1388" />
- </DataNode>
- <DataNode TextLabel="ROS" GraphId="sa396" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="792.0" CenterY="1714.0" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="obo.chebi" ID="CHEBI:26523" />
- </DataNode>
- <DataNode TextLabel="GGT1" GraphId="sa307" Type="GeneProduct">
- <Comment></Comment>
- <Graphics CenterX="983.0" CenterY="918.0" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ffff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="PRDX1" GraphId="sa281" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1480.0" CenterY="1770.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="CDK5R1" GraphId="sa386" Type="Protein" GroupRef="csa11">
- <Comment></Comment>
- <Graphics CenterX="177.090909090909" CenterY="1376.9870129870126" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="MAPK3K5" GraphId="sa413" Type="Protein" GroupRef="csa20">
- <Comment></Comment>
- <Graphics CenterX="246.0" CenterY="1803.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="glutathione" GraphId="sa238" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="3348.0" CenterY="1013.0" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="obo.chebi" ID="CHEBI:16856" />
- </DataNode>
- <DataNode TextLabel="PARK7" GraphId="sa358" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="395.52941176470586" CenterY="2121.9411764705883" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="MAPK8" GraphId="sa277" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="696.0" CenterY="1602.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="NFE2L2" GraphId="sa316" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="659.5454545454545" CenterY="791.181818181818" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="PRDX2" GraphId="sa383" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="911.1428571428573" CenterY="1223.1428571428573" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="SLC6A3" GraphId="sa264" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1862.0" CenterY="1662.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="MPP-SG" GraphId="sa271" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="2193.9411764705883" CenterY="1786.0882352941178" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="GSH Depletion" GraphId="sa403" Type="Pathway">
- <Comment></Comment>
- <Graphics CenterX="1107.5" CenterY="1247.5" Width="125.0" Height="35.0" ZOrder="32883" FillColor="cc99ff" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="glutathione" GraphId="sa412" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="1064.0" CenterY="2300.0" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="obo.chebi" ID="CHEBI:16856" />
- </DataNode>
- <DataNode TextLabel="MPP+" GraphId="sa398" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="834.0" CenterY="1655.0" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="pubchem.compound" ID="39484" />
- </DataNode>
- <DataNode TextLabel="GGT1" GraphId="sa310" Type="Rna">
- <Comment></Comment>
- <Graphics CenterX="1161.0" CenterY="918.0" Width="90.0" Height="25.0" ZOrder="32883" FillColor="66ff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="CDK5R1 (p25)" GraphId="sa392" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="639.6666666666667" CenterY="1320.5" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ffcccc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="PRDX6" GraphId="sa407" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1480.0" CenterY="1820.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="SLC7A11" GraphId="sa336" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="4495.666666666667" CenterY="963.6666666666667" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="GCLM" GraphId="sa258" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1564.0902255639094" CenterY="1316.2796574770261" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="ROS/RNS" GraphId="sa322" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="574.5454545454545" CenterY="1017.681818181818" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="obo.chebi" ID="CHEBI:62764" />
- </DataNode>
- <DataNode TextLabel="L-cysteine" GraphId="sa250" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="2286.7142857142862" CenterY="1296.5" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="obo.chebi" ID="CHEBI:17561" />
- </DataNode>
- <DataNode TextLabel="generic protein" GraphId="sa287" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1210.0" CenterY="1614.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="PRKAB1" GraphId="sa408" Type="Protein" GroupRef="csa17">
- <Comment></Comment>
- <Graphics CenterX="1302.0" CenterY="2350.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="ANPEP" GraphId="sa247" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1856.0" CenterY="1227.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="UPS" GraphId="sa345">
- <Comment></Comment>
- <Graphics CenterX="674.0" CenterY="1072.0" Width="30.0" Height="30.0" ZOrder="32883" FillColor="ffcccc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="pubmed" ID="18990698" />
- </DataNode>
- <DataNode TextLabel="glutathione" GraphId="sa406" Type="Metabolite">
- <Comment></Comment>
- <Graphics CenterX="1294.0" CenterY="1000.0" Width="70.0" Height="25.0" ZOrder="32883" FillColor="ccff66" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="obo.chebi" ID="CHEBI:16856" />
- </DataNode>
- <DataNode TextLabel="PRKAB2" GraphId="sa409" Type="Protein" GroupRef="csa17">
- <Comment></Comment>
- <Graphics CenterX="1304.0" CenterY="2394.0" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="GSH/GSSG ratio" GraphId="sa401" Type="Pathway">
- <Comment></Comment>
- <Graphics CenterX="1136.0" CenterY="1312.0" Width="126.0" Height="38.0" ZOrder="32883" FillColor="cc99ff" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="generic protein" GraphId="sa289" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="1211.625" CenterY="1862.375" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="generic protein" GraphId="sa284" Type="Protein">
- <Comment></Comment>
- <Graphics CenterX="2190.875" CenterY="1882.375" Width="80.0" Height="40.0" ZOrder="32883" FillColor="ccffcc" FontSize="10" Valign="Middle" Color="0000ff" />
- <Xref Database="" ID="" />
- </DataNode>
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- </Graphics>
- <Xref Database="" ID="" />
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- <Shape TextLabel="nucleus" GraphId="ca7">
- <Comment>GSTP1;TXN;GSS;SLC1A1;GGT1;TXN;GSTP1;SLC1A1;GSS;GGT1;NFE2L2;</Comment>
- <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
- <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double" />
- <Graphics CenterX="998.0" CenterY="921.0" Width="490.0" Height="304.0" ZOrder="16384" FontSize="20" Valign="Bottom" ShapeType="Rectangle" LineThickness="3.0" Color="ffcc66" Rotation="0.0" />
- </Shape>
- <Shape TextLabel="Astrocyte" GraphId="ca3">
- <Comment>GLUT?;ABCB1;yGluCys;SLC7A11;glucose;GGT1;cystine;GSS;L-glutamic acid;glycine;MAOB;MTPT;generic
-proteine;Paraquat-SG;MRP1;ABCB1;glutathione;lactate;electrophile-SG;MRP5;MPP+;MPP-SG;SLC3A2;L-cysteine;L-glutamic acid;GLUT1;GCLM;GCLC;</Comment>
- <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
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- <Graphics CenterX="3239.0" CenterY="1722.0" Width="1732.0" Height="1936.0" ZOrder="16384" FontSize="20" Valign="Bottom" ShapeType="Rectangle" LineThickness="3.0" Color="ffcc66" Rotation="0.0" />
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- <Shape TextLabel="Mitochondria" GraphId="ca8">
- <Comment>SLC25A10;Complex I;glutathione;SLC25A11;</Comment>
- <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
- <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double" />
- <Graphics CenterX="1662.5" CenterY="923.0" Width="201.0" Height="276.0" ZOrder="16384" FontSize="20" Valign="Bottom" ShapeType="Rectangle" LineThickness="3.0" Color="ffcc66" Rotation="0.0" />
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- <Shape TextLabel="endothelial cell" GraphId="ca6">
- <Comment>cystine;SLC7A11;SLC7A5;</Comment>
- <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
- <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double" />
- <Graphics CenterX="4400.0" CenterY="1689.0" Width="200.0" Height="1900.0" ZOrder="16384" FontSize="20" Valign="Bottom" ShapeType="Rectangle" LineThickness="3.0" Color="ffcc66" Rotation="0.0" />
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- <Shape TextLabel="blood vessel" GraphId="ca5">
- <Comment></Comment>
- <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
- <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double" />
- <Graphics CenterX="7414.0" CenterY="3000.0" Width="5172.0" Height="6000.0" ZOrder="16384" FontSize="20" Valign="Bottom" ShapeType="Rectangle" LineThickness="3.0" Color="ffcc66" Rotation="0.0" />
- </Shape>
- <Shape TextLabel="blood vessel" GraphId="ca4">
- <Comment>glutathione;generic
-protein;cystine;electrophile-SG;L-glutamic acid;CysGly;MPP-SG;Paraquat-SG;L-cysteine;MPP+;</Comment>
- <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
- <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double" />
- <Graphics CenterX="2260.5" CenterY="3000.0" Width="4521.0" Height="6000.0" ZOrder="16384" FontSize="20" Valign="Bottom" ShapeType="Rectangle" LineThickness="3.0" Color="ffcc66" Rotation="0.0" />
- </Shape>
- <Shape TextLabel="Neuron" GraphId="ca1">
- <Comment>Apotosis;glutathione;pyruvate;GLRX2;Proliferation;glycine;GCLC;TRAF2-GSTP1;Thioredoxin-ASK1;CAPN1;MRP/ABCC;glutathione
- disulfide;L-cysteine;CDK5R1;MPP+;ROS;PRDX1;MPP+;PARK-DAXX;PARK7-DAXX;JUN;ROS/RNS;PARK7;JUN;PRDX2;MAPK8;NFE2L2;PRDX2;SLC6A3;GSH Depletion;glutathione;MPP+;UPS;TRAF2;PARK7-KEAP1;CDK5R1 (p25);PRDX6;GSH Depletion;GCLM;ROS/RNS;generic
-protein;generic
-protein;GSTP1-CDK5;glutathione;ANPEP;UPS;MAP3K5;glutathione;ASK1-DAXX;ROS;GSH/GSSG ratio;generic
-protein;PARK7;Paraquat;electrophile-SG;GLUT?;20S core;DAXX;GSTP1;JNK-GSTP1;PARK7;L-glutamic acid;KEAP1;SLC1A1;TRX;PARK7;AMPK;glutathione
- disulfide;CDK5-p25;glutathione;MPP-SG;GSS;electrophile;GSR;CDK5-p35;yGluCys;TRX;glutathione;Paraquat-SG;electrophile;CDK5;AMPK;GLRX;lactate;20S core;generic
- protein;E1/E2;GSTP1;glutathione;Apotosis;DAXX;ROS/RNS;UPS;</Comment>
- <Attribute Key="org.pathvisio.CellularComponentProperty" Value="Cell" />
- <Attribute Key="org.pathvisio.DoubleLineProperty" Value="Double" />
- <Graphics CenterX="983.0" CenterY="1712.0" Width="1772.0" Height="1924.0" ZOrder="16384" FontSize="20" Valign="Bottom" ShapeType="Rectangle" LineThickness="3.0" Color="ffcc66" Rotation="0.0" />
- </Shape>
- <Group GroupId="csa7" GraphId="csa7" />
- <Group GroupId="csa8" GraphId="csa8" />
- <Group GroupId="csa5" GraphId="csa5" />
- <Group GroupId="csa9" GraphId="csa9" />
- <Group GroupId="csa15" GraphId="csa15" />
- <Group GroupId="csa11" GraphId="csa11" />
- <Group GroupId="csa16" GraphId="csa16" />
- <Group GroupId="csa20" GraphId="csa20" />
- <Group GroupId="csa4" GraphId="csa4" />
- <Group GroupId="csa12" GraphId="csa12" />
- <Group GroupId="csa3" GraphId="csa3" />
- <Group GroupId="csa19" GraphId="csa19" GroupRef="csa18" />
- <Group GroupId="csa18" GraphId="csa18" />
- <Group GroupId="csa10" GraphId="csa10" />
- <Group GroupId="csa14" GraphId="csa14" />
- <Group GroupId="csa13" GraphId="csa13" />
- <Group GroupId="csa17" GraphId="csa17" GroupRef="csa16" />
- <InfoBox CenterX="0.0" CenterY="0.0" />
-</Pathway>
-
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java b/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
index c480231a2a77c021ca268509c0bdb5e46e287170..63bc73e8f3ce796d7c4d51b2da4b82761f0d4b52 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
@@ -28,7 +28,7 @@ public final class ApplicationContextLoader {
private static ConfigurableApplicationContext applicationContext;
/**
- * Default constructor. Prevents instatiation.
+ * Default constructor. Prevents instantiation.
*/
private ApplicationContextLoader() {
diff --git a/persist/src/main/resources/db/migration/15.0.0/V15.0.0.20191022__font_color_is_obligatory.sql b/persist/src/main/resources/db/migration/15.0.0/V15.0.0.20191022__font_color_is_obligatory.sql
new file mode 100644
index 0000000000000000000000000000000000000000..f79af3ae4ab07ba4f51a8a444c0b9a607997a08b
--- /dev/null
+++ b/persist/src/main/resources/db/migration/15.0.0/V15.0.0.20191022__font_color_is_obligatory.sql
@@ -0,0 +1,2 @@
+update element_table set font_color = E'\\xaced00057372000e6a6176612e6177742e436f6c6f7201a51783108f337502000546000666616c70686149000576616c75654c0002637374001b4c6a6176612f6177742f636f6c6f722f436f6c6f7253706163653b5b00096672676276616c75657400025b465b00066676616c756571007e0002787000000000ff000000707070' where font_color is null;
+ALTER TABLE element_table ALTER COLUMN font_color SET NOT NULL;
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index f9d2e9f26b3547b7aabcd49ff87948df258faba7..3560c6db610553db2ed7985bf285cac908ae3b84 100644
--- a/rest-api/pom.xml
+++ b/rest-api/pom.xml
@@ -26,6 +26,12 @@
<version>1.0</version>
</dependency>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>pathvisio</artifactId>
+ <version>1.0</version>
+ </dependency>
+
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>jsr311-api</artifactId>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index bc9c4366ab4c056f74a422392e16135c94007e6c..5ab4674620e75aa3225032ac375ad9e410ba9b4f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -23,9 +23,6 @@ import lcsb.mapviewer.annotation.services.*;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.converter.Converter;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
-import lcsb.mapviewer.converter.model.sbml.SbmlParser;
import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -60,6 +57,9 @@ public abstract class BaseRestImpl {
@Autowired
private PubmedParser pubmedParser;
+ @Autowired
+ private List<Converter> modelConverters;
+
private ElementMatcher elementMatcher = new ElementMatcher();
private Transformer mathMlTransformer;
@@ -161,7 +161,7 @@ public abstract class BaseRestImpl {
* @param modelId
* list of model identifiers separated by "," or '*' when all models
* should be returned
- * @throws QueryException
+ * @throws QueryException
*/
protected List<Model> getModels(String projectId, String modelId) throws QueryException {
Model model = modelService.getLastModelByProjectId(projectId);
@@ -318,11 +318,7 @@ public abstract class BaseRestImpl {
}
protected List<Converter> getModelConverters() {
- List<Converter> result = new ArrayList<>();
- result.add(new CellDesignerXmlParser());
- result.add(new SbgnmlXmlConverter());
- result.add(new SbmlParser());
- return result;
+ return modelConverters;
}
protected String getFirstValue(List<Object> list) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java b/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
index 28365629698bf7a2625b0cefd7899d2d3cde31cb..57b92597b0c411165ef847f29e13de0a0f0856fa 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
@@ -8,7 +8,7 @@ import lcsb.mapviewer.services.SpringServiceConfig;
@Configuration
@EnableWebMvc
@Import({ SpringServiceConfig.class })
-@ComponentScan(basePackages = { "lcsb.mapviewer.api" })
+@ComponentScan(basePackages = { "lcsb.mapviewer" })
public class SpringRestApiConfig {
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
index 77e415ea34e49fd29215be138e0ad97e0e2fc4ba..84d9f956a0b7e8aa72e65fbc4de242593ce407b0 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
@@ -15,16 +15,21 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.api.projects.ProjectRestImpl;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.user.annotator.AnnotatorData;
public class BaseRestImplTest extends RestTestFunctions {
- Logger logger = LogManager.getLogger(BaseRestImplTest.class);
+ Logger logger = LogManager.getLogger();
@Autowired
MiriamConnector mc;
+ @Autowired
+ ProjectRestImpl restImpl;
+
@Autowired
PubmedParser pubmedParser;
@@ -107,4 +112,11 @@ public class BaseRestImplTest extends RestTestFunctions {
Integer x = controller.parseInteger(null);
assertNull(x);
}
+
+ @Test
+ public void testGetConverters() throws Exception {
+ List<Converter> list = restImpl.getModelConverters();
+ assertTrue(list.size() > 0);
+ }
+
}