export of reaction layout added

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java

@@ -3,6 +3,7 @@ package lcsb.mapviewer.converter.model.sbml;
 import java.awt.geom.Line2D;
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 import org.apache.log4j.Logger;
@@ -18,6 +19,7 @@ import org.sbml.jsbml.ext.layout.ReactionGlyph;
 import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
 import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
 
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.modifier.Inhibition;
 import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -41,12 +43,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   @Override
   public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
     String reactionId = getReactionId(reaction);
-    logger.debug(reactionId);
     org.sbml.jsbml.Reaction result = super.sbmlElementByElementId.get(reactionId);
     if (result != null) {
       return result;
     }
     result = sbmlModel.createReaction(reactionId);
+    result.setReversible(reaction.isReversible());
     for (Product product : reaction.getProducts()) {
       Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
       SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
@@ -79,7 +81,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     if (separatorIndex > 0) {
       glyphId = glyphId.substring(separatorIndex + 2);
     }
-    logger.debug(glyphId);
     ReactionGlyph reactionGlyph;
     try {
       // handle case when input data cannot doesn't come from SBML parser and contains
@@ -135,18 +136,24 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   private SpeciesReferenceGlyph createNodeGlyph(ReactionGlyph reactionGlyph, ReactionNode node) {
     SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
     reactantGlyph.setSpeciesGlyph(speciesExporter.sbmlGlyphByElementId.get(node.getElement().getElementId()).getId());
-    reactantGlyph.setCurve(createCurve(node));
+    reactantGlyph.setCurve(createCurve(node, node instanceof Reactant));
     reactantGlyph.setSpeciesReference(speciesReferenceByReactionNode.get(node));
     return reactantGlyph;
   }
 
-  private Curve createCurve(ReactionNode reactant) {
+  private Curve createCurve(ReactionNode reactant, boolean reverse) {
     Curve curve = new Curve();
-    for (Line2D line : reactant.getLine().getLines()) {
-      LineSegment segment = new LineSegment();
-      segment.setStart(new Point(line.getX1(), line.getY1()));
-      segment.setEnd(new Point(line.getX2(), line.getY2()));
-      curve.addCurveSegment(segment);
+    List<Line2D> lines = reactant.getLine().getLines();    
+    if (reverse) {
+      lines = reactant.getLine().reverse().getLines();
+    }
+    for (Line2D line : lines) {
+      if (line.getP1().distance(line.getP2())>Configuration.EPSILON) {
+        LineSegment segment = new LineSegment();
+        segment.setStart(new Point(line.getX1(), line.getY1()));
+        segment.setEnd(new Point(line.getX2(), line.getY2()));
+        curve.addCurveSegment(segment);
+      }
     }
     return curve;
   }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

@@ -231,14 +231,6 @@ public class SbmlExporterTest {
 
     Model model2 = converter.createModel(new ConverterParams().filename("tmp.xml"));
     model2.setName(null);
-    
-    for (Reaction r: model.getReactions()) {
-      logger.debug(r.getIdReaction());
-    }
-    logger.debug("---");
-    for (Reaction r: model2.getReactions()) {
-      logger.debug(r.getIdReaction());
-    }
 
     assertNotNull(model2);
     ModelComparator comparator = new ModelComparator(1.0);

model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java

@@ -17,115 +17,127 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
  * 
  */
 public class PolylineDataComparator implements Comparator<PolylineData> {
-	/**
-	 * Default class logger.
-	 */
-	private Logger logger	= Logger.getLogger(PolylineDataComparator.class);
-
-	/**
-	 * Epsilon value used for comparison of doubles.
-	 */
-	private double epsilon;
-
-	/**
-	 * Constructor that requires {@link #epsilon} parameter.
-	 * 
-	 * @param epsilon
-	 *          {@link #epsilon}
-	 */
-	public PolylineDataComparator(double epsilon) {
-		this.epsilon = epsilon;
-	}
-
-	/**
-	 * Default constructor.
-	 */
-	public PolylineDataComparator() {
-		this(Configuration.EPSILON);
-	}
-
-	@Override
-	public int compare(PolylineData arg0, PolylineData arg1) {
-		if (arg0 == null) {
-			if (arg1 == null) {
-				return 0;
-			} else {
-				return 1;
-			}
-		} else if (arg1 == null) {
-			return -1;
-		}
-
-		if (arg0.getClass().equals(arg1.getClass())) {
-			if (arg0.getClass().equals(PolylineData.class)) {
-				return internalCompare(arg0, arg1);
-			} else {
-				throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
-			}
-		} else {
-			return -1;
-		}
-	}
-
-	/**
-	 * This method compares only the fields that are defined in
-	 * {@link PolylineData} class in inheritence tree.
-	 * 
-	 * @param arg0
-	 *          first object to compare
-	 * @param arg1
-	 *          second object to compare
-	 * @return if all fields are qual then returns 0. If they are different then
-	 *         -1/1 is returned.
-	 */
-	private int internalCompare(PolylineData arg0, PolylineData arg1) {
-		IntegerComparator integerComparator = new IntegerComparator();
-		DoubleComparator doubleComparator = new DoubleComparator(epsilon);
-		ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
-
-		if (integerComparator.compare(arg0.getPoints().size(), arg1.getPoints().size()) != 0) {
-			logger.debug("Lines have different size: " + arg0.getPoints().size() + ", " + arg1.getPoints().size());
-			return integerComparator.compare(arg0.getPoints().size(), arg1.getPoints().size());
-		}
-		// TODO this should be fixed
-		// for (int i = 0; i < arg0.getPoints().size(); i++) {
-		// if
-		// (doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
-		// 0.0) != 0) {
-		// logger.debug("Lines have different points: " + arg0.getPoints().get(i) +
-		// ", " + arg1.getPoints().get(i));
-		// return
-		// doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
-		// 0.0);
-		// }
-		// }
-
-		if (atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd()) != 0) {
-			logger.debug("Lines have different begin adt: " + arg0.getBeginAtd() + ", " + arg1.getBeginAtd());
-			return atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd());
-		}
-
-		if (atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd()) != 0) {
-			logger.debug("Lines have different end adt: " + arg0.getEndAtd() + ", " + arg1.getEndAtd());
-			return atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd());
-		}
-
-		if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
-			logger.debug("Lines have different width: " + arg0.getWidth() + ", " + arg1.getWidth());
-			return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
-		}
-
-		if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
-			logger.debug("Lines have different color: " + arg0.getColor() + ", " + arg1.getColor());
-			return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
-		}
-
-		if (arg0.getType().compareTo(arg1.getType()) != 0) {
-			logger.debug("Lines have different type: " + arg0.getType() + ", " + arg1.getType());
-			return arg0.getType().compareTo(arg1.getType());
-		}
-
-		return 0;
-	}
+  /**
+   * Default class logger.
+   */
+  private Logger logger = Logger.getLogger(PolylineDataComparator.class);
+
+  /**
+   * Epsilon value used for comparison of doubles.
+   */
+  private double epsilon;
+
+  /**
+   * Constructor that requires {@link #epsilon} parameter.
+   * 
+   * @param epsilon
+   *          {@link #epsilon}
+   */
+  public PolylineDataComparator(double epsilon) {
+    this.epsilon = epsilon;
+  }
+
+  /**
+   * Default constructor.
+   */
+  public PolylineDataComparator() {
+    this(Configuration.EPSILON);
+  }
+
+  @Override
+  public int compare(PolylineData arg0, PolylineData arg1) {
+    if (arg0 == null) {
+      if (arg1 == null) {
+        return 0;
+      } else {
+        return 1;
+      }
+    } else if (arg1 == null) {
+      return -1;
+    }
+
+    if (arg0.getClass().equals(arg1.getClass())) {
+      if (arg0.getClass().equals(PolylineData.class)) {
+        return internalCompare(arg0, arg1);
+      } else {
+        throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
+      }
+    } else {
+      return -1;
+    }
+  }
+
+  /**
+   * This method compares only the fields that are defined in {@link PolylineData}
+   * class in inheritance tree.
+   * 
+   * @param arg0
+   *          first object to compare
+   * @param arg1
+   *          second object to compare
+   * @return if all fields are equal then returns 0. If they are different then
+   *         -1/1 is returned.
+   */
+  private int internalCompare(PolylineData arg0, PolylineData arg1) {
+    IntegerComparator integerComparator = new IntegerComparator();
+    DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+    ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
+
+    int different1=0;
+    int different2=0;
+    for (int i=1;i<arg0.getPoints().size();i++) {
+      if (arg0.getPoints().get(i).distance(arg0.getPoints().get(i-1))>Configuration.EPSILON) {
+        different1++;
+      }
+    }
+    for (int i=1;i<arg1.getPoints().size();i++) {
+      if (arg1.getPoints().get(i).distance(arg1.getPoints().get(i-1))>Configuration.EPSILON) {
+        different2++;
+      }
+    }
+    if (integerComparator.compare(different1, different2) != 0) {
+      logger.debug("Lines have different size: " + different1 + ", " + different2);
+      return integerComparator.compare(arg0.getPoints().size(), arg1.getPoints().size());
+    }
+    // TODO this should be fixed
+    // for (int i = 0; i < arg0.getPoints().size(); i++) {
+    // if
+    // (doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
+    // 0.0) != 0) {
+    // logger.debug("Lines have different points: " + arg0.getPoints().get(i) +
+    // ", " + arg1.getPoints().get(i));
+    // return
+    // doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
+    // 0.0);
+    // }
+    // }
+
+    if (atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd()) != 0) {
+      logger.debug("Lines have different begin adt: " + arg0.getBeginAtd() + ", " + arg1.getBeginAtd());
+      return atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd());
+    }
+
+    if (atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd()) != 0) {
+      logger.debug("Lines have different end adt: " + arg0.getEndAtd() + ", " + arg1.getEndAtd());
+      return atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd());
+    }
+
+    if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+      logger.debug("Lines have different width: " + arg0.getWidth() + ", " + arg1.getWidth());
+      return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+    }
+
+    if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
+      logger.debug("Lines have different color: " + arg0.getColor() + ", " + arg1.getColor());
+      return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
+    }
+
+    if (arg0.getType().compareTo(arg1.getType()) != 0) {
+      logger.debug("Lines have different type: " + arg0.getType() + ", " + arg1.getType());
+      return arg0.getType().compareTo(arg1.getType());
+    }
+
+    return 0;
+  }
 
 }

model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java

@@ -58,7 +58,7 @@ public class AbstractNodeComparator implements Comparator<AbstractNode> {
 
 		// now check class types
 		if (arg0.getClass().equals(arg1.getClass())) {
-			// and call comparator of apropriate subclass
+			// and call comparator of appropriate subclass
 			if (arg0 instanceof NodeOperator) {
 				NodeOperatorComparator nodeOperatorComparator = new NodeOperatorComparator(epsilon);
 				return nodeOperatorComparator.compare((NodeOperator) arg0, (NodeOperator) arg1);
@@ -75,13 +75,13 @@ public class AbstractNodeComparator implements Comparator<AbstractNode> {
 
 	/**
 	 * This method compares only the fields that are defined in AbstractNode class
-	 * in inheritence tree. By the design it is called by subclass comparator.
+	 * in inheritance tree. By the design it is called by subclass comparator.
 	 * 
 	 * @param arg0
 	 *          first object to compare
 	 * @param arg1
 	 *          second object to compare
-	 * @return if all fields are qual then returns 0. If they are different then
+	 * @return if all fields are equal then returns 0. If they are different then
 	 *         -1/1 is returned.
 	 */
 	protected int internalCompare(AbstractNode arg0, AbstractNode arg1) {