From 6eab06f8a1784f15f3b8ad89aeac94c317556957 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 13 Jul 2018 14:13:32 +0200
Subject: [PATCH] rest API provide information about all modifications
---
.../element/species/SpeciesConverter.java | 3 +-
.../element/species/SpeciesConverterTest.java | 3 +-
.../src/main/js/gui/leftPanel/GuiUtils.js | 36 ++++++++----
.../resources/applicationContext-persist.xml | 1 +
.../elements/ElementsRestImpl.java | 55 ++++++++++++++++---
5 files changed, 74 insertions(+), 24 deletions(-)
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 f9e547396a..c707b3b147 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
@@ -592,8 +592,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
double y = modificationSite.getPosition().getY();
- Point2D p = modificationSite.getPosition();
- p.setLocation(p.getX(), p.getY() - DEFAULT_MODIFICATION_DIAMETER);
+ Point2D p = new Point2D.Double(modificationSite.getPosition().getX(), y - DEFAULT_MODIFICATION_DIAMETER);
Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
Color c = graphics.getColor();
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
index 16bdf0a9a1..4f67a317af 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
@@ -25,8 +25,10 @@ import org.mockito.Mockito;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -328,5 +330,4 @@ public class SpeciesConverterTest {
return protein;
}
-
}
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index b8815fc72e..e5ffcbc892 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -60,6 +60,12 @@ GuiUtils.prototype.createLabel = function (value) {
return result;
};
+/**
+ *
+ * @param {string} label
+ * @param {Object[]} value
+ * @returns {HTMLDivElement}
+ */
GuiUtils.prototype.createPostTranslationalModifications = function (label, value) {
var result = document.createElement("div");
if (value !== undefined && value.length > 0) {
@@ -71,19 +77,25 @@ GuiUtils.prototype.createPostTranslationalModifications = function (label, value
});
for (var i = 0; i < value.length; i++) {
var name = value[i].name;
- var modificationStateType = self.getConfiguration().getModificationStateTypeByName(value[i].state);
- var state = modificationStateType.getCommonName();
- var desc;
- if (name !== null && name !== undefined && name !== "") {
- desc = state + " at position " + name + ", ";
- } else {
- desc = state + ",";
+ var desc = undefined;
+ if (value[i].state !== undefined && value[i].name !== null) {
+ var modificationStateType = self.getConfiguration().getModificationStateTypeByName(value[i].state);
+ var state = modificationStateType.getCommonName();
+
+ if (name !== null && name !== undefined && name !== "") {
+ desc = state + " at position " + name + ", ";
+ } else {
+ desc = state + ",";
+ }
+ }
+
+ if (desc !== undefined) {
+ var row = Functions.createElement({
+ type: "li"
+ });
+ row.appendChild(self.createLabelText(desc));
+ list.appendChild(row);
}
- var row = Functions.createElement({
- type: "li"
- });
- row.appendChild(self.createLabelText(desc));
- list.appendChild(row);
}
result.appendChild(list);
}
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 22f563b1a0..104c0fb09f 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -180,6 +180,7 @@
<value>lcsb.mapviewer.model.map.species.field.CodingRegion</value>
<value>lcsb.mapviewer.model.map.species.field.ModificationSite</value>
<value>lcsb.mapviewer.model.map.species.field.ProteinBindingDomain</value>
+ <value>lcsb.mapviewer.model.map.species.field.RegulatoryRegion</value>
<value>lcsb.mapviewer.model.map.species.field.Residue</value>
<value>lcsb.mapviewer.model.map.species.field.TranscriptionSite</value>
<value>lcsb.mapviewer.model.map.species.field.UniprotRecord</value>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index ab6009bf4c..d2f3739d54 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -12,18 +12,27 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.model.map.species.field.Structure;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import lcsb.mapviewer.services.SecurityException;
@@ -215,12 +224,16 @@ public class ElementsRestImpl extends BaseRestImpl {
structuralState = protein.getStructuralState();
} else if (element instanceof Rna) {
Rna rna = ((Rna) element);
- modifications = getModifications(((Rna) element).getRegions());
+ modifications = getModifications(rna.getRegions());
structuralState = rna.getState();
} else if (element instanceof AntisenseRna) {
AntisenseRna antisenseRna = ((AntisenseRna) element);
- modifications = getModifications(((AntisenseRna) element).getRegions());
+ modifications = getModifications(antisenseRna.getRegions());
structuralState = antisenseRna.getState();
+ } else if (element instanceof Gene) {
+ Gene gene = ((Gene) element);
+ modifications = getModifications(gene.getModificationResidues());
+ structuralState = gene.getState();
}
if (element instanceof Species) {
structures = getStructures(((Species) element).getUniprots());
@@ -235,15 +248,39 @@ public class ElementsRestImpl extends BaseRestImpl {
private List<Map<String, Object>> getModifications(List<? extends ModificationResidue> elements) {
List<Map<String, Object>> result = new ArrayList<>();
for (ModificationResidue region : elements) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("name", region.getName());
+ row.put("modificationId", region.getIdModificationResidue());
if (region instanceof AbstractSiteModification) {
- ModificationState state = ((AbstractSiteModification) region).getState();
- if (state != null) {
- Map<String, Object> row = new TreeMap<>();
- row.put("name", region.getName());
- row.put("state", state.name());
- result.add(row);
+ AbstractSiteModification siteModification = ((AbstractSiteModification) region);
+ if (siteModification.getState() != null) {
+ row.put("state", siteModification.getState().name());
}
}
+ String type = null;
+ if (region instanceof Residue) {
+ type = ModificationType.RESIDUE.name();
+ } else if (region instanceof BindingRegion) {
+ type = ModificationType.BINDING_REGION.name();
+ } else if (region instanceof CodingRegion) {
+ type = ModificationType.CODING_REGION.name();
+ } else if (region instanceof ProteinBindingDomain) {
+ type = ModificationType.PROTEIN_BINDING_DOMAIN.name();
+ } else if (region instanceof RegulatoryRegion) {
+ type = ModificationType.REGULATORY_REGION.name();
+ } else if (region instanceof TranscriptionSite) {
+ if (((TranscriptionSite) region).getDirection().equals("LEFT")) {
+ type = ModificationType.TRANSCRIPTION_SITE_LEFT.name();
+ } else {
+ type = ModificationType.TRANSCRIPTION_SITE_RIGHT.name();
+ }
+ } else if (region instanceof ModificationSite) {
+ type = ModificationType.MODIFICATION_SITE.name();
+ } else {
+ throw new InvalidArgumentException("Unknown class: " + region.getClass());
+ }
+ row.put("type", type);
+ result.add(row);
}
return result;
}
--
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