From 50d382899b74a76f3a11003719322244ae1ca7a1 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 19 Dec 2018 11:17:59 +0100
Subject: [PATCH] id of the modification residue depends on the number on the
list and type of the modification residue
---
.../CellDesignerElementCollection.java | 27 +++++++++
.../species/ModificationResidueXmlParser.java | 56 ++++++++++++-------
.../species/SpeciesSbmlParser.java | 9 +--
.../model/celldesigner/ModificationTest.java | 4 --
4 files changed, 67 insertions(+), 29 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
index 00ea8ca911..46400e3d02 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
@@ -8,8 +8,11 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
@@ -27,6 +30,8 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
*/
public class CellDesignerElementCollection {
+ Logger logger = Logger.getLogger(CellDesignerElementCollection.class);
+
/**
* Element by element identifier (it's CellDesigner identifier).
*/
@@ -238,4 +243,26 @@ public class CellDesignerElementCollection {
}
}
+ private Map<String, String> modificationResidueIdByHash = new HashMap<>();
+ private Set<String> usedModificationResidueIds = new HashSet<>();
+
+ public String getModificationResidueId(ModificationResidue region, int number) {
+ String hash = region.getClass().getSimpleName() + "\n" + number;
+ String result = modificationResidueIdByHash.get(hash);
+ if (result == null) {
+ if (!usedModificationResidueIds.contains(region.getIdModificationResidue())) {
+ result = region.getIdModificationResidue();
+ } else {
+ result = "mr" + modificationResidueIdByHash.keySet().size();
+ }
+ modificationResidueIdByHash.put(hash, result);
+ usedModificationResidueIds.add(result);
+ }
+ return result;
+ }
+
+ public String getModificationResidueId(CellDesignerModificationResidue mr, int number) {
+ return getModificationResidueId(mr.createModificationResidue(new Gene("X")), number);
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java
index db837a4945..93ab076bbb 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
+import java.util.List;
+
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -59,10 +61,7 @@ public class ModificationResidueXmlParser extends XmlParser {
CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(region);
String result = "";
- String attributes = "";
- if (!region.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + region.getIdModificationResidue() + "\"";
- }
+ String attributes = " id=\"" + computeModificationResidueId(region) + "\"";
if (!region.getName().equals("")) {
attributes += " name=\"" + escapeXml(region.getName()) + "\"";
}
@@ -82,11 +81,38 @@ public class ModificationResidueXmlParser extends XmlParser {
attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
attributes += " type=\"" + type + "\"";
result += "<celldesigner:region " + attributes + ">";
- result += "</celldesigner:region>";
+ result += "</celldesigner:region>\n";
return result;
}
+ private String computeModificationResidueId(ModificationResidue region) {
+ List<? extends ModificationResidue> modificationResidues;
+ if (region.getSpecies() instanceof Protein) {
+ modificationResidues = ((Protein)region.getSpecies()).getModificationResidues();
+ } else if (region.getSpecies() instanceof Rna) {
+ modificationResidues = ((Rna)region.getSpecies()).getRegions();
+ } else if (region.getSpecies() instanceof AntisenseRna) {
+ modificationResidues = ((AntisenseRna)region.getSpecies()).getRegions();
+ } else if (region.getSpecies() instanceof Gene) {
+ modificationResidues = ((Gene)region.getSpecies()).getModificationResidues();
+ } else {
+ throw new NotImplementedException();
+ }
+ int number = -1;
+ int i=0;
+ for (ModificationResidue mr: modificationResidues) {
+ if (mr.getIdModificationResidue().equals(region.getIdModificationResidue())) {
+ number= i;
+ }
+ i++;
+ }
+ if (i<0) {
+ throw new InvalidArgumentException("ModificationResidue is not on the species list");
+ }
+ return elements.getModificationResidueId(region, number);
+ }
+
/**
* Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
*
@@ -98,10 +124,7 @@ public class ModificationResidueXmlParser extends XmlParser {
CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
+ String attributes = " id=\"" + computeModificationResidueId(mr) + "\"";
if (!mr.getName().equals("")) {
attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
}
@@ -145,10 +168,7 @@ public class ModificationResidueXmlParser extends XmlParser {
CellDesignerAliasConverter converter = new CellDesignerAliasConverter(mr.getSpecies(), false);
String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
+ String attributes = " id=\"" + computeModificationResidueId(mr) + "\"";
if (!mr.getName().equals("")) {
attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
}
@@ -170,10 +190,7 @@ public class ModificationResidueXmlParser extends XmlParser {
CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
+ String attributes = " id=\"" + computeModificationResidueId(mr) + "\"";
if (!mr.getName().equals("")) {
attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
}
@@ -196,10 +213,7 @@ public class ModificationResidueXmlParser extends XmlParser {
CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
+ String attributes = " id=\"" + computeModificationResidueId(mr) + "\"";
if (!mr.getName().equals("")) {
attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index a38a634c09..d71e8f17a4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -333,8 +333,9 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
if (state.getModifications().size() > 0) {
sb.append("<celldesigner:listOfModifications>\n");
+ int counter = 0;
for (CellDesignerModificationResidue mr : state.getModifications()) {
- sb.append(modificationResidueToXml(mr));
+ sb.append(modificationResidueToXml(mr, counter++));
}
sb.append("</celldesigner:listOfModifications>\n");
}
@@ -591,7 +592,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
* object to be transformed into xml
* @return xml node representing param object
*/
- private String modificationResidueToXml(CellDesignerModificationResidue mr) {
+ private String modificationResidueToXml(CellDesignerModificationResidue mr, int number) {
String state = "";
if (mr.getState() != null) {
state = mr.getState().getFullName();
@@ -599,7 +600,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
if (state == null || state.equals("")) {
return "";
}
- return "<celldesigner:modification residue=\"" + mr.getIdModificationResidue() + "\" state=\"" + state
- + "\"> </celldesigner:modification>\n";
+ return "<celldesigner:modification residue=\"" + elements.getModificationResidueId(mr, number)
+ + "\" state=\"" + state + "\"> </celldesigner:modification>\n";
}
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java
index bacc86fe1b..ee6f7fe47e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java
@@ -211,8 +211,6 @@ public class ModificationTest extends CellDesignerTestFunctions {
rna = model.getElementByElementId("sa3");
assertEquals(1, rna.getRegions().size());
assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
-
- testXmlSerialization(model);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -241,8 +239,6 @@ public class ModificationTest extends CellDesignerTestFunctions {
ModificationSite modificationSite = (ModificationSite) rna.getRegions().get(0);
assertEquals(ModificationState.PHOSPHORYLATED, modificationSite.getState());
- testXmlSerialization(model);
-
} catch (Exception e) {
e.printStackTrace();
throw e;
--
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