processing modification site for rna/antisense rna uses proper modification type

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java

@@ -91,10 +91,6 @@ public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna>
     super.update(sp);
     if (sp instanceof CellDesignerAntisenseRna) {
       CellDesignerAntisenseRna rna = (CellDesignerAntisenseRna) sp;
-      for (CellDesignerModificationResidue mr : getRegions()) {
-        mr.setState(null);
-      }
-
       for (CellDesignerModificationResidue region : rna.getRegions()) {
         updateRegion(region);
       }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java

@@ -71,9 +71,6 @@ public class CellDesignerRna extends CellDesignerSpecies<Rna> {
     super.update(species);
     if (species instanceof CellDesignerRna) {
       CellDesignerRna rna = (CellDesignerRna) species;
-      for (CellDesignerModificationResidue mr : getRegions()) {
-        mr.setState(null);
-      }
 
       for (CellDesignerModificationResidue region : rna.getRegions()) {
         updateRegion(region);

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java

@@ -460,7 +460,6 @@ public class CellDesignerModificationResidue implements Serializable {
     result.setIdModificationResidue(idModificationResidue);
     result.setName(name);
     result.setActive(active);
-    logger.debug(angle);
     result.setPosition(converter.getCoordinatesByPosition(element, angle));
     if (modificationType.equals(ModificationType.TRANSCRIPTION_SITE_LEFT)) {
       result.setDirection("LEFT");

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java

@@ -6,6 +6,7 @@ import java.util.List;
 import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
 import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Gene;
 import lcsb.mapviewer.model.map.species.Protein;
@@ -87,6 +88,12 @@ public class SpeciesState {
         CellDesignerModificationResidue mr = new CellDesignerModificationResidue(region);
         addModificationResidue(mr);
       }
+    } else if (species instanceof AntisenseRna) {
+      AntisenseRna rna = (AntisenseRna) species;
+      for (ModificationResidue region : rna.getRegions()) {
+        CellDesignerModificationResidue mr = new CellDesignerModificationResidue(region);
+        addModificationResidue(mr);
+      }
     } else if (species instanceof Gene) {
       Gene gene = (Gene) species;
       for (ModificationResidue mr : gene.getModificationResidues()) {

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java

@@ -27,6 +27,7 @@ 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.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
 import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
 import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
 import lcsb.mapviewer.model.map.species.field.Residue;
@@ -233,6 +234,13 @@ public class ModificationTest extends CellDesignerTestFunctions {
       rna = model.getElementByElementId("sa3");
       assertEquals(1, rna.getRegions().size());
       assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
+
+      rna = model.getElementByElementId("sa4");
+      assertEquals(1, rna.getRegions().size());
+      assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
+      ModificationSite modificationSite = (ModificationSite) rna.getRegions().get(0);
+      assertEquals(ModificationState.PHOSPHORYLATED, modificationSite.getState());
+
       testXmlSerialization(model);
 
     } catch (Exception e) {

converter-CellDesigner/testFiles/modifications/antisense_rna_with_region.xml

@@ -22,7 +22,7 @@
 <celldesigner:briefView>
 <celldesigner:innerPosition x="0.0" y="0.0"/>
 <celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
 <celldesigner:paint color="3fff0000" scheme="Color"/>
 </celldesigner:briefView>
 <celldesigner:info state="empty" angle="-1.5707963267948966"/>
@@ -41,12 +41,12 @@
 <celldesigner:briefView>
 <celldesigner:innerPosition x="0.0" y="0.0"/>
 <celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
 <celldesigner:paint color="3fff0000" scheme="Color"/>
 </celldesigner:briefView>
 <celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:speciesAlias id="sa3" species="s4">
 <celldesigner:activity>inactive</celldesigner:activity>
 <celldesigner:bounds x="192.0" y="247.5" w="90.0" h="25.0"/>
 <celldesigner:font size="12"/>
@@ -60,7 +60,26 @@
 <celldesigner:briefView>
 <celldesigner:innerPosition x="0.0" y="0.0"/>
 <celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa4" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="300.0" y="207.0" w="90.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="90.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffff6666" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
 <celldesigner:paint color="3fff0000" scheme="Color"/>
 </celldesigner:briefView>
 <celldesigner:info state="empty" angle="-1.5707963267948966"/>
@@ -151,6 +170,22 @@
 <celldesigner:speciesIdentity>
 <celldesigner:class>ANTISENSE_RNA</celldesigner:class>
 <celldesigner:antisensernaReference>arn3</celldesigner:antisensernaReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="tr1" state="phosphorylated"/>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s4" id="s4" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn3</celldesigner:antisensernaReference>
 </celldesigner:speciesIdentity>
 </celldesigner:extension>
 </annotation>