JAL-2632 corrected lookup of residue colour

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index fbac400..38ce476 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -27,7 +27,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
@@ -49,8 +49,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javajs.awt.Dimension;
-
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolSelectionListener;
@@ -74,7 +72,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   Vector<String> atomsPicked = new Vector<String>();
 
-  public Vector<String> chainNames;
+  private List<String> chainNames;
 
   Hashtable<String, String> chainFile;
 
@@ -99,10 +97,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public Viewer viewer;
 
   public JalviewJmolBinding(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          DataSourceType protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
      * "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -1083,7 +1081,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
-    chainNames = new Vector<String>();
+    chainNames = new ArrayList<String>();
     chainFile = new Hashtable<String, String>();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
@@ -1143,13 +1141,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       for (int pe = 0; pe < getPdbCount(); pe++)
       {
         boolean matches = false;
+        addSequence(pe, getSequence()[pe]);
         if (fileName == null)
         {
           if (false)
           // see JAL-623 - need method of matching pasted data up
           {
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    pdbfile, AppletFormatAdapter.PASTE);
+                    pdbfile, DataSourceType.PASTE);
             getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
@@ -1167,12 +1166,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             // needs
             // to be tested. See mantis bug
             // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-            String protocol = AppletFormatAdapter.URL;
+            DataSourceType protocol = DataSourceType.URL;
             try
             {
               if (fl.exists())
               {
-                protocol = AppletFormatAdapter.FILE;
+                protocol = DataSourceType.FILE;
               }
             } catch (Exception e)
             {
@@ -1194,7 +1193,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             String chid = new String(pdb.getId() + ":"
                     + pdb.getChains().elementAt(i).id);
             chainFile.put(chid, fileName);
-            chainNames.addElement(chid);
+            chainNames.add(chid);
           }
           notifyLoaded = true;
         }
@@ -1242,6 +1241,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     setLoadingFromArchive(false);
   }
 
+  @Override
+  public List<String> getChainNames()
+  {
+    return chainNames;
+  }
+
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
   {
     notifyAtomPicked(iatom, strMeasure, null);
@@ -1295,10 +1300,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     command.append("select *;color white;");
     List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
             false);
-    for (String res : residueSet)
+    for (String resName : residueSet)
     {
-      Color col = cs.findColour(res.charAt(0));
-      command.append("select " + res + ";color[" + col.getRed() + ","
+      char res = resName.length() == 3 ? ResidueProperties
+              .getSingleCharacterCode(resName) : resName.charAt(0);
+      Color col = cs.findColour(res);
+      command.append("select " + resName + ";color[" + col.getRed() + ","
               + col.getGreen() + "," + col.getBlue() + "];");
     }
 
@@ -1404,7 +1411,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     // Jalview doesn't honour resize panel requests
     return null;