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 56287a9..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;
@@ -100,7 +98,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   public JalviewJmolBinding(StructureSelectionManager ssm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
-          String protocol)
+          DataSourceType protocol)
   {
     super(ssm, pdbentry, sequenceIs, protocol);
     /*
@@ -1150,7 +1148,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           // 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;
@@ -1168,12 +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)
             {
@@ -1302,10 +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() + "];");
     }
 
@@ -1411,7 +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;