JAL-1757 match only first altloc CA in PDB structure for superposition

[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 18b04ec..50e156f 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,22 +20,6 @@
  */
 package jalview.ext.jmol;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
 import java.awt.Color;
 import java.awt.Container;
 import java.awt.event.ComponentEvent;
@@ -43,8 +27,8 @@ import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
 import java.security.AccessControlException;
-import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
@@ -56,6 +40,22 @@ import org.jmol.api.JmolViewer;
 import org.jmol.constant.EnumCallback;
 import org.jmol.popup.JmolPopup;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
@@ -507,7 +507,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         command.append(1 + pdbfnum);
         command.append(".1} {");
         command.append(1 + refStructure);
-        command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
+        // conformation=1 excludes alternate locations for CA (JAL-1757)
+        command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
 
         // form the matched pair strings
         String sep = "";
@@ -1328,24 +1329,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       return;
     }
 
-    String res;
-    int index;
-    Color col;
     jmolHistory(false);
-    // TODO: Switch between nucleotide or aa selection expressions
-    Enumeration en = ResidueProperties.aa3Hash.keys();
-    StringBuffer command = new StringBuffer("select *;color white;");
-    while (en.hasMoreElements())
+    StringBuilder command = new StringBuilder(128);
+    command.append("select *;color white;");
+    List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
+            false);
+    for (String res : residueSet)
     {
-      res = en.nextElement().toString();
-      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
-      if (index > 20)
-      {
-        continue;
-      }
-
-      col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
+      Color col = cs.findColour(res.charAt(0));
       command.append("select " + res + ";color[" + col.getRed() + ","
               + col.getGreen() + "," + col.getBlue() + "];");
     }