X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=603202a84ef71776fb441992bdac1e7d606f51fa;hb=1450fb2e94eea45507c0147e7e3d993dc98f1633;hp=a809caecc1b7126cae8d62fb243590c64ccdaa01;hpb=799c26111d6936a2e70cb5f1fd7d7312311e6db9;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index a809cae..603202a 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -21,11 +21,13 @@
 package jalview.ext.jmol;
 
 import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
@@ -53,17 +55,20 @@ public class JmolCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignViewportI viewport)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
-    ColumnSelection cs = viewport.getColumnSelection();
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+    AlignViewportI viewport = viewPanel.getAlignViewport();
+    HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
     AlignmentI al = viewport.getAlignment();
     List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
 
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-      StringBuffer command = new StringBuffer();
+      StringBuilder command = new StringBuilder();
       StructureMappingcommandSet smc;
       ArrayList<String> str = new ArrayList<String>();
 
@@ -72,7 +77,6 @@ public class JmolCommands
         continue;
       }
 
-      int lastPos = -1;
       for (int s = 0; s < sequence[pdbfnum].length; s++)
       {
         for (int sp, m = 0; m < mapping.length; m++)
@@ -80,6 +84,7 @@ public class JmolCommands
           if (mapping[m].getSequence() == sequence[pdbfnum][s]
                   && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
           {
+            int lastPos = StructureMapping.UNASSIGNED_VALUE;
             SequenceI asp = al.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
             {
@@ -90,44 +95,47 @@ public class JmolCommands
               }
               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 
-              if (pos < 1 || pos == lastPos)
+              if (pos == lastPos)
               {
                 continue;
               }
+              if (pos == StructureMapping.UNASSIGNED_VALUE)
+              {
+                // terminate current colour op
+                if (command.length() > 0
+                        && command.charAt(command.length() - 1) != ';')
+                {
+                  command.append(";");
+                }
+                // reset lastPos
+                lastPos = StructureMapping.UNASSIGNED_VALUE;
+                continue;
+              }
 
               lastPos = pos;
 
-              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-
-              if (fr != null)
-              {
-                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
-              }
+              Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+                      finder);
 
               /*
                * shade hidden regions darker
                */
               if (!cs.isVisible(r))
               {
-                // col = ColorUtils.darkerThan(col);
                 col = Color.GRAY;
               }
 
-              String newSelcom = (mapping[m].getChain() != " " ? ":"
-                      + mapping[m].getChain() : "")
-                      + "/"
-                      + (pdbfnum + 1)
-                      + ".1"
-                      + ";color["
-                      + col.getRed()
-                      + ","
-                      + col.getGreen()
-                      + ","
+              // todo JAL-3152 handle 'no chain' case without errors
+              boolean hasChain = true || mapping[m].getChain() != " ";
+			  String chainSpec = hasChain
+                      ? ":" + mapping[m].getChain()
+                      : "";
+			  String newSelcom = chainSpec + "/" + (pdbfnum + 1) + ".1" + ";color["
+                      + col.getRed() + "," + col.getGreen() + ","
                       + col.getBlue() + "]";
-              if (command.length() > newSelcom.length()
-                      && command.substring(
-                              command.length() - newSelcom.length())
-                              .equals(newSelcom))
+              if (command.length() > newSelcom.length() && command
+                      .substring(command.length() - newSelcom.length())
+                      .equals(newSelcom))
               {
                 command = JmolCommands.condenseCommand(command, pos);
                 continue;
@@ -135,7 +143,12 @@ public class JmolCommands
               // TODO: deal with case when buffer is too large for Jmol to parse
               // - execute command and flush
 
-              command.append(";");
+              if (command.length() > 0
+                      && command.charAt(command.length() - 1) != ';')
+              {
+                command.append(";");
+              }
+
               if (command.length() > 51200)
               {
                 // add another chunk
@@ -162,7 +175,7 @@ public class JmolCommands
     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
   }
 
-  public static StringBuffer condenseCommand(StringBuffer command, int pos)
+  public static StringBuilder condenseCommand(StringBuilder command, int pos)
   {
 
     // work back to last 'select'
@@ -177,7 +190,7 @@ public class JmolCommands
       ;
     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 
-    StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
+    StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
 
     command = command.delete(0, q + 7);