X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=3e7ca591c1b79ae0668cab24825a5561206b4357;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=17a622dad6653a522eabe653c717a7b28b3028af;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 17a622d..3e7ca59 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -1,33 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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.HiddenColumns;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Routines for generating Jmol commands for Jalview/Jmol binding another
@@ -48,11 +55,15 @@ public class JmolCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
-
-    ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+    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++)
     {
@@ -62,7 +73,9 @@ public class JmolCommands
       ArrayList<String> str = new ArrayList<String>();
 
       if (mapping == null || mapping.length < 1)
+      {
         continue;
+      }
 
       int lastPos = -1;
       for (int s = 0; s < sequence[pdbfnum].length; s++)
@@ -70,9 +83,9 @@ public class JmolCommands
         for (int sp, m = 0; m < mapping.length; m++)
         {
           if (mapping[m].getSequence() == sequence[pdbfnum][s]
-                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+                  && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
           {
-            SequenceI asp = alignment.getSequenceAt(sp);
+            SequenceI asp = al.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
             {
               // no mapping to gaps in sequence
@@ -83,14 +96,23 @@ public class JmolCommands
               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 
               if (pos < 1 || pos == lastPos)
+              {
                 continue;
+              }
 
               lastPos = pos;
 
-              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+              Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+                      finder);
+
+              /*
+               * shade hidden regions darker
+               */
+              if (!cs.isVisible(r))
+              {
+                col = Color.GRAY;
+              }
 
-              if (fr != null)
-                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")
                       + "/"
@@ -123,7 +145,7 @@ public class JmolCommands
               command.append("select " + pos);
               command.append(newSelcom);
             }
-            break;
+            // break;
           }
         }
       }