JAL-3148 SequenceRenderer, ResidueColourFinder overloads and

[jalview.git] / src / jalview / gui / AppJmol.java

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 29f02d6..12bb21d 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -26,6 +26,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.structures.models.AAStructureBindingModel.ColourBy;
 import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -57,7 +58,7 @@ public class AppJmol extends StructureViewerBase
 
   private static final String SPACE = " ";
 
-  private static final String BACKSLASH = "\"";
+  private static final String QUOTE = "\"";
 
   AppJmolBinding jmb;
 
@@ -113,14 +114,14 @@ public class AppJmol extends StructureViewerBase
     initMenus();
     if (leaveColouringToJmol || !usetoColour)
     {
-      jmb.setColourBySequence(false);
+      jmb.setColourBy(ColourBy.Viewer);
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
     else if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
-      jmb.setColourBySequence(true);
+      jmb.setColourBy(ColourBy.Sequence);
       seqColour.setSelected(true);
       viewerColour.setSelected(false);
     }
@@ -175,10 +176,13 @@ public class AppJmol extends StructureViewerBase
   {
     progressBar = ap.alignFrame;
 
-    openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+    openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+            new SequenceI[][]
+            { seq });
   }
 
-  private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+  private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+          PDBEntry[] pdbentrys,
           SequenceI[][] seqs)
   {
     progressBar = ap.alignFrame;
@@ -187,10 +191,10 @@ public class AppJmol extends StructureViewerBase
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
 
-    alignAddedStructures = true;
-      useAlignmentPanelForSuperposition(ap);
+    alignAddedStructures = alignAdded;
+    useAlignmentPanelForSuperposition(ap);
 
-    jmb.setColourBySequence(true);
+    jmb.setColourBy(ColourBy.Sequence);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
     addingStructures = false;
@@ -210,16 +214,19 @@ public class AppJmol extends StructureViewerBase
   }
 
   /**
-   * create a new Jmol containing several structures superimposed using the
-   * given alignPanel.
+   * create a new Jmol containing several structures optionally superimposed
+   * using the given alignPanel.
    * 
    * @param ap
+   * @param alignAdded
+   *          - true to superimpose
    * @param pe
    * @param seqs
    */
-  public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+  public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+          SequenceI[][] seqs)
   {
-    openNewJmol(ap, pe, seqs);
+    openNewJmol(ap, alignAdded, pe, seqs);
   }
 
 
@@ -253,8 +260,6 @@ public class AppJmol extends StructureViewerBase
     jmb.setFinishedInit(true);
   }
 
-  boolean allChainsSelected = false;
-
   @Override
   void showSelectedChains()
   {
@@ -321,8 +326,8 @@ public class AppJmol extends StructureViewerBase
     StringBuilder fileList = new StringBuilder();
     for (String s : files)
     {
-      fileList.append(SPACE).append(BACKSLASH)
-              .append(Platform.escapeString(s)).append(BACKSLASH);
+      fileList.append(SPACE).append(QUOTE)
+              .append(Platform.escapeString(s)).append(QUOTE);
     }
     String filesString = fileList.toString();
 
@@ -397,7 +402,7 @@ public class AppJmol extends StructureViewerBase
       jmb.updateColours(ap);
     }
     // do superposition if asked to
-    if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+    if (alignAddedStructures)
     {
       alignAddedStructures();
     }
@@ -431,7 +436,7 @@ public class AppJmol extends StructureViewerBase
         }
       }
     });
-    alignAddedStructures = false;
+
   }
 
   /**
@@ -460,6 +465,7 @@ public class AppJmol extends StructureViewerBase
         String file = jmb.getPdbEntry(pi).getFile();
         if (file == null)
         {
+          // todo: extract block as method and pull up (also ChimeraViewFrame)
           // retrieve the pdb and store it locally
           AlignmentI pdbseq = null;
           pdbid = jmb.getPdbEntry(pi).getId();