Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 55288d0..4379c20 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -147,9 +147,7 @@ public class AppJmol extends StructureViewerBase
     PDBEntry[] pdbentrys = new PDBEntry[files.length];
     for (int i = 0; i < pdbentrys.length; i++)
     {
-      PDBEntry pdbentry = new PDBEntry();
-      pdbentry.setFile(files[i]);
-      pdbentry.setId(ids[i]);
+      PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
       pdbentrys[i] = pdbentry;
     }
     // / TODO: check if protocol is needed to be set, and if chains are
@@ -169,7 +167,7 @@ public class AppJmol extends StructureViewerBase
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    if (usetoColour)
+    else if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
       jmb.setColourBySequence(true);
@@ -427,118 +425,6 @@ public class AppJmol extends StructureViewerBase
     openNewJmol(ap, pe, seqs);
   }
 
-  public AlignmentPanel[] getAllAlignmentPanels()
-  {
-    AlignmentPanel[] t;
-    AlignmentPanel[] list = new AlignmentPanel[0];
-    for (String setid : _aps)
-    {
-      AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
-      if (panels != null)
-      {
-        t = new AlignmentPanel[list.length + panels.length];
-        System.arraycopy(list, 0, t, 0, list.length);
-        System.arraycopy(panels, 0, t, list.length, panels.length);
-        list = t;
-      }
-    }
-
-    return list;
-  }
-
-  /**
-   * set the primary alignmentPanel reference and add another alignPanel to the
-   * list of ones to use for colouring and aligning
-   * 
-   * @param nap
-   */
-  public void addAlignmentPanel(AlignmentPanel nap)
-  {
-    if (getAlignmentPanel() == null)
-    {
-      setAlignmentPanel(nap);
-    }
-    if (!_aps.contains(nap.av.getSequenceSetId()))
-    {
-      _aps.add(nap.av.getSequenceSetId());
-    }
-  }
-
-  /**
-   * remove any references held to the given alignment panel
-   * 
-   * @param nap
-   */
-  public void removeAlignmentPanel(AlignmentPanel nap)
-  {
-    try
-    {
-      _alignwith.remove(nap);
-      _colourwith.remove(nap);
-      if (getAlignmentPanel() == nap)
-      {
-        setAlignmentPanel(null);
-        for (AlignmentPanel aps : getAllAlignmentPanels())
-        {
-          if (aps != nap)
-          {
-            setAlignmentPanel(aps);
-            break;
-          }
-        }
-      }
-    } catch (Exception ex)
-    {
-    }
-    if (getAlignmentPanel() != null)
-    {
-      buildActionMenu();
-    }
-  }
-
-  public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
-  {
-    addAlignmentPanel(nap);
-    if (!_alignwith.contains(nap))
-    {
-      _alignwith.add(nap);
-    }
-  }
-
-  public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
-  {
-    if (_alignwith.contains(nap))
-    {
-      _alignwith.remove(nap);
-    }
-  }
-
-  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
-          boolean enableColourBySeq)
-  {
-    useAlignmentPanelForColourbyseq(nap);
-    getBinding().setColourBySequence(enableColourBySeq);
-    seqColour.setSelected(enableColourBySeq);
-    viewerColour.setSelected(!enableColourBySeq);
-  }
-
-  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
-  {
-    addAlignmentPanel(nap);
-    if (!_colourwith.contains(nap))
-    {
-      _colourwith.add(nap);
-    }
-  }
-
-  public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
-  {
-    if (_colourwith.contains(nap))
-    {
-      _colourwith.remove(nap);
-    }
-  }
-
   /**
    * pdb retrieval thread.
    */
@@ -1052,7 +938,7 @@ public class AppJmol extends StructureViewerBase
       // Set the colour using the current view for the associated alignframe
       for (AlignmentPanel ap : _colourwith)
       {
-        jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+        jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
       }
     }
   }