X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=dca904710f0096e8df615f5aab3cac62e1f992a5;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hp=6024cf995bf2cbdefeeee3cfe493178ad99e4514;hpb=adcef27f5747b4e70e89a56c3735bc3afb8ce9bf;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 6024cf9..dca9047 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -74,6 +74,14 @@ import javax.swing.JInternalFrame;
 public class AlignViewport extends AlignmentViewport
         implements SelectionSource
 {
+
+  public final static int NO_SPLIT = 0;
+
+  public final static int SPLIT_FRAME = 1;
+
+  public final static int NEW_WINDOW = 2;
+
+
   Font font;
 
   boolean cursorMode = false;
@@ -163,7 +171,7 @@ public class AlignViewport extends AlignmentViewport
    * @param hiddenColumns
    * @param seqsetid
    *          (may be null)
-   */
+f   */
   public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid)
   {
@@ -216,7 +224,7 @@ public class AlignViewport extends AlignmentViewport
 
     setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
     setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
-    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+    autoCalculateConsensusAndConservation = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
     setPadGaps(Cache.getDefault("PAD_GAPS", true));
     setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
@@ -392,7 +400,7 @@ public class AlignViewport extends AlignmentViewport
     if (align != null)
     {
       StructureSelectionManager ssm = StructureSelectionManager
-              .getStructureSelectionManager(Desktop.instance);
+              .getStructureSelectionManager(Desktop.getInstance());
       ssm.registerMappings(align.getCodonFrames());
     }
 
@@ -414,7 +422,7 @@ public class AlignViewport extends AlignmentViewport
       if (mappings != null)
       {
         StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager(Desktop.instance);
+                .getStructureSelectionManager(Desktop.getInstance());
         for (AlignedCodonFrame acf : mappings)
         {
           if (noReferencesTo(acf))
@@ -541,7 +549,7 @@ public class AlignViewport extends AlignmentViewport
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance)
+            .getStructureSelectionManager(Desktop.getInstance())
             .sendSelection(new SequenceGroup(getSelectionGroup()),
                     new ColumnSelection(getColumnSelection()),
                     new HiddenColumns(getAlignment().getHiddenColumns()),
@@ -587,7 +595,7 @@ public class AlignViewport extends AlignmentViewport
   public StructureSelectionManager getStructureSelectionManager()
   {
     return StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
+            .getStructureSelectionManager(Desktop.getInstance());
   }
   
   @Override
@@ -755,7 +763,8 @@ public void setNormaliseSequenceLogo(boolean state)
     }
 
     ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
-    firePropertyChange("alignment", null, getAlignment().getSequences());
+    notifyAlignment();
+
   }
 
   /**
@@ -781,48 +790,55 @@ public void setNormaliseSequenceLogo(boolean state)
      * dialog responses 0, 1, 2 (even though JOptionPane shows them
      * in reverse order)
      */
-    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
-            .setResponseHandler(0, new Runnable()
+    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
+            .setResponseHandler(NO_SPLIT, new Runnable()
             {
               @Override
               public void run()
               {
                   addDataToAlignment(al);
               }
-            }).setResponseHandler(1, new Runnable()
+            }).setResponseHandler(SPLIT_FRAME, new Runnable()
             {
               @Override
               public void run()
               {
-                us.openLinkedAlignmentAs(al, title, true);
+                openLinkedAlignmentAs(getAlignPanel().alignFrame,
+                        new Alignment(getAlignment()), al, title,
+                        SPLIT_FRAME);
+//                us.openLinkedAlignmentAs(al, title, true);
               }
-            }).setResponseHandler(2, new Runnable()
+            }).setResponseHandler(NEW_WINDOW, new Runnable()
             {
               @Override
               public void run()
               {
-                us.openLinkedAlignmentAs(al, title, false);
+                openLinkedAlignmentAs(null, getAlignment(), al, title,
+                        NEW_WINDOW);
               }
             });
-	dialog.showDialog(question,
+      dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
   }
-
-  protected void openLinkedAlignmentAs(AlignmentI al, String title,
-          boolean newWindowOrSplitPane)
-    {
+  /**
+   * Open a split frame or a new window
+   * 
+   * @param al
+   * @param title
+   * @param mode
+   *          SPLIT_FRAME or NEW_WINDOW
+   */
+  public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+          AlignmentI thisAlignment, AlignmentI al, String title, int mode)
+  {
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
      */
-    AlignmentI thisAlignment = newWindowOrSplitPane
-            ? new Alignment(getAlignment())
-            : getAlignment();
     AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
-    final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
-
+    AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
     /*
      * Map sequences. At least one should get mapped as we have already passed
      * the test for 'mappability'. Any mappings made will be added to the
@@ -850,7 +866,7 @@ public void setNormaliseSequenceLogo(boolean state)
     // alignFrame.setFileName(file, format);
     // }
 
-    if (!newWindowOrSplitPane)
+    if (mode == NEW_WINDOW)
     {
       Desktop.addInternalFrame(newAlignFrame, title,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -864,10 +880,10 @@ public void setNormaliseSequenceLogo(boolean state)
     {
     }
 
-    if (newWindowOrSplitPane)
+    if (mode == SPLIT_FRAME)
     {
       al.alignAs(thisAlignment);
-      protein = openSplitFrame(newAlignFrame, thisAlignment);
+      openSplitFrame(thisFrame, newAlignFrame, thisAlignment);
     }
   }
 
@@ -881,8 +897,8 @@ public void setNormaliseSequenceLogo(boolean state)
    *          cdna/protein complement alignment to show in the other split half
    * @return the protein alignment in the split frame
    */
-  protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
-          AlignmentI complement)
+  static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
+          AlignFrame newAlignFrame, AlignmentI complement)
   {
     /*
      * Make a new frame with a copy of the alignment we are adding to. If this
@@ -891,7 +907,8 @@ public void setNormaliseSequenceLogo(boolean state)
      */
     AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
-    copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+    copyMe.setTitle(thisFrame.getTitle());
+
 
     AlignmentI al = newAlignFrame.viewport.getAlignment();
     final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
@@ -1148,4 +1165,5 @@ public void setNormaliseSequenceLogo(boolean state)
   {
     this.viewName = viewName;
   }
+
 }