X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=6635ef01bed0dd24c0dab7c2dc37915565fa89ce;hb=e4496f5b27c5a01a1cc494653bd3f9f49080d544;hp=de1d0035c858341194379ada9e65208cd47c0a1e;hpb=050133c52e350a0e76b94ab0c1243aea7613b042;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index de1d003..6635ef0 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -372,7 +372,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        new CalculationChooser(AlignFrame.this);
+        openTreePcaDialog();
       }
     });
     buildColourMenu();
@@ -2760,6 +2760,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     newap.av.replaceMappings(viewport.getAlignment());
 
+    /*
+     * start up cDNA consensus (if applicable) now mappings are in place
+     */
+    if (newap.av.initComplementConsensus())
+    {
+      newap.refresh(true); // adjust layout of annotations
+    }
+
     newap.av.viewName = getNewViewName(viewTitle);
 
     addAlignmentPanel(newap, true);
@@ -3337,7 +3345,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     if (ResidueColourScheme.USER_DEFINED.equals(name))
     {
-      new UserDefinedColours(alignPanel, null);
+      new UserDefinedColours(alignPanel);
       return;
     }
 
@@ -3358,10 +3366,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void changeColour(ColourSchemeI cs)
   {
     // TODO: pull up to controller method
-    if (cs != null)
-    {
-      ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
-    }
+    ColourMenuHelper.setColourSelected(colourMenu, cs);
 
     viewport.setGlobalColourScheme(cs);
 
@@ -3649,21 +3654,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      // are the visible sequences aligned?
-      if (!viewport.getAlignment().isAligned(false))
-      {
-        JvOptionPane
-                .showMessageDialog(
-                        Desktop.desktop,
-                        MessageManager
-                                .getString("label.sequences_must_be_aligned_before_creating_tree"),
-                        MessageManager
-                                .getString("label.sequences_not_aligned"),
-                        JvOptionPane.WARNING_MESSAGE);
-
-        return;
-      }
-
       if (viewport.getAlignment().getHeight() < 2)
       {
         return;
@@ -4692,14 +4682,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (FileFormat.ScoreMatrix == format)
           {
+            // load and register the score matrix
             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
                     sourceType));
-            sm.parse();
-            // todo: i18n this message
-            statusBar
-                    .setText(MessageManager.formatMessage(
-                            "label.successfully_loaded_matrix",
-                            sm.getMatrixName()));
+            statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_loaded_file_type",
+                    format.getName(), sm.getMatrixName()));
           }
           else if (FileFormat.Jnet.equals(format))
           {
@@ -5634,10 +5622,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
-    String schemeName = colourScheme == null ? null : colourScheme
-            .getSchemeName();
+    ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
+  }
 
-    ColourMenuHelper.setColourSelected(colourMenu, schemeName);
+  /**
+   * Open a dialog (if not already open) that allows the user to select and
+   * calculate PCA or Tree analysis
+   */
+  protected void openTreePcaDialog()
+  {
+    if (alignPanel.getCalculationDialog() == null)
+    {
+      new CalculationChooser(AlignFrame.this);
+    }
   }
 }