JAL-1620 version bump and release notes

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8b47302..216db0e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.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.
@@ -30,10 +30,12 @@ import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
 import jalview.commands.OrderCommand;
 import jalview.commands.RemoveGapColCommand;
 import jalview.commands.RemoveGapsCommand;
@@ -114,6 +116,7 @@ import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
@@ -279,7 +282,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Make a new AlignFrame from exisiting alignmentPanels
+   * Make a new AlignFrame from existing alignmentPanels
    * 
    * @param ap
    *          AlignmentPanel
@@ -746,10 +749,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     scaleRight.setVisible(av.wrapAlignment);
     annotationPanelMenuItem.setState(av.showAnnotation);
     /*
-     * Show/hide all annotations only enabled if annotation panel is shown
+     * Show/hide annotations only enabled if annotation panel is shown
      */
-    showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -1408,7 +1413,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      CommandI command = (CommandI) viewport.historyList.peek();
+      CommandI command = viewport.historyList.peek();
       undoMenuItem.setText(MessageManager.formatMessage(
               "label.undo_command", new String[]
               { command.getDescription() }));
@@ -1423,7 +1428,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       redoMenuItem.setEnabled(true);
 
-      CommandI command = (CommandI) viewport.redoList.peek();
+      CommandI command = viewport.redoList.peek();
       redoMenuItem.setText(MessageManager.formatMessage(
               "label.redo_command", new String[]
               { command.getDescription() }));
@@ -1487,7 +1492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    CommandI command = (CommandI) viewport.historyList.pop();
+    CommandI command = viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand(getViewAlignments());
 
@@ -1526,7 +1531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    CommandI command = (CommandI) viewport.redoList.pop();
+    CommandI command = viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand(getViewAlignments());
 
@@ -1988,7 +1993,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // /////
         // ADD HISTORY ITEM
         //
-        addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
+        addHistoryItem(new EditCommand(
+                MessageManager.getString("label.add_sequences"),
+                Action.PASTE,
                 sequences, 0, alignment.getWidth(), alignment));
       }
       // Add any annotations attached to sequences
@@ -2259,8 +2266,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * //ADD HISTORY ITEM
      */
-    addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
-            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+    addHistoryItem(new EditCommand(
+            MessageManager.getString("label.cut_sequences"), Action.CUT,
+            cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
             viewport.getAlignment()));
 
     viewport.setSelectionGroup(null);
@@ -3104,8 +3112,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final boolean setVisible = annotationPanelMenuItem.isSelected();
     viewport.setShowAnnotation(setVisible);
     alignPanel.setAnnotationVisible(setVisible);
-    this.showAllAnnotations.setEnabled(setVisible);
-    this.hideAllAnnotations.setEnabled(setVisible);
+    this.showAllSeqAnnotations.setEnabled(setVisible);
+    this.hideAllSeqAnnotations.setEnabled(setVisible);
+    this.showAllAlAnnotations.setEnabled(setVisible);
+    this.hideAllAlAnnotations.setEnabled(setVisible);
   }
 
   @Override
@@ -4176,16 +4186,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
        */
       msa = viewport.getAlignmentView(true);
     }
+    else if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() == 1)
+    {
+      int option = JOptionPane.showConfirmDialog(this,
+              MessageManager.getString("warn.oneseq_msainput_selection"),
+              MessageManager.getString("label.invalid_selection"),
+              JOptionPane.OK_CANCEL_OPTION);
+      if (option == JOptionPane.OK_OPTION)
+      {
+        msa = viewport.getAlignmentView(false);
+      }
+    }
     else
     {
-      /*
-       * Vector seqs = viewport.getAlignment().getSequences();
-       * 
-       * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
-       * 
-       * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
-       * seqs.elementAt(i); } }
-       */
       msa = viewport.getAlignmentView(false);
     }
     return msa;
@@ -5055,7 +5069,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 PDBEntry pe = new AssociatePdbFileWithSeq()
                         .associatePdbWithSeq((String) fm[0],
-                                (String) fm[1], toassoc, false);
+                                (String) fm[1], toassoc, false,
+                                Desktop.instance);
                 if (pe != null)
                 {
                   System.err.println("Associated file : "
@@ -5770,19 +5785,51 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Action on selection of menu option to Show or Hide all annotations.
+   * Action on selection of menu options to Show or Hide annotations.
    * 
-   * @param visibile
+   * @param visible
+   * @param forSequences
+   *          update sequence-related annotations
+   * @param forAlignment
+   *          update non-sequence-related annotations
    */
   @Override
-  protected void setAllAnnotationsVisibility(boolean visible)
+  protected void setAnnotationsVisibility(boolean visible,
+          boolean forSequences, boolean forAlignment)
   {
     for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
-      aa.visible = visible;
+      boolean apply = (aa.sequenceRef == null && forAlignment)
+              || (aa.sequenceRef != null && forSequences);
+      if (apply)
+      {
+        aa.visible = visible;
+      }
     }
-    this.alignPanel.paintAlignment(true);
+    alignPanel.validateAnnotationDimensions(false);
+    alignPanel.alignmentChanged();
+  }
+
+  /**
+   * Store selected annotation sort order for the view and repaint.
+   */
+  @Override
+  protected void sortAnnotations_actionPerformed()
+  {
+    this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+    this.alignPanel.av
+            .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * 
+   * @return alignment panels in this alignemnt frame
+   */
+  public List<AlignmentViewPanel> getAlignPanels()
+  {
+    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
   }
 }