JAL-2446 merged to spike branch

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 8b9168a..8ca1a4e 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -27,6 +27,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.util.MessageManager;
 
@@ -219,6 +220,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
 
+    boolean fullRepaint = false;
     if (evt.getActionCommand().equals(ADDNEW))
     {
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
@@ -231,11 +233,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
       ap.av.getAlignment().addAnnotation(newAnnotation);
       ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(EDITNAME))
     {
+      String name = aa[selectedRow].label;
       editLabelDescription(aa[selectedRow]);
-      repaint();
+      if (!name.equalsIgnoreCase(aa[selectedRow].label))
+      {
+        fullRepaint = true;
+      }
     }
     else if (evt.getActionCommand().equals(HIDE))
     {
@@ -244,6 +251,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (evt.getActionCommand().equals(DELETE))
     {
       ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+      ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(SHOWALL))
     {
@@ -254,6 +263,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           aa[i].visible = true;
         }
       }
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
@@ -282,21 +292,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    refresh();
+    ap.refresh(fullRepaint);
 
   }
 
   /**
-   * Redraw sensibly.
-   */
-  protected void refresh()
-  {
-    ap.validateAnnotationDimensions(false);
-    ap.addNotify();
-    ap.repaint();
-  }
-
-  /**
    * DOCUMENT ME!
    * 
    * @param e
@@ -304,6 +304,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   boolean editLabelDescription(AlignmentAnnotation annotation)
   {
+    // TODO i18n
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, "       Annotation Name ",
             "Annotation Description ", "Edit Annotation Name/Description",
@@ -331,12 +332,20 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   {
     getSelectedRow(evt.getY() - getScrollOffset());
     oldY = evt.getY();
-    if (!evt.isPopupTrigger())
+    if (evt.isPopupTrigger())
     {
-      return;
+      showPopupMenu(evt);
     }
+  }
+
+  /**
+   * Build and show the Pop-up menu at the right-click mouse position
+   * 
+   * @param evt
+   */
+  void showPopupMenu(MouseEvent evt)
+  {
     evt.consume();
-    // handle popup menu event
     final AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
 
@@ -389,7 +398,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // ann.visible = false;
             // }
             // }
-            refresh();
+            ap.refresh(true);
           }
         });
         pop.add(hideType);
@@ -451,6 +460,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
             }
+            ap.alignmentChanged();
           }
         });
         pop.add(cbmi);
@@ -594,7 +604,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       }
     }
     pop.show(this, evt.getX(), evt.getY());
-
   }
 
   /**
@@ -606,6 +615,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    if (evt.isPopupTrigger())
+    {
+      showPopupMenu(evt);
+      return;
+    }
+
     int start = selectedRow;
     getSelectedRow(evt.getY() - getScrollOffset());
     int end = selectedRow;
@@ -802,8 +817,45 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // todo: make the ap scroll to the selection - not necessary, first
             // click highlights/scrolls, second selects
             ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
-            ap.av.setSelectionGroup(// new SequenceGroup(
-            aa[selectedRow].groupRef); // );
+            // process modifiers
+            SequenceGroup sg = ap.av.getSelectionGroup();
+            if (sg == null
+                    || sg == aa[selectedRow].groupRef
+                    || !(jalview.util.Platform.isControlDown(evt) || evt
+                            .isShiftDown()))
+            {
+              if (jalview.util.Platform.isControlDown(evt)
+                      || evt.isShiftDown())
+              {
+                // clone a new selection group from the associated group
+                ap.av.setSelectionGroup(new SequenceGroup(
+                        aa[selectedRow].groupRef));
+              }
+              else
+              {
+                // set selection to the associated group so it can be edited
+                ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+              }
+            }
+            else
+            {
+              // modify current selection with associated group
+              int remainToAdd = aa[selectedRow].groupRef.getSize();
+              for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+              {
+                if (jalview.util.Platform.isControlDown(evt))
+                {
+                  sg.addOrRemove(sgs, --remainToAdd == 0);
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
+                  sg.addSequence(sgs, --remainToAdd == 0);
+                }
+              }
+            }
+
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
@@ -862,9 +914,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               sg.addSequence(aa[selectedRow].sequenceRef, false);
             }
             ap.av.setSelectionGroup(sg);
-            ap.av.sendSelection();
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
           }
 
         }
@@ -895,19 +947,21 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
+      omitHidden = av.getAlignment().getHiddenColumns()
+              .getVisibleSequenceStrings(0,
               sq.getLength(), seqs);
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
-    List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
+    List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
+            .getHiddenRegions();
     if (hiddenCols != null)
     {
       alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
               hiddenCols);
     }
-    String output = new FormatAdapter().formatSequences("Fasta", seqs,
-            omitHidden, alignmentStartEnd);
+    String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
+            seqs, omitHidden, alignmentStartEnd);
 
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
@@ -916,7 +970,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     if (av.hasHiddenColumns())
     {
       hiddenColumns = new ArrayList<int[]>();
-      for (int[] region : av.getColumnSelection().getHiddenColumns())
+      for (int[] region : av.getAlignment().getHiddenColumns()
+              .getHiddenRegions())
       {
         hiddenColumns.add(new int[] { region[0], region[1] });
       }