Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 92c6dc6..4b774d6 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))
     {
@@ -245,6 +252,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     {
       ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
       ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(SHOWALL))
     {
@@ -255,6 +263,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           aa[i].visible = true;
         }
       }
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
@@ -283,18 +292,30 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    refresh();
+    refresh(fullRepaint);
 
   }
 
   /**
    * Redraw sensibly.
+   * 
+   * @adjustHeight if true, try to recalculate panel height for visible
+   *               annotations
    */
-  protected void refresh()
+  protected void refresh(boolean adjustHeight)
   {
-    ap.validateAnnotationDimensions(false);
+    ap.validateAnnotationDimensions(adjustHeight);
     ap.addNotify();
-    ap.repaint();
+    if (adjustHeight)
+    {
+      // sort, repaint, update overview
+      ap.paintAlignment(true);
+    }
+    else
+    {
+      // lightweight repaint
+      ap.repaint();
+    }
   }
 
   /**
@@ -305,6 +326,7 @@ 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",
@@ -398,7 +420,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // ann.visible = false;
             // }
             // }
-            refresh();
+            refresh(true);
           }
         });
         pop.add(hideType);
@@ -460,6 +482,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
             }
+            ap.alignmentChanged();
           }
         });
         pop.add(cbmi);
@@ -957,8 +980,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       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);