JAL-2591 Refactor HiddenColumns to use ArrayList instead of Vector

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index c72cfaf..e16867a 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -52,7 +52,6 @@ import java.awt.image.BufferedImage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.List;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -220,6 +219,7 @@ 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,
@@ -232,11 +232,16 @@ 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 +250,8 @@ 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))
     {
@@ -255,6 +262,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           aa[i].visible = true;
         }
       }
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
@@ -283,21 +291,11 @@ 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
@@ -305,6 +303,7 @@ 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",
@@ -332,12 +331,20 @@ 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();
 
@@ -390,7 +397,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // ann.visible = false;
             // }
             // }
-            refresh();
+            ap.refresh(true);
           }
         });
         pop.add(hideType);
@@ -452,6 +459,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
             }
+            ap.alignmentChanged();
           }
         });
         pop.add(cbmi);
@@ -595,7 +603,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       }
     }
     pop.show(this, evt.getX(), evt.getY());
-
   }
 
   /**
@@ -607,6 +614,12 @@ 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;
@@ -933,17 +946,18 @@ 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();
-    if (hiddenCols != null)
+    if (av.hasHiddenColumns())
     {
-      alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
-              hiddenCols);
+      alignmentStartEnd = av.getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
     }
+
     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
             seqs, omitHidden, alignmentStartEnd);
 
@@ -951,13 +965,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             .setContents(new StringSelection(output), Desktop.instance);
 
     ArrayList<int[]> hiddenColumns = null;
+
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<int[]>();
-      for (int[] region : av.getColumnSelection().getHiddenColumns())
-      {
-        hiddenColumns.add(new int[] { region[0], region[1] });
-      }
+      hiddenColumns = av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopy();
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset