X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=294b8db964023849c80b70be9564548496649089;hb=80e3ac6ebcb27e0d13ce639d1c3105f7cd6f83fe;hp=15f1fe059a9d3c1165e79091913c584b385f01ba;hpb=3ab70c7242fba39a5106deb39882648bacfc2ba6;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 15f1fe0..294b8db 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -25,6 +25,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -33,6 +34,7 @@ import jalview.io.FormatAdapter;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.dialogrunner.RunResponse;
 
 import java.awt.Color;
 import java.awt.Cursor;
@@ -50,9 +52,9 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -207,41 +209,33 @@ public class AnnotationLabels extends JPanel
     AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
 
-    boolean fullRepaint = false;
-    if (evt.getActionCommand().equals(ADDNEW))
+    String action = evt.getActionCommand();
+    if (ADDNEW.equals(action))
     {
+      /*
+       * non-returning dialog
+       */
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
               null, new Annotation[ap.av.getAlignment().getWidth()]);
-
-      if (!editLabelDescription(newAnnotation))
-      {
-        return;
-      }
-
-      ap.av.getAlignment().addAnnotation(newAnnotation);
-      ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
-      fullRepaint = true;
+      editLabelDescription(newAnnotation, true);
     }
-    else if (evt.getActionCommand().equals(EDITNAME))
+    else if (EDITNAME.equals(action))
     {
-      String name = aa[selectedRow].label;
-      editLabelDescription(aa[selectedRow]);
-      if (!name.equalsIgnoreCase(aa[selectedRow].label))
-      {
-        fullRepaint = true;
-      }
+      /*
+       * non-returning dialog
+       */
+      editLabelDescription(aa[selectedRow], false);
     }
-    else if (evt.getActionCommand().equals(HIDE))
+    else if (HIDE.equals(action))
     {
       aa[selectedRow].visible = false;
     }
-    else if (evt.getActionCommand().equals(DELETE))
+    else if (DELETE.equals(action))
     {
       ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
       ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
-      fullRepaint = true;
     }
-    else if (evt.getActionCommand().equals(SHOWALL))
+    else if (SHOWALL.equals(action))
     {
       for (int i = 0; i < aa.length; i++)
       {
@@ -250,15 +244,12 @@ public class AnnotationLabels extends JPanel
           aa[i].visible = true;
         }
       }
-      fullRepaint = true;
     }
-    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    else if (OUTPUT_TEXT.equals(action))
     {
-      new AnnotationExporter().exportAnnotations(ap,
-              new AlignmentAnnotation[]
-              { aa[selectedRow] });
+      new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
     }
-    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+    else if (COPYCONS_SEQ.equals(action))
     {
       SequenceI cons = null;
       if (aa[selectedRow].groupRef != null)
@@ -273,46 +264,54 @@ public class AnnotationLabels extends JPanel
       {
         copy_annotseqtoclipboard(cons);
       }
-
     }
-    else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+    else if (TOGGLE_LABELSCALE.equals(action))
     {
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    ap.refresh(fullRepaint);
-
+    ap.refresh(true);
   }
 
   /**
-   * DOCUMENT ME!
+   * Shows a dialog where the annotation name and description may be edited. If
+   * parameter addNew is true, then on confirmation, a new AlignmentAnnotation
+   * is added, else an existing annotation is updated.
    * 
-   * @param e
-   *          DOCUMENT ME!
+   * @param annotation
+   * @param addNew
    */
-  boolean editLabelDescription(AlignmentAnnotation annotation)
+  void editLabelDescription(AlignmentAnnotation annotation, boolean addNew)
   {
-    // TODO i18n
+    String name = MessageManager.getString("label.annotation_name");
+    String description = MessageManager
+            .getString("label.annotation_description");
+    String title = MessageManager
+            .getString("label.edit_annotation_name_description");
     EditNameDialog dialog = new EditNameDialog(annotation.label,
-            annotation.description, "       Annotation Name ",
-            "Annotation Description ", "Edit Annotation Name/Description",
-            ap.alignFrame);
-
-    if (!dialog.accept)
-    {
-      return false;
-    }
-
-    annotation.label = dialog.getName();
-
-    String text = dialog.getDescription();
-    if (text != null && text.length() == 0)
-    {
-      text = null;
-    }
-    annotation.description = text;
+            annotation.description, name, description);
 
-    return true;
+    dialog.showDialog(ap.alignFrame, title,
+            new RunResponse(JvOptionPane.OK_OPTION)
+            {
+              @Override
+              public void run()
+              {
+                annotation.label = dialog.getName();
+                String text = dialog.getDescription();
+                if (text != null && text.length() == 0)
+                {
+                  text = null;
+                }
+                annotation.description = text;
+                if (addNew)
+                {
+                  ap.av.getAlignment().addAnnotation(annotation);
+                  ap.av.getAlignment().setAnnotationIndex(annotation, 0);
+                }
+                ap.refresh(true);
+              }
+            });
   }
 
   @Override
@@ -782,12 +781,13 @@ public class AnnotationLabels extends JPanel
   protected void showOrHideAdjuster(MouseEvent evt)
   {
     boolean was = resizePanel;
-    resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+    resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+            && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
 
     if (resizePanel != was)
     {
-      setCursor(Cursor.getPredefinedCursor(
-              resizePanel ? Cursor.S_RESIZE_CURSOR
+      setCursor(Cursor
+              .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR
                       : Cursor.DEFAULT_CURSOR));
       repaint();
     }
@@ -934,8 +934,9 @@ public class AnnotationLabels extends JPanel
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getAlignment().getHiddenColumns()
-              .getVisibleSequenceStrings(0, sq.getLength(), seqs);
+      Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+              .getVisContigsIterator(0, sq.getLength(), false);
+      omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
@@ -951,12 +952,12 @@ public class AnnotationLabels extends JPanel
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
 
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy();
+      hiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset