X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=d498ca5aa9bcb290b29eb90eb9f3f8136bfb8042;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=e8cbd2e7091cdf2d400d4ddd520250d92aa94dfe;hpb=5a60f6428df1108a96524aae0c34d615ae48c227;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index e8cbd2e..d498ca5 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,67 +1,76 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Vector;
 
 import jalview.datamodel.*;
 
-public class AnnotationLabels
-    extends Panel implements ActionListener
+public class AnnotationLabels extends Panel implements ActionListener,
+        MouseListener, MouseMotionListener
 {
+  Image image;
+
   boolean active = false;
+
   AlignmentPanel ap;
+
   AlignViewport av;
+
   boolean resizing = false;
+
   int oldY, mouseX;
-  static String ADDNEW = "Add new row";
-  static String HIDE = "Hide this row";
-  static String DELETE = "Delete this row";
-  static String SHOWALL = "Show all hidden rows";
+
+  static String ADDNEW = "Add New Row";
+
+  static String EDITNAME = "Edit Label/Description";
+
+  static String HIDE = "Hide This Row";
+
+  static String SHOWALL = "Show All Hidden Rows";
+
   static String OUTPUT_TEXT = "Show Values In Textbox";
+
   static String COPYCONS_SEQ = "Copy Consensus Sequence";
-  
-  int selectedRow = 0;
+
   int scrollOffset = 0;
 
+  int selectedRow = -1;
+
+  Tooltip tooltip;
+
   public AnnotationLabels(AlignmentPanel ap)
   {
     this.ap = ap;
     this.av = ap.av;
     setLayout(null);
-    addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      {
-        doMousePressed(evt);
-      }
-    });
+    addMouseListener(this);
+    addMouseMotionListener(this);
   }
 
   public AnnotationLabels(AlignViewport av)
-{
-  this.av = av;
-}
-
+  {
+    this.av = av;
+  }
 
   public void setScrollOffset(int y)
   {
@@ -69,11 +78,57 @@ public class AnnotationLabels
     repaint();
   }
 
+  int getSelectedRow(int y)
+  {
+    int row = -1;
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    if (aa == null)
+    {
+      return row;
+    }
+
+    int height = 0;
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (!aa[i].visible)
+      {
+        continue;
+      }
+
+      height += aa[i].height;
+      if (y < height)
+      {
+        row = i;
+        break;
+      }
+    }
+
+    return row;
+  }
+
   public void actionPerformed(ActionEvent evt)
   {
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    if (evt.getActionCommand().equals(HIDE))
+    if (evt.getActionCommand().equals(ADDNEW))
+    {
+      AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
+              new Annotation[ap.av.alignment.getWidth()]);
+
+      if (!editLabelDescription(newAnnotation))
+      {
+        return;
+      }
+
+      ap.av.alignment.addAnnotation(newAnnotation);
+      ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+    }
+    else if (evt.getActionCommand().equals(EDITNAME))
+    {
+      editLabelDescription(aa[selectedRow]);
+    }
+    else if (evt.getActionCommand().equals(HIDE))
     {
       aa[selectedRow].visible = false;
     }
@@ -81,119 +136,203 @@ public class AnnotationLabels
     {
       for (int i = 0; i < aa.length; i++)
       {
-        aa[i].visible = true;
+        aa[i].visible = (aa[i].annotations == null) ? false : true;
       }
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
+              ap.alignFrame);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
-                                       ap.alignFrame.getTitle() + " - " +
-                                       aa[selectedRow].label, 500, 100);
+      jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
+              + " - " + aa[selectedRow].label, 500, 100);
       cap.setText(aa[selectedRow].toString());
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
-      SequenceI cons=av.getConsensusSeq();
-      if (cons!=null)
+      SequenceI cons = av.getConsensusSeq();
+      if (cons != null)
+      {
         copy_annotseqtoclipboard(cons);
-      
+      }
+
     }
     ap.annotationPanel.adjustPanelHeight();
     setSize(getSize().width, ap.annotationPanel.getSize().height);
     ap.validate();
-    ap.repaint();
+    ap.paintAlignment(true);
   }
 
-  public void doMousePressed(MouseEvent evt)
+  boolean editLabelDescription(AlignmentAnnotation annotation)
   {
-    int y = evt.getY() - scrollOffset;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-    int height = 0;
-    for (int i = 0; i < aa.length; i++)
+    Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
+            + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+
+    EditNameDialog dialog = new EditNameDialog(annotation.label,
+            annotation.description, "      Annotation Label",
+            "Annotation Description", ap.alignFrame,
+            "Edit Annotation Name / Description", 500, 180, false);
+
+    Panel empty = new Panel(new FlowLayout());
+    empty.add(padGaps);
+    dialog.add(empty);
+    dialog.pack();
+
+    dialog.setVisible(true);
+
+    if (dialog.accept)
     {
-      if (!aa[i].visible)
+      annotation.label = dialog.getName();
+      annotation.description = dialog.getDescription();
+      annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
+      repaint();
+      return true;
+    }
+    else
+      return false;
+
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    int row = getSelectedRow(evt.getY() - scrollOffset);
+
+    if (row > -1)
+    {
+      if (tooltip == null)
       {
-        continue;
+        tooltip = new Tooltip(ap.av.alignment.getAlignmentAnnotation()[row]
+                .getDescription(true), this);
       }
-
-      height += aa[i].height;
-      if (y < height)
+      else
       {
-        selectedRow = i;
-        break;
+        tooltip.setTip(ap.av.alignment.getAlignmentAnnotation()[row]
+                .getDescription(true));
       }
     }
+    else if (tooltip != null)
+    {
+      tooltip.setTip("");
+    }
+
+  }
 
-    PopupMenu pop = new PopupMenu("Annotations");
-    MenuItem item = new MenuItem(HIDE);
+  public void mouseDragged(MouseEvent evt)
+  {
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    selectedRow = getSelectedRow(evt.getY() - scrollOffset);
+
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    PopupMenu popup = new PopupMenu("Annotations");
+
+    MenuItem item = new MenuItem(ADDNEW);
+    item.addActionListener(this);
+    popup.add(item);
+    item = new MenuItem(EDITNAME);
+    item.addActionListener(this);
+    popup.add(item);
+    item = new MenuItem(HIDE);
     item.addActionListener(this);
-    pop.add(item);
+    popup.add(item);
     item = new MenuItem(SHOWALL);
     item.addActionListener(this);
-    pop.add(item);
-    this.add(pop);
+    popup.add(item);
+    this.add(popup);
     item = new MenuItem(OUTPUT_TEXT);
     item.addActionListener(this);
-    pop.add(item);
+    popup.add(item);
 
-    if (aa[selectedRow].label.equals("Consensus"))
+    if (aa[selectedRow] == ap.av.consensus)
     {
-      pop.addSeparator();
+      popup.addSeparator();
       final CheckboxMenuItem cbmi = new CheckboxMenuItem(
-          "Ignore Gaps In Consensus",
-          ap.av.getIgnoreGapsConsensus());
+              "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
 
       cbmi.addItemListener(new ItemListener()
       {
         public void itemStateChanged(ItemEvent e)
         {
           ap.av.setIgnoreGapsConsensus(cbmi.getState());
-          ap.repaint();
+          ap.paintAlignment(true);
         }
       });
-      pop.add(cbmi);
-      final MenuItem cpcons=new MenuItem(COPYCONS_SEQ);
-      cpcons.addActionListener(this);
-      pop.add(cpcons);
+      popup.add(cbmi);
+      item = new MenuItem(COPYCONS_SEQ);
+      item.addActionListener(this);
+      popup.add(item);
     }
 
-     pop.show(this, evt.getX(), evt.getY());
+    popup.show(this, evt.getX(), evt.getY());
 
   }
-/**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void copy_annotseqtoclipboard(SequenceI sq)
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
+   */
+  protected void copy_annotseqtoclipboard(SequenceI sq)
+  {
+    if (sq == null || sq.getLength() < 1)
     {
-      if (sq==null || sq.getLength()<1)
-        return;
-      jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-      jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
-          sq.getStart() + "\t" +
-          sq.getEnd() + "\t" +
-          sq.getSequenceAsString() + "\n");
-      if (av.hasHiddenColumns)
+      return;
+    }
+    jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
+    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+            + sq.getStart() + "\t" + sq.getEnd() + "\t"
+            + sq.getSequenceAsString() + "\n");
+    if (av.hasHiddenColumns)
+    {
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
+      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
       {
-        jalview.appletgui.AlignFrame.copiedHiddenColumns=new Vector();
-        for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
-        {
-          int[] region = (int[])
-              av.getColumnSelection().getHiddenColumns().elementAt(i);
+        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+                .elementAt(i);
 
-          jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]{region[0],
-                            region[1]});
-        }
+        jalview.appletgui.AlignFrame.copiedHiddenColumns
+                .addElement(new int[]
+                { region[0], region[1] });
       }
     }
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
 
   public void paint(Graphics g)
   {
-    drawComponent(g, getSize().width);
+    int w = getSize().width;
+    if (image == null || w != image.getWidth(this))
+    {
+      image = createImage(w, ap.annotationPanel.getSize().height);
+    }
+
+    drawComponent(image.getGraphics(), w);
+    g.drawImage(image, 0, 0, this);
   }
 
   public void drawComponent(Graphics g, int width)
@@ -221,14 +360,14 @@ public class AnnotationLabels
 
         x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (aa[i].graph>0)
+        if (aa[i].graph > 0)
         {
           y += (aa[i].height / 3);
         }
 
         g.drawString(aa[i].label, x, y);
 
-        if (aa[i].graph>0)
+        if (aa[i].graph > 0)
         {
           y += (2 * aa[i].height / 3);
         }