X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=a952f9d870ce5bd06ee6b3f5698ef9179689e8a9;hb=ad52f1ddcaefa09c6a3e85329b28dad155613f49;hp=651d44cac97d856cdbcf4656f4dba6fb52e44945;hpb=d65fda1b7cee986dadd46083e25bdd274f3055df;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 651d44c..a952f9d 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -19,37 +19,47 @@
 
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
 
 import jalview.datamodel.*;
 
 public class AnnotationLabels
-    extends Panel implements ActionListener
+    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";
-  int selectedRow = 0;
+  static String COPYCONS_SEQ = "Copy Consensus Sequence";
+
   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;
   }
 
   public void setScrollOffset(int y)
@@ -58,11 +68,58 @@ public class AnnotationLabels
     repaint();
   }
 
-  public void actionPerformed(ActionEvent evt)
+  int getSelectedRow(int y)
   {
+    int row = -1;
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-    if (evt.getActionCommand().equals(HIDE))
+    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(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;
     }
@@ -75,7 +132,7 @@ public class AnnotationLabels
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame,
@@ -83,50 +140,115 @@ public class AnnotationLabels
                                        aa[selectedRow].label, 500, 100);
       cap.setText(aa[selectedRow].toString());
     }
+    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+    {
+      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++)
+    EditNameDialog dialog = new EditNameDialog(
+        annotation.label,
+        annotation.description,
+        "       Annotation Label",
+        "Annotation Description",
+        ap.alignFrame,
+        "Edit Annotation Name / Description",
+        500, 100);
+
+    if (dialog.accept)
     {
-      if (!aa[i].visible)
+      annotation.label = dialog.getName();
+      annotation.description = dialog.getDescription();
+      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].
+                              description,
+                              this);
       }
-
-      height += aa[i].height;
-      if (y < height)
+      else
       {
-        selectedRow = i;
-        break;
+        tooltip.setTip(ap.av.alignment.
+                       getAlignmentAnnotation()[row].description);
       }
     }
+    else if (tooltip != null)
+    {
+      tooltip.setTip("");
+    }
+
+  }
+
+  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)
+  {}
 
-    PopupMenu pop = new PopupMenu("Annotations");
-    MenuItem item = new MenuItem(HIDE);
+  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);
-    pop.add(item);
+    popup.add(item);
+    item = new MenuItem(HIDE);
+    item.addActionListener(this);
+    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",
+          "Ignore Gaps In Consensus",
           ap.av.getIgnoreGapsConsensus());
 
       cbmi.addItemListener(new ItemListener()
@@ -134,31 +256,78 @@ public class AnnotationLabels
         public void itemStateChanged(ItemEvent e)
         {
           ap.av.setIgnoreGapsConsensus(cbmi.getState());
-          ap.repaint();
+          ap.paintAlignment(true);
         }
       });
-      pop.add(cbmi);
+      popup.add(cbmi);
+      item = new MenuItem(COPYCONS_SEQ);
+      item.addActionListener(this);
+      popup.add(item);
+    }
+
+    popup.show(this, evt.getX(), evt.getY());
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void copy_annotseqtoclipboard(SequenceI sq)
+  {
+    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)
+    {
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
+      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      {
+        int[] region = (int[])
+            av.getColumnSelection().getHiddenColumns().elementAt(i);
 
-     pop.show(this, evt.getX(), evt.getY());
+        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);
+    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)
+  public void drawComponent(Graphics g, int width)
   {
-    FontMetrics fm = g.getFontMetrics(g.getFont());
+    g.setFont(av.getFont());
+    FontMetrics fm = g.getFontMetrics(av.getFont());
     g.setColor(Color.white);
     g.fillRect(0, 0, getSize().width, getSize().height);
 
     g.translate(0, scrollOffset);
     g.setColor(Color.black);
 
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
     int y = g.getFont().getSize();
     int x = 0;
 
@@ -171,16 +340,16 @@ public class AnnotationLabels
           continue;
         }
 
-        x = getSize().width - fm.stringWidth(aa[i].label) - 3;
+        x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (aa[i].isGraph)
+        if (aa[i].graph > 0)
         {
           y += (aa[i].height / 3);
         }
 
         g.drawString(aa[i].label, x, y);
 
-        if (aa[i].isGraph)
+        if (aa[i].graph > 0)
         {
           y += (2 * aa[i].height / 3);
         }