X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=cef84ccd25edb687b97bdaabdb65ebc5a6992099;hb=af1471fa3d7d3cb32d203e81d394838608dd1c96;hp=1884a08633aa7c2dae4cf0e7448bc48f81b7a181;hpb=6951479b7dc56bd022ce2c370b7f88b5571004fd;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 1884a08..cef84cc 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,58 +1,97 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package jalview.appletgui;
 
 import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
+import java.awt.image.BufferedImage;
 
 import jalview.datamodel.*;
 
-public class AnnotationLabels
-    extends Panel implements ActionListener, MouseListener, MouseMotionListener
+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 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 scrollOffset = 0;
+
   int selectedRow = -1;
 
   Tooltip tooltip;
 
+  private boolean hasHiddenRows;
+
   public AnnotationLabels(AlignmentPanel ap)
   {
     this.ap = ap;
     this.av = ap.av;
     setLayout(null);
+
+    /**
+     * this retrieves the adjustable height glyph from resources. we don't use it at the moment.
+    java.net.URL url = getClass().getResource("/images/idwidth.gif");
+    Image temp = null;
+
+    if (url != null)
+    {
+      temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+    }
+
+    try
+    {
+      MediaTracker mt = new MediaTracker(this);
+      mt.addImage(temp, 0);
+      mt.waitForID(0);
+    } catch (Exception ex)
+    {
+    }
+
+    BufferedImage bi = new BufferedImage(temp.getHeight(this),
+            temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
+    Graphics2D g = (Graphics2D) bi.getGraphics();
+    g.rotate(Math.toRadians(90));
+    g.drawImage(temp, 0, -bi.getWidth(this), this);
+    image = (Image) bi;
+*/
     addMouseListener(this);
     addMouseMotionListener(this);
   }
@@ -68,24 +107,29 @@ public class AnnotationLabels
     repaint();
   }
 
+  /**
+   * 
+   * @param y
+   * @return -2 if no rows are visible at all, -1 if no visible rows were
+   *         selected
+   */
   int getSelectedRow(int y)
   {
-    int row = -1;
+    int row = -2;
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
     if (aa == null)
     {
       return row;
     }
-
     int height = 0;
     for (int i = 0; i < aa.length; i++)
     {
+      row = -1;
       if (!aa[i].visible)
       {
         continue;
       }
-
       height += aa[i].height;
       if (y < height)
       {
@@ -103,9 +147,8 @@ public class AnnotationLabels
 
     if (evt.getActionCommand().equals(ADDNEW))
     {
-      AlignmentAnnotation newAnnotation = new AlignmentAnnotation("",
-          null,
-          new Annotation[ap.av.alignment.getWidth()]);
+      AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
+              new Annotation[ap.av.alignment.getWidth()]);
 
       if (!editLabelDescription(newAnnotation))
       {
@@ -127,17 +170,17 @@ public class AnnotationLabels
     {
       for (int i = 0; i < aa.length; i++)
       {
-        aa[i].visible = (aa[i].annotations==null) ? false : 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))
@@ -157,19 +200,26 @@ public class AnnotationLabels
 
   boolean editLabelDescription(AlignmentAnnotation annotation)
   {
-    EditNameDialog dialog = new EditNameDialog(
-        annotation.label,
-        annotation.description,
-        "       Annotation Label",
-        "Annotation Description",
-        ap.alignFrame,
-        "Edit Annotation Name / Description",
-        500, 100);
+    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)
     {
       annotation.label = dialog.getName();
       annotation.description = dialog.getDescription();
+      annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
       repaint();
       return true;
     }
@@ -178,23 +228,27 @@ public class AnnotationLabels
 
   }
 
+  boolean resizePanel = false;
+
   public void mouseMoved(MouseEvent evt)
   {
-    int row = getSelectedRow(evt.getY() - scrollOffset);
+    resizePanel = evt.getY() < 10;
+
+    int row = getSelectedRow(evt.getY() + scrollOffset);
 
     if (row > -1)
     {
       if (tooltip == null)
       {
-        tooltip = new Tooltip(ap.av.alignment.
-                              getAlignmentAnnotation()[row].
-                              description,
-                              this);
+        tooltip = new Tooltip(
+                ap.av.alignment.getAlignmentAnnotation()[row]
+                        .getDescription(true),
+                this);
       }
       else
       {
-        tooltip.setTip(ap.av.alignment.
-                       getAlignmentAnnotation()[row].description);
+        tooltip.setTip(ap.av.alignment.getAlignmentAnnotation()[row]
+                .getDescription(true));
       }
     }
     else if (tooltip != null)
@@ -204,75 +258,204 @@ public class AnnotationLabels
 
   }
 
+  MouseEvent dragEvent = null;
+
   public void mouseDragged(MouseEvent evt)
-  {}
+  {
+    dragEvent = evt;
+
+    if (resizePanel)
+    {
+      Dimension d = ap.annotationPanelHolder.getSize(),e = ap.annotationSpaceFillerHolder.getSize();;
+      int dif = evt.getY() - oldY;
+
+      dif /= ap.av.charHeight;
+      dif *= ap.av.charHeight;
+
+      if ((d.height - dif) > 20)
+      {
+        
+        setSize(new Dimension(e.width,d.height-dif));
+        ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width, d.height - dif));
+        ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height - dif));
+        ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height-dif, 0, ap.annotationPanel.adjustPanelHeight(false));
+        
+        ap.validate();
+        //ap.paintAlignment(true);
+      }
+
+      ap.addNotify();
+    }
+    else
+    {
+      repaint();
+    }
+  }
 
   public void mouseClicked(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseReleased(MouseEvent evt)
-  {}
+  {
+    resizePanel = false;
+    dragEvent = null;
+    repaint();
+    ap.annotationPanel.repaint();
+  }
 
   public void mouseEntered(MouseEvent evt)
-  {}
+  {
+    if (evt.getY() < 10)
+    {
+      resizePanel = true;
+      repaint();
+    }
+  }
 
   public void mouseExited(MouseEvent evt)
-  {}
+  {
+
+    if (dragEvent == null)
+    {
+      resizePanel = false;
+    }
+    else
+    {
+      if (!resizePanel)
+      {
+        dragEvent = null;
+      }
+    }
+    repaint();
+  }
 
   public void mousePressed(MouseEvent evt)
   {
-    selectedRow = getSelectedRow(evt.getY() - scrollOffset);
+    oldY = evt.getY();
+    // todo: move below to mouseClicked ?
+    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);
-    popup.add(item);
-    item = new MenuItem(SHOWALL);
-    item.addActionListener(this);
-    popup.add(item);
-    this.add(popup);
-    item = new MenuItem(OUTPUT_TEXT);
-    item.addActionListener(this);
-    popup.add(item);
-
-    if (aa[selectedRow] == ap.av.consensus)
+    // DETECT RIGHT MOUSE BUTTON IN AWT
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      popup.addSeparator();
-      final CheckboxMenuItem cbmi = new CheckboxMenuItem(
-          "Ignore Gaps In Consensus",
-          ap.av.getIgnoreGapsConsensus());
 
-      cbmi.addItemListener(new ItemListener()
+      PopupMenu popup = new PopupMenu("Annotations");
+
+      MenuItem item = new MenuItem(ADDNEW);
+      item.addActionListener(this);
+      popup.add(item);
+      if (selectedRow < 0)
       {
-        public void itemStateChanged(ItemEvent e)
+        // this never happens at moment: - see comment on JAL-563
+        if (hasHiddenRows)
         {
-          ap.av.setIgnoreGapsConsensus(cbmi.getState());
-          ap.paintAlignment(true);
+          item = new MenuItem(SHOWALL);
+          item.addActionListener(this);
+          popup.add(item);
         }
-      });
-      popup.add(cbmi);
-      item = new MenuItem(COPYCONS_SEQ);
+        this.add(popup);
+        popup.show(this, evt.getX(), evt.getY());
+        return;
+      }
+      // add the rest if there are actually rows to show
+      item = new MenuItem(EDITNAME);
       item.addActionListener(this);
       popup.add(item);
+      item = new MenuItem(HIDE);
+      item.addActionListener(this);
+      popup.add(item);
+      if (hasHiddenRows)
+      {
+        item = new MenuItem(SHOWALL);
+        item.addActionListener(this);
+        popup.add(item);
+      }
+      this.add(popup);
+      item = new MenuItem(OUTPUT_TEXT);
+      item.addActionListener(this);
+      popup.add(item);
+
+      if (aa[selectedRow] == ap.av.consensus)
+      {
+        popup.addSeparator();
+        final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+                "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
+
+        cbmi.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            ap.av.setIgnoreGapsConsensus(cbmi.getState());
+            ap.paintAlignment(true);
+          }
+        });
+        popup.add(cbmi);
+        item = new MenuItem(COPYCONS_SEQ);
+        item.addActionListener(this);
+        popup.add(item);
+      }
+
+      popup.show(this, evt.getX(), evt.getY());
     }
+    else
+    {
+      // selection action.
+      if (selectedRow > -1 && selectedRow < aa.length)
+      {
+        if (aa[selectedRow].groupRef != null)
+        {
+          if (evt.getClickCount() >= 2)
+          {
+            // todo: make the ap scroll to the selection - not necessary, first
+            // click highlights/scrolls, second selects
+            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            ap.av.setSelectionGroup(// new SequenceGroup(
+            aa[selectedRow].groupRef); // );
+            ap.av.sendSelection();
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+          }
+          else
+          {
+            ap.seqPanel.ap.idPanel
+                    .highlightSearchResults(aa[selectedRow].groupRef
+                            .getSequences(null));
+          }
+          return;
+        }
+        else if (aa[selectedRow].sequenceRef != null)
+        {
+          Vector sr = new Vector();
+          sr.addElement(aa[selectedRow].sequenceRef);
+          if (evt.getClickCount() == 1)
+          {
+            ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+          }
+          else if (evt.getClickCount() >= 2)
+          {
+            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            SequenceGroup sg = new SequenceGroup();
+            sg.addSequence(aa[selectedRow].sequenceRef, false);
+            ap.av.setSelectionGroup(sg);
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
+          }
 
-    popup.show(this, evt.getX(), evt.getY());
+        }
+      }
 
+    }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
    */
   protected void copy_annotseqtoclipboard(SequenceI sq)
   {
@@ -281,21 +464,20 @@ public class AnnotationLabels
       return;
     }
     jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
-        sq.getStart() + "\t" +
-        sq.getEnd() + "\t" +
-        sq.getSequenceAsString() + "\n");
+    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);
+        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] });
       }
     }
   }
@@ -324,41 +506,53 @@ public class AnnotationLabels
     g.setColor(Color.white);
     g.fillRect(0, 0, getSize().width, getSize().height);
 
-    g.translate(0, scrollOffset);
+    g.translate(0, -scrollOffset);
     g.setColor(Color.black);
 
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    int y = g.getFont().getSize();
-    int x = 0;
+    int y = 0, fy = g.getFont().getSize();
+    int x = 0, offset;
 
     if (aa != null)
     {
+      hasHiddenRows = false;
       for (int i = 0; i < aa.length; i++)
       {
         if (!aa[i].visible)
         {
+          hasHiddenRows = true;
           continue;
         }
 
         x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (aa[i].graph > 0)
-        {
-          y += (aa[i].height / 3);
-        }
-
-        g.drawString(aa[i].label, x, y);
+        y += aa[i].height;
+        offset = -(aa[i].height - fy) / 2;
 
-        if (aa[i].graph > 0)
-        {
-          y += (2 * aa[i].height / 3);
-        }
-        else
-        {
-          y += aa[i].height;
-        }
+        g.drawString(aa[i].label, x, y + offset);
       }
     }
+    g.translate(0, +scrollOffset);
+    if (resizePanel)
+    {
+      g.setColor(Color.red);
+      g.setPaintMode();
+      g.drawLine(2, 8, 5, 2);
+      g.drawLine(5, 2, 8, 8);
+    }
+    else if (dragEvent != null && aa != null)
+    {
+      g.setColor(Color.lightGray);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(),
+              dragEvent.getY());
+    }
+
+    if ((aa == null) || (aa.length < 1))
+    {
+      g.setColor(Color.black);
+      g.drawString("Right click", 2, 8);
+      g.drawString("to add annotation", 2, 18);
+    }
   }
 
 }