X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=8561e640b1020c397f1d26d5ad2771ba024cd3da;hb=dea32f71ff7f8a80cc8494864b6605921d81fafa;hp=f2603ea3e349eac0f766f836a0fed1b01edd71a4;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index f2603ea..8561e64 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,255 +1,434 @@
-
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
+ * Copyright (C) 2005 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.gui;
 
-import javax.swing.*;
-import java.awt.event.*;
+import jalview.datamodel.*;
+
 import java.awt.*;
+import java.awt.event.*;
 import java.awt.image.*;
-import jalview.datamodel.*;
-import jalview.io.FormatAdapter;
 
-public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationLabels extends JPanel implements MouseListener,
+    MouseMotionListener, ActionListener
 {
-  boolean active = false;
-  Image image;
-  AlignmentPanel ap ;
-  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 OUTPUT_TEXT="Show Values In Textbox";
-  int selectedRow = 0;
-  int scrollOffset = 0;
-
-  public AnnotationLabels(AlignmentPanel ap)
-  {
-    this.ap = ap;
-
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-    Image temp = null;
-    if (url != null)
-      temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-
-    try
+    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 OUTPUT_TEXT = "Show Values In Textbox";
+    boolean active = false;
+    Image image;
+    AlignmentPanel ap;
+    AlignViewport av;
+    boolean resizing = false;
+    int oldY;
+    int mouseX;
+    int selectedRow = 0;
+    int scrollOffset = 0;
+
+
+    /**
+     * Creates a new AnnotationLabels object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public AnnotationLabels(AlignmentPanel ap)
+    {
+        this.ap = ap;
+        av = ap.av;
+
+        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);
+    }
+
+    public AnnotationLabels(AlignViewport av)
     {
-      MediaTracker mt = new MediaTracker(this);
-      mt.addImage(temp, 0);
-      mt.waitForID(0);
+      this.av = av;
     }
-    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);
-  }
-
-  public void setScrollOffset(int y)
-  {
-    scrollOffset = y;
-    repaint();
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-    if(evt.getActionCommand().equals(ADDNEW))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param y DOCUMENT ME!
+     */
+    public void setScrollOffset(int y)
     {
-      String label = JOptionPane.showInputDialog(this, "Label for annotation");
-      if(label==null)
-        label = "";
-      ap.av.alignment.addAnnotation(new AlignmentAnnotation
-                                      (label,
-                                       "New description",
-                                       new Annotation[ap.av.alignment.getWidth()]));
+        scrollOffset = y;
+        repaint();
     }
-   else if(evt.getActionCommand().equals(HIDE))
-   {
-     aa[selectedRow].visible = false;
-     if(aa[selectedRow].label.equals("Conservation"))
-       ap.av.showConservation = false;
-     if(aa[selectedRow].label.equals("Quality"))
-       ap.av.showQuality = false;
-     if(aa[selectedRow].label.equals("Consensus"))
-       ap.av.showIdentity = false;
-   }
-   else if(evt.getActionCommand().equals(DELETE))
-   {
-     ap.av.alignment.deleteAnnotation(aa[selectedRow]);
-   }
-   else if(evt.getActionCommand().equals(SHOWALL))
-   {
-       for(int i=0; i<aa.length; i++)
-         aa[i].visible = true;
-   }
-   else if(evt.getActionCommand().equals(OUTPUT_TEXT))
-   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-     Desktop.addInternalFrame(cap, ap.alignFrame.getTitle()+" - "+ aa[selectedRow].label, 500, 100);
-     cap.setText( aa[selectedRow].toString() );
-   }
-
-   ap.annotationPanel.adjustPanelHeight();
-   ap.repaint();
-
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    int y = evt.getY() - scrollOffset;
-
-      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-       if(aa==null || aa.length==0)
-       {
-            JPopupMenu pop = new JPopupMenu("Annotations");
-            JMenuItem item = new JMenuItem(ADDNEW);
-            item.addActionListener(this);
-            pop.add(item);
-            pop.show(this, evt.getX(), evt.getY());
-            return;
-       }
-
-       int height = 0;
-       for (int i = 0; i < aa.length; i++)
-       {
-         if(!aa[i].visible)
-           continue;
-
-         height += aa[i].height;
-         if(y<height)
-         {
-           selectedRow = i;
-           break;
-         }
-       }
-
-      JPopupMenu pop = new JPopupMenu("Annotations");
-      JMenuItem item = new JMenuItem(ADDNEW);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(HIDE);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(DELETE);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(SHOWALL);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(OUTPUT_TEXT);
-      item.addActionListener(this);
-      pop.add(item);
-      pop.show(this, evt.getX(), evt.getY());
-
-    oldY = evt.getY();
-  }
-
-  public void mouseReleased(MouseEvent evt){ active = false; repaint(); }
-  public void mouseEntered(MouseEvent evt) { active = true;  repaint();}
-  public void mouseExited(MouseEvent evt)  { active = false; repaint();}
-  public void mouseDragged(MouseEvent evt)
-  {
-    active = true;
-    Dimension d = ap.annotationScroller.getPreferredSize();
-    int dif = evt.getY() - oldY;
-
-    dif /= ap.av.charHeight;
-    dif *= ap.av.charHeight;
-
-    if(d.height-dif>20)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void actionPerformed(ActionEvent evt)
+    {
+        int dif = 0;
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+        if (evt.getActionCommand().equals(ADDNEW))
+        {
+            String label = JOptionPane.showInputDialog(this,
+                    "Label for annotation");
+
+            if (label == null)
+            {
+                label = "";
+            }
+
+            ap.av.alignment.addAnnotation(new AlignmentAnnotation(label,
+                    "New description",
+                    new Annotation[ap.av.alignment.getWidth()]));
+
+            dif = aa[aa.length - 1].height;
+        }
+        else if (evt.getActionCommand().equals(HIDE))
+        {
+            aa[selectedRow].visible = false;
+
+            if (aa[selectedRow].label.equals("Conservation"))
+            {
+                ap.av.showConservation = false;
+            }
+
+            if (aa[selectedRow].label.equals("Quality"))
+            {
+                ap.av.showQuality = false;
+            }
+
+            if (aa[selectedRow].label.equals("Consensus"))
+            {
+                ap.av.showIdentity = false;
+            }
+
+            dif = aa[selectedRow].height * -1;
+        }
+        else if (evt.getActionCommand().equals(DELETE))
+        {
+            ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+            dif = aa[selectedRow].height * -1;
+        }
+        else if (evt.getActionCommand().equals(SHOWALL))
+        {
+            for (int i = 0; i < aa.length; i++)
+            {
+                if (!aa[i].visible)
+                {
+                    dif += aa[i].height;
+                    aa[i].visible = true;
+                }
+            }
+        }
+        else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+        {
+            CutAndPasteTransfer cap = new CutAndPasteTransfer();
+            Desktop.addInternalFrame(cap,
+                ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
+                100);
+            cap.setText(aa[selectedRow].toString());
+        }
+
+
+        ap.annotationPanel.adjustPanelHeight();
+
+        Dimension d = ap.annotationScroller.getPreferredSize();
+        ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+                d.height + dif));
+        d = ap.annotationSpaceFillerHolder.getPreferredSize();
+        ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,
+                d.height + dif));
+
+        ap.addNotify();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
+    {
+        oldY = evt.getY();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
     {
-      ap.annotationScroller.setPreferredSize(new Dimension(d.width,d.height - dif));
-      d = ap.annotationSpaceFillerHolder.getPreferredSize();
-      ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,d.height - dif));
-      ap.repaint();
+        active = false;
+        repaint();
     }
-    ap.addNotify();
-  }
 
-  public void mouseMoved(MouseEvent evt)   {}
-  public void mouseClicked(MouseEvent evt) {}
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
+    {
+        active = true;
+        repaint();
+    }
 
-  public void paintComponent(Graphics g1)
-  {
-    Graphics2D g = (Graphics2D)g1;
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
+    {
+        active = false;
+        repaint();
+    }
 
-    drawComponent(g);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
+    {
+        active = true;
 
-  public void drawComponent(Graphics2D g)
-  {
-    FontMetrics fm = g.getFontMetrics(g.getFont());
-    g.setColor(Color.white);
-    g.fillRect(0,0, getWidth(), getHeight());
+        Dimension d = ap.annotationScroller.getPreferredSize();
+        int dif = evt.getY() - oldY;
 
-    g.translate(0, scrollOffset);
-    g.setColor(Color.black);
+        dif /= ap.av.charHeight;
+        dif *= ap.av.charHeight;
 
-   AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-   int y = g.getFont().getSize();
-   int x = 0;
+        if ((d.height - dif) > 20)
+        {
+            ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+                    d.height - dif));
+            d = ap.annotationSpaceFillerHolder.getPreferredSize();
+            ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+                    d.width, d.height - dif));
+            ap.repaint();
+        }
 
-   if(aa!=null)
-   for(int i=0; i<aa.length; i++)
-   {
-     if(!aa[i].visible)
-       continue;
+        ap.addNotify();
+    }
 
-     x = getWidth() - fm.stringWidth(aa[i].label)-3;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
+    {
+    }
 
-     if(aa[i].isGraph)
-       y+=(aa[i].height/3);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
+    {
+        int y = evt.getY() - scrollOffset;
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-     g.drawString(aa[i].label, x, y);
+        if ((aa == null) || (aa.length == 0))
+        {
+            JPopupMenu pop = new JPopupMenu("Annotations");
+            JMenuItem item = new JMenuItem(ADDNEW);
+            item.addActionListener(this);
+            pop.add(item);
+            pop.show(this, evt.getX(), evt.getY());
 
-     if(aa[i].isGraph)
-       y+=(2*aa[i].height/3);
-    else
-       y+=aa[i].height;
-   }
+            return;
+        }
+
+        int height = 0;
+
+        for (int i = 0; i < aa.length; i++)
+        {
+            if (!aa[i].visible)
+            {
+                continue;
+            }
+
+            height += aa[i].height;
+
+            if (y < height)
+            {
+                selectedRow = i;
+
+                break;
+            }
+        }
+
+        JPopupMenu pop = new JPopupMenu("Annotations");
+        JMenuItem item = new JMenuItem(ADDNEW);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(HIDE);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(DELETE);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(SHOWALL);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(OUTPUT_TEXT);
+        item.addActionListener(this);
+        pop.add(item);
+
+        if (aa[selectedRow].label.equals("Consensus"))
+        {
+          pop.addSeparator();
+          final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+              "Ignore Gaps In Consensus",
+              ap.av.getIgnoreGapsConsensus());
+          cbmi.addActionListener(new ActionListener()
+              {public void actionPerformed(ActionEvent e)
+               {
+                 ap.av.setIgnoreGapsConsensus(cbmi.getState());
+                 ap.repaint();
+               }
+              });
+          pop.add(cbmi);
+
+        }
+
+        pop.show(this, evt.getX(), evt.getY());
+    }
 
-   if (active)
-   {
-     if (image != null)
-       g.drawImage(image, 2, 0, this);
-   }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g1 DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
+    {
 
-   if (aa == null || aa.length<1)
-   {
-     g.drawString("Right click", 2, 8);
-     g.drawString("to add annotation", 2, 18);
-   }
+        int width = getWidth();
+        if(width==0)
+         width = ap.calculateIdWidth().width + 4;
 
+       Graphics2D g2 = (Graphics2D) g;
+        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
 
+       drawComponent(g2, width);
 
-  }
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void drawComponent(Graphics g, int width)
+    {
+        FontMetrics fm = g.getFontMetrics(g.getFont());
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
+
+        g.translate(0, scrollOffset);
+        g.setColor(Color.black);
+
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        int y = g.getFont().getSize();
+        int x = 0;
+
+
+        if (aa != null)
+        {
+            for (int i = 0; i < aa.length; i++)
+            {
+                if (!aa[i].visible)
+                {
+                    continue;
+                }
+
+                x = width - fm.stringWidth(aa[i].label) - 3;
+
+                if (aa[i].isGraph)
+                {
+                    y += (aa[i].height / 3);
+                }
+
+                g.drawString(aa[i].label, x, y);
+
+                if (aa[i].isGraph)
+                {
+                    y += ((2 * aa[i].height) / 3);
+                }
+                else
+                {
+                    y += aa[i].height;
+                }
+            }
+        }
+
+        if (active)
+        {
+            if (image != null)
+            {
+                g.drawImage(image, 2, 0, this);
+            }
+        }
+
+        if ((aa == null) || (aa.length < 1))
+        {
+            g.drawString("Right click", 2, 8);
+            g.drawString("to add annotation", 2, 18);
+        }
+    }
 }