X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=50849e136bca4ca2671d4b48048d9ed5ed9a70d7;hb=ea49c8f1b0d681ec87547fc4055eb35a1165aee3;hp=c600b8272721e37c80beafa8deda17eb52557080;hpb=c59fb56cb143b05c5643a71f5b39996ac1cd2fef;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index c600b82..50849e1 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,213 +1,533 @@
-
+/*
+ * 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.*;
 
-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";
-  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 resizePanel = false;
+    Image image;
+    AlignmentPanel ap;
+    AlignViewport av;
+    boolean resizing = false;
+    MouseEvent dragEvent;
+    int oldY;
+    int selectedRow;
+    int scrollOffset = 0;
+    Font font = new Font("Arial", Font.PLAIN, 11);
+
+
+    /**
+     * Creates a new AnnotationLabels object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public AnnotationLabels(AlignmentPanel ap)
     {
-      MediaTracker mt = new MediaTracker(this);
-      mt.addImage(temp, 0);
-      mt.waitForID(0);
+        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);
     }
-    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))
+
+    public AnnotationLabels(AlignViewport av)
     {
-      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()]));
+      this.av = av;
     }
-   else if(evt.getActionCommand().equals(HIDE))
-   {
-     aa[selectedRow].visible = 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;
-   }
-
-   ap.annotationPanel.adjustPanelHeight();
-   ap.RefreshPanels();
-
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    int y = evt.getY() - scrollOffset;
-
-    if (SwingUtilities.isRightMouseButton(evt))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param y DOCUMENT ME!
+     */
+    public void setScrollOffset(int y)
     {
-       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);
-      pop.show(this, evt.getX(), evt.getY());
-      return;
+        scrollOffset = y;
+        repaint();
     }
 
-    oldY = evt.getY();
-  }
+    void getSelectedRow(int y)
+    {
+      int height = 0;
+      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
+
+        height += aa[i].height;
 
-  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;
+        if (y < height)
+        {
+          selectedRow = i;
 
-    dif /= ap.av.charHeight;
-    dif *= ap.av.charHeight;
+          break;
+        }
+      }
+    }
+
+    /**
+     * 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 = "";
+            }
+
+            AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,
+                    "New description",
+                    new Annotation[ap.av.alignment.getWidth()]);
+
+            ap.av.alignment.addAnnotation(newAnnotation);
+            ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+            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();
+        ap.annotationScroller.validate();
+        ap.repaint();
+    }
 
-    if(d.height-dif>20)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(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.RefreshPanels();
+        getSelectedRow(evt.getY() - scrollOffset);
+        oldY = evt.getY();
     }
-    ap.addNotify();
-  }
 
-  public void mouseMoved(MouseEvent evt)   {}
-  public void mouseClicked(MouseEvent evt) {}
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
+    {
+        int start = selectedRow;
+        getSelectedRow(evt.getY() - scrollOffset);
+        int end = selectedRow;
+
+        if(start!=end)
+        {
+          //Swap these annotations
+          AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
+          AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
 
-  public void paintComponent(Graphics g1)
-  {
-    Graphics2D g = (Graphics2D)g1;
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
 
-    FontMetrics fm = g.getFontMetrics(g.getFont());
+          ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
+          ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+        }
+
+        resizePanel = false;
+        dragEvent = null;
+        repaint();
+        ap.annotationPanel.repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
+    {
+      if(evt.getY()<10)
+      {
+        resizePanel = true;
+        repaint();
+      }
+    }
 
-    g.setColor(Color.white);
-    g.fillRect(0,0, getWidth(), getHeight());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
+    {       }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
+    {
+      dragEvent = evt;
+
+      if (resizePanel)
+      {
+        Dimension d = ap.annotationScroller.getPreferredSize();
+        int dif = evt.getY() - oldY;
+
+        dif /= ap.av.charHeight;
+        dif *= ap.av.charHeight;
+
+        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();
+        }
+
+        ap.addNotify();
+      }
+      else
+        repaint();
+    }
 
-    g.translate(0, scrollOffset);
-    g.setColor(Color.black);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
+    {
+      resizePanel = evt.getY()<10;
 
-   AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-   int y = g.getFont().getSize();
-   int x = 0;
+      repaint();
+    }
 
-   if(aa!=null)
-   for(int i=0; i<aa.length; i++)
-   {
-     if(!aa[i].visible)
-       continue;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
+    {
+       if(!SwingUtilities.isRightMouseButton(evt))
+         return;
 
-     x = getWidth() - fm.stringWidth(aa[i].label)-3;
+        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());
 
-     y+=aa[i].height;
-   }
+            return;
+        }
+
+
+        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;
+       if(av.antiAlias)
+        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)
+    {
+        if(av.getFont().getSize()<10)
+          g.setFont(new Font("Arial", Font.PLAIN, av.getFont().getSize()-1));
+        else
+          g.setFont(font);
+
+        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 fontHeight = g.getFont().getSize();
+        int y = fontHeight;
+        int x = 0;
+        int graphExtras = 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].graph>0)
+                {
+                    graphExtras = y;
+
+                    y += (aa[i].height / 3);
+
+                    if(aa[i].graphGroup<0)
+                        graphExtras = y + fontHeight;
+                }
+
+                if(aa[i].graphGroup>-1)
+                {
+                  int groupSize = 0;
+                  for (int gg = 0; gg < aa.length; gg++)
+                  {
+                    if (aa[gg].graphGroup == aa[i].graphGroup)
+                      groupSize++;
+                  }
+
+                  if(groupSize * (fontHeight+8) < aa[i].height)
+                    graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;
+
+                 for(int gg=0; gg<aa.length; gg++)
+                 {
+                   if(aa[gg].graphGroup==aa[i].graphGroup)
+                   {
+                     x = width - fm.stringWidth(aa[gg].label) - 3;
+                     g.drawString(aa[gg].label, x, graphExtras );
+                     if(aa[gg].annotations[0]!=null)
+                       g.setColor(aa[gg].annotations[0].colour);
+
+                     g.drawLine( x, graphExtras+3,
+                                 x+fm.stringWidth(aa[gg].label),
+                                 graphExtras+3);
+
+                     g.setColor(Color.black);
+                     graphExtras += fontHeight+8;
+                   }
+                 }
+                }
+                else
+                  g.drawString(aa[i].label, x, y);
+
+                if (aa[i].graph>0)
+                {
+                /*  if (aa[i].graphLines != null)
+                  {
+                    for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
+                    {
+                       x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
+                      g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
+                      g.setColor(aa[i].getGraphLine(gl).colour);
+                      Graphics2D g2 = (Graphics2D) g;
+                      g2.setStroke(new BasicStroke(1,
+                          BasicStroke.CAP_SQUARE,
+                          BasicStroke.JOIN_ROUND, 3f,
+                          new float[]
+                          {5f, 3f}, 0f));
+
+                      graphExtras += 3;
+
+                      g.drawLine(x, graphExtras,
+                                 x+fm.stringWidth(aa[i].label),
+                                 graphExtras);
+                      g2.setStroke(new BasicStroke());
+                    }
+                  }*/
+                    y += ((2 * aa[i].height) / 3);
+                }
+                else
+                {
+                    y += aa[i].height;
+                }
+            }
+        }
+
+        if (resizePanel)
+        {
+          g.drawImage(image, 2, 0 - scrollOffset, this);
+        }
+        else if (dragEvent != null)
+        {
+          g.setColor(Color.lightGray);
+          g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
+        }
+
+
+        if ((aa == null) || (aa.length < 1))
+        {
+            g.drawString("Right click", 2, 8);
+            g.drawString("to add annotation", 2, 18);
+        }
+    }
 }