X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=1577477d78d94a203cfeb18658bd56cb8a78343d;hb=59d682209891099d46b960509907c79e3fb276fe;hp=b77fab6d0e4caae0eb9ebbaa3f1a94a3af8c57e1;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index b77fab6..1577477 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 
@@ -18,10 +18,12 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.regex.Pattern;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.event.*;
+import java.awt.geom.AffineTransform;
 import java.awt.image.*;
 import javax.swing.*;
 
@@ -113,6 +115,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     addMouseListener(this);
     addMouseMotionListener(this);
+    addMouseWheelListener(ap.annotationPanel);
   }
 
   public AnnotationLabels(AlignViewport av)
@@ -142,7 +145,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   void getSelectedRow(int y)
   {
     int height = 0;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
     selectedRow = -2;
     if (aa != null)
     {
@@ -174,20 +178,21 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void actionPerformed(ActionEvent evt)
   {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
 
     if (evt.getActionCommand().equals(ADDNEW))
     {
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
-              null, new Annotation[ap.av.alignment.getWidth()]);
+              null, new Annotation[ap.av.getAlignment().getWidth()]);
 
       if (!editLabelDescription(newAnnotation))
       {
         return;
       }
 
-      ap.av.alignment.addAnnotation(newAnnotation);
-      ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+      ap.av.getAlignment().addAnnotation(newAnnotation);
+      ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
     }
     else if (evt.getActionCommand().equals(EDITNAME))
     {
@@ -197,15 +202,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (evt.getActionCommand().equals(HIDE))
     {
       aa[selectedRow].visible = false;
-
-      if (aa[selectedRow].label.equals("Quality"))
-      {
-        ap.av.quality = null;
-      }
     }
     else if (evt.getActionCommand().equals(DELETE))
     {
-      ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+      ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
     }
     else if (evt.getActionCommand().equals(SHOWALL))
     {
@@ -245,9 +245,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    ap.annotationPanel.adjustPanelHeight();
-    ap.annotationScroller.validate();
-    ap.paintAlignment(true);
+    ap.validateAnnotationDimensions(false);
+    ap.addNotify();
+    ap.repaint();
+    // validate();
+    // ap.paintAlignment(true);
   }
 
   /**
@@ -307,16 +309,17 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     if (start != end)
     {
       // Swap these annotations
-      AlignmentAnnotation startAA = ap.av.alignment
+      AlignmentAnnotation startAA = ap.av.getAlignment()
               .getAlignmentAnnotation()[start];
       if (end == -1)
       {
-        end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+        end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
       }
-      AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+      AlignmentAnnotation endAA = ap.av.getAlignment()
+              .getAlignmentAnnotation()[end];
 
-      ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
-      ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+      ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+      ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
     }
 
     resizePanel = false;
@@ -404,25 +407,57 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     getSelectedRow(evt.getY() - scrollOffset);
 
     if (selectedRow > -1
-            && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+            && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
     {
-      AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
-
-      StringBuffer desc = new StringBuffer("<html>");
+      AlignmentAnnotation aa = ap.av.getAlignment()
+              .getAlignmentAnnotation()[selectedRow];
 
+      StringBuffer desc = new StringBuffer();
       if (aa.description != null
               && !aa.description.equals("New description"))
       {
-        desc.append(aa.getDescription(true));
-        if (aa.hasScore)
-          desc.append("<br>");
+        // TODO: we could refactor and merge this code with the code in
+        // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
+        // tooltips
+        desc.append(aa.getDescription(true).trim());
+        // check to see if the description is an html fragment.
+        if (desc.length() < 6
+                || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
+        {
+          // clean the description ready for embedding in html
+          desc = new StringBuffer(Pattern.compile("<").matcher(desc)
+                  .replaceAll("&lt;"));
+          desc.insert(0, "<html>");
+        }
+        else
+        {
+          // remove terminating html if any
+          int i = desc.substring(desc.length() - 7).toLowerCase()
+                  .lastIndexOf("</html>");
+          if (i > -1)
+          {
+            desc.setLength(desc.length() - 7 + i);
+          }
+        }
+        if (aa.hasScore())
+        {
+          desc.append("<br/>");
+        }
+
+      }
+      else
+      {
+        // begin the tooltip's html fragment
+        desc.append("<html>");
       }
       if (aa.hasScore())
       {
-        desc.append("Score: " + aa.score);
+        // TODO: limit precision of score to avoid noise from imprecise doubles
+        // (64.7 becomes 64.7+/some tiny value).
+        desc.append(" Score: " + aa.score);
       }
 
-      if (desc.length() != 6)
+      if (desc.length() > 6)
       {
         desc.append("</html>");
         this.setToolTipText(desc.toString());
@@ -441,7 +476,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
     if (SwingUtilities.isLeftMouseButton(evt))
     {
       if (selectedRow > -1 && selectedRow < aa.length)
@@ -450,13 +486,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
           if (evt.getClickCount() >= 2)
           {
-            // todo: make the ap scroll to the selection
+            // 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());
+            ap.av.sendSelection();
           }
           else
           {
@@ -611,6 +648,28 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             }
           });
           pop.add(cprofl);
+          final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+                  "Normalise Group Logo",
+                  aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+          cproflnorm.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+              // automatically enable logo display if we're clicked
+              aaa.groupRef.setshowSequenceLogo(true);
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cproflnorm);
         }
         else
         {
@@ -627,6 +686,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // can be
               // updated.
               av.setShowConsensusHistogram(chist.getState());
+              ap.alignFrame.setMenusForViewport();
               ap.repaint();
               // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
             }
@@ -645,11 +705,32 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // can be
               // updated.
               av.setShowSequenceLogo(cprof.getState());
+              ap.alignFrame.setMenusForViewport();
               ap.repaint();
               // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
             }
           });
           pop.add(cprof);
+          final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+                  "Normalise Logo", av.isNormaliseSequenceLogo());
+          cprofnorm.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowSequenceLogo(true);
+              av.setNormaliseSequenceLogo(cprofnorm.getState());
+              ap.alignFrame.setMenusForViewport();
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprofnorm);
         }
         final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
         consclipbrd.addActionListener(this);
@@ -681,7 +762,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       sq.setDatasetSequence(dseqs[0]);
     }
     Alignment ds = new Alignment(dseqs);
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
               sq.getLength(), seqs);
@@ -694,7 +775,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             .setContents(new StringSelection(output), Desktop.instance);
 
     Vector hiddenColumns = null;
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       hiddenColumns = new Vector();
       for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
@@ -763,18 +844,22 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     g.translate(0, scrollOffset);
     g.setColor(Color.black);
 
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int fontHeight = g.getFont().getSize();
     int y = 0;
     int x = 0;
     int graphExtras = 0;
     int offset = 0;
-
+    Font baseFont = g.getFont();
+    FontMetrics baseMetrics = fm;
+    int ofontH = fontHeight;
+    boolean visible = true;
     if (aa != null)
     {
       hasHiddenRows = false;
       for (int i = 0; i < aa.length; i++)
       {
+        visible = true;
         g.setColor(Color.black);
 
         if (!aa[i].visible)
@@ -807,30 +892,55 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               groupSize++;
             }
           }
-
           if (groupSize * (fontHeight + 8) < aa[i].height)
           {
             graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
           }
-
-          for (int gg = 0; gg < aa.length; gg++)
+          else
           {
-            if (aa[gg].graphGroup == aa[i].graphGroup)
+            // scale font to fit
+            float h = aa[i].height / (float) groupSize, s;
+            if (h < 9)
+            {
+              visible = false;
+            }
+            else
             {
-              x = width - fm.stringWidth(aa[gg].label) - 3;
-              g.drawString(aa[gg].label, x, y - graphExtras);
-              if (aa[gg].annotations[0] != null)
+              fontHeight = -8 + (int) h;
+              s = ((float) fontHeight) / (float) ofontH;
+              Font f = baseFont.deriveFont(AffineTransform
+                      .getScaleInstance(s, s));
+              g.setFont(f);
+              fm = g.getFontMetrics();
+              graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+            }
+          }
+          if (visible)
+          {
+            for (int gg = 0; gg < aa.length; gg++)
+            {
+              if (aa[gg].graphGroup == aa[i].graphGroup)
               {
-                g.setColor(aa[gg].annotations[0].colour);
-              }
+                x = width - fm.stringWidth(aa[gg].label) - 3;
+                g.drawString(aa[gg].label, x, y - graphExtras);
+
+                if (aa[gg]._linecolour != null)
+                {
 
-              g.drawLine(x, y - graphExtras - 3,
-                      x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+                  g.setColor(aa[gg]._linecolour);
+                  g.drawLine(x, y - graphExtras + 3,
+                          x + fm.stringWidth(aa[gg].label), y - graphExtras
+                                  + 3);
+                }
 
-              g.setColor(Color.black);
-              graphExtras += fontHeight + 8;
+                g.setColor(Color.black);
+                graphExtras += fontHeight + 8;
+              }
             }
           }
+          g.setFont(baseFont);
+          fm = baseMetrics;
+          fontHeight = ofontH;
         }
         else
         {