X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=082692400d1840b605d2660f7b9a4c2aa385f6ae;hb=d83c0095dae033f5b4b7c81eb1493083b5cbe346;hp=bd46613380d4962af60dd9e75199fed036931fcb;hpb=5dc1f2c2e2827d06041127686c9f33ed1c06a31d;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index bd46613..0826924 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
@@ -18,6 +18,7 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.regex.Pattern;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
@@ -73,6 +74,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
   Font font = new Font("Arial", Font.PLAIN, 11);
 
+  private boolean hasHiddenRows;
+
   /**
    * Creates a new AnnotationLabels object.
    * 
@@ -102,8 +105,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     {
     }
 
-    BufferedImage bi = new BufferedImage(temp.getHeight(this), temp
-            .getWidth(this), BufferedImage.TYPE_INT_RGB);
+    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);
@@ -130,15 +133,23 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     repaint();
   }
 
+  /**
+   * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
+   * y
+   * 
+   * @param y
+   *          coordinate position to search for a row
+   */
   void getSelectedRow(int y)
   {
     int height = 0;
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
+    selectedRow = -2;
     if (aa != null)
     {
       for (int i = 0; i < aa.length; i++)
       {
+        selectedRow = -1;
         if (!aa[i].visible)
         {
           continue;
@@ -153,8 +164,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           break;
         }
       }
-    } else {
-      selectedRow = -1;
     }
   }
 
@@ -189,11 +198,6 @@ 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))
     {
@@ -237,9 +241,11 @@ 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);
   }
 
   /**
@@ -252,7 +258,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   {
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, "       Annotation Name ",
-            "Annotation Description ", "Edit Annotation Name/Description");
+            "Annotation Description ", "Edit Annotation Name/Description",
+            ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -300,6 +307,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       // Swap these annotations
       AlignmentAnnotation startAA = ap.av.alignment
               .getAlignmentAnnotation()[start];
+      if (end == -1)
+      {
+        end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+      }
       AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
 
       ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
@@ -394,22 +405,43 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
     {
       AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
-
-      StringBuffer desc = new StringBuffer("<html>");
-
+      
+      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());
@@ -431,17 +463,19 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
     if (SwingUtilities.isLeftMouseButton(evt))
     {
-      if (aa!=null && selectedRow < aa.length)
+      if (selectedRow > -1 && selectedRow < aa.length)
       {
         if (aa[selectedRow].groupRef != null)
         {
           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); // );
+            aa[selectedRow].groupRef); // );
             ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
           }
           else
           {
@@ -465,6 +499,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             SequenceGroup sg = new SequenceGroup();
             sg.addSequence(aa[selectedRow].sequenceRef, false);
             ap.av.setSelectionGroup(sg);
+            ap.av.sendSelection();
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
           }
@@ -480,17 +515,18 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     JPopupMenu pop = new JPopupMenu("Annotations");
     JMenuItem item = new JMenuItem(ADDNEW);
     item.addActionListener(this);
-
-    if ((aa == null) || (aa.length == 0))
+    pop.add(item);
+    if (selectedRow < 0)
     {
-      item = new JMenuItem(SHOWALL);
-      item.addActionListener(this);
-      pop.add(item);
+      if (hasHiddenRows)
+      { // let the user make everything visible again
+        item = new JMenuItem(SHOWALL);
+        item.addActionListener(this);
+        pop.add(item);
+      }
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
-
-    pop.add(item);
     item = new JMenuItem(EDITNAME);
     item.addActionListener(this);
     pop.add(item);
@@ -500,9 +536,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     item = new JMenuItem(DELETE);
     item.addActionListener(this);
     pop.add(item);
-    item = new JMenuItem(SHOWALL);
-    item.addActionListener(this);
-    pop.add(item);
+    if (hasHiddenRows)
+    {
+      item = new JMenuItem(SHOWALL);
+      item.addActionListener(this);
+      pop.add(item);
+    }
     item = new JMenuItem(OUTPUT_TEXT);
     item.addActionListener(this);
     pop.add(item);
@@ -530,8 +569,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
                 "Ignore Gaps In Consensus",
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
-                        .getIgnoreGapsConsensus()
-                        : ap.av.getIgnoreGapsConsensus());
+                        .getIgnoreGapsConsensus() : ap.av
+                        .getIgnoreGapsConsensus());
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {
@@ -554,8 +593,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  "Show Group Histogram", aa[selectedRow].groupRef
-                          .isShowConsensusHistogram());
+                  "Show Group Histogram",
+                  aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -572,10 +611,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             }
           });
           pop.add(chist);
-          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                  "Show Group Logo", aa[selectedRow].groupRef
-                          .isShowSequenceLogo());
-          cprof.addActionListener(new ActionListener()
+          final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+                  "Show Group Logo",
+                  aa[selectedRow].groupRef.isShowSequenceLogo());
+          cprofl.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
             {
@@ -585,12 +624,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // view
               // can be
               // updated.
-              aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
+              aaa.groupRef.setshowSequenceLogo(cprofl.getState());
               ap.repaint();
               // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
             }
           });
-          pop.add(cprof);
+          pop.add(cprofl);
         }
         else
         {
@@ -670,8 +709,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
             omitHidden);
 
-    Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
-            new StringSelection(output), Desktop.instance);
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+            .setContents(new StringSelection(output), Desktop.instance);
 
     Vector hiddenColumns = null;
     if (av.hasHiddenColumns)
@@ -752,12 +791,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     if (aa != null)
     {
+      hasHiddenRows = false;
       for (int i = 0; i < aa.length; i++)
       {
         g.setColor(Color.black);
 
         if (!aa[i].visible)
         {
+          hasHiddenRows = true;
           continue;
         }
 
@@ -802,8 +843,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                 g.setColor(aa[gg].annotations[0].colour);
               }
 
-              g.drawLine(x, y - graphExtras - 3, x
-                      + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+              g.drawLine(x, y - graphExtras - 3,
+                      x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
 
               g.setColor(Color.black);
               graphExtras += fontHeight + 8;
@@ -824,9 +865,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
-      g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent
-              .getY()
-              - scrollOffset);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(),
+              dragEvent.getY() - scrollOffset);
     }
 
     if ((aa == null) || (aa.length < 1))