X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=7967ae63cd2e4a34fdec448120ef0f67ee0ed049;hb=57c960648b550f10c7db40e39c7bb6a761d732b1;hp=b8c81ce0d592139aeee3a40a308319fc6398f453;hpb=ecb2c593fb296f6908deb65492835fac476b2378;p=jalview.git
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index b8c81ce..7967ae6 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,6 +1,6 @@
/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.*;
@@ -58,7 +59,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
Image image;
AlignmentPanel ap;
-
+
AlignViewport av;
boolean resizing = false;
@@ -404,22 +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("");
-
+
+ StringBuffer desc = new StringBuffer();
if (aa.description != null
&& !aa.description.equals("New description"))
{
- desc.append(aa.getDescription(true));
- if (aa.hasScore)
- desc.append("
");
+ // 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("")<0))
+ {
+ // clean the description ready for embedding in html
+ desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("<"));
+ desc.insert(0, "");
+ } else {
+ // remove terminating html if any
+ int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf("");
+ if (i>-1) {
+ desc.setLength(desc.length()-7+i);
+ }
+ }
+ if (aa.hasScore())
+ {
+ desc.append("
");
+ }
+
+
+ } else {
+ // begin the tooltip's html fragment
+ desc.append("");
}
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("");
this.setToolTipText(desc.toString());
@@ -439,7 +461,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
public void mouseClicked(MouseEvent evt)
{
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
if (SwingUtilities.isLeftMouseButton(evt))
{
if (selectedRow > -1 && selectedRow < aa.length)
@@ -495,7 +516,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
-
if (selectedRow < 0)
{
if (hasHiddenRows)
@@ -610,6 +630,28 @@ 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
{
@@ -626,6 +668,7 @@ 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());
}
@@ -644,11 +687,32 @@ 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);