X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=a286e0685004b7fc3885a83da4fedbf3239d7761;hb=3b4233b78bba3c53c98fc9b9166b267e5b744411;hp=e383e9d15641d616ace5563299d5601950daea63;hpb=2e5393f81c78a3bb60a99f6e7eaa075d993c8eaa;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index e383e9d..a286e06 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,19 +1,22 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
- *
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
@@ -21,9 +24,9 @@ import java.util.*;
import java.awt.*;
import java.awt.event.*;
-import java.awt.image.BufferedImage;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
import jalview.util.ParseHtmlBodyAndLinks;
public class AnnotationLabels extends Panel implements ActionListener,
@@ -92,10 +95,13 @@ public class AnnotationLabels extends Panel implements ActionListener,
this.av = av;
}
- public void setScrollOffset(int y)
+ public void setScrollOffset(int y, boolean repaint)
{
scrollOffset = y;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
/**
@@ -107,7 +113,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
int getSelectedRow(int y)
{
int row = -2;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (aa == null)
{
@@ -134,20 +141,20 @@ public class AnnotationLabels extends Panel implements ActionListener,
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
- new Annotation[ap.av.alignment.getWidth()]);
+ 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))
{
@@ -228,7 +235,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
if (row > -1)
{
- ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(av.alignment.getAlignmentAnnotation()[row].getDescription(true), true, "\n");
+ ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+ av.getAlignment().getAlignmentAnnotation()[row]
+ .getDescription(true),
+ true, "\n");
if (tooltip == null)
{
tooltip = new Tooltip(phb.getNonHtmlContent(), this);
@@ -290,7 +300,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
- dif));
ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
- ap.annotationPanel.calcPanelHeight());
+ av.calcPanelHeight());
f.height += dif;
ap.seqPanelHolder.setPreferredSize(f);
ap.setScrollValues(av.getStartRes(), av.getStartSeq());
@@ -334,20 +344,20 @@ public class AnnotationLabels extends Panel implements ActionListener,
int end = getSelectedRow(evt.getY() + scrollOffset);
- if (start>-1 && start != end)
+ if (start > -1 && 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
+ 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;
@@ -391,17 +401,19 @@ public class AnnotationLabels extends Panel implements ActionListener,
{
return;
}
- dragCancelled=false;
+ dragCancelled = false;
// todo: move below to mouseClicked ?
selectedRow = getSelectedRow(evt.getY() + scrollOffset);
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- PopupMenu popup = new PopupMenu("Annotations");
+ PopupMenu popup = new PopupMenu(
+ MessageManager.getString("label.annotations"));
MenuItem item = new MenuItem(ADDNEW);
item.addActionListener(this);
@@ -505,7 +517,28 @@ public class AnnotationLabels extends Panel implements ActionListener,
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
+
popup.add(cprofl);
+ final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+ "Normalise Group Logo",
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cprofn.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(true);
+ aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprofn);
}
else
{
@@ -522,6 +555,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
// can be
// updated.
av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.showConsensusHistogram.setState(chist
+ .getState()); // TODO: implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for applet
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
@@ -540,11 +577,40 @@ public class AnnotationLabels extends Panel implements ActionListener,
// can be
// updated.
av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
popup.add(cprof);
+ final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+ "Normalise Logo", av.isNormaliseSequenceLogo());
+ cprofn.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
+ av.setNormaliseSequenceLogo(cprofn.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprofn);
}
item = new MenuItem(COPYCONS_SEQ);
@@ -622,7 +688,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+ sq.getStart() + "\t" + sq.getEnd() + "\t"
+ sq.getSequenceAsString() + "\n");
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
@@ -646,7 +712,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
{
int w = getSize().width;
int h = getSize().height;
- if (image == null || w != image.getWidth(this) || h!=image.getHeight(this) )
+ if (image == null || w != image.getWidth(this)
+ || h != image.getHeight(this))
{
image = createImage(w, ap.annotationPanel.getSize().height);
}
@@ -665,7 +732,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
g.translate(0, -scrollOffset);
g.setColor(Color.black);
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int y = 0, fy = g.getFont().getSize();
int x = 0, offset;
@@ -703,11 +770,12 @@ public class AnnotationLabels extends Panel implements ActionListener,
dragEvent.getY());
}
- if ((aa == null) || (aa.length < 1))
+ if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
{
g.setColor(Color.black);
- g.drawString("Right click", 2, 8);
- g.drawString("to add annotation", 2, 18);
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
}
}
}