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JAL-1078 - extend applet cut'n'paste features/annotation to support t-coffee file
[jalview.git]
/
src
/
jalview
/
appletgui
/
AnnotationLabels.java
diff --git
a/src/jalview/appletgui/AnnotationLabels.java
b/src/jalview/appletgui/AnnotationLabels.java
index
5140024
..
635535c
100755
(executable)
--- a/
src/jalview/appletgui/AnnotationLabels.java
+++ b/
src/jalview/appletgui/AnnotationLabels.java
@@
-1,6
+1,6
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-107,7
+107,7
@@
public class AnnotationLabels extends Panel implements ActionListener,
int getSelectedRow(int y)
{
int row = -2;
int getSelectedRow(int y)
{
int row = -2;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
if (aa == null)
{
@@
-134,20
+134,20
@@
public class AnnotationLabels extends Panel implements ActionListener,
public void actionPerformed(ActionEvent evt)
{
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,
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;
}
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))
{
}
else if (evt.getActionCommand().equals(EDITNAME))
{
@@
-228,7
+228,7
@@
public class AnnotationLabels extends Panel implements ActionListener,
if (row > -1)
{
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);
if (tooltip == null)
{
tooltip = new Tooltip(phb.getNonHtmlContent(), this);
@@
-337,17
+337,17
@@
public class AnnotationLabels extends Panel implements ActionListener,
if (start>-1 && start != end)
{
// Swap these annotations
if (start>-1 && start != end)
{
// Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment
+ AlignmentAnnotation startAA = ap.av.getAlignment()
.getAlignmentAnnotation()[start];
if (end == -1)
{
.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];
.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;
}
}
resizePanel = false;
@@
-395,7
+395,7
@@
public class AnnotationLabels extends Panel implements ActionListener,
// todo: move below to mouseClicked ?
selectedRow = getSelectedRow(evt.getY() + scrollOffset);
// 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)
// DETECT RIGHT MOUSE BUTTON IN AWT
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
@@
-622,7
+622,7
@@
public class AnnotationLabels extends Panel implements ActionListener,
jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+ sq.getStart() + "\t" + sq.getEnd() + "\t"
+ sq.getSequenceAsString() + "\n");
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++)
{
jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
@@
-665,7
+665,7
@@
public class AnnotationLabels extends Panel implements ActionListener,
g.translate(0, -scrollOffset);
g.setColor(Color.black);
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;
int y = 0, fy = g.getFont().getSize();
int x = 0, offset;