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JAL-1628 employ new AnnotationFile reader method to allow the current view's ColumnSe...
author
Jim Procter
<jprocter@dundee.ac.uk>
Sun, 18 Jan 2015 15:43:17 +0000
(15:43 +0000)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Sun, 18 Jan 2015 15:43:17 +0000
(15:43 +0000)
src/jalview/appletgui/CutAndPasteTransfer.java
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src/jalview/bin/JalviewLite.java
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src/jalview/gui/AlignFrame.java
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src/jalview/io/packed/ParsePackedSet.java
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diff --git
a/src/jalview/appletgui/CutAndPasteTransfer.java
b/src/jalview/appletgui/CutAndPasteTransfer.java
index
636dd7f
..
ce2a3ac
100644
(file)
--- a/
src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/
src/jalview/appletgui/CutAndPasteTransfer.java
@@
-203,8
+203,8
@@
public class CutAndPasteTransfer extends Panel implements ActionListener,
}
if (tcf == null)
{
}
if (tcf == null)
{
- if (new AnnotationFile().readAnnotationFile(
- alignFrame.viewport.getAlignment(), textarea.getText(),
+ if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+ textarea.getText(),
jalview.io.AppletFormatAdapter.PASTE))
{
alignFrame.alignPanel.fontChanged();
jalview.io.AppletFormatAdapter.PASTE))
{
alignFrame.alignPanel.fontChanged();
diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
833dd7e
..
dab649e
100644
(file)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-709,8
+709,8
@@
public class JalviewLite extends Applet implements
*/
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
*/
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
- if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
- .getAlignment(), annotation, AppletFormatAdapter.PASTE))
+ if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
+ annotation, AppletFormatAdapter.PASTE))
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
@@
-1999,8
+1999,8
@@
public class JalviewLite extends Applet implements
{
param = setProtocolState(param);
{
param = setProtocolState(param);
- if (new AnnotationFile().readAnnotationFile(
- newAlignFrame.viewport.getAlignment(), param, protocol))
+ if (new AnnotationFile().annotateAlignmentView(
+ newAlignFrame.viewport, param, protocol))
{
newAlignFrame.alignPanel.fontChanged();
newAlignFrame.alignPanel.setScrollValues(0, 0);
{
newAlignFrame.alignPanel.fontChanged();
newAlignFrame.alignPanel.setScrollValues(0, 0);
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
269e103
..
5c42418
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-5148,7
+5148,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// try to parse as annotation.
boolean isAnnotation = (format == null || format
.equalsIgnoreCase("PFAM")) ? new AnnotationFile()
// try to parse as annotation.
boolean isAnnotation = (format == null || format
.equalsIgnoreCase("PFAM")) ? new AnnotationFile()
- .readAnnotationFile(viewport.getAlignment(), file, protocol)
+ .annotateAlignmentView(viewport, file, protocol)
: false;
if (!isAnnotation)
: false;
if (!isAnnotation)
diff --git
a/src/jalview/io/packed/ParsePackedSet.java
b/src/jalview/io/packed/ParsePackedSet.java
index
df1acf1
..
8980e2c
100644
(file)
--- a/
src/jalview/io/packed/ParsePackedSet.java
+++ b/
src/jalview/io/packed/ParsePackedSet.java
@@
-123,8
+123,9
@@
public class ParsePackedSet
{
br = new BufferedReader(src.getReader());
}
{
br = new BufferedReader(src.getReader());
}
+ // TODO: add columnSelection to context
if (new jalview.io.AnnotationFile().parseAnnotationFrom(
if (new jalview.io.AnnotationFile().parseAnnotationFrom(
- context.getLastAlignment(), br))
+ context.getLastAlignment(), null, br))
{
context.updateSetModified(true);
}
{
context.updateSetModified(true);
}