git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-1015 refactor tooltip html generation code to jalview.io.SequenceAnnotationReport
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationExporter.java
diff --git
a/src/jalview/gui/AnnotationExporter.java
b/src/jalview/gui/AnnotationExporter.java
index
a6ccc7b
..
9c6231a
100755
(executable)
--- a/
src/jalview/gui/AnnotationExporter.java
+++ b/
src/jalview/gui/AnnotationExporter.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
\r
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
\r
*
\r
* This file is part of Jalview.
\r
*
\r
*
\r
* This file is part of Jalview.
\r
*
\r
@@
-18,6
+18,7
@@
package jalview.gui;
\r
\r
import java.util.*;
\r
package jalview.gui;
\r
\r
import java.util.*;
\r
+import java.util.List;
\r
\r
import java.awt.*;
\r
import java.awt.event.*;
\r
\r
import java.awt.*;
\r
import java.awt.event.*;
\r
@@
-44,7
+45,7
@@
public class AnnotationExporter extends JPanel
\r
AlignmentAnnotation[] annotations;
\r
\r
\r
AlignmentAnnotation[] annotations;
\r
\r
- Vector sequenceGroups;
\r
+ List<SequenceGroup> sequenceGroups;
\r
\r
Hashtable alignmentProperties;
\r
\r
\r
Hashtable alignmentProperties;
\r
\r
@@
-73,7
+74,7
@@
public class AnnotationExporter extends JPanel
}
\r
\r
public void exportAnnotations(AlignmentPanel ap,
\r
}
\r
\r
public void exportAnnotations(AlignmentPanel ap,
\r
- AlignmentAnnotation[] annotations, Vector sequenceGroups,
\r
+ AlignmentAnnotation[] annotations, List<SequenceGroup> list,
\r
Hashtable alProperties)
\r
{
\r
this.ap = ap;
\r
Hashtable alProperties)
\r
{
\r
this.ap = ap;
\r
@@
-81,7
+82,7
@@
public class AnnotationExporter extends JPanel
GFFFormat.setVisible(false);
\r
CSVFormat.setVisible(true);
\r
this.annotations = annotations;
\r
GFFFormat.setVisible(false);
\r
CSVFormat.setVisible(true);
\r
this.annotations = annotations;
\r
- this.sequenceGroups = sequenceGroups;
\r
+ this.sequenceGroups = list;
\r
this.alignmentProperties = alProperties;
\r
frame.setTitle("Export Annotations");
\r
}
\r
this.alignmentProperties = alProperties;
\r
frame.setTitle("Export Annotations");
\r
}
\r
@@
-105,13
+106,13
@@
public class AnnotationExporter extends JPanel
{
\r
if (GFFFormat.isSelected())
\r
{
\r
{
\r
if (GFFFormat.isSelected())
\r
{
\r
- text = new FeaturesFile().printGFFFormat(ap.av.alignment
\r
+ text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
\r
.getDataset().getSequencesArray(),
\r
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
\r
}
\r
else
\r
{
\r
.getDataset().getSequencesArray(),
\r
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
\r
}
\r
else
\r
{
\r
- text = new FeaturesFile().printJalviewFormat(ap.av.alignment
\r
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
\r
.getDataset().getSequencesArray(),
\r
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
\r
}
\r
.getDataset().getSequencesArray(),
\r
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
\r
}
\r
@@
-152,13
+153,13
@@
public class AnnotationExporter extends JPanel
{
\r
if (GFFFormat.isSelected())
\r
{
\r
{
\r
if (GFFFormat.isSelected())
\r
{
\r
- text = new FeaturesFile().printGFFFormat(ap.av.alignment
\r
+ text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
\r
.getDataset().getSequencesArray(),
\r
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
\r
}
\r
else
\r
{
\r
.getDataset().getSequencesArray(),
\r
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
\r
}
\r
else
\r
{
\r
- text = new FeaturesFile().printJalviewFormat(ap.av.alignment
\r
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
\r
.getDataset().getSequencesArray(),
\r
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
\r
}
\r
.getDataset().getSequencesArray(),
\r
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
\r
}
\r