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JAL-2668 add tests for HMMER commands, annotation and io
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationExporter.java
diff --git
a/src/jalview/gui/AnnotationExporter.java
b/src/jalview/gui/AnnotationExporter.java
index
d688ddd
..
0d47e36
100644
(file)
--- a/
src/jalview/gui/AnnotationExporter.java
+++ b/
src/jalview/gui/AnnotationExporter.java
@@
-20,6
+20,7
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
@@
-155,18
+156,26
@@
public class AnnotationExporter extends JPanel
.getString("label.no_features_on_alignment");
if (features)
{
.getString("label.no_features_on_alignment");
if (features)
{
+ Map<String, FeatureColourI> displayedFeatureColours = ap
+ .getFeatureRenderer().getDisplayedFeatureCols();
FeaturesFile formatter = new FeaturesFile();
SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
FeaturesFile formatter = new FeaturesFile();
SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
- Map<String, Object> featureColours = ap.getFeatureRenderer()
+ Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
.getDisplayedFeatureCols();
boolean includeNonPositional = ap.av.isShowNPFeats();
if (GFFFormat.isSelected())
{
.getDisplayedFeatureCols();
boolean includeNonPositional = ap.av.isShowNPFeats();
if (GFFFormat.isSelected())
{
+ text = new FeaturesFile().printGffFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(), displayedFeatureColours,
+ true, ap.av.isShowNPFeats());
text = formatter.printGffFormat(sequences, featureColours, true,
includeNonPositional);
}
else
{
text = formatter.printGffFormat(sequences, featureColours, true,
includeNonPositional);
}
else
{
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(), displayedFeatureColours,
+ true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
text = formatter.printJalviewFormat(sequences, featureColours,
true, includeNonPositional);
}
text = formatter.printJalviewFormat(sequences, featureColours,
true, includeNonPositional);
}