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
AlignmentAnnotation[] annotations;\r
\r
- Vector sequenceGroups;\r
+ List<SequenceGroup> sequenceGroups;\r
\r
Hashtable alignmentProperties;\r
\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
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
{\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
- 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
{\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
- 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