Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges...

[jalview.git] / src / jalview / gui / AnnotationLabels.java

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 15f1fe0..6f8b225 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -25,6 +25,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -50,9 +51,11 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -254,9 +257,7 @@ public class AnnotationLabels extends JPanel
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      new AnnotationExporter().exportAnnotations(ap,
-              new AlignmentAnnotation[]
-              { aa[selectedRow] });
+      new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
@@ -934,8 +935,9 @@ public class AnnotationLabels extends JPanel
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getAlignment().getHiddenColumns()
-              .getVisibleSequenceStrings(0, sq.getLength(), seqs);
+      Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+              .getVisContigsIterator(0, sq.getLength(), false);
+      omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
@@ -951,12 +953,12 @@ public class AnnotationLabels extends JPanel
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
 
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy();
+      hiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset