JAL-1486 fixed flatfile output of visible region for consensus sequence

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 68d7397..b37b442 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1291,7 +1291,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return ed;
   }
 
-  private static int[] getStartEnd(int[] aligmentStartEnd,
+  public static int[] getStartEnd(int[] aligmentStartEnd,
           List<int[]> hiddenCols)
   {
     int startPos = aligmentStartEnd[0];
@@ -1303,7 +1303,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     for (int[] hiddenCol : hiddenCols)
     {
       // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
-
       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
     }

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index fad9dcd..4e625e1 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,6 +20,16 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
@@ -41,6 +51,7 @@ import java.awt.image.BufferedImage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.List;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -50,16 +61,6 @@ import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -874,8 +875,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               sq.getLength(), seqs);
     }
 
+    int[] alignmentStartEnd = new int[]
+    { 0, ds.getWidth() - 1 };
+    List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
+    if (hiddenCols != null)
+    {
+      alignmentStartEnd = AlignFrame.getStartEnd(alignmentStartEnd,
+              hiddenCols);
+    }
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
-            omitHidden, null);
+            omitHidden, alignmentStartEnd);
 
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8a563fa..63a14d7 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -108,11 +108,11 @@ public class FormatAdapter extends AppletFormatAdapter
         startRes = seqs[i].getStart();
         endRes = seqs[i].getEnd();
 
-        startIndex = startEnd[0];
-        endIndex = startEnd[1];
 
         if (startEnd != null)
         {
+          startIndex = startEnd[0];
+          endIndex = startEnd[1];
           // get first non-gaped residue start position
           while (jalview.util.Comparison.isGap(seqs[i]
                   .getCharAt(startIndex)) && startIndex < endIndex)