JAL-1488 bug-fix for incorrect start/end position in flatfiles exported from alignmen...

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ad2bbc3..6481855 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1126,7 +1126,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       String output = f.formatSequences(format,
               exportData.getAlignment(), // class cast exceptions will
               // occur in the distant future
-              exportData.getOmitHidden(), f.getCacheSuffixDefault(format),
+              exportData.getOmitHidden(), exportData.getStartEndPostions(),
+              f.getCacheSuffixDefault(format),
               viewport.getColumnSelection());
 
       if (output == null)
@@ -1202,7 +1203,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       cap.setText(new FormatAdapter(viewport).formatSequences(
               e.getActionCommand(),
  exportData.getAlignment(),
-              exportData.getOmitHidden(),
+              exportData.getOmitHidden(), exportData.getStartEndPostions(),
               viewport.getColumnSelection()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
               "label.alignment_output_command", new Object[]
@@ -1219,10 +1220,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
+    int[] alignmentStartEnd = new int[2];
     FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
     viewport.setFeatureRenderer(fr);
     HiddenSequences hiddenSeqs = viewport.getAlignment()
             .getHiddenSequences();
+
+
+    alignmentToExport = viewport.getAlignment();
+    alignmentStartEnd = new int[]
+    { 0, alignmentToExport.getWidth() - 1 };
+
     if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
     {
       int reply = JOptionPane
@@ -1237,19 +1245,81 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (reply == JOptionPane.YES_OPTION)
       {
+        // export only visible region
         omitHidden = viewport.getViewAsString(false);
+        alignmentToExport = viewport.getAlignment();
+        alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+                .getColumnSelection().getHiddenColumns());
       }
       else
       {
-        alignmentToExport = viewport.getAlignment().getHiddenSequences()
-                .getFullAlignment();
+        // export all region including visible
+        alignmentToExport = hiddenSeqs.getFullAlignment();
       }
     }
-    if (alignmentToExport == null)
+
+    return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
+  }
+
+  private static int[] getStartEnd(int[] aligmentStartEnd,
+          List<int[]> hiddenCols)
+  {
+    int startPos = aligmentStartEnd[0];
+    int endPos = aligmentStartEnd[1];
+
+    int[] lowestRange = new int[2];
+    int[] higestRange = new int[2];
+
+    for (int[] hiddenCol : hiddenCols)
+    {
+      // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
+
+      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+    }
+    // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
+    // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
+
+    if (lowestRange[0] == 0 && lowestRange[1] == 0)
+    {
+      startPos = aligmentStartEnd[0];
+    }
+    else
+    {
+      startPos = lowestRange[1] + 1;
+    }
+
+    if (higestRange[0] == 0 && higestRange[1] == 0)
+    {
+      endPos = aligmentStartEnd[1];
+    }
+    else
     {
-      alignmentToExport = viewport.getAlignment();
+      endPos = higestRange[0];
     }
-    return new ExportData(alignmentToExport, omitHidden);
+
+    // System.out.println("Export range : " + minPos + " - " + maxPos);
+    return new int[]
+    { startPos, endPos };
+  }
+
+  public static void main(String[] args)
+  {
+    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
+    hiddenCols.add(new int[]
+    { 0, 4 });
+    hiddenCols.add(new int[]
+    { 6, 9 });
+    hiddenCols.add(new int[]
+    { 11, 12 });
+    hiddenCols.add(new int[]
+    { 33, 33 });
+    hiddenCols.add(new int[]
+    { 45, 50 });
+
+    int[] x = getStartEnd(new int[]
+    { 0, 50 }, hiddenCols);
+    // System.out.println("Export range : " + x[0] + " - " + x[1]);
   }
 
   /**
@@ -1776,7 +1846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
-            omitHidden);
+            omitHidden, null);
 
     StringSelection ss = new StringSelection(output);
 
@@ -6001,11 +6071,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     private String[] omitHidden;
 
-    public ExportData(AlignmentI align, String[] ommit)
+    private int[] startEnd;
+
+    public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
     {
       this.alignment = align;
       this.omitHidden = ommit;
-      System.out.println();
+      this.startEnd = startEnd;
     }
 
     public AlignmentI getAlignment()
@@ -6027,6 +6099,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       this.omitHidden = omitHidden;
     }
+
+    public int[] getStartEndPostions()
+    {
+      return startEnd;
+    }
+
+    public void setStartEndPostions(int[] startEnd)
+    {
+      this.startEnd = startEnd;
+    }
   }
 
   @Override

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index a544813..fad9dcd 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -875,7 +875,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     }
 
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
-            omitHidden);
+            omitHidden, null);
 
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 7c117b9..d241308 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -70,10 +70,11 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   public String formatSequences(String format, SequenceI[] seqs,
-          String[] omitHiddenColumns)
+          String[] omitHiddenColumns, int[] exportRange)
   {
 
-    return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+    return formatSequences(format,
+            replaceStrings(seqs, omitHiddenColumns, exportRange));
   }
 
   /**
@@ -85,15 +86,48 @@ public class FormatAdapter extends AppletFormatAdapter
    * @return new sequences
    */
   public SequenceI[] replaceStrings(SequenceI[] seqs,
-          String[] omitHiddenColumns)
+          String[] omitHiddenColumns, int[] startEnd)
   {
     if (omitHiddenColumns != null)
     {
       SequenceI[] tmp = new SequenceI[seqs.length];
+
+      int startRes;
+      int endRes;
+      int startIndex;
+      int endIndex;
       for (int i = 0; i < seqs.length; i++)
       {
+        startRes = seqs[i].getStart();
+        endRes = seqs[i].getEnd();
+
+        startIndex = startEnd[0];
+        endIndex = startEnd[1];
+
+        if (startEnd != null)
+        {
+          // get first non-gaped residue start position
+          while (jalview.util.Comparison.isGap(seqs[i]
+                  .getCharAt(startIndex)) && startIndex < endIndex)
+          {
+            startIndex++;
+          }
+
+          // get last non-gaped residue end position
+          while (jalview.util.Comparison.isGap(seqs[i].getCharAt(endIndex))
+                  && endIndex > startIndex)
+          {
+            endIndex--;
+          }
+
+          startRes = seqs[i].findPosition(startIndex);
+          startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
+                  : startRes;
+          endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+        }
+
         tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
-                seqs[i].getStart(), seqs[i].getEnd());
+                startRes, endRes);
         tmp[i].setDescription(seqs[i].getDescription());
       }
       seqs = tmp;
@@ -199,16 +233,17 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, ColumnSelection colSel)
+          String[] omitHidden, int[] exportRange, ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden,
+    return formatSequences(format, alignment, omitHidden, exportRange,
             getCacheSuffixDefault(format), colSel, null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
+          String[] omitHidden, int[] exportRange, ColumnSelection colSel,
+          SequenceGroup sgp)
   {
-    return formatSequences(format, alignment, omitHidden,
+    return formatSequences(format, alignment, omitHidden, exportRange,
             getCacheSuffixDefault(format), colSel, sgp);
   }
 
@@ -225,14 +260,17 @@ public class FormatAdapter extends AppletFormatAdapter
    * @return string representation of the alignment formatted as format
    */
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, boolean suffix, ColumnSelection colSel)
+          String[] omitHidden, int[] exportRange, boolean suffix,
+          ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden, suffix, colSel,
+    return formatSequences(format, alignment, omitHidden, exportRange,
+            suffix, colSel,
             null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, boolean suffix, ColumnSelection colSel,
+          String[] omitHidden, int[] exportRange, boolean suffix,
+          ColumnSelection colSel,
           jalview.datamodel.SequenceGroup selgp)
   {
     if (omitHidden != null)
@@ -242,7 +280,7 @@ public class FormatAdapter extends AppletFormatAdapter
       // TODO: JAL-1486 - set start and end for output correctly. basically,
       // AlignmentView.getVisibleContigs does this.
       Alignment alv = new Alignment(replaceStrings(
-              alignment.getSequencesArray(), omitHidden));
+              alignment.getSequencesArray(), omitHidden, exportRange));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
       if (ala != null)
       {