JAL-2054 Renamed getStartEnd in AlignFrame to getVisibleStartAndEndIndex, and refacto...

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d1ea70d..a9b0d53 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1793,4 +1793,40 @@ public class Alignment implements AlignmentI
     }
     return null;
   }
+
+  @Override
+  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+  {
+    int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
+    int startPos = alignmentStartEnd[0];
+    int endPos = alignmentStartEnd[1];
+
+    int[] lowestRange = new int[] { -1, -1 };
+    int[] higestRange = new int[] { -1, -1 };
+
+    for (int[] hiddenCol : hiddenCols)
+    {
+      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+    }
+
+    if (lowestRange[0] == -1 && lowestRange[1] == -1)
+    {
+      startPos = alignmentStartEnd[0];
+    }
+    else
+    {
+      startPos = lowestRange[1] + 1;
+    }
+
+    if (higestRange[0] == -1 && higestRange[1] == -1)
+    {
+      endPos = alignmentStartEnd[1];
+    }
+    else
+    {
+      endPos = higestRange[0] - 1;
+    }
+    return new int[] { startPos, endPos };
+  }
 }

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 396ef2d..76d1a48 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -543,4 +543,13 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+
+  /**
+   * Calculate the visible start and end index of an alignment. The result is
+   * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+   * 
+   * @param hiddenCols
+   * @return
+   */
+  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d1f3421..cb769bb 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1276,13 +1276,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentI alignmentToExport = null;
     AlignExportSettingI settings = exportSettings;
     String[] omitHidden = null;
-    int[] alignmentStartEnd = new int[2];
 
     HiddenSequences hiddenSeqs = viewport.getAlignment()
             .getHiddenSequences();
 
     alignmentToExport = viewport.getAlignment();
-    alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
 
     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
     if (settings == null)
@@ -1297,6 +1295,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       omitHidden = viewport.getViewAsString(false);
     }
 
+    int[] alignmentStartEnd = new int[2];
     if (hasHiddenSeqs && settings.isExportHiddenSequences())
     {
       alignmentToExport = hiddenSeqs.getFullAlignment();
@@ -1304,7 +1303,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       alignmentToExport = viewport.getAlignment();
-      alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+      alignmentStartEnd = viewport.getAlignment()
+              .getVisibleStartAndEndIndex(
+                      viewport
               .getColumnSelection().getHiddenColumns());
     }
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
@@ -1312,55 +1313,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return ed;
   }
 
-  public static int[] getStartEnd(int[] aligmentStartEnd,
-          List<int[]> hiddenCols)
-  {
-    int startPos = aligmentStartEnd[0];
-    int endPos = aligmentStartEnd[1];
-
-    int[] lowestRange = new int[] { -1, -1 };
-    int[] higestRange = new int[] { -1, -1 };
-
-    for (int[] hiddenCol : hiddenCols)
-    {
-      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
-      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
-    }
-
-    if (lowestRange[0] == -1 && lowestRange[1] == -1)
-    {
-      startPos = aligmentStartEnd[0];
-    }
-    else
-    {
-      startPos = lowestRange[1] + 1;
-    }
-
-    if (higestRange[0] == -1 && higestRange[1] == -1)
-    {
-      endPos = aligmentStartEnd[1];
-    }
-    else
-    {
-      endPos = higestRange[0] - 1;
-    }
-
-    // System.out.println("Export range : " + startPos + " - " + endPos);
-    return new int[] { startPos, endPos };
-  }
-
-  public static void main(String[] args)
-  {
-    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
-    hiddenCols.add(new int[] { 0, 0 });
-    hiddenCols.add(new int[] { 6, 9 });
-    hiddenCols.add(new int[] { 11, 12 });
-    hiddenCols.add(new int[] { 33, 33 });
-    hiddenCols.add(new int[] { 50, 50 });
-
-    int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
-    // System.out.println("Export range : " + x[0] + " - " + x[1]);
-  }
 
   /**
    * DOCUMENT ME!

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index d4300e4..3105ab9 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -213,6 +213,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     AlignmentAnnotation[] aa = ap.av.getAlignment()
@@ -331,6 +332,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     getSelectedRow(evt.getY() - getScrollOffset());
@@ -343,6 +345,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     int start = selectedRow;
@@ -377,6 +380,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
     if (evt.getY() < 10)
@@ -392,6 +396,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseExited(MouseEvent evt)
   {
     if (dragEvent == null)
@@ -407,6 +412,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     dragEvent = evt;
@@ -443,6 +449,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     resizePanel = evt.getY() < 10;
@@ -527,6 +534,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
     final AlignmentAnnotation[] aa = ap.av.getAlignment()
@@ -711,6 +719,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             if (aaa.groupRef != null)
@@ -735,6 +744,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -754,6 +764,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   aa[selectedRow].groupRef.isShowSequenceLogo());
           cprofl.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -773,6 +784,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   aa[selectedRow].groupRef.isNormaliseSequenceLogo());
           cproflnorm.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
 
@@ -798,6 +810,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   av.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -818,6 +831,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   av.isShowSequenceLogo());
           cprof.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -838,6 +852,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   av.isNormaliseSequenceLogo());
           cprofnorm.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -893,7 +908,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
     if (hiddenCols != null)
     {
-      alignmentStartEnd = AlignFrame.getStartEnd(alignmentStartEnd,
+      alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
               hiddenCols);
     }
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
@@ -926,6 +941,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param g1
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
 

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index bd445c4..5a45176 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -32,6 +32,7 @@ import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
@@ -474,4 +475,33 @@ public class AlignmentTest
     align.addCodonFrame(acf2);
     assertTrue(align.getDataset().getCodonFrames().contains(acf));
   }
+
+  @Test(groups = "Functional")
+  public void getVisibleStartAndEndIndexTest()
+  {
+    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+    AlignmentI align = new Alignment(new SequenceI[] { seq });
+    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
+
+    int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
+    assertEquals(0, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hiddenCols.add(new int[] { 0, 0 });
+    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
+    assertEquals(1, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hiddenCols.add(new int[] { 6, 9 });
+    hiddenCols.add(new int[] { 11, 12 });
+    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
+    assertEquals(1, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hiddenCols.add(new int[] { 24, 25 });
+    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
+    System.out.println(startEnd[0] + " : " + startEnd[1]);
+    assertEquals(1, startEnd[0]);
+    assertEquals(23, startEnd[1]);
+  }
 }