X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=be4f9e63e30f27afc99f8be969a54c2838bc8f5d;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=2d2e3fdc06cda4a1ffcd14d490caabcbe5639769;hpb=1499d3297cf70ff34df05362449dbf36873c5bc1;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 2d2e3fd..be4f9e6 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -54,6 +54,10 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.ListIterator;
 import java.util.Vector;
 
 public class SeqPanel extends Panel implements MouseMotionListener,
@@ -130,8 +134,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (editCommand != null && editCommand.getSize() > 0)
     {
       ap.alignFrame.addHistoryItem(editCommand);
-      av.firePropertyChange("alignment", null, av.getAlignment()
-              .getSequences());
+      av.firePropertyChange("alignment", null,
+              av.getAlignment().getSequences());
     }
 
     startseq = -1;
@@ -181,23 +185,21 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
-    if (av.hasHiddenColumns()
-            && !av.getAlignment().getHiddenColumns()
-                    .isVisible(seqCanvas.cursorX))
+    if (av.hasHiddenColumns() && !av.getAlignment().getHiddenColumns()
+            .isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
       while (!av.getAlignment().getHiddenColumns()
-              .isVisible(seqCanvas.cursorX)
-              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+              .isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth
+              && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
-      if (seqCanvas.cursorX >= maxWidth
-              || !av.getAlignment().getHiddenColumns()
-                      .isVisible(seqCanvas.cursorX))
+      if (seqCanvas.cursorX >= maxWidth || !av.getAlignment()
+              .getHiddenColumns().isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -228,7 +230,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     endEditing();
     if (av.getWrapAlignment())
     {
-      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+      av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
     }
     else
     {
@@ -236,25 +238,25 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       while (seqCanvas.cursorY < ranges.getStartSeq())
       {
-        ap.scrollUp(true);
+        ranges.scrollUp(true);
       }
       while (seqCanvas.cursorY > ranges.getEndSeq())
       {
-        ap.scrollUp(false);
+        ranges.scrollUp(false);
       }
-      while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges
-              .getStartRes()))
+      while (seqCanvas.cursorX < hidden
+              .adjustForHiddenColumns(ranges.getStartRes()))
       {
 
-        if (!ap.scrollRight(false))
+        if (!ranges.scrollRight(false))
         {
           break;
         }
       }
-      while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges
-              .getEndRes()))
+      while (seqCanvas.cursorX > hidden
+              .adjustForHiddenColumns(ranges.getEndRes()))
       {
-        if (!ap.scrollRight(true))
+        if (!ranges.scrollRight(true))
         {
           break;
         }
@@ -441,9 +443,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
-              .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
-              .get(displayChar));
+      residue = "X".equalsIgnoreCase(displayChar) ? "X"
+              : ("*".equals(displayChar) ? "STOP"
+                      : ResidueProperties.aa2Triplet.get(displayChar));
       if (residue != null)
       {
         text.append(" Residue: ").append(residue);
@@ -505,7 +507,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     // For now, ignore the mouseWheel font resizing on Macs
     // As the Button2_mask always seems to be true
-    if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
+    if ((evt.getModifiers()
+            & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
             && !av.MAC)
     {
       mouseWheelPressed = true;
@@ -563,20 +566,23 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(sequence,
-              sequence.findPosition(findRes(evt)));
+      int column = findRes(evt);
+      boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+      List<SequenceFeature> features = findFeaturesAtRes(sequence,
+              sequence.findPosition(column));
+      if (isGapped)
+      {
+        removeAdjacentFeatures(features, column + 1, sequence);
+      }
 
-      if (features != null && features.length > 0)
+      if (!features.isEmpty())
       {
         SearchResultsI highlight = new SearchResults();
-        highlight.addResult(sequence, features[0].getBegin(),
-                features[0].getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(),
+                features.get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
-      }
-      if (features != null && features.length > 0)
-      {
         seqCanvas.getFeatureRenderer().amendFeatures(
-                new SequenceI[] { sequence }, features, false, ap);
+                Collections.singletonList(sequence), features, false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -586,13 +592,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    boolean didDrag = mouseDragging; // did we come here after a drag
     mouseDragging = false;
     mouseWheelPressed = false;
-    ap.paintAlignment(true);
 
     if (!editingSeqs)
     {
-      doMouseReleasedDefineMode(evt);
+      doMouseReleasedDefineMode(evt, didDrag);
       return;
     }
 
@@ -609,6 +615,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     int res = 0;
     int x = evt.getX();
 
+    int startRes = av.getRanges().getStartRes();
     if (av.getWrapAlignment())
     {
 
@@ -623,7 +630,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       int y = evt.getY();
       y -= hgap;
-      x -= seqCanvas.LABEL_WEST;
+      x = Math.max(0, x - seqCanvas.LABEL_WEST);
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
       if (cwidth < 1)
@@ -632,14 +639,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getRanges().getStartRes() / cwidth;
-
-      res = wrappedBlock * cwidth + x / av.getCharWidth();
-
+      wrappedBlock += startRes / cwidth;
+      int startOffset = startRes % cwidth; // in case start is scrolled right
+                                           // from 0
+      res = wrappedBlock * cwidth + startOffset
+              + +Math.min(cwidth - 1, x / av.getCharWidth());
     }
     else
     {
-      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+      res = (x / av.getCharWidth()) + startRes;
     }
 
     if (av.hasHiddenColumns())
@@ -681,8 +689,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       y -= hgap;
 
-      seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
-              .getHeight() - 1);
+      seq = Math.min((y % cHeight) / av.getCharHeight(),
+              av.getAlignment().getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -690,10 +698,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight())
-              + av.getRanges().getStartSeq(),
-              av
-              .getAlignment().getHeight() - 1);
+      seq = Math.min(
+              (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
+              av.getAlignment().getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -747,10 +754,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (av.isFollowHighlight())
     {
+      // don't allow highlight of protein/cDNA to also scroll a complementary
+      // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+      // over residue to change abruptly, causing highlighted residue in panel 2
+      // to change, causing a scroll in panel 1 etc)
+      ap.setToScrollComplementPanel(false);
       if (ap.scrollToPosition(results, true))
       {
         ap.alignFrame.repaint();
       }
+      ap.setToScrollComplementPanel(true);
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);
@@ -796,9 +809,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     final char ch = sequence.getCharAt(column);
-    int respos = Comparison.isGap(ch) ? -1 : sequence.findPosition(column);
+    boolean isGapped = Comparison.isGap(ch);
+    // find residue at column (or nearest if at a gap)
+    int respos = sequence.findPosition(column);
 
-    if (ssm != null && respos != -1)
+    if (ssm != null && !isGapped)
     {
       mouseOverSequence(sequence, column, respos);
     }
@@ -807,30 +822,20 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     text.append("Sequence ").append(Integer.toString(seq + 1))
             .append(" ID: ").append(sequence.getName());
 
-    String obj = null;
-    if (respos != -1)
+    if (!isGapped)
     {
       if (av.getAlignment().isNucleotide())
       {
-        obj = ResidueProperties.nucleotideName.get(ch);
-        if (obj != null)
-        {
-          text.append(" Nucleotide: ").append(obj);
-        }
+        String base = ResidueProperties.nucleotideName.get(ch);
+        text.append(" Nucleotide: ").append(base == null ? ch : base);
       }
       else
       {
-        obj = (ch == 'x' || ch == 'X') ? "X" : ResidueProperties.aa2Triplet
-                .get(String.valueOf(ch));
-        if (obj != null)
-        {
-          text.append(" Residue: ").append(obj);
-        }
-      }
-      if (obj != null)
-      {
-        text.append(" (").append(Integer.toString(respos)).append(")");
+        String residue = (ch == 'x' || ch == 'X') ? "X"
+                : ResidueProperties.aa2Triplet.get(String.valueOf(ch));
+        text.append(" Residue: ").append(residue == null ? ch : residue);
       }
+      text.append(" (").append(Integer.toString(respos)).append(")");
     }
 
     ap.alignFrame.statusBar.setText(text.toString());
@@ -841,7 +846,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       for (int g = 0; g < groups.length; g++)
       {
-        if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column)
+        if (groups[g].getStartRes() <= column
+                && groups[g].getEndRes() >= column)
         {
           if (!groups[g].getName().startsWith("JTreeGroup")
                   && !groups[g].getName().startsWith("JGroup"))
@@ -858,18 +864,19 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     /*
-     * add feature details to tooltip if over one or more features
+     * add feature details to tooltip, including any that straddle
+     * a gapped position
      */
-    if (respos != -1)
+    if (av.isShowSequenceFeatures())
     {
-      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+      List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
               sequence.findPosition(column));
-
-      int index = 0;
-      while (index < allFeatures.length)
+      if (isGapped)
+      {
+        removeAdjacentFeatures(allFeatures, column + 1, sequence);
+      }
+      for (SequenceFeature sf : allFeatures)
       {
-        SequenceFeature sf = allFeatures[index];
-
         tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
 
         if (sf.getDescription() != null)
@@ -886,8 +893,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           }
         }
         tooltipText.append("\n");
-
-        index++;
       }
     }
 
@@ -901,24 +906,51 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
-  SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+  /**
+   * Removes from the list of features any that start after, or end before, the
+   * given column position. This allows us to retain only those features
+   * adjacent to a gapped position that straddle the position. Contact features
+   * that 'straddle' the position are also removed, since they are not 'at' the
+   * position.
+   * 
+   * @param features
+   * @param column
+   *          alignment column (1..)
+   * @param sequence
+   */
+  protected void removeAdjacentFeatures(List<SequenceFeature> features,
+          int column, SequenceI sequence)
+  {
+    // TODO should this be an AlignViewController method (shared by gui)?
+    ListIterator<SequenceFeature> it = features.listIterator();
+    while (it.hasNext())
+    {
+      SequenceFeature sf = it.next();
+      if (sf.isContactFeature()
+              || sequence.findIndex(sf.getBegin()) > column
+              || sequence.findIndex(sf.getEnd()) < column)
+      {
+        it.remove();
+      }
+    }
+  }
+
+  List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
   {
-    Vector tmp = new Vector();
+    List<SequenceFeature> result = new ArrayList<>();
     SequenceFeature[] features = sequence.getSequenceFeatures();
     if (features != null)
     {
       for (int i = 0; i < features.length; i++)
       {
-        if (av.getFeaturesDisplayed() == null
-                || !av.getFeaturesDisplayed().isVisible(
-                        features[i].getType()))
+        if (av.getFeaturesDisplayed() == null || !av.getFeaturesDisplayed()
+                .isVisible(features[i].getType()))
         {
           continue;
         }
 
-        if (features[i].featureGroup != null
-                && !seqCanvas.fr.checkGroupVisibility(
-                        features[i].featureGroup, false))
+        if (features[i].featureGroup != null && !seqCanvas.fr
+                .checkGroupVisibility(features[i].featureGroup, false))
         {
           continue;
         }
@@ -926,15 +958,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         if ((features[i].getBegin() <= res)
                 && (features[i].getEnd() >= res))
         {
-          tmp.addElement(features[i]);
+          result.add(features[i]);
         }
       }
     }
 
-    features = new SequenceFeature[tmp.size()];
-    tmp.copyInto(features);
-
-    return features;
+    return result;
   }
 
   Tooltip tooltip;
@@ -955,8 +984,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       int oldWidth = av.getCharWidth();
 
       // Which is bigger, left-right or up-down?
-      if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
-              - lastMousePress.x))
+      if (Math.abs(evt.getY() - lastMousePress.y) > Math
+              .abs(evt.getX() - lastMousePress.x))
       {
         int fontSize = av.font.getSize();
 
@@ -1065,8 +1094,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     StringBuffer message = new StringBuffer();
     if (groupEditing)
     {
-      message.append(MessageManager.getString("action.edit_group")).append(
-              ":");
+      message.append(MessageManager.getString("action.edit_group"))
+              .append(":");
       if (editCommand == null)
       {
         editCommand = new EditCommand(
@@ -1084,8 +1113,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.formatMessage(
-                "label.edit_params", new String[] { label }));
+        editCommand = new EditCommand(MessageManager
+                .formatMessage("label.edit_params", new String[]
+                { label }));
       }
     }
 
@@ -1102,9 +1132,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     ap.alignFrame.statusBar.setText(message.toString());
 
     // Are we editing within a selection group?
-    if (groupEditing
-            || (sg != null && sg.getSequences(av.getHiddenRepSequences())
-                    .contains(seq)))
+    if (groupEditing || (sg != null
+            && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
     {
       fixedColumns = true;
 
@@ -1204,8 +1233,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
-                      - j)))
+              if (!jalview.util.Comparison
+                      .isGap(gs.getCharAt(fixedRight - j)))
               {
                 blank = false;
                 break;
@@ -1326,9 +1355,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(Action.INSERT_GAP,
-                  new SequenceI[] { seq }, lastres, startres - lastres,
-                  av.getAlignment(), true);
+          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] { seq },
+                  lastres, startres - lastres, av.getAlignment(), true);
         }
       }
       else
@@ -1362,8 +1390,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (max > 0)
           {
             editCommand.appendEdit(Action.DELETE_GAP,
-                    new SequenceI[] { seq }, startres, max,
-                    av.getAlignment(), true);
+                    new SequenceI[]
+                    { seq }, startres, max, av.getAlignment(), true);
           }
         }
       }
@@ -1458,26 +1486,24 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiers()
+            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+      List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
               sequence.findPosition(res));
 
       Vector<String> links = null;
-      if (allFeatures != null)
+      for (SequenceFeature sf : allFeatures)
       {
-        for (int i = 0; i < allFeatures.length; i++)
+        if (sf.links != null)
         {
-          if (allFeatures[i].links != null)
+          if (links == null)
           {
-            if (links == null)
-            {
-              links = new Vector<String>();
-            }
-            for (int j = 0; j < allFeatures[i].links.size(); j++)
-            {
-              links.addElement(allFeatures[i].links.elementAt(j));
-            }
+            links = new Vector<>();
+          }
+          for (int j = 0; j < sf.links.size(); j++)
+          {
+            links.addElement(sf.links.elementAt(j));
           }
         }
       }
@@ -1521,7 +1547,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
-  public void doMouseReleasedDefineMode(MouseEvent evt)
+  public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
   {
     if (stretchGroup == null)
     {
@@ -1531,7 +1557,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // but defer colourscheme update until hidden sequences are passed in
     boolean vischange = stretchGroup.recalcConservation(true);
     // here we rely on stretchGroup == av.getSelection()
-    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+            && afterDrag;
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1770,24 +1797,23 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (mouseDragging && evt.getY() < 0
                   && av.getRanges().getStartSeq() > 0)
           {
-            running = ap.scrollUp(true);
+            running = av.getRanges().scrollUp(true);
           }
 
-          if (mouseDragging && evt.getY() >= getSize().height
-                  && av.getAlignment().getHeight() > av.getRanges()
-                          .getEndSeq())
+          if (mouseDragging && evt.getY() >= getSize().height && av
+                  .getAlignment().getHeight() > av.getRanges().getEndSeq())
           {
-            running = ap.scrollUp(false);
+            running = av.getRanges().scrollUp(false);
           }
 
           if (mouseDragging && evt.getX() < 0)
           {
-            running = ap.scrollRight(false);
+            running = av.getRanges().scrollRight(false);
           }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
           {
-            running = ap.scrollRight(true);
+            running = av.getRanges().scrollRight(true);
           }
         }
 
@@ -1812,9 +1838,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // handles selection messages...
     // TODO: extend config options to allow user to control if selections may be
     // shared between viewports.
-    if (av != null
-            && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
-                    .getSequenceSetId().equals(av.getSequenceSetId()))))
+    if (av != null && (av == source || !av.followSelection
+            || (source instanceof AlignViewport
+                    && ((AlignmentViewport) source).getSequenceSetId()
+                            .equals(av.getSequenceSetId()))))
     {
       return;
     }
@@ -1843,11 +1870,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       {
         if (av.getAlignment() == null)
         {
-          System.out
-                  .println("Selection message: alignviewport av SeqSetId="
-                          + av.getSequenceSetId() + " ViewId="
-                          + av.getViewId()
-                          + " 's alignment is NULL! returning immediatly.");
+          System.out.println("Selection message: alignviewport av SeqSetId="
+                  + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+                  + " 's alignment is NULL! returning immediatly.");
           return;
         }
         sgroup = seqsel.intersect(av.getAlignment(),
@@ -1867,9 +1892,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       repaint = av.isSelectionGroupChanged(true);
     }
-    if (copycolsel
-            && (av.getColumnSelection() == null || !av
-                    .isColSelChanged(true)))
+    if (copycolsel && (av.getColumnSelection() == null
+            || !av.isColSelChanged(true)))
     {
       // the current selection is unset or from a previous message
       // so import the new colsel.
@@ -1895,10 +1919,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       repaint |= av.isColSelChanged(true);
     }
-    if (copycolsel
-            && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getAlignment()
-                    .getHiddenColumns().getHiddenRegions() == null))
+    if (copycolsel && av.hasHiddenColumns()
+            && (av.getColumnSelection() == null))
     {
       System.err.println("Bad things");
     }
@@ -1932,8 +1954,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
 
     row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
-    ap.scrollTo(ap.av.getRanges().getStartRes(), ap.av.getRanges()
-            .getStartRes(), row, true, true);
+    ap.scrollTo(ap.av.getRanges().getStartRes(),
+            ap.av.getRanges().getStartRes(), row, true, true);
   }
 
   /**
@@ -1945,7 +1967,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
 
     column = column < 0 ? ap.av.getRanges().getStartRes() : column;
-    ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, true);
+    ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true,
+            true);
   }
 
   /**