X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=e4e3640a7885c544ed3f8884e71282c3d66e00b3;hb=b4d2b6a2ed131265ed599db27de9b82aaf010400;hp=4b200adf73c3954fcb689f5155200983854ed66b;hpb=521b4513449cabf0e64b9c70c70c304d6bf2f7e3;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 4b200ad..e4e3640 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -25,6 +25,7 @@ import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -38,6 +39,7 @@ import jalview.structure.SelectionSource;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
@@ -52,6 +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,
@@ -180,19 +186,22 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
     if (av.hasHiddenColumns()
-            && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+            && !av.getAlignment().getHiddenColumns()
+                    .isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
-      while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+      while (!av.getAlignment().getHiddenColumns()
+              .isVisible(seqCanvas.cursorX)
               && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-              || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+              || !av.getAlignment().getHiddenColumns()
+                      .isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -223,32 +232,33 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     endEditing();
     if (av.getWrapAlignment())
     {
-      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+      av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
     }
     else
     {
       ViewportRanges ranges = av.getRanges();
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       while (seqCanvas.cursorY < ranges.getStartSeq())
       {
-        ap.scrollUp(true);
+        ranges.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > ranges.getEndSeq())
+      while (seqCanvas.cursorY > ranges.getEndSeq())
       {
-        ap.scrollUp(false);
+        ranges.scrollUp(false);
       }
-      while (seqCanvas.cursorX < av.getColumnSelection()
-              .adjustForHiddenColumns(ranges.getStartRes()))
+      while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges
+              .getStartRes()))
       {
 
-        if (!ap.scrollRight(false))
+        if (!ranges.scrollRight(false))
         {
           break;
         }
       }
-      while (seqCanvas.cursorX > av.getColumnSelection()
-              .adjustForHiddenColumns(ranges.getEndRes()))
+      while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges
+              .getEndRes()))
       {
-        if (!ap.scrollRight(true))
+        if (!ranges.scrollRight(true))
         {
           break;
         }
@@ -407,13 +417,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    * 
    * @param sequence
    *          aligned sequence object
-   * @param res
+   * @param column
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of res in sequence
+   * @return position of column in sequence or -1 if at gap
    */
-  void setStatusMessage(SequenceI sequence, int res, int seq)
+  void setStatusMessage(SequenceI sequence, int column, int seq)
   {
     // TODO remove duplication of identical gui method
     StringBuilder text = new StringBuilder(32);
@@ -424,7 +434,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     /*
      * Try to translate the display character to residue name (null for gap).
      */
-    final String displayChar = String.valueOf(sequence.getCharAt(res));
+    final String displayChar = String.valueOf(sequence.getCharAt(column));
     if (av.getAlignment().isNucleotide())
     {
       residue = ResidueProperties.nucleotideName.get(displayChar);
@@ -447,7 +457,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     int pos = -1;
     if (residue != null)
     {
-      pos = sequence.findPosition(res);
+      pos = sequence.findPosition(column);
       text.append(" (").append(Integer.toString(pos)).append(")");
     }
 
@@ -557,20 +567,23 @@ 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);
       }
@@ -580,13 +593,13 @@ 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;
     }
 
@@ -603,6 +616,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     int res = 0;
     int x = evt.getX();
 
+    int startRes = av.getRanges().getStartRes();
     if (av.getWrapAlignment())
     {
 
@@ -617,7 +631,7 @@ 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)
@@ -626,19 +640,21 @@ 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
+              + Math.min(cwidth - 1, startOffset + x / av.getCharWidth());
     }
     else
     {
-      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+      res = (x / av.getCharWidth()) + startRes;
     }
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(res);
     }
 
     return res;
@@ -740,10 +756,16 @@ 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);
@@ -766,10 +788,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   @Override
   public void mouseMoved(MouseEvent evt)
   {
-    int res = findRes(evt);
+    final int column = findRes(evt);
     int seq = findSeq(evt);
 
-    if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
+    if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
     {
       if (tooltip != null)
       {
@@ -779,7 +801,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    if (res > sequence.getLength())
+    if (column > sequence.getLength())
     {
       if (tooltip != null)
       {
@@ -788,38 +810,34 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return;
     }
 
-    int respos = sequence.findPosition(res);
-    if (ssm != null)
+    final char ch = sequence.getCharAt(column);
+    boolean isGapped = Comparison.isGap(ch);
+    // find residue at column (or nearest if at a gap)
+    int respos = sequence.findPosition(column);
+
+    if (ssm != null && !isGapped)
     {
-      mouseOverSequence(sequence, res, respos);
+      mouseOverSequence(sequence, column, respos);
     }
 
     StringBuilder text = new StringBuilder();
     text.append("Sequence ").append(Integer.toString(seq + 1))
             .append(" ID: ").append(sequence.getName());
 
-    String obj = null;
-    final String ch = String.valueOf(sequence.getCharAt(res));
-    if (av.getAlignment().isNucleotide())
+    if (!isGapped)
     {
-      obj = ResidueProperties.nucleotideName.get(ch);
-      if (obj != null)
+      if (av.getAlignment().isNucleotide())
       {
-        text.append(" Nucleotide: ").append(obj);
+        String base = ResidueProperties.nucleotideName.get(ch);
+        text.append(" Nucleotide: ").append(base == null ? ch : base);
       }
-    }
-    else
-    {
-      obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
-              .get(ch);
-      if (obj != null)
+      else
       {
-        text.append(" Residue: ").append(obj);
+        String residue = (ch == 'x' || ch == 'X') ? "X"
+                : ResidueProperties.aa2Triplet
+                .get(String.valueOf(ch));
+        text.append(" Residue: ").append(residue == null ? ch : residue);
       }
-    }
-
-    if (obj != null)
-    {
       text.append(" (").append(Integer.toString(respos)).append(")");
     }
 
@@ -831,7 +849,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       for (int g = 0; g < groups.length; g++)
       {
-        if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+        if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column)
         {
           if (!groups[g].getName().startsWith("JTreeGroup")
                   && !groups[g].getName().startsWith("JGroup"))
@@ -847,33 +865,37 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
 
-    // use aa to see if the mouse pointer is on a
-    SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
-            sequence.findPosition(res));
-
-    int index = 0;
-    while (index < allFeatures.length)
+    /*
+     * add feature details to tooltip, including any that straddle
+     * a gapped position
+     */
+    if (av.isShowSequenceFeatures())
     {
-      SequenceFeature sf = allFeatures[index];
-
-      tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
-
-      if (sf.getDescription() != null)
+      List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
+              sequence.findPosition(column));
+      if (isGapped)
       {
-        tooltipText.append(" " + sf.getDescription());
+        removeAdjacentFeatures(allFeatures, column + 1, sequence);
       }
-
-      if (sf.getValue("status") != null)
+      for (SequenceFeature sf : allFeatures)
       {
-        String status = sf.getValue("status").toString();
-        if (status.length() > 0)
+        tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+
+        if (sf.getDescription() != null)
         {
-          tooltipText.append(" (" + sf.getValue("status") + ")");
+          tooltipText.append(" " + sf.getDescription());
         }
-      }
-      tooltipText.append("\n");
 
-      index++;
+        if (sf.getValue("status") != null)
+        {
+          String status = sf.getValue("status").toString();
+          if (status.length() > 0)
+          {
+            tooltipText.append(" (" + sf.getValue("status") + ")");
+          }
+        }
+        tooltipText.append("\n");
+      }
     }
 
     if (tooltip == null)
@@ -886,9 +908,38 @@ 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)
   {
-    Vector tmp = new Vector();
+    // 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)
+  {
+    List<SequenceFeature> result = new ArrayList<>();
     SequenceFeature[] features = sequence.getSequenceFeatures();
     if (features != null)
     {
@@ -911,15 +962,12 @@ 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;
@@ -1133,8 +1181,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (av.hasHiddenColumns())
     {
       fixedColumns = true;
-      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+      int y1 = av.getAlignment().getHiddenColumns()
+              .getHiddenBoundaryLeft(startres);
+      int y2 = av.getAlignment().getHiddenColumns()
+              .getHiddenBoundaryRight(startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1205,8 +1255,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           if (sg.getSize() == av.getAlignment().getHeight())
           {
-            if ((av.hasHiddenColumns() && startres < av
-                    .getColumnSelection().getHiddenBoundaryRight(startres)))
+            if ((av.hasHiddenColumns() && startres < av.getAlignment()
+                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
@@ -1443,24 +1493,21 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // DETECT RIGHT MOUSE BUTTON IN AWT
     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));
           }
         }
       }
@@ -1504,7 +1551,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
-  public void doMouseReleasedDefineMode(MouseEvent evt)
+  public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
   {
     if (stretchGroup == null)
     {
@@ -1514,7 +1561,8 @@ 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,
@@ -1753,24 +1801,24 @@ 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())
           {
-            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);
           }
         }
 
@@ -1789,7 +1837,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    */
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          SelectionSource source)
+          HiddenColumns hidden, SelectionSource source)
   {
     // TODO: fix this hack - source of messages is align viewport, but SeqPanel
     // handles selection messages...
@@ -1806,7 +1854,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
      * Check for selection in a view of which this one is a dna/protein
      * complement.
      */
-    if (selectionFromTranslation(seqsel, colsel, source))
+    if (selectionFromTranslation(seqsel, colsel, hidden, source))
     {
       return;
     }
@@ -1872,15 +1920,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          av.getColumnSelection().setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel,
+                  av.getAlignment().getHiddenColumns());
         }
       }
       repaint |= av.isColSelChanged(true);
     }
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getColumnSelection()
-                    .getHiddenColumns() == null))
+            && (av.getColumnSelection() == null))
     {
       System.err.println("Bad things");
     }
@@ -1940,7 +1988,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    * @param source
    */
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
-          ColumnSelection colsel, SelectionSource source)
+          ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     if (!(source instanceof AlignViewportI))
     {
@@ -1963,9 +2012,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     /*
      * Map column selection
      */
-    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
-            av);
+    // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+    // av);
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
+    MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
+    av.getAlignment().setHiddenColumns(hs);
 
     ap.scalePanelHolder.repaint();
     ap.repaint();