X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=0e12703b0bb7360e9e8583165c7fff48e38c2877;hb=6134e7137677ce608564d35d2874064e47c565c2;hp=700f82d4ebdb4a1d0f14794fd9f97475413b721d;hpb=c97f556291e878a0c8e82ebf521a07f67c90234a;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 700f82d..0e12703 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -25,8 +25,9 @@ import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -40,6 +41,7 @@ import jalview.structure.VamsasSource;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Font;
@@ -225,16 +227,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.startSeq)
+      ViewportRanges ranges = av.getRanges();
+      while (seqCanvas.cursorY < ranges.getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.endSeq)
+      while (seqCanvas.cursorY + 1 > ranges.getEndSeq())
       {
         ap.scrollUp(false);
       }
       while (seqCanvas.cursorX < av.getColumnSelection()
-              .adjustForHiddenColumns(av.startRes))
+              .adjustForHiddenColumns(ranges.getStartRes()))
       {
 
         if (!ap.scrollRight(false))
@@ -243,7 +246,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
       }
       while (seqCanvas.cursorX > av.getColumnSelection()
-              .adjustForHiddenColumns(av.endRes))
+              .adjustForHiddenColumns(ranges.getEndRes()))
       {
         if (!ap.scrollRight(true))
         {
@@ -432,8 +435,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      residue = "X".equalsIgnoreCase(displayChar) ? "X"
-              : ResidueProperties.aa2Triplet.get(displayChar);
+      residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
+              .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
+              .get(displayChar));
       if (residue != null)
       {
         text.append(" Residue: ").append(residue);
@@ -446,36 +450,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       pos = sequence.findPosition(res);
       text.append(" (").append(Integer.toString(pos)).append(")");
     }
-    // Object obj = null;
-    // if (av.getAlignment().isNucleotide())
-    // {
-    // obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
-    // + "");
-    // if (obj != null)
-    // {
-    // text.append(" Nucleotide: ");
-    // }
-    // }
-    // else
-    // {
-    // obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-    // if (obj != null)
-    // {
-    // text.append("  Residue: ");
-    // }
-    // }
-    //
-    // if (obj != null)
-    // {
-    //
-    // if (obj != "")
-    // {
-    // text.append(obj + " (" + sequence.findPosition(res) + ")");
-    // }
-    // }
 
     ap.alignFrame.statusBar.setText(text.toString());
-
   }
 
   /**
@@ -485,7 +461,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    * @param results
    * @return true if results were matched, false if not
    */
-  private boolean setStatusMessage(SearchResults results)
+  private boolean setStatusMessage(SearchResultsI results)
   {
     AlignmentI al = this.av.getAlignment();
     int sequenceIndex = al.findIndex(results);
@@ -494,9 +470,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return false;
     }
     SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
-    for (Match m : results.getResults())
+    for (SearchResultMatchI m : results.getResults())
     {
       SequenceI seq = m.getSequence();
+      if (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
 
       if (seq == ds)
       {
@@ -504,7 +484,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
          * Convert position in sequence (base 1) to sequence character array
          * index (base 0)
          */
-        int start = m.getStart() - 1;
+        int start = m.getStart() - m.getSequence().getStart();
         setStatusMessage(seq, start, sequenceIndex);
         return true;
       }
@@ -512,6 +492,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     return false;
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     lastMousePress = evt.getPoint();
@@ -562,6 +543,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     return;
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
     SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
@@ -580,21 +562,22 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       if (features != null && features.length > 0)
       {
-        SearchResults highlight = new SearchResults();
+        SearchResultsI highlight = new SearchResults();
         highlight.addResult(sequence, features[0].getBegin(),
                 features[0].getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
       if (features != null && features.length > 0)
       {
-        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
-        { sequence }, features, false, ap);
+        seqCanvas.getFeatureRenderer().amendFeatures(
+                new SequenceI[] { sequence }, features, false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
     }
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     mouseDragging = false;
@@ -630,8 +613,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
@@ -644,14 +626,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getStartRes() / cwidth;
+      wrappedBlock += av.getRanges().getStartRes() / cwidth;
 
       res = wrappedBlock * cwidth + x / av.getCharWidth();
 
     }
     else
     {
-      res = (x / av.getCharWidth()) + av.getStartRes();
+      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
     }
 
     if (av.hasHiddenColumns())
@@ -688,8 +670,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
 
@@ -702,7 +683,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+      seq = Math.min((y / av.getCharHeight())
+              + av.getRanges().getStartSeq(),
+              av
               .getAlignment().getHeight() - 1);
       if (seq < 0)
       {
@@ -740,6 +723,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   String lastMessage;
 
+  @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
     String tmp = sequence.hashCode() + index + "";
@@ -751,7 +735,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     lastMessage = tmp;
   }
 
-  public void highlightSequence(SearchResults results)
+  @Override
+  public void highlightSequence(SearchResultsI results)
   {
     if (av.isFollowHighlight())
     {
@@ -771,12 +756,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     return this.ap == null ? null : this.ap.av;
   }
 
+  @Override
   public void updateColours(SequenceI seq, int index)
   {
     System.out.println("update the seqPanel colours");
     // repaint();
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     int res = findRes(evt);
@@ -823,8 +810,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      obj = "X".equalsIgnoreCase(ch) ? "X"
-              : ResidueProperties.aa2Triplet.get(ch);
+      obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
+              .get(ch);
       if (obj != null)
       {
         text.append(" Residue: ").append(obj);
@@ -908,13 +895,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       for (int i = 0; i < features.length; i++)
       {
         if (av.getFeaturesDisplayed() == null
-                || !av.getFeaturesDisplayed().isVisible(features[i].getType()))
+                || !av.getFeaturesDisplayed().isVisible(
+                        features[i].getType()))
         {
           continue;
         }
 
         if (features[i].featureGroup != null
-                && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))
+                && !seqCanvas.fr.checkGroupVisibility(
+                        features[i].featureGroup, false))
         {
           continue;
         }
@@ -935,6 +924,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   Tooltip tooltip;
 
+  /**
+   * set when the current UI interaction has resulted in a change that requires
+   * overview shading to be recalculated. this could be changed to something
+   * more expressive that indicates what actually has changed, so selective
+   * redraws can be applied
+   */
+  private boolean needOverviewUpdate; // TODO: refactor to avcontroller
+
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     if (mouseWheelPressed)
@@ -1070,8 +1068,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (editCommand == null)
       {
         editCommand = new EditCommand(MessageManager.formatMessage(
-                "label.edit_params", new String[]
-                { label }));
+                "label.edit_params", new String[] { label }));
       }
     }
 
@@ -1305,14 +1302,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           for (int j = lastres; j < startres; j++)
           {
-            insertChar(j, new SequenceI[]
-            { seq }, fixedRight);
+            insertChar(j, new SequenceI[] { seq }, fixedRight);
           }
         }
         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
@@ -1327,8 +1324,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
               endEditing();
               break;
             }
-            deleteChar(startres, new SequenceI[]
-            { seq }, fixedRight);
+            deleteChar(startres, new SequenceI[] { seq }, fixedRight);
           }
         }
         else
@@ -1346,8 +1342,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
           if (max > 0)
           {
-            editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
-            { seq }, startres, max, av.getAlignment(), true);
+            editCommand.appendEdit(Action.DELETE_GAP,
+                    new SequenceI[] { seq }, startres, max,
+                    av.getAlignment(), true);
           }
         }
       }
@@ -1430,41 +1427,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     stretchGroup = av.getSelectionGroup();
 
-    if (stretchGroup == null)
+    if (stretchGroup == null || !stretchGroup.contains(sequence, res))
     {
-      stretchGroup = av.getAlignment().findGroup(sequence);
-      if (stretchGroup != null && res > stretchGroup.getStartRes()
-              && res < stretchGroup.getEndRes())
+      stretchGroup = av.getAlignment().findGroup(sequence, res);
+      if (stretchGroup != null)
       {
+        // only update the current selection if the popup menu has a group to
+        // focus on
         av.setSelectionGroup(stretchGroup);
       }
-      else
-      {
-        stretchGroup = null;
-      }
-    }
-
-    else if (!stretchGroup.getSequences(null).contains(sequence)
-            || stretchGroup.getStartRes() > res
-            || stretchGroup.getEndRes() < res)
-    {
-      stretchGroup = null;
-
-      SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
-
-      if (allGroups != null)
-      {
-        for (int i = 0; i < allGroups.length; i++)
-        {
-          if (allGroups[i].getStartRes() <= res
-                  && allGroups[i].getEndRes() >= res)
-          {
-            stretchGroup = allGroups[i];
-            break;
-          }
-        }
-      }
-      av.setSelectionGroup(stretchGroup);
     }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
@@ -1519,13 +1490,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       if (av.getConservationSelected())
       {
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
-                "Background");
+        SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+                ap.getViewName());
       }
       if (av.getAbovePIDThreshold())
       {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                "Background");
+        SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+                ap.getViewName());
       }
 
     }
@@ -1537,9 +1508,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       return;
     }
-
-    stretchGroup.recalcConservation(); // always do this - annotation has own
-                                       // state
+    // always do this - annotation has own state
+    // 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();
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1550,17 +1523,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                 stretchGroup.getName());
       }
-      else
+      if (stretchGroup.cs.getThreshold() > 0)
       {
         SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
                 stretchGroup.getName());
       }
     }
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
+    ap.paintAlignment(needOverviewUpdate);
+    needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.paintAlignment(true);
     av.sendSelection();
   }
 
@@ -1612,6 +1586,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1619,6 +1594,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1652,6 +1628,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1661,6 +1638,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1669,8 +1647,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = -1;
     }
 
-    if (res > av.endRes || res < av.startRes || y < av.startSeq
-            || y > av.endSeq)
+    if (res > av.getRanges().getEndRes()
+            || res < av.getRanges().getStartRes()
+            || y < av.getRanges().getStartSeq()
+            || y > av.getRanges().getEndSeq())
     {
       mouseExited(evt);
     }
@@ -1683,6 +1663,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     seqCanvas.repaint();
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (oldSeq < 0)
@@ -1697,6 +1678,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -1756,6 +1738,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       running = false;
     }
 
+    @Override
     public void run()
     {
       running = true;
@@ -1765,13 +1748,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         if (evt != null)
         {
 
-          if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+          if (mouseDragging && evt.getY() < 0
+                  && av.getRanges().getStartSeq() > 0)
           {
             running = ap.scrollUp(true);
           }
 
           if (mouseDragging && evt.getY() >= getSize().height
-                  && av.getAlignment().getHeight() > av.getEndSeq())
+                  && av.getAlignment().getHeight() > av.getRanges()
+                          .getEndSeq())
           {
             running = ap.scrollUp(false);
           }
@@ -1800,6 +1785,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   /**
    * modify current selection according to a received message.
    */
+  @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
           SelectionSource source)
   {
@@ -1825,9 +1811,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     // do we want to thread this ? (contention with seqsel and colsel locks, I
     // suspect)
-    // rules are: colsel is copied if there is a real intersection between
-    // sequence selection
-    boolean repaint = false, copycolsel = true;
+    /*
+     * only copy colsel if there is a real intersection between
+     * sequence selection and this panel's alignment
+     */
+    boolean repaint = false;
+    boolean copycolsel = false;
     if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
     {
       SequenceGroup sgroup = null;
@@ -1844,11 +1833,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         sgroup = seqsel.intersect(av.getAlignment(),
                 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
-        if ((sgroup == null || sgroup.getSize() == 0)
-                && (colsel == null || colsel.size() == 0))
+        if ((sgroup != null && sgroup.getSize() > 0))
         {
-          // don't copy columns if the region didn't intersect.
-          copycolsel = false;
+          copycolsel = true;
         }
       }
       if (sgroup != null && sgroup.getSize() > 0)
@@ -1867,7 +1854,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       // the current selection is unset or from a previous message
       // so import the new colsel.
-      if (colsel == null || colsel.size() == 0)
+      if (colsel == null || colsel.isEmpty())
       {
         if (av.getColumnSelection() != null)
         {
@@ -1911,8 +1898,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollTo(int row, int column)
   {
 
-    row = row < 0 ? ap.av.startSeq : row;
-    column = column < 0 ? ap.av.startRes : column;
+    row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+    column = column < 0 ? ap.av.getRanges().getStartRes() : column;
     ap.scrollTo(column, column, row, true, true);
   }
 
@@ -1924,8 +1911,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToRow(int row)
   {
 
-    row = row < 0 ? ap.av.startSeq : row;
-    ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
+    row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+    ap.scrollTo(ap.av.getRanges().getStartRes(), ap.av.getRanges()
+            .getStartRes(), row, true, true);
   }
 
   /**
@@ -1936,8 +1924,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToColumn(int column)
   {
 
-    column = column < 0 ? ap.av.startRes : column;
-    ap.scrollTo(column, column, ap.av.startSeq, true, true);
+    column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+    ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, true);
   }
 
   /**
@@ -1952,33 +1940,34 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
           ColumnSelection colsel, SelectionSource source)
   {
-    if (!(source instanceof AlignViewportI)) {
+    if (!(source instanceof AlignViewportI))
+    {
       return false;
     }
     final AlignViewportI sourceAv = (AlignViewportI) source;
-    if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+    if (sourceAv.getCodingComplement() != av
+            && av.getCodingComplement() != sourceAv)
     {
       return false;
     }
-  
+
     /*
      * Map sequence selection
      */
     SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
     av.setSelectionGroup(sg);
     av.isSelectionGroupChanged(true);
-  
+
     /*
      * Map column selection
      */
     ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
             av);
     av.setColumnSelection(cs);
-    av.isColSelChanged(true);
-  
+
     ap.scalePanelHolder.repaint();
     ap.repaint();
-  
+
     return true;
   }