X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2884c501cc87f2dc65bed280e3a59041f01ed054;hb=c3d92b4b7a6cb00f9e596dbb7cd6c8508da5c252;hp=16415ccf503d93980942db91cc3c4260105b6105;hpb=d559b47886de6427219011e6e355320a0babd757;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 16415cc..2884c50 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,6 +27,7 @@ import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -59,6 +60,7 @@ import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 import javax.swing.JPanel;
@@ -181,7 +183,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * @param evt
    * @return
    */
-  int findRes(MouseEvent evt)
+  int findColumn(MouseEvent evt)
   {
     int res = 0;
     int x = evt.getX();
@@ -209,7 +211,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getStartRes() / cwidth;
+      wrappedBlock += av.getRanges().getStartRes() / cwidth;
 
       res = wrappedBlock * cwidth + x / av.getCharWidth();
 
@@ -222,17 +224,18 @@ public class SeqPanel extends JPanel implements MouseListener,
         // right-hand gutter
         x = seqCanvas.getX() + seqCanvas.getWidth();
       }
-      res = (x / av.getCharWidth()) + av.getStartRes();
-      if (res > av.getEndRes())
+      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+      if (res > av.getRanges().getEndRes())
       {
         // moused off right
-        res = av.getEndRes();
+        res = av.getRanges().getEndRes();
       }
     }
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(res);
     }
 
     return res;
@@ -262,7 +265,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+      seq = Math.min((y / av.getCharHeight())
+              + av.getRanges().getStartSeq(),
+              av
               .getAlignment().getHeight() - 1);
     }
 
@@ -336,20 +341,23 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
+
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
     if (av.hasHiddenColumns()
-            && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ && !hidden.isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
-      while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+      while (!hidden.isVisible(seqCanvas.cursorX)
               && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-              || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+              || !hidden.isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -385,26 +393,27 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.getStartSeq())
+      while (seqCanvas.cursorY < av.getRanges().getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.getEndSeq())
+      while (seqCanvas.cursorY > av.getRanges().getEndSeq())
       {
         ap.scrollUp(false);
       }
       if (!av.getWrapAlignment())
       {
-        while (seqCanvas.cursorX < av.getColumnSelection()
-                .adjustForHiddenColumns(av.getStartRes()))
+        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+        while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av
+                .getRanges().getStartRes()))
         {
           if (!ap.scrollRight(false))
           {
             break;
           }
         }
-        while (seqCanvas.cursorX > av.getColumnSelection()
-                .adjustForHiddenColumns(av.getEndRes()))
+        while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av
+                .getRanges().getEndRes()))
         {
           if (!ap.scrollRight(true))
           {
@@ -633,7 +642,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     int seq = findSeq(evt);
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (seq < 0 || res < 0)
     {
@@ -732,25 +741,27 @@ public class SeqPanel extends JPanel implements MouseListener,
       mouseDragged(evt);
     }
 
-    int res = findRes(evt);
+    final int column = findColumn(evt);
     int seq = findSeq(evt);
-    int pos;
-    if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+    if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
     {
       return;
     }
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    if (res >= sequence.getLength())
+    if (column >= sequence.getLength())
     {
       return;
     }
 
-    pos = setStatusMessage(sequence, res, seq);
+    /*
+     * set status bar message, returning residue position in sequence
+     */
+    final int pos = setStatusMessage(sequence, column, seq);
     if (ssm != null && pos > -1)
     {
-      mouseOverSequence(sequence, res, pos);
+      mouseOverSequence(sequence, column, pos);
     }
 
     tooltipText.setLength(6); // Cuts the buffer back to <html>
@@ -760,7 +771,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       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"))
@@ -776,14 +788,11 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    // use aa to see if the mouse pointer is on a
-    if (av.isShowSequenceFeatures())
+    if (av.isShowSequenceFeatures() && pos != -1)
     {
-      int rpos;
       List<SequenceFeature> features = ap.getFeatureRenderer()
-              .findFeaturesAtRes(sequence.getDatasetSequence(),
-                      rpos = sequence.findPosition(res));
-      seqARep.appendFeatures(tooltipText, rpos, features,
+              .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
+      seqARep.appendFeatures(tooltipText, pos, features,
               this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
     if (tooltipText.length() == 6) // <html>
@@ -850,17 +859,20 @@ public class SeqPanel extends JPanel implements MouseListener,
   // avcontroller or viewModel
 
   /**
-   * Set status message in alignment panel
+   * Sets the status message in alignment panel, showing the sequence number
+   * (index) and id, residue and residue position for the given sequence and
+   * column position. Returns the calculated residue position in the sequence,
+   * or -1 for a gapped column position.
    * 
    * @param sequence
    *          aligned sequence object
-   * @param res
+   * @param column
    *          alignment column
    * @param seq
    *          index of sequence in alignment
    * @return position of res in sequence
    */
-  int setStatusMessage(SequenceI sequence, int res, int seq)
+  int setStatusMessage(SequenceI sequence, final int column, int seq)
   {
     StringBuilder text = new StringBuilder(32);
 
@@ -875,7 +887,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     /*
      * 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);
@@ -898,7 +910,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     int pos = -1;
     if (residue != null)
     {
-      pos = sequence.findPosition(res);
+      pos = sequence.findPosition(column);
       text.append(" (").append(Integer.toString(pos)).append(")");
     }
     ap.alignFrame.statusBar.setText(text.toString());
@@ -942,30 +954,36 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
+   * {@inheritDoc}
    */
   @Override
   public void mouseDragged(MouseEvent evt)
   {
     if (mouseWheelPressed)
     {
+      boolean inSplitFrame = ap.av.getCodingComplement() != null;
+      boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
+
       int oldWidth = av.getCharWidth();
 
       // Which is bigger, left-right or up-down?
       if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
               .getX() - lastMousePress.getX()))
       {
+        /*
+         * on drag up or down, decrement or increment font size
+         */
         int fontSize = av.font.getSize();
+        boolean fontChanged = false;
 
         if (evt.getY() < lastMousePress.getY())
         {
+          fontChanged = true;
           fontSize--;
         }
         else if (evt.getY() > lastMousePress.getY())
         {
+          fontChanged = true;
           fontSize++;
         }
 
@@ -974,24 +992,56 @@ public class SeqPanel extends JPanel implements MouseListener,
           fontSize = 1;
         }
 
-        av.setFont(
-                new Font(av.font.getName(), av.font.getStyle(), fontSize),
-                true);
-        av.setCharWidth(oldWidth);
-        ap.fontChanged();
+        if (fontChanged)
+        {
+          Font newFont = new Font(av.font.getName(), av.font.getStyle(),
+                  fontSize);
+          av.setFont(newFont, true);
+          av.setCharWidth(oldWidth);
+          ap.fontChanged();
+          if (copyChanges)
+          {
+            ap.av.getCodingComplement().setFont(newFont, true);
+            SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+                    .getSplitViewContainer();
+            splitFrame.adjustLayout();
+            splitFrame.repaint();
+          }
+        }
       }
       else
       {
+        /*
+         * on drag left or right, decrement or increment character width
+         */
+        int newWidth = 0;
         if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
         {
-          av.setCharWidth(av.getCharWidth() - 1);
+          newWidth = av.getCharWidth() - 1;
+          av.setCharWidth(newWidth);
         }
         else if (evt.getX() > lastMousePress.getX())
         {
-          av.setCharWidth(av.getCharWidth() + 1);
+          newWidth = av.getCharWidth() + 1;
+          av.setCharWidth(newWidth);
+        }
+        if (newWidth > 0)
+        {
+          ap.paintAlignment(false);
+          if (copyChanges)
+          {
+            /*
+             * need to ensure newWidth is set on cdna, regardless of which
+             * panel the mouse drag happened in; protein will compute its 
+             * character width as 1:1 or 3:1
+             */
+            av.getCodingComplement().setCharWidth(newWidth);
+            SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+                    .getSplitViewContainer();
+            splitFrame.adjustLayout();
+            splitFrame.repaint();
+          }
         }
-
-        ap.paintAlignment(false);
       }
 
       FontMetrics fm = getFontMetrics(av.getFont());
@@ -1008,7 +1058,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (res < 0)
     {
@@ -1141,8 +1191,10 @@ public class SeqPanel extends JPanel implements MouseListener,
     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))
@@ -1217,8 +1269,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           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;
@@ -1482,6 +1534,11 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
   }
 
+  /**
+   * Handler for double-click on a position with one or more sequence features.
+   * Opens the Amend Features dialog to allow feature details to be amended, or
+   * the feature deleted.
+   */
   @Override
   public void mouseClicked(MouseEvent evt)
   {
@@ -1498,22 +1555,25 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
               .findFeaturesAtRes(sequence.getDatasetSequence(),
-                      sequence.findPosition(findRes(evt)));
+                      sequence.findPosition(findColumn(evt)));
 
-      if (features != null && features.size() > 0)
+      if (!features.isEmpty())
       {
+        /*
+         * highlight the first feature at the position on the alignment
+         */
         SearchResultsI highlight = new SearchResults();
         highlight.addResult(sequence, features.get(0).getBegin(), features
                 .get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
-      }
-      if (features != null && features.size() > 0)
-      {
-        seqCanvas.getFeatureRenderer().amendFeatures(
-                new SequenceI[] { sequence },
-                features.toArray(new SequenceFeature[features.size()]),
-                false, ap);
 
+        /*
+         * open the Amend Features dialog; clear highlighting afterwards,
+         * whether changes were made or not
+         */
+        List<SequenceI> seqs = Collections.singletonList(sequence);
+        seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
+                ap);
         seqCanvas.highlightSearchResults(null);
       }
     }
@@ -1557,7 +1617,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   public void doMousePressedDefineMode(MouseEvent evt)
   {
-    final int res = findRes(evt);
+    final int res = findColumn(evt);
     final int seq = findSeq(evt);
     oldSeq = seq;
     needOverviewUpdate = false;
@@ -1616,7 +1676,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.cursorMode)
     {
-      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorX = findColumn(evt);
       seqCanvas.cursorY = findSeq(evt);
       seqCanvas.repaint();
       return;
@@ -1668,11 +1728,11 @@ public class SeqPanel extends JPanel implements MouseListener,
    * 
    * @param evt
    * @param res
-   * @param sequence
+   * @param sequences
    */
   void showPopupMenu(MouseEvent evt)
   {
-    final int res = findRes(evt);
+    final int res = findColumn(evt);
     final int seq = findSeq(evt);
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
     List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
@@ -1743,7 +1803,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = findRes(evt);
+    int res = findColumn(evt);
     int y = findSeq(evt);
 
     if (wrappedBlock != startWrapBlock)
@@ -1772,9 +1832,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       changeStartRes = true;
     }
 
-    if (res < av.getStartRes())
+    if (res < av.getRanges().getStartRes())
     {
-      res = av.getStartRes();
+      res = av.getRanges().getStartRes();
     }
 
     if (changeEndRes)
@@ -1908,13 +1968,15 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         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() >= getHeight())
-                  && (av.getAlignment().getHeight() > av.getEndSeq()))
+                  && (av.getAlignment().getHeight() > av.getRanges()
+                          .getEndSeq()))
           {
             running = ap.scrollUp(false);
           }
@@ -1944,7 +2006,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   @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...
@@ -1952,9 +2014,20 @@ public class SeqPanel extends JPanel implements MouseListener,
     // shared between viewports.
     boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
             .getSequenceSetId().equals(av.getSequenceSetId())));
-    if (iSentTheSelection || !av.followSelection)
+
+    if (iSentTheSelection)
     {
-      return;
+      // respond to our own event by updating dependent dialogs
+      if (ap.getCalculationDialog() != null)
+      {
+        ap.getCalculationDialog().validateCalcTypes();
+      }
+
+      // process further ?
+      if (!av.followSelection)
+      {
+        return;
+      }
     }
 
     /*
@@ -1969,7 +2042,7 @@ public class SeqPanel extends JPanel implements MouseListener,
      * 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;
     }
@@ -2032,7 +2105,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          av.getColumnSelection().setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel,
+                  av.getAlignment().getHiddenColumns());
         }
       }
       av.isColSelChanged(true);
@@ -2041,8 +2115,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getColumnSelection()
-                    .getHiddenColumns() == null))
+            && (av.getAlignment().getHiddenColumns() == null || av
+                    .getAlignment().getHiddenColumns().getHiddenRegions() == null))
     {
       System.err.println("Bad things");
     }
@@ -2052,6 +2126,13 @@ public class SeqPanel extends JPanel implements MouseListener,
       PaintRefresher.Refresh(this, av.getSequenceSetId());
       // ap.paintAlignment(false);
     }
+
+    // lastly, update dependent dialogs
+    if (ap.getCalculationDialog() != null)
+    {
+      ap.getCalculationDialog().validateCalcTypes();
+    }
+
   }
 
   /**
@@ -2064,7 +2145,8 @@ public class SeqPanel extends JPanel implements MouseListener,
    * @param source
    */
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
-          ColumnSelection colsel, SelectionSource source)
+          ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     if (!(source instanceof AlignViewportI))
     {
@@ -2087,9 +2169,19 @@ public class SeqPanel extends JPanel implements MouseListener,
     /*
      * 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);
+
+    // lastly, update any dependent dialogs
+    if (ap.getCalculationDialog() != null)
+    {
+      ap.getCalculationDialog().validateCalcTypes();
+    }
 
     PaintRefresher.Refresh(this, av.getSequenceSetId());