Merge branch 'documentation/JAL-2418_release2102' into develop

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 063ab7d..a2c2bd9 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -60,6 +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;
@@ -396,7 +397,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.getRanges().getEndSeq())
+      while (seqCanvas.cursorY > av.getRanges().getEndSeq())
       {
         ap.scrollUp(false);
       }
@@ -950,30 +951,36 @@ 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++;
         }
 
@@ -982,24 +989,56 @@ 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());
@@ -1492,6 +1531,11 @@ 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)
   {
@@ -1510,20 +1554,23 @@ public class SeqPanel extends JPanel implements MouseListener,
               .findFeaturesAtRes(sequence.getDatasetSequence(),
                       sequence.findPosition(findRes(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, null);
         seqCanvas.highlightSearchResults(null);
       }
     }
@@ -1678,7 +1725,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * 
    * @param evt
    * @param res
-   * @param sequence
+   * @param sequences
    */
   void showPopupMenu(MouseEvent evt)
   {
@@ -1964,9 +2011,20 @@ 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;
+      }
     }
 
     /*
@@ -2044,7 +2102,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          av.getColumnSelection().setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel,
+                  av.getAlignment().getHiddenColumns());
         }
       }
       av.isColSelChanged(true);
@@ -2054,7 +2113,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (copycolsel
             && av.hasHiddenColumns()
             && (av.getAlignment().getHiddenColumns() == null || av
-                    .getAlignment().getHiddenColumns().getListOfCols() == null))
+                    .getAlignment().getHiddenColumns().getHiddenRegions() == null))
     {
       System.err.println("Bad things");
     }
@@ -2064,6 +2123,13 @@ 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();
+    }
+
   }
 
   /**
@@ -2108,6 +2174,12 @@ public class SeqPanel extends JPanel implements MouseListener,
     av.setColumnSelection(cs);
     av.getAlignment().setHiddenColumns(hs);
 
+    // lastly, update any dependent dialogs
+    if (ap.getCalculationDialog() != null)
+    {
+      ap.getCalculationDialog().validateCalcTypes();
+    }
+
     PaintRefresher.Refresh(this, av.getSequenceSetId());
 
     return true;