spike branch updated from latest features/JAL-2446

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 5634ead..2b1b0e5 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -201,6 +201,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     int res = 0;
     int x = evt.getX();
 
+    int startRes = av.getRanges().getStartRes();
     if (av.getWrapAlignment())
     {
 
@@ -215,7 +216,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       int y = evt.getY();
       y -= hgap;
-      x -= seqCanvas.LABEL_WEST;
+      x = Math.max(0, x - seqCanvas.labelWidthWest);
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
       if (cwidth < 1)
@@ -224,10 +225,11 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getRanges().getStartRes() / cwidth;
-
-      res = wrappedBlock * cwidth + x / av.getCharWidth();
-
+      wrappedBlock += startRes / cwidth;
+      // allow for wrapped view scrolled right (possible from Overview)
+      int startOffset = startRes % cwidth;
+      res = wrappedBlock * cwidth
+              + Math.min(cwidth - 1, startOffset + x / av.getCharWidth());
     }
     else
     {
@@ -237,7 +239,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         // right-hand gutter
         x = seqCanvas.getX() + seqCanvas.getWidth();
       }
-      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+      res = (x / av.getCharWidth()) + startRes;
       if (res > av.getRanges().getEndRes())
       {
         // moused off right
@@ -681,6 +683,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     lastSearchResults = results;
 
+    boolean wasScrolled = false;
+
     if (av.isFollowHighlight())
     {
       // don't allow highlight of protein/cDNA to also scroll a complementary
@@ -688,14 +692,19 @@ public class SeqPanel extends JPanel implements MouseListener,
       // 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, false))
+      wasScrolled = ap.scrollToPosition(results, false);
+      if (wasScrolled)
       {
         seqCanvas.revalidate();
       }
       ap.setToScrollComplementPanel(true);
     }
-    setStatusMessage(results);
-    seqCanvas.highlightSearchResults(results);
+
+    boolean noFastPaint = wasScrolled && av.getWrapAlignment();
+    if (seqCanvas.highlightSearchResults(results, noFastPaint))
+    {
+      setStatusMessage(results);
+    }
   }
 
   @Override
@@ -1592,7 +1601,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         SearchResultsI highlight = new SearchResults();
         highlight.addResult(sequence, features.get(0).getBegin(), features
                 .get(0).getEnd());
-        seqCanvas.highlightSearchResults(highlight);
+        seqCanvas.highlightSearchResults(highlight, false);
 
         /*
          * open the Amend Features dialog; clear highlighting afterwards,
@@ -1601,7 +1610,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         List<SequenceI> seqs = Collections.singletonList(sequence);
         seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
                 ap);
-        seqCanvas.highlightSearchResults(null);
+        av.setSearchResults(null); // clear highlighting
+        seqCanvas.repaint(); // draw new/amended features
       }
     }
   }
@@ -2147,8 +2157,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getAlignment().getHiddenColumns() == null || av
-                    .getAlignment().getHiddenColumns().getHiddenRegions() == null))
+            && (av.getAlignment().getHiddenColumns() == null))
     {
       System.err.println("Bad things");
     }