X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=d06251c7694de626e8dd9140ec6475f5986e7475;hb=ecf2d49dbf1d62c024845715f141a596cff8b065;hp=84e5efe56d5ff3e8bea4d9d856697ad176c1e634;hpb=5dc1f2c2e2827d06041127686c9f33ed1c06a31d;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 84e5efe..d06251c 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -179,8 +179,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     AlignmentI al = av.getAlignment();
     int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
-    int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth
-            / 3));
+    int maxwidth = Math.max(20,
+            Math.min(afwidth - 200, (int) 2 * afwidth / 3));
     int i = 0;
     int idWidth = 0;
     String id;
@@ -223,10 +223,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Highlight the given results on the alignment.
    * 
-   * @param results
-   *          DOCUMENT ME!
    */
   public void highlightSearchResults(SearchResults results)
   {
@@ -271,19 +269,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
         return false;
       }
       SequenceI seq = av.alignment.getSequenceAt(seqIndex);
-
-      int[] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq,
-      // seq.getStart(),
-      // seq.getEnd());
-      // TODO: VAMSAS: fix hidden column issue where scroll to left from C
-      // terminus is not visible
+      
+      int[] r=results.getResults(seq, 0, av.alignment.getWidth());
       if (r == null)
       {
         return false;
       }
       int start = r[0];
       int end = r[1];
-      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // DEBUG
+      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
+      // DEBUG
       if (start < 0)
       {
         return false;
@@ -292,6 +287,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         return false;
       }
+      if (av.hasHiddenColumns)
+      {
+        start = av.getColumnSelection().findColumnPosition(start);
+        end = av.getColumnSelection().findColumnPosition(end);
+        if (start==end)
+        {
+          if (!av.colSel.isVisible(r[0]))
+          {
+            // don't scroll - position isn't visible
+            return false;
+          }
+        }
+      }
       if (!av.wrapAlignment)
       {
         if ((startv = av.getStartRes()) >= start)
@@ -500,12 +508,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Adjust row/column scrollers to show a visible position in the alignment.
    * 
-   * @param x
-   *          DOCUMENT ME!
-   * @param y
+   * @param x visible column to scroll to
    *          DOCUMENT ME!
+   * @param y visible row to scroll to
+   *          
    */
   public void setScrollValues(int x, int y)
   {
@@ -577,9 +585,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av
-              .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av
-                      .getCharWidth())) - 1);
+      av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -859,8 +865,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
 
       pg.setColor(currentColor);
-      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av
-              .getCharHeight());
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+              av.getCharHeight());
 
       pg.setColor(currentTextColor);
 
@@ -873,7 +879,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 - 4;
       }
 
-      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+      pg.drawString(
+              seq.getDisplayId(av.getShowJVSuffix()),
+              xPos,
               (((i - startSeq) * av.charHeight) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
@@ -1327,6 +1335,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public void updateAnnotation(boolean applyGlobalSettings)
   {
+    // TODO: this should be merged with other annotation update stuff - that
+    // sits on AlignViewport
     boolean updateCalcs = false;
     boolean conv = av.isShowGroupConservation();
     boolean cons = av.isShowGroupConsensus();
@@ -1345,46 +1355,46 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Hashtable oldrfs = new Hashtable();
     if (aan != null)
     {
-    for (int an = 0; an < aan.length; an++)
-    {
-      if (aan[an].autoCalculated && aan[an].groupRef != null)
+      for (int an = 0; an < aan.length; an++)
       {
-        oldrfs.put(aan[an].groupRef, aan[an].groupRef);
-        av.alignment.deleteAnnotation(aan[an]);
-        aan[an] = null;
+        if (aan[an].autoCalculated && aan[an].groupRef != null)
+        {
+          oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+          av.alignment.deleteAnnotation(aan[an]);
+          aan[an] = null;
+        }
       }
     }
-    }
     SequenceGroup sg;
     if (gr != null)
     {
-    for (int g = 0; g < gr.size(); g++)
-    {
-      updateCalcs = false;
-      sg = (SequenceGroup) gr.elementAt(g);
-      if (applyGlobalSettings || !oldrfs.containsKey(sg))
-      {
-        // set defaults for this group's conservation/consensus
-        sg.setIncludeAllConsSymbols(showprf);
-        sg.setShowConsensusHistogram(showConsHist);
-      }
-      if (conv)
-      {
-        updateCalcs = true;
-        av.alignment.addAnnotation(sg.getConservationRow(), 0);
-      }
-      if (cons)
-      {
-        updateCalcs = true;
-        av.alignment.addAnnotation(sg.getConsensus(), 0);
-      }
-      // refresh the annotation rows
-      if (updateCalcs)
+      for (int g = 0; g < gr.size(); g++)
       {
-        sg.recalcConservation();
+        updateCalcs = false;
+        sg = (SequenceGroup) gr.elementAt(g);
+        if (applyGlobalSettings || !oldrfs.containsKey(sg))
+        {
+          // set defaults for this group's conservation/consensus
+          sg.setshowSequenceLogo(showprf);
+          sg.setShowConsensusHistogram(showConsHist);
+        }
+        if (conv)
+        {
+          updateCalcs = true;
+          av.alignment.addAnnotation(sg.getConservationRow(), 0);
+        }
+        if (cons)
+        {
+          updateCalcs = true;
+          av.alignment.addAnnotation(sg.getConsensus(), 0);
+        }
+        // refresh the annotation rows
+        if (updateCalcs)
+        {
+          sg.recalcConservation();
+        }
       }
     }
-    }
     oldrfs.clear();
     adjustAnnotationHeight();
   }