X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=af7e9cde3ea9e0e512f2de7ab6178e5f93b4fd72;hb=d559b47886de6427219011e6e355320a0babd757;hp=813ab84753593307045e62171ed08c9fc542f080;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 813ab84..af7e9cd 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -25,7 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;
 
@@ -293,7 +293,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    * Highlight the given results on the alignment.
    * 
    */
-  public void highlightSearchResults(SearchResults results)
+  public void highlightSearchResults(SearchResultsI results)
   {
     scrollToPosition(results);
     seqPanel.seqCanvas.highlightSearchResults(results);
@@ -306,7 +306,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    * @param results
    * @return false if results were not found
    */
-  public boolean scrollToPosition(SearchResults results)
+  public boolean scrollToPosition(SearchResultsI results)
   {
     return scrollToPosition(results, true);
   }
@@ -320,10 +320,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    *          - when set, the overview will be recalculated (takes longer)
    * @return false if results were not found
    */
-  public boolean scrollToPosition(SearchResults results,
+  public boolean scrollToPosition(SearchResultsI results,
           boolean redrawOverview)
   {
-    return scrollToPosition(results, redrawOverview, false);
+    return scrollToPosition(results, 0, redrawOverview, false);
   }
 
   /**
@@ -335,7 +335,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    *          - when set, the overview will be recalculated (takes longer)
    * @return false if results were not found
    */
-  public boolean scrollToPosition(SearchResults results,
+  public boolean scrollToPosition(SearchResultsI results,
+          int verticalOffset,
           boolean redrawOverview, boolean centre)
   {
     // do we need to scroll the panel?
@@ -347,6 +348,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         return false;
       }
+      /*
+       * allow for offset of target sequence (actually scroll to one above it)
+       */
+
       SequenceI seq = alignment.getSequenceAt(seqIndex);
       int[] r = results.getResults(seq, 0, alignment.getWidth());
       if (r == null)
@@ -391,6 +396,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         return false;
       }
+
+      /*
+       * allow for offset of target sequence (actually scroll to one above it)
+       */
+      seqIndex = Math.max(0, seqIndex - verticalOffset);
       return scrollTo(start, end, seqIndex, false, redrawOverview);
     }
     return true;
@@ -419,6 +429,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       start = ostart;
     }
+
     if (!av.getWrapAlignment())
     {
       /*
@@ -508,7 +519,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue(res / cwidth);
-      av.startRes = vscroll.getValue() * cwidth;
+      av.setStartRes(vscroll.getValue() * cwidth);
     }
   }
 
@@ -621,8 +632,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   public void setWrapAlignment(boolean wrap)
   {
-    av.startSeq = 0;
-    av.startRes = 0;
+    av.setStartSeq(0);
+    av.setStartRes(0);
     scalePanelHolder.setVisible(!wrap);
 
     hscroll.setVisible(!wrap);
@@ -821,8 +832,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       overviewPanel.setBoxPosition();
     }
 
-    int scrollX = av.startRes - oldX;
-    int scrollY = av.startSeq - oldY;
+    int scrollX = av.getStartRes() - oldX;
+    int scrollY = av.getStartSeq() - oldY;
 
     if (av.getWrapAlignment() || !fastPaint || av.MAC)
     {
@@ -832,13 +843,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if (scrollX > av.endRes - av.startRes)
+      if (scrollX > av.getEndRes() - av.getStartRes())
       {
-        scrollX = av.endRes - av.startRes;
+        scrollX = av.getEndRes() - av.getStartRes();
       }
-      else if (scrollX < av.startRes - av.endRes)
+      else if (scrollX < av.getStartRes() - av.getEndRes())
       {
-        scrollX = av.startRes - av.endRes;
+        scrollX = av.getStartRes() - av.getEndRes();
       }
 
       idPanel.idCanvas.fastPaint(scrollY);
@@ -902,14 +913,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    * @param seqOffset
    *          the number of visible sequences to show above the mapped region
    */
-  protected void scrollToCentre(SearchResults sr, int seqOffset)
+  protected void scrollToCentre(SearchResultsI sr, int seqOffset)
   {
     /*
      * To avoid jumpy vertical scrolling (if some sequences are gapped or not
      * mapped), we can make the scroll-to location a sequence above the one
      * actually mapped.
      */
-    SequenceI mappedTo = sr.getResultSequence(0);
+    SequenceI mappedTo = sr.getResults().get(0).getSequence();
     List<SequenceI> seqs = av.getAlignment().getSequences();
 
     /*
@@ -931,23 +942,21 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       return; // failsafe, shouldn't happen
     }
-    sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
-    sr.getResults().get(0)
-            .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
 
     /*
      * Scroll to position but centring the target residue. Also set a state flag
      * to prevent adjustmentValueChanged performing this recursively.
      */
     setFollowingComplementScroll(true);
-    scrollToPosition(sr, true, true);
+    // this should be scrollToPosition(sr,verticalOffset,
+    scrollToPosition(sr, seqOffset, true, true);
   }
 
   private void sendViewPosition()
   {
     StructureSelectionManager.getStructureSelectionManager(av.applet)
-            .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
-                    av.endSeq);
+            .sendViewPosition(this, av.getStartRes(), av.getEndRes(),
+                    av.getStartSeq(), av.getEndSeq());
   }
 
   /**