X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FOverviewDimensionsShowHidden.java;h=0bda56ecca1ed046f91b2134035f0a275eaa100e;hb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;hp=c4b69a86e37d1fc124b7fcc79163e59eea2cafa6;hpb=58fb14c48ecb086be7422f92addf14f930656523;p=jalview.git

diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index c4b69a8..0bda56e 100644
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -81,7 +81,9 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
     yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
             hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
+    yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
     int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    visYAsSeq = Math.max(visYAsSeq, 0); // -1 if before first visible sequence
 
     // update viewport accordingly
     updateViewportFromTopLeft(visXAsRes, visYAsSeq, hiddenSeqs, hiddenCols);
@@ -102,9 +104,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
 
     // update viewport accordingly
-    updateViewportFromTopLeft(visXAsRes, visYAsRes,
-            hiddenSeqs,
-            hiddenCols);
+    updateViewportFromTopLeft(visXAsRes, visYAsRes, hiddenSeqs, hiddenCols);
   }
 
   @Override
@@ -125,6 +125,11 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       visYAsSeq = 0;
     }
 
+    if (ranges.isWrappedMode())
+    {
+      visYAsSeq = 0; // sorry, no vertical scroll when wrapped
+    }
+
     // Determine where scrollCol should be, given visXAsRes
 
     // get viewport width in residues
@@ -161,8 +166,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       // went past the end of the alignment, adjust backwards
       if (ranges.getEndSeq() < visAlignHeight)
       {
-        visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
-                .subtractVisibleRows(vpheight - 1, alheight - 1));
+        visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(
+                hiddenSeqs.subtractVisibleRows(vpheight - 1, alheight - 1));
       }
       else
       {
@@ -198,22 +203,21 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
     int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
 
-    setBoxPosition(startRes, startSeq, endRes - startRes + 1, endSeq
-            - startSeq + 1);
+    setBoxPosition(startRes, startSeq, endRes - startRes + 1,
+            endSeq - startSeq + 1);
   }
 
   @Override
   public AlignmentColsCollectionI getColumns(AlignmentI al)
   {
-    return new AllColsCollection(0,
-            ranges.getAbsoluteAlignmentWidth() - 1, al);
+    return new AllColsCollection(0, ranges.getAbsoluteAlignmentWidth() - 1,
+            al);
   }
 
   @Override
   public AlignmentRowsCollectionI getRows(AlignmentI al)
   {
-    return new AllRowsCollection(0,
-            ranges.getAbsoluteAlignmentHeight() - 1,
+    return new AllRowsCollection(0, ranges.getAbsoluteAlignmentHeight() - 1,
             al);
   }