X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FViewportRanges.java;h=04db165334d2ca6af4f15772767a3d2d3e661272;hb=e57f77dc13f5a295cf49a403da05770a68a6e22b;hp=c7a3fa1174c81b4c4dcb1b49a1c99d4a5955d0a0;hpb=66e2ef1a1a7767b8ca8d40f108f29e9036166236;p=jalview.git

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index c7a3fa1..04db165 100644
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -97,7 +97,7 @@ public class ViewportRanges extends ViewportProperties
    */
   public int getVisibleAlignmentWidth()
   {
-    return al.getWidth() - al.getHiddenColumns().getSize();
+    return al.getVisibleWidth();
   }
 
   /**
@@ -224,6 +224,8 @@ public class ViewportRanges extends ViewportProperties
    */
   public void setStartEndSeq(int start, int end)
   {
+    // jalview.bin.Console.outPrintln("ViewportRange setStartEndSeq " + start +
+    // " " + end);
     int[] oldvalues = updateStartEndSeq(start, end);
     int oldstartseq = oldvalues[0];
     int oldendseq = oldvalues[1];
@@ -285,12 +287,12 @@ public class ViewportRanges extends ViewportProperties
    * event.
    * 
    * @param seq
-   *          sequence position
+   *          sequence position in the range [0, height)
    */
   public void setEndSeq(int seq)
   {
-    int height = getViewportHeight();
-    setStartEndSeq(seq - height + 1, seq);
+    // BH 2018.04.18 added safety for seq < 0; comment about not being >= height
+    setStartEndSeq(Math.max(0, seq + 1 - getViewportHeight()), seq);
   }
 
   /**
@@ -425,17 +427,22 @@ public class ViewportRanges extends ViewportProperties
   public void setViewportStartAndHeight(int start, int h)
   {
     int vpstart = start;
+
+    int visHeight = getVisibleAlignmentHeight();
     if (vpstart < 0)
     {
       vpstart = 0;
     }
-    else if ((h <= getVisibleAlignmentHeight())
-            && (vpstart + h - 1 > getVisibleAlignmentHeight() - 1))
+    else if (h <= visHeight && vpstart + h > visHeight)
     // viewport height is less than the full alignment and we are running off
     // the bottom
     {
-      vpstart = getVisibleAlignmentHeight() - h;
+      vpstart = visHeight - h;
     }
+    // jalview.bin.Console.outPrintln("ViewportRanges setviewportStartAndHeight
+    // " + vpstart
+    // + " " + start + " " + h + " " + getVisibleAlignmentHeight());
+
     setStartEndSeq(vpstart, vpstart + h - 1);
   }
 
@@ -580,8 +587,8 @@ public class ViewportRanges extends ViewportProperties
     }
 
     int residuesToScroll = width * widthsToScroll;
-    int newStartRes = up ? oldStartRes - residuesToScroll : oldStartRes
-            + residuesToScroll;
+    int newStartRes = up ? oldStartRes - residuesToScroll
+            : oldStartRes + residuesToScroll;
     if (newStartRes < 0)
     {
       newStartRes = 0;
@@ -607,16 +614,16 @@ public class ViewportRanges extends ViewportProperties
     {
       scrollUp(false);
     }
-    
+
     HiddenColumns hidden = al.getHiddenColumns();
-    while (x < hidden.adjustForHiddenColumns(startRes))
+    while (x < hidden.visibleToAbsoluteColumn(startRes))
     {
       if (!scrollRight(false))
       {
         break;
       }
     }
-    while (x > hidden.adjustForHiddenColumns(endRes))
+    while (x > hidden.visibleToAbsoluteColumn(endRes))
     {
       if (!scrollRight(true))
       {
@@ -638,7 +645,7 @@ public class ViewportRanges extends ViewportProperties
     boolean changedLocation = false;
 
     // convert the x,y location to visible coordinates
-    int visX = al.getHiddenColumns().findColumnPosition(x);
+    int visX = al.getHiddenColumns().absoluteToVisibleColumn(x);
     int visY = al.getHiddenSequences().findIndexWithoutHiddenSeqs(y);
 
     // if (vis_x,vis_y) is already visible don't do anything