From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Thu, 18 Apr 2019 17:54:08 +0000 (-0500)
Subject: Corrects incorrect calls to ViewportRanges.setEndSeq()
X-Git-Tag: Release_2_11_4_0~45^2~18^2~143
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c0b77a767e71bffd8f55704f9a64f943f559e4f6;p=jalview.git

Corrects incorrect calls to ViewportRanges.setEndSeq()

This function has the limit of height - 1, not height. Also adds safety
for start < 0 in ViewportRanges.setEndSeq();
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index bad2383..2cf33ac 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2071,7 +2071,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             seqs, 0, viewport.getAlignment().getWidth(),
             viewport.getAlignment()));
 
-    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
+    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
+                                                                             // 2019.04.18
     viewport.getAlignment().getWidth();
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index d10591e..2bead46 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -253,7 +253,7 @@ public class AlignViewport extends AlignmentViewport
 
   public void resetSeqLimits(int height)
   {
-    ranges.setEndSeq(height / getCharHeight());
+    ranges.setEndSeq(height / getCharHeight() - 1); // BH 2019.04.18
   }
 
   boolean centreColumnLabels;
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 77b8552..27a0f76 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2224,7 +2224,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
 
         // propagate alignment changed.
-        viewport.getRanges().setEndSeq(alignment.getHeight());
+        viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
         if (annotationAdded)
         {
           // Duplicate sequence annotation in all views.
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5ef2568..7d01222 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -743,7 +743,7 @@ public class AlignViewport extends AlignmentViewport
       }
     }
 
-    ranges.setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 6f817bb..4f671da 100644
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -224,6 +224,7 @@ public class ViewportRanges extends ViewportProperties
    */
   public void setStartEndSeq(int start, int end)
   {
+    // System.out.println("ViewportRange setStartEndSeq " + start + " " + end);
     int[] oldvalues = updateStartEndSeq(start, end);
     int oldstartseq = oldvalues[0];
     int oldendseq = oldvalues[1];
@@ -285,12 +286,12 @@ 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 +426,21 @@ 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;
     }
+    // System.out.println("ViewportRanges setviewportStartAndHeight " + vpstart
+    // + " " + start + " " + h + " " + getVisibleAlignmentHeight());
+
     setStartEndSeq(vpstart, vpstart + h - 1);
   }