From b21b4cdb3d8bbf84d0b86c6d3ea724aa3c1ea3f8 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 15 May 2017 12:27:53 +0100
Subject: [PATCH] JAL-2491 Better merge but not quite right yet

---
 src/jalview/viewmodel/OverviewDimensions.java           |   13 +++++--------
 src/jalview/viewmodel/OverviewDimensionsHideHidden.java |   15 ++++-----------
 src/jalview/viewmodel/OverviewDimensionsShowHidden.java |   14 +++++++-------
 3 files changed, 16 insertions(+), 26 deletions(-)

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index dd7eb1e..d2912d8 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -225,8 +225,8 @@ public abstract class OverviewDimensions
    */
   protected abstract void resetAlignmentDims();
 
-  protected void setBoxPosition(int startRes, int endRes, int startSeq,
-          int endSeq)
+  protected void setBoxPosition(int startRes, int startSeq, int vpwidth,
+          int vpheight)
   {
     resetAlignmentDims();
 
@@ -235,12 +235,9 @@ public abstract class OverviewDimensions
     boxY = Math.round((float) startSeq * sequencesHeight / alheight);
 
     // boxWidth is the width in residues translated to pixels
-    // since the box includes both the start and end residues, add 1 to the
-    // difference
-    boxWidth = Math
-            .round((float) (endRes - startRes + 1) * width / alwidth);
+    boxWidth = Math.round((float) vpwidth * width / alwidth);
+
     // boxHeight is the height in sequences translated to pixels
-    boxHeight = Math.round((float) (endSeq - startSeq + 1)
-            * sequencesHeight / alheight);
+    boxHeight = Math.round((float) vpheight * sequencesHeight / alheight);
   }
 }
\ No newline at end of file
diff --git a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
index 9236151..cb9c535 100644
--- a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
@@ -64,7 +64,7 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
       }
       else
       {
-        xAsRes = ranges.getEndRes();
+        xAsRes = ranges.getStartRes();
       }
     }
 
@@ -89,7 +89,7 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
       }
       else
       {
-        yAsSeq = ranges.getEndSeq();
+        yAsSeq = ranges.getStartSeq();
       }
     }
 
@@ -103,15 +103,8 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public void setBoxPosition(HiddenSequences hiddenSeqs,
           HiddenColumns hiddenCols)
   {
-    // work with visible values of startRes and endRes
-    int startRes = ranges.getStartRes();
-    int endRes = ranges.getEndRes();
-
-    // work with visible values of startSeq and endSeq
-    int startSeq = ranges.getStartSeq();
-    int endSeq = ranges.getEndSeq();
-
-    setBoxPosition(startRes, endRes, startSeq, endSeq);
+    setBoxPosition(ranges.getStartRes(), ranges.getStartSeq(),
+            ranges.getViewportWidth(), ranges.getViewportHeight());
   }
 
   @Override
diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index 4f7d6c2..3506332 100644
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -115,7 +115,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       }
       else
       {
-        visXAsRes = ranges.getEndRes();
+        visXAsRes = ranges.getStartRes();
       }
     }
 
@@ -149,13 +149,13 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       }
       else
       {
-        visYAsSeq = ranges.getEndSeq();
+        visYAsSeq = ranges.getStartSeq();
       }
     }
 
     // update viewport
-    ranges.setStartRes(xAsRes);
-    ranges.setStartSeq(yAsSeq);
+    ranges.setStartRes(visXAsRes);
+    ranges.setStartSeq(visYAsSeq);
 
   }
 
@@ -175,15 +175,15 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
           HiddenColumns hiddenCols)
   {
     // work with absolute values of startRes and endRes
-    int startRes = hiddenCols
-            .adjustForHiddenColumns(ranges.getStartRes());
+    int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
     int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
 
     // work with absolute values of startSeq and endSeq
     int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
     int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
 
-    setBoxPosition(startRes, endRes, startSeq, endSeq);
+    setBoxPosition(startRes, startSeq, endRes - startRes + 1, endSeq
+            - startSeq + 1);
   }
 
   @Override
-- 
1.7.10.2