Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / viewmodel / OverviewDimensionsShowHidden.java

diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index b897189..4b396a6 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -93,7 +93,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int xAsRes = Math.round((float) x * alwidth / width);
 
     // get viewport width in residues
-    int vpwidth = ranges.getEndRes() - ranges.getStartRes() + 1;
+    int vpwidth = ranges.getViewportWidth();
 
     // get where x should be when accounting for hidden cols
     // if x is in a hidden col region, shift to left - but we still need
@@ -108,14 +108,14 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       // went past the end of the alignment, adjust backwards
 
       // if last position was before the end of the alignment, need to update
-      if ((scrollCol + vpwidth - 1) < visAlignWidth)
+      if (ranges.getEndRes() < visAlignWidth)
       {
         visXAsRes = hiddenCols.findColumnPosition(hiddenCols
                 .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
       }
       else
       {
-        visXAsRes = scrollCol;
+        visXAsRes = ranges.getStartRes();
       }
     }
 
@@ -127,8 +127,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
 
     // get viewport height in sequences
-    // add 1 because height includes both endSeq and startSeq
-    int vpheight = ranges.getEndSeq() - ranges.getStartSeq() + 1;
+    int vpheight = ranges.getViewportHeight();
 
     // get where y should be when accounting for hidden rows
     // if y is in a hidden row region, shift up - but we still need absolute
@@ -143,20 +142,20 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     if (visYAsSeq + vpheight - 1 > visAlignHeight)
     {
       // went past the end of the alignment, adjust backwards
-      if ((scrollRow + vpheight - 1) < visAlignHeight)
+      if (ranges.getEndSeq() < visAlignHeight)
       {
         visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
                 .subtractVisibleRows(vpheight - 1, alheight - 1));
       }
       else
       {
-        visYAsSeq = scrollRow;
+        visYAsSeq = ranges.getStartSeq();
       }
     }
 
-    // update scroll values
-    scrollCol = visXAsRes;
-    scrollRow = visYAsSeq;
+    // update viewport
+    ranges.setStartRes(visXAsRes);
+    ranges.setStartSeq(visYAsSeq);
 
   }
 
@@ -176,15 +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