JAL-2388 Tidies and unit tests

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

diff --git a/src/jalview/viewmodel/OverviewDimensionsWithHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
similarity index 77%
rename from src/jalview/viewmodel/OverviewDimensionsWithHidden.java
rename to src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index e718d5a..b897189 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensionsWithHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -28,9 +28,9 @@ import jalview.datamodel.AllRowsCollection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 
-public class OverviewDimensionsWithHidden extends OverviewDimensions
+public class OverviewDimensionsShowHidden extends OverviewDimensions
 {
-  private ViewportRanges alRanges;
+  private ViewportRanges ranges;
 
   /**
    * Create an OverviewDimensions object
@@ -40,11 +40,11 @@ public class OverviewDimensionsWithHidden extends OverviewDimensions
    * @param showAnnotationPanel
    *          true if the annotation panel is to be shown, false otherwise
    */
-  public OverviewDimensionsWithHidden(ViewportRanges ranges,
+  public OverviewDimensionsShowHidden(ViewportRanges vpranges,
           boolean showAnnotationPanel)
   {
-    super(ranges, showAnnotationPanel);
-    alRanges = ranges;
+    super(vpranges, showAnnotationPanel);
+    ranges = vpranges;
     resetAlignmentDims();
   }
 
@@ -93,7 +93,7 @@ public class OverviewDimensionsWithHidden extends OverviewDimensions
     int xAsRes = Math.round((float) x * alwidth / width);
 
     // get viewport width in residues
-    int vpwidth = alRanges.getEndRes() - alRanges.getStartRes() + 1;
+    int vpwidth = ranges.getEndRes() - ranges.getStartRes() + 1;
 
     // 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
@@ -128,7 +128,7 @@ public class OverviewDimensionsWithHidden extends OverviewDimensions
 
     // get viewport height in sequences
     // add 1 because height includes both endSeq and startSeq
-    int vpheight = alRanges.getEndSeq() - alRanges.getStartSeq() + 1;
+    int vpheight = ranges.getEndSeq() - ranges.getStartSeq() + 1;
 
     // 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
@@ -175,52 +175,37 @@ public class OverviewDimensionsWithHidden extends OverviewDimensions
   public void setBoxPosition(HiddenSequences hiddenSeqs,
           HiddenColumns hiddenCols)
   {
-    resetAlignmentDims();
-
     // work with absolute values of startRes and endRes
     int startRes = hiddenCols
-            .adjustForHiddenColumns(alRanges.getStartRes());
-    int endRes = hiddenCols.adjustForHiddenColumns(alRanges.getEndRes());
+            .adjustForHiddenColumns(ranges.getStartRes());
+    int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
 
     // work with absolute values of startSeq and endSeq
-    int startSeq = hiddenSeqs.adjustForHiddenSeqs(alRanges.getStartSeq());
-    int endSeq = hiddenSeqs.adjustForHiddenSeqs(alRanges.getEndSeq());
-
-    // boxX, boxY is the x,y location equivalent to startRes, startSeq
-    boxX = Math.round((float) startRes * width / alwidth);
-    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);
-    // boxHeight is the height in sequences translated to pixels
-    boxHeight = Math.round((float) (endSeq - startSeq + 1)
-            * sequencesHeight
-            / alheight);
+    int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
+    int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
+
+    setBoxPosition(startRes, endRes, startSeq, endSeq);
   }
 
   @Override
-  public AlignmentColsCollectionI getColumns(HiddenColumns hiddenCols)
+  public AlignmentColsCollectionI getColumns(AlignmentI al)
   {
     return new AllColsCollection(0,
-            alRanges.getAbsoluteAlignmentWidth() - 1,
-            hiddenCols);
+            ranges.getAbsoluteAlignmentWidth() - 1, al);
   }
 
   @Override
   public AlignmentRowsCollectionI getRows(AlignmentI al)
   {
     return new AllRowsCollection(0,
-            alRanges.getAbsoluteAlignmentHeight() - 1,
+            ranges.getAbsoluteAlignmentHeight() - 1,
             al);
   }
 
   @Override
   protected void resetAlignmentDims()
   {
-    alwidth = alRanges.getAbsoluteAlignmentWidth();
-    alheight = alRanges.getAbsoluteAlignmentHeight();
+    alwidth = ranges.getAbsoluteAlignmentWidth();
+    alheight = ranges.getAbsoluteAlignmentHeight();
   }
 }