* the alignment's hidden columns
* @return a column collection
*/
- public abstract AlignmentColsCollectionI getColumns(
- HiddenColumns hiddenCols);
+ public abstract AlignmentColsCollectionI getColumns(AlignmentI al);
/**
* Get the collection of rows used by this overview dimensions object
* Updates overview dimensions to account for current alignment dimensions
*/
protected abstract void resetAlignmentDims();
+
+ protected void setBoxPosition(int startRes, int endRes, int startSeq,
+ int endSeq)
+ {
+ resetAlignmentDims();
+
+ // 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);
+ }
}
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