+ /**
+ * Get the collection of rows used by this overview dimensions object
+ *
+ * @param al
+ * the alignment
+ * @return a row collection
+ */
+ public abstract AlignmentRowsCollectionI getRows(AlignmentI al);
+
+ /**
+ * Updates overview dimensions to account for current alignment dimensions
+ */
+ protected abstract void resetAlignmentDims();
+
+ protected void setBoxPosition(int startRes, int startSeq, int vpwidth,
+ int vpheight)
+ {
+ 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
+ boxWidth = Math.round((float) vpwidth * width / alwidth);
+
+ // boxHeight is the height in sequences translated to pixels
+ boxHeight = Math.round((float) vpheight * sequencesHeight / alheight);
+ }
+
+ /**
+ * Answers if a mouse position is in the overview's red box
+ *
+ * @param x
+ * mouse x position
+ * @param y
+ * mouse y position
+ * @return true if (x,y) is inside the box
+ */
+ protected boolean isPositionInBox(int x, int y)
+ {
+ return (x > boxX && y > boxY && boxX + x < boxWidth
+ && boxY + y < boxHeight);
+ }