}
/**
+ * add a series of start,end (inclusive) ranges to the column selection
+ *
+ * @param rng
+ * [start_0, end_0, start_1, end_1, ... ]
+ * @param baseOne
+ * - when true, ranges are base 1 and will be mapped to base 0
+ */
+ public void addRangeOfElements(int[] rng, boolean baseOne)
+ {
+ int base = baseOne ? -1 : 0;
+ for (int c = 0; c < rng.length; c += 2)
+ {
+ for (int p = rng[c]; p <= rng[c + 1]; p++)
+ {
+ selection.add(base + p);
+ }
+ }
+
+ }
+
+ /**
* clears column selection
*/
public void clear()
// viewmodel package
this.clear();
- if (ann_row.graph == AlignmentAnnotation.CUSTOMRENDERER && (filterParams
+ if (ann_row.graph == AlignmentAnnotation.CONTACT_MAP && (filterParams
.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
|| filterParams
.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD))
int cpos = ann_row.sequenceRef.findPosition(column) - 1;
ContactListI clist = ann_row.sequenceRef
.getContactListFor(ann_row, cpos);
- for (int row = column + 8,
- rowEnd = clist.getContactHeight(); row < rowEnd; row++)
+ for (int row = column + 8, rowEnd = clist
+ .getContactHeight(); row < rowEnd; row++)
{
if (filterParams
.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD