+ boolean showUnconserved=false;
+ public boolean getShowUnconserved()
+ {
+ return showUnconserved;
+ }
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ showUnconserved=showunconserved;
+ }
+ /**
+ * return the alignPanel containing the given viewport. Use this to get the
+ * components currently handling the given viewport.
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame reference
+ */
+ public AlignmentPanel getAlignPanel()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this.getSequenceSetId());
+ AlignmentPanel ap=null;
+ for (int p=0;aps!=null && p<aps.length; p++)
+ {
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
+ }
+ return null;
+ }
+ public boolean getSortByTree()
+ {
+ return sortByTree;
+ }
+ public void setSortByTree(boolean sort) {
+ sortByTree = sort;
+ }