/**
* Routines for manipulating the order of a multiple sequence alignment
- * TODO: this class retains some global states concerning sort-order which should be made attributes for the caller's alignment visualization.
+ * TODO: this class retains some global states concerning sort-order which should be made attributes for the caller's alignment visualization.
+ * TODO: refactor to allow a subset of selected sequences to be sorted within the context of a whole alignment.
+ * Sort method template is: SequenceI[] tobesorted, [ input data mapping to each tobesorted element to use ], Alignment context of tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie seuqence to be sorted w.r.t.])
+ * sortinplace implies that the sorted vector resulting from applying the operation to tobesorted should be mapped back to the original positions in alignment.
+ * Otherwise, normal behaviour is to re order alignment so that tobesorted is sorted and grouped together starting from the first tobesorted position in the alignment.
+ * e.g. (a,tb2,b,tb1,c,tb3 becomes a,tb1,tb2,tb3,b,c)
*/
public class AlignmentSorter
{
private static String lastSortByScore;
/**
- * Sort by Percentage Identity
+ * Sort by Percentage Identity w.r.t. s
*
* @param align AlignmentI
* @param s SequenceI
+ * @param tosort sequences from align that are to be sorted.
*/
- public static void sortByPID(AlignmentI align, SequenceI s)
+ public static void sortByPID(AlignmentI align, SequenceI s, SequenceI[] tosort)
{
int nSeq = align.getHeight();
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(),
- viewport.getAlignment().getSequenceAt(0));
+ viewport.getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.alignment));
alignPanel.paintAlignment(true);
{
SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(),
- viewport.getAlignment().getSequenceAt(0));
+ viewport.getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.alignment));
alignPanel.paintAlignment(true);
public void actionPerformed(ActionEvent e)
{
SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
+ AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());//,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
alignPanel.paintAlignment(true);
}