this.alignment=alignment;
this.selection = selection;
}
-
+
public Finder(AlignmentI alignment, SequenceGroup selectionGroup, int seqIndex, int resIndex) {
this(alignment, selectionGroup);
this.seqIndex=seqIndex;
{
int res = Integer.parseInt(searchString);
found = true;
- if (selection == null || selection.getSize(false) < 1)
+ if (selection == null || selection.getSize() < 1)
{
seq = (Sequence) alignment.getSequenceAt(0);
}
int end = alignment.getHeight();
-
+
if (selection != null)
{
- if ((selection.getSize(false) < 1) ||
+ if ((selection.getSize() < 1) ||
((selection.getEndRes() - selection.getStartRes()) < 2))
{
selection = null;
{
seq = (Sequence) alignment.getSequenceAt(seqIndex);
- if ((selection != null) && !selection.getSequences(false).contains(seq))
+ if ((selection != null) && !selection.getSequences(null).contains(seq))
{
seqIndex++;
resIndex = 0;
{
item = item.substring(0, selection.getEndRes() + 1);
}
-
+
///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
StringBuffer noGapsSB = new StringBuffer();
int insertCount = 0;