public void analyze(String name, Object data) {
if (!(data instanceof SequenceGroup)) {
ErrorWindow.showErrorWindow(
new Exception("Got a non-sequencegroup object for a dot plot analysis"));
}
SequenceGroup sg = (SequenceGroup) data;
currentSG = sg;
titleLabel.setText(name);
DefaultComboBoxModel cModel1 = new DefaultComboBoxModel();
DefaultComboBoxModel cModel2 = new DefaultComboBoxModel();
for (int j = 0; j < sg.size(); j++) {
cModel1.addElement(sg.get(j).getName());
cModel2.addElement(sg.get(j).getName());
}
seq1Box.setModel(cModel1);
seq2Box.setModel(cModel2);
seq1Box.setSelectedIndex(0);
seq2Box.setSelectedIndex(1);
dotPlot.setBlockWidth((Integer) blockWidthSpinner.getValue());
changeSequences();
}
/**
* Returns true if there is more than one base in this column Gap characters (as defined by
* Sequence.GAP) don't count one way or the other. All gaps in this colum return false
*/
public boolean isPolymorphic(int site) {
if (sg.size() == 0) return false;
char base = sg.get(0).at(site);
int seqNum = 0;
while (seqNum < sg.size() && charIsGap(base)) {
base = sg.get(seqNum).at(site);
seqNum++;
}
// Every base is a gap in this column, I guess we return false here
if (seqNum == sg.size()) {
return false;
}
boolean same = true;
for (int i = seqNum; i < sg.size() && same; i++) {
char compBase = sg.get(i).at(site);
if ((!charIsGap(compBase)) && compBase != base) same = false;
}
return !same;
}
/** Returns true if any sequence has a gap at this site */
public boolean hasGap(int site) {
for (int i = 0; i < sg.size(); i++) if (sg.get(i).isGap(site)) return true;
return false;
}
