@Override
protected DefaultMutableTreeNode doInBackground() {
myNode = new DefaultMutableTreeNode(this.mouseID);
message("startedLoadingTree", "Doh");
setMessage("Creating Mouse Tree ...");
if (0 == "FindAncestors".compareTo(this.function)) {
ped.FindAncestors(0, this.mouseID, myNode);
return (myNode);
} else if (0 == "FindDescendants".compareTo(this.function)) {
ped.FindDescendants(0, this.mouseID, myNode);
return (myNode);
} else return (null);
}
private void redirect(String pedigreeFileS, String biparentalStr) {
Pedigree ped = new Pedigree(pedigreeFileS);
String[] NAMfamily = ped.getFamilyStartWith(biparentalStr, 100);
String[][] samples = ped.getSampleOfFamilies(NAMfamily, 100);
for (int i = 0; i < samples.length; i++) {
Arrays.sort(samples[i]);
}
tbt2anchorRedirect = new int[NAMfamily.length][theTBTs[0].getTaxaNames().length];
IdGroup anchorIdGroup = theAnchorChrInBits[0].getIdGroup();
String[] taxaNameAnchor = new String[anchorIdGroup.getIdCount()];
int[] taxaNameIndexAnchor = new int[anchorIdGroup.getIdCount()];
int[] familyMark = new int[taxaNameAnchor.length];
for (int i = 0; i < taxaNameAnchor.length; i++) {
taxaNameAnchor[i] = anchorIdGroup.getIdentifier(i).getFullName();
taxaNameIndexAnchor[i] = i;
}
for (int i = 0; i < taxaNameAnchor.length - 1; i++) {
for (int j = i + 1; j < taxaNameAnchor.length; j++) {
if (taxaNameAnchor[i].compareTo(taxaNameAnchor[j]) > 0) {
String temp;
temp = taxaNameAnchor[i];
taxaNameAnchor[i] = taxaNameAnchor[j];
taxaNameAnchor[j] = temp;
int tem;
tem = taxaNameIndexAnchor[i];
taxaNameIndexAnchor[i] = taxaNameIndexAnchor[j];
taxaNameIndexAnchor[j] = tem;
}
}
}
for (int i = 0; i < taxaNameAnchor.length; i++) {
familyMark[i] = -1;
int hit = -1;
for (int j = 0; j < samples.length; j++) {
hit = Arrays.binarySearch(samples[j], taxaNameAnchor[i]);
if (hit >= 0) {
familyMark[i] = j;
break;
}
}
// System.out.println(taxaNameAnchor[i]+"\t"+hit);
}
for (int i = 0; i < theTBTs[0].getTaxaNames().length; i++) {
String query = theTBTs[0].getTaxaName(i);
int hit = Arrays.binarySearch(taxaNameAnchor, query);
if (hit >= 0 && familyMark[hit] != -1) {
tbt2anchorRedirect[familyMark[hit]][i] = taxaNameIndexAnchor[hit];
for (int j = 0; j < tbt2anchorRedirect.length; j++) {
if (j == familyMark[hit]) continue;
tbt2anchorRedirect[j][i] = -1;
}
} else {
for (int j = 0; j < tbt2anchorRedirect.length; j++) {
tbt2anchorRedirect[j][i] = -1;
}
}
}
family2TBTIndex = new int[tbt2anchorRedirect.length][];
for (int i = 0; i < tbt2anchorRedirect.length; i++) {
ArrayList<Integer> temp = new ArrayList();
for (int j = 0; j < tbt2anchorRedirect[i].length; j++) {
if (tbt2anchorRedirect[i][j] > -1) temp.add(j);
}
family2TBTIndex[i] = new int[temp.size()];
for (int j = 0; j < family2TBTIndex[i].length; j++) {
family2TBTIndex[i][j] = temp.get(j);
}
}
}
