public void calMFBPCCsize(GoSet aGoSet) {
this.MFOsize = 0;
this.BPOsize = 0;
this.CCOsize = 0;
for (int node : this.Annotation) {
if (aGoSet.getSpace(node) == 'F') this.MFOsize++;
if (aGoSet.getSpace(node) == 'P') this.BPOsize++;
if (aGoSet.getSpace(node) == 'C') this.CCOsize++;
}
}
public void removeRedunAnn(GoSet aGoSet) {
ArrayList<Integer> Ann = new ArrayList<Integer>();
for (int ann : this.Annotation) Ann.add(ann);
for (int i = 0; i < Ann.size() - 1; i++)
for (int j = 0; j < Ann.size(); j++) {
int ann1 = Ann.get(i);
int ann2 = Ann.get(j);
if (aGoSet.checkFather(ann1, ann2) != 0) {
int father = aGoSet.checkFather(ann1, ann2);
this.Annotation.remove(father);
}
}
}
public void filterGoNotIn(GoSet aGo) {
HashSet<Integer> aAnnotation = new HashSet<Integer>();
for (Integer i : this.Annotation) {
if (aGo.containNode(i)) aAnnotation.add(i);
else System.out.println("remove" + this.access + " : " + i);
}
this.Annotation = aAnnotation;
}
public void OutputType3Annotation(PrintWriter Fout, GoSet aGoSet) {
ArrayList<Integer> Ann = new ArrayList<Integer>();
for (Integer i : Annotation) {
Ann.add(i);
}
Collections.sort(Ann);
for (Integer i : Ann) {
if (this.getStoreAnnotationSize(aGoSet.getSpace(i)) == 0)
Fout.println(this.access + "\t" + proteinCommon.GOInt2Str(i));
}
}
public void addIEAFather(GoSet aGoSet) {
ArrayList<Integer> tempor = new ArrayList<Integer>(IEA_Annotation);
for (int i = 0; i < tempor.size(); i++) {
int gonum = tempor.get(i);
Set<Integer> fatherList = aGoSet.getFatherList(gonum);
for (Integer father : fatherList) {
if (!IEA_Annotation.contains(father)) {
IEA_Annotation.add(father);
tempor.add(father);
}
}
}
}
