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); } } } }