public void setGOtcha(proteinSet train) {
if (this.blastResult.size() == 0) {
System.out.println(access + " have no blast result; We use Naive Score");
this.PredictionScore = train.getNaiveList();
}
ArrayList<Integer> ann = new ArrayList<Integer>();
HashMap<Integer, Double> pred = new HashMap<Integer, Double>();
double SumBitScore = 0;
double bitscore;
for (Pair<String, Double> pair : blastResult) {
bitscore = pair.getSecond();
SumBitScore = SumBitScore + bitscore;
String access = pair.getFirst();
if (train.containProtein(access)) {
ann = train.getAnnotation(access);
for (int node : ann) {
if (!pred.containsKey(node)) {
pred.put(node, bitscore);
} else {
pred.put(node, pred.get(node) + bitscore);
}
}
}
}
for (Map.Entry<Integer, Double> entry : pred.entrySet()) {
this.PredictionScore.add(
new Pair<Integer, Double>(entry.getKey(), (double) entry.getValue() / SumBitScore));
}
}
public void knn(proteinSet train) {
ArrayList<Integer> ann = new ArrayList<Integer>();
HashMap<Integer, Double> pred = new HashMap<Integer, Double>();
double SumBitScore = 0;
double sim;
for (Pair<String, Double> pair : this.Similiar) {
sim = pair.getSecond();
SumBitScore = SumBitScore + sim;
String access = pair.getFirst();
if (train.containProtein(access)) {
ann = train.getAnnotation(access);
for (int node : ann) {
if (!pred.containsKey(node)) {
pred.put(node, sim);
} else {
pred.put(node, pred.get(node) + sim);
}
}
}
}
for (Map.Entry<Integer, Double> entry : pred.entrySet()) {
double knnScore = 0.0;
if (SumBitScore > Parameter.resolution) knnScore = (double) entry.getValue() / SumBitScore;
this.PredictionScore.add(new Pair<Integer, Double>(entry.getKey(), knnScore));
}
}
public double miniscore() {
double miniscore = 1.0;
for (Pair<Integer, Double> entry : PredictionScore) {
if (miniscore > entry.getSecond()) miniscore = entry.getSecond();
}
return miniscore;
}
public void OutputPredScore(PrintWriter Fout) {
Fout.println(this.access);
Fout.print(this.PredictionScore.size());
for (Pair<Integer, Double> entry : this.PredictionScore) {
Fout.printf(" %d:%.4f", entry.getFirst(), entry.getSecond());
}
Fout.println();
}
public oneProtein getSubProtein(char space) {
oneProtein aProtein = new oneProtein(this.access, getSubAnnotation(space));
for (Pair<Integer, Double> entry : PredictionScore) {
int Annotation = entry.getFirst();
if (learning.aGoSet.getSpace(Annotation) == space) aProtein.addPred(entry);
}
return aProtein;
}
public void setLiblinearFeatureFromSparseFeature() {
List<Feature> x = new ArrayList<Feature>();
for (Pair<Integer, Double> pair : this.SparseFeature) {
Feature node = new FeatureNode(pair.getFirst(), pair.getSecond());
x.add(node);
}
this.liblinearFeature = new Feature[x.size()];
this.liblinearFeature = x.toArray(this.liblinearFeature);
this.SparseFeature.clear();
}
public void recordblastScore() {
for (Pair<Integer, Double> pair : this.PredictionScore) {
int label = pair.getFirst();
if ((this.MFOL2RCandidate.contains(label))
|| (this.BPOL2RCandidate.contains(label))
|| (this.CCOL2RCandidate.contains(label))) {
this.blastScore.put(pair.getFirst(), pair.getSecond());
}
}
}
public void removeLowPred(int count) {
ArrayList<Pair<Double, Integer>> ArrSort = new ArrayList<Pair<Double, Integer>>();
for (Pair<Integer, Double> pair : this.PredictionScore) {
ArrSort.add(new Pair<Double, Integer>(pair.getSecond(), pair.getFirst()));
}
Collections.sort(ArrSort);
this.PredictionScore.clear();
int index = Math.max(0, ArrSort.size() - count);
for (int i = ArrSort.size() - 1; i >= index; i--) {
this.PredictionScore.add(
new Pair<Integer, Double>(ArrSort.get(i).getSecond(), ArrSort.get(i).getFirst()));
}
}
public void setBlastPred(proteinSet train) {
ArrayList<Integer> ann = new ArrayList<Integer>();
HashMap<Integer, Double> pred = new HashMap<Integer, Double>();
for (Pair<String, Double> pair : blastResult) {
double bitscore = pair.getSecond();
String access = pair.getFirst();
ann = train.getAnnotation(access);
for (int node : ann) {
if (!pred.containsKey(node)) {
pred.put(node, bitscore);
PredictionScore.add(new Pair<Integer, Double>(node, bitscore));
}
}
}
}
public void OutputSparseFeature(PrintWriter Fout) {
for (Pair<Integer, Double> e : this.SparseFeature) {
Fout.print(" " + e.getFirst() + ":" + e.getSecond());
Fout.printf(" %d:%.4f", e.getFirst(), e.getSecond());
}
}