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package proteinstructure; |
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import java.util.TreeMap; |
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import java.util.ArrayList; |
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public class NbhProbDistribution { |
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final static int MAXRANK = 21; |
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double entropy; |
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TreeMap<String,Double> dist; |
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TreeMap<String,Integer> ranks; |
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public NbhProbDistribution(TreeMap<String,Double> dist) { |
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this.dist=dist; |
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this.entropy=calculateEntropy(); |
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getRanks(); //initialises ranks TreeMap |
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} |
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|
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public double getProb(String res){ |
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return dist.get(res); |
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} |
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public int getRank(String res) { |
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return ranks.get(res); |
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} |
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public double getEntropy(){ |
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return entropy; |
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} |
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public ArrayList<String> getResiduesSortedByRank(){ |
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ArrayList<String> sortedResidues = new ArrayList<String>(); |
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for (int i=1;i<=21;i++){ |
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for (String res:ranks.keySet()){ |
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if (ranks.get(res)<=i && !sortedResidues.contains(res)){ |
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sortedResidues.add(res); |
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} |
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} |
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} |
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return sortedResidues; |
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} |
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private void getRanks(){ |
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ranks = new TreeMap<String, Integer>(); |
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// first we set the residues with prob=0.0 to MAXRANK |
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for (String res:dist.keySet()){ |
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if (!ranks.containsKey(res)) { // we don't check the ones already assigned |
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double prob = dist.get(res); |
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if (prob==0.0){ |
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ranks.put(res,MAXRANK); |
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} |
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} |
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} |
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// now we set ranks for the rest |
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int lastRank = 0; |
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double lastMax = 0.0; |
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int numberNonZeroProb = dist.size()-ranks.size(); |
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for (int rank=1;rank<=numberNonZeroProb;rank++){ |
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double max = 0.0; |
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String maxres=""; |
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for (String res:dist.keySet()){ |
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if (!ranks.containsKey(res)) { |
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double prob = dist.get(res); |
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if (prob>=max){ |
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max = prob; |
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maxres = res; |
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} |
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} |
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} |
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if (max==lastMax){ |
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ranks.put(maxres, lastRank); |
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} else { |
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ranks.put(maxres,rank); |
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lastRank = rank; |
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} |
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lastMax = max; |
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} |
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} |
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private double calculateEntropy(){ |
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double sumplogp=0.0; |
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for (double prob:dist.values()){ |
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if (prob!=0){ // plogp is defined to be 0 when p=0 (because of limit). If we let java calculate it, it gives NaN (-infinite) because it tries to compute log(0) |
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sumplogp += prob*(Math.log(prob)/Math.log(2)); |
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} |
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} |
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return (double) (-1)*sumplogp; |
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} |
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} |
