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package pp2.prediction.knn;
/**
* Stores a BLAST hit with associated information such as E-value etc.
* @author Thomas Hopf
*
*/
public class BlastHit implements Comparable<BlastHit>{
// FASTA identifier of the hit
private String hitID;
// list of all associated go terms
private String[] goTerms;
// all measures of the hit
private double eValue;
private double bitScore;
private int length;
private int sequenceIdentity;
private int sequenceIdentityLength;
private int gaps;
private int gapsLength;
// PSI-Blast iteration in which the hit was found
private int iteration;
// holds which ontologies are supported by this hit (important for calculating normalization values)
private boolean[] supports;
// private boolean supportsMolecularFunction = false;
// private boolean supportsBiologicalProcess = false;
// private boolean supportsCellularComponent = false;
public BlastHit(String hitLine)
{
try {
String[] split = hitLine.split("\t");
//System.out.println(Arrays.toString(split));
// extract all information from the hitLine
hitID = split[0];
goTerms = split[1].split(",");
// if eValue has format e-117, we need to add a "1" as prefix to avoid a NumberFormatException
eValue = Double.parseDouble(split[2].startsWith("e") ? ("1"+split[2]): split[2]);
bitScore = Double.parseDouble(split[3]);
length = Integer.parseInt(split[4]);
sequenceIdentity = Integer.parseInt(split[5].split("/")[0]);
sequenceIdentityLength = Integer.parseInt(split[5].split("/")[1]);
if(split[6].equals("0"))
{
gaps = 0;
gapsLength = length;
}
else
{
gaps = Integer.parseInt(split[6].split("/")[0]);
gapsLength = Integer.parseInt(split[6].split("/")[1]);
}
iteration = Integer.parseInt(split[7]);
supports = new boolean[PredictionTarget.NUM_ONTOLOGIES];
} catch(Exception e) {
System.err.println("an error occurred while parsing a blast hit line:");
System.err.println(hitLine);
e.printStackTrace();
//System.err.println(e);
}
//System.out.println(hitID + "->" + goTerms + ", " + eValue);
}
// deprecated
public BlastHit(String goTerms, double eValue)
{
this.goTerms = goTerms.split(",");
this.eValue = eValue;
}
public double getEValue()
{
return eValue;
}
public String[] getGoTerms()
{
return goTerms;
}
public double getBitScore()
{
return bitScore;
}
public String getHitID()
{
return hitID;
}
public boolean supports(int ontologyType) {
return supports[ontologyType];
}
public void activateOntologySupport(String ontology)
{
if(ontology.equals("molecular_function"))
supports[PredictionTarget.MOLECULAR_FUNCTION] = true;
else {
if(ontology.equals("biological_process"))
supports[PredictionTarget.BIOLOGICAL_PROCESS] = true;
else
supports[PredictionTarget.CELLULAR_COMPONENT] = true;
}
}
@Override
public int compareTo(BlastHit o) {
if(this.eValue < o.eValue)
return -1;
else {
if (this.eValue > o.eValue)
return 1;
else
return 0;
}
}
}
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