/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.ws.hmmer;
import java.io.Serializable;
import java.util.SortedSet;
/** The results of a Hmmer search for a single sequence
*
* @author Andreas Prlic
* @since 3.0.3
*/
public class HmmerResult implements Comparable<HmmerResult>, Serializable{
/**
*
*/
private static final long serialVersionUID = -6016026193090737943L;
String desc ;
Float score;
Float evalue;
Double pvalue;
String acc;
Integer dcl;
String name;
Integer ndom;
Integer nreported;
SortedSet<HmmerDomain>domains;
public SortedSet<HmmerDomain> getDomains() {
return domains;
}
public void setDomains(SortedSet<HmmerDomain> domains) {
this.domains = domains;
}
public String getDesc() {
return desc;
}
public void setDesc(String desc) {
this.desc = desc;
}
public Float getScore() {
return score;
}
public void setScore(Float score) {
this.score = score;
}
public Float getEvalue() {
return evalue;
}
public void setEvalue(Float evalue) {
this.evalue = evalue;
}
public Double getPvalue() {
return pvalue;
}
public void setPvalue(Double pvalue) {
this.pvalue = pvalue;
}
public String getAcc() {
return acc;
}
public void setAcc(String acc) {
this.acc = acc;
}
public Integer getDcl() {
return dcl;
}
public void setDcl(Integer dcl) {
this.dcl = dcl;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public Integer getNdom() {
return ndom;
}
public void setNdom(Integer ndom) {
this.ndom = ndom;
}
public Integer getNreported() {
return nreported;
}
public void setNreported(Integer nreported) {
this.nreported = nreported;
}
@Override
public String toString() {
return "HmmerResult [acc=" + acc + ", desc=" + desc + ", score=" + score + ", evalue="
+ evalue + ", pvalue=" + pvalue + ", dcl="
+ dcl + ", name=" + name + ", ndom=" + ndom + ", nreported="
+ nreported + ", domains=" + domains + "]";
}
@Override
public int compareTo(HmmerResult o) {
// sort by the start position of the first domain
if ( emptyDomains(this) && emptyDomains(o)){
return 0;
}
if ( ! emptyDomains(this) && emptyDomains(o))
return -1;
if ( emptyDomains(this) && (! emptyDomains(o)))
return 1;
// ok when we are here, both domains are not empty
HmmerDomain me = this.getDomains().first();
HmmerDomain other = o.getDomains().first();
//System.out.println(" domains: " + me.getHmmAcc() + " " + other.getHmmAcc()+ " " + me.getSqFrom().compareTo(other.getSqFrom()));
return(me.getSqFrom().compareTo(other.getSqFrom()));
}
private boolean emptyDomains(HmmerResult o) {
if ( o.getDomains() == null || o.getDomains().size() == 0)
return true;
return false;
}
/** Get the overlap between two HmmerResult objects
*
* @param other
* @return 0 if no overlap, otherwise the length of the overlap
*/
public int getOverlapLength(HmmerResult other){
int overlap = 0;
for ( HmmerDomain d1 : getDomains()){
for (HmmerDomain d2 : other.getDomains()){
overlap += getOverlap(d1, d2);
}
}
return overlap;
}
private int getOverlap(HmmerDomain one, HmmerDomain other){
int xs = one.getSqFrom();
int ys = one.getSqTo();
int as = other.getSqFrom();
int bs = other.getSqTo();
int overlap = 0;
//1:
if ((( xs< as) && ( as<ys)) || ((xs < bs) && ( bs <= ys)) || (as<xs && ys<bs)) {
//2:
if ( xs < as) {
if ( ys < bs)
overlap = ys-as;
else
overlap = bs-as;
} else {
if ( ys < bs)
overlap = ys -xs;
else
overlap = bs - xs;
}
}
return overlap;
}
}