/*
* 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;
/** Provides the details of a domain hit
*
* @author Andreas Prlic
* @since 3.0.3
*/
public class HmmerDomain implements Comparable<HmmerDomain>, Serializable{
/**
*
*/
private static final long serialVersionUID = 8004302800150892757L;
Integer sqFrom;
Integer sqTo;
Integer aliLenth;
Integer simCount;
Integer hmmFrom;
Integer hmmTo;
String hmmName;
String hmmDesc;
String hmmAcc;
Float evalue;
public Float getEvalue() {
return evalue;
}
public void setEvalue(Float evalue) {
this.evalue = evalue;
}
public Integer getSqFrom() {
return sqFrom;
}
public void setSqFrom(Integer sqFrom) {
this.sqFrom = sqFrom;
}
public Integer getSqTo() {
return sqTo;
}
public void setSqTo(Integer sqTo) {
this.sqTo = sqTo;
}
public Integer getAliLenth() {
return aliLenth;
}
public void setAliLenth(Integer aliLenth) {
this.aliLenth = aliLenth;
}
public Integer getSimCount() {
return simCount;
}
public void setSimCount(Integer simCount) {
this.simCount = simCount;
}
public Integer getHmmFrom() {
return hmmFrom;
}
public void setHmmFrom(Integer hmmFrom) {
this.hmmFrom = hmmFrom;
}
public Integer getHmmTo() {
return hmmTo;
}
public void setHmmTo(Integer hmmTo) {
this.hmmTo = hmmTo;
}
public String getHmmName() {
return hmmName;
}
public void setHmmName(String hmmName) {
this.hmmName = hmmName;
}
public String getHmmDesc() {
return hmmDesc;
}
public void setHmmDesc(String hmmDesc) {
this.hmmDesc = hmmDesc;
}
public String getHmmAcc() {
return hmmAcc;
}
public void setHmmAcc(String hmmAcc) {
this.hmmAcc = hmmAcc;
}
@Override
public String toString() {
return "HmmerDomain [hmmAcc=" + hmmAcc + ", hmmDesc=" + hmmDesc
+ "sqFrom=" + sqFrom + ", sqTo=" + sqTo
+ ", aliLenth=" + aliLenth + ", simCount=" + simCount
+ ", hmmFrom=" + hmmFrom + ", hmmTo=" + hmmTo + ", hmmName="
+ hmmName + "]" ;
}
@Override
public int compareTo(HmmerDomain o) {
if (emptyDomain(this) &&emptyDomain(o))
return 0;
if ( ! emptyDomain(this) &&emptyDomain(o))
return -1;
if (emptyDomain(this) && (! emptyDomain(o)))
return 1;
return (this.getSqFrom().compareTo(o.getSqFrom()));
}
private boolean emptyDomain(HmmerDomain o) {
if ( o.getSqFrom() == null)
return true;
return false;
}
/*
*
* that's the full data that is currently responded from the JSON api:
[{"ievalue":"0.021","cevalue":"1.0e-05",
"alimline":"+++Wc+ ++++ +GW+ ++ +","jali":62,
"alicsline":0,"aliIdCount":4,"aliSimCount":17,
"aliM":55,"alisqto":"62","aliL":164,"alimemsize":
"kenWcrvradGatGWiyqslL\u0000+++Wc+ ++++ +GW+ ++ +\u0000NGEWCEAQTKNGQGWVPSNYI\u000089**************98765\u0000000010555\u0000PF06347.7\u0000Bacterial SH3 domain\u0000seq\u0000\u0000",
"alihmmacc":"PF06347.7","oasc":"0.88",
"aliaseq":"NGEWCEAQTKNGQGWVPSNYI","aliN":21,
"iali":42,"alihindex":"10555","is_reported":"1",
"alimodel":"kenWcrvradGatGWiyqslL","alippline":"89**************98765",
"aliSim":0.80952380952381,"alisqacc":"","jenv":"64",
"alihmmname":"SH3_4","alihmmdesc":"Bacterial SH3 domain",
"alihmmto":"53","alirfline":0,
"bitscore":14.0345134735107,"bias":"0.20",
"alisqfrom":"42",
"alisqname":"1","aliappline":0,
"alihmmfrom":"33","alimem":46912854337136,
"aliId":0.19047619047619,"is_included":"0",
"alisqdesc":"","ienv":"36"}] */
}