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Copy pathResidueNumber.java
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279 lines (241 loc) · 6.47 KB
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/*
* 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/
*
* Created on Jun 17, 2010
* Author: ap3
*
*/
package org.biojava.nbio.structure;
import java.io.Serializable;
import java.io.StringWriter;
/**
* Everything that is needed to uniquely describe a residue position
*
* @author Andreas Prlic
*
*/
public class ResidueNumber implements Serializable, Comparable<ResidueNumber>
{
private static final long serialVersionUID = 1773011704758536083L;
private String chainName;
private Character insCode;
private Integer seqNum;
public ResidueNumber() {
}
public ResidueNumber(ResidueNumber o) {
this.chainName = o.chainName;
this.insCode = o.insCode;
this.seqNum = o.seqNum;
}
public ResidueNumber(String chainName, Integer residueNumber, Character insCode) {
this.chainName = chainName;
this.seqNum = residueNumber;
this.insCode = insCode;
}
public String getChainName()
{
return chainName;
}
public void setChainName(String chainName)
{
this.chainName = chainName;
}
public Character getInsCode()
{
return insCode;
}
public void setInsCode(Character insCode)
{
this.insCode = insCode;
}
public Integer getSeqNum()
{
return seqNum;
}
public void setSeqNum(Integer seqNum)
{
this.seqNum = seqNum;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
ResidueNumber other = (ResidueNumber) obj;
if (chainName == null) {
if (other.chainName != null)
return false;
} else if (!chainName.equals(other.chainName))
return false;
if (insCode == null) {
if (other.insCode != null)
return false;
} else if (!insCode.equals(other.insCode))
return false;
if (seqNum == null) {
if (other.seqNum != null)
return false;
} else if (!seqNum.equals(other.seqNum))
return false;
return true;
}
/**
* Check if the seqNum and insertion code are equivalent,
* ignoring the chain
* @param obj
* @return
*/
public boolean equalsPositional(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
ResidueNumber other = (ResidueNumber) obj;
if (insCode == null) {
if (other.insCode != null)
return false;
} else if (!insCode.equals(other.insCode))
return false;
if (seqNum == null) {
if (other.seqNum != null)
return false;
} else if (!seqNum.equals(other.seqNum))
return false;
return true;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((chainName == null) ? 0 : chainName.hashCode());
result = prime * result + ((insCode == null) ? 0 : insCode.hashCode());
result = prime * result + ((seqNum == null) ? 0 : seqNum.hashCode());
return result;
}
/**
* @return The residue number and insertion code as a string, eg "74A"
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
StringWriter writer = new StringWriter();
// if ( chainName != null){
// writer.append(chainName);
// writer.append(":");
// }
writer.append(String.valueOf(seqNum));
if ( insCode != null && ( insCode != ' '))
writer.append(insCode);
return writer.toString();
}
/**
* @return The chain, number, and insertion code as a string, eg "B 74A" or "A 1 "
*/
public String toPDB() {
String insCodeS ;
if ( insCode != null)
insCodeS = insCode+"";
else insCodeS = " ";
return String.format("%s%4d%-2s", chainName, seqNum, insCodeS);
}
/** Convert a string representation of a residue number to a residue number object.
* The string representation can be a integer followed by a character.
*
* @param pdb_code
* @return a ResidueNumber object, or null if the input was null
*/
public static ResidueNumber fromString(String pdb_code) {
if(pdb_code == null)
return null;
ResidueNumber residueNumber = new ResidueNumber();
Integer resNum = null;
String icode = null;
try {
resNum = Integer.parseInt(pdb_code);
} catch ( NumberFormatException e){
// there is an insertion code..
// Split at any position that's either:
// preceded by a digit and followed by a non-digit, or
// preceded by a non-digit and followed by a digit.
String[] spl = pdb_code.split("(?<=\\d)(?=\\D)|(?<=\\D)(?=\\d)");
if ( spl.length == 2){
resNum = Integer.parseInt(spl[0]);
icode = spl[1];
}
}
residueNumber.setSeqNum(resNum);
if ( icode == null)
residueNumber.setInsCode(null);
else if ( icode.length() > 0)
residueNumber.setInsCode(icode.charAt(0));
return residueNumber;
}
/**
* Compare residue numbers by chain, sequence number, and insertion code
*/
@Override
public int compareTo(ResidueNumber other) {
// chain id
if (chainName != null && other.chainName != null) {
if (!chainName.equals(other.chainName)) return chainName.compareTo(other.chainName);
}
if (chainName != null && other.chainName == null) {
return 1;
} else if (chainName == null && other.chainName != null) {
return -1;
}
return compareToPositional(other);
}
/**
* Compare residue numbers by sequence number and insertion code,
* ignoring the chain
* @param other
* @return
*/
public int compareToPositional(ResidueNumber other) {
// sequence number
if (seqNum != null && other.seqNum != null) {
if (!seqNum.equals(other.seqNum)) return seqNum.compareTo(other.seqNum);
}
if (seqNum != null && other.seqNum == null) {
return 1;
} else if (seqNum == null && other.seqNum != null) {
return -1;
}
// insertion code
if (insCode != null && other.insCode != null) {
if (!insCode.equals(other.insCode)) return insCode.compareTo(other.insCode);
}
if (insCode != null && other.insCode == null) {
return 1;
} else if (insCode == null && other.insCode != null) {
return -1;
}
return 0;
}
public String printFull() {
final String chain = chainName==null? "" : chainName;
return chain + "_" + toString();
}
}