/*
* 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 May 27, 2010
* Author: Jianjiong Gao
*
*/
package org.biojava.nbio.protmod;
import java.util.Collection;
import java.util.LinkedHashSet;
import java.util.Set;
/**
* This class contains information about a specific protein
* modification.
*
* @author Jianjiong Gao
* @since 3.0
*/
public class ProteinModificationImpl
implements ProteinModification , Comparable<ProteinModification> {
private final String id;
private final ModificationCondition condition;
private final ModificationCategory category;
private final ModificationOccurrenceType occurrenceType;
private final String pdbccId;
private final String pdbccName;
private final String residId;
private final String residName;
private final String psimodId;
private final String psimodName;
private final String sysName;
private final String formula;
private final Set<String> keywords;
@Override
public String getId() {
return id;
}
@Override
public String getPdbccId() {
return pdbccId;
}
@Override
public String getPdbccName() {
return pdbccName;
}
@Override
public String getResidId() {
return residId;
}
@Override
public String getResidName() {
return residName;
}
@Override
public String getPsimodId() {
return psimodId;
}
@Override
public String getPsimodName() {
return psimodName;
}
@Override
public String getSystematicName() {
return sysName;
}
@Override
public String getDescription() {
return toString();
//return description;
}
@Override
public Set<String> getKeywords() {
return keywords;
}
@Override
public ModificationCondition getCondition() {
return condition;
}
@Override
public String getFormula() {
return formula;
}
@Override
public ModificationCategory getCategory() {
return category;
}
@Override
public ModificationOccurrenceType getOccurrenceType() {
return occurrenceType;
}
@Override
public String toString() {
return "ProteinModificationImpl [id=" + id + ", condition=" + condition
+ ", category=" + category + ", occurrenceType="
+ occurrenceType + ", pdbccId=" + pdbccId + ", pdbccName="
+ pdbccName + ", residId=" + residId + ", residName="
+ residName + ", psimodId=" + psimodId + ", psimodName="
+ psimodName + ", sysName=" + sysName + ", formula=" + formula
+ ", keywords=" + keywords + "]";
}
/*
private String printModification(ProteinModificationImpl mod) {
StringBuilder sb = new StringBuilder();
String name = getBestPossibleName(mod);
boolean hasName = true;
if ( name.equals(""))
hasName = false;
sb.append(name);
Set<String> keywords = mod.getKeywords();
if (keywords!=null && !keywords.isEmpty()) {
if ( hasName)
sb.append(" (");
for (String keyword : keywords) {
sb.append(keyword);
sb.append(", ");
}
sb.delete(sb.length()-2,sb.length());
}
if ( hasName)
sb.append(")");
return sb.toString();
}
private String getBestPossibleName(ProteinModificationImpl mod) {
//System.out.println(mod.getResidName() + " : " + mod.getPsimodName() + " : " + mod.getPdbccName() + " : " + mod.getSystematicName());
// first: get resid
String resid = mod.getResidId();
if (resid != null) {
String residname = mod.getResidName();
if (residname != null) {
return residname;
}
}
// 2nd: PSI-MOD
String name = mod.getPsimodName();
if ( name != null) {
//System.out.println("PSI_MOD name:" + name);
return name;
}
// 3rd PDB-CC
String pdbcc = mod.getPdbccName();
if ( pdbcc != null ) {
//System.out.println("PDBCC name: " + pdbcc);
return pdbcc;
}
// no public name know, use the systematic name
String systematic = mod.getSystematicName();
if ( systematic != null) {
//System.out.println("SYSTEMATIC NAME: " + mod.getSystematicName());
return systematic;
}
return "";
}
*/
@Override
public int hashCode() {
int ret = id.hashCode();
ret = ret * 31 + category.hashCode();
return ret;
}
@Override
public boolean equals(Object obj) {
if (!(obj instanceof ProteinModification))
return false;
ProteinModification mod = (ProteinModification)obj;
if (!id.equals(mod.getId()))
return false;
if (category != mod.getCategory())
return false;
return true;
}
/**
* Uses Builder pattern to build a ProteinModification.
*/
public static class Builder {
private final String id;
private ModificationCondition condition;
private ModificationCategory category;
private ModificationOccurrenceType occurrenceType;
private String pdbccId = null;
private String pdbccName = null;
private String residId = null;
private String residName = null;
private String psimodId = null;
private String psimodName = null;
private String sysName = null;
private String formula = null;
private Set<String> keywords = new LinkedHashSet<String>();
/**
*
* @param id
* @param cat
* @param occType
* @param condition
*/
public Builder(final String id, final ModificationCategory cat,
final ModificationOccurrenceType occType,
final ModificationCondition condition) {
if ( id == null) throw new IllegalArgumentException("id == null!");
if ( cat == null) throw new IllegalArgumentException("cat == null!");
if ( occType == null) throw new IllegalArgumentException("occType == null!");
if ( condition == null) throw new IllegalArgumentException("condition == null!");
this.id = id;
this.category = cat;
this.occurrenceType = occType;
this.condition = condition;
}
/**
* Create a Builder from an existing ProteinModification.
* @param copyFrom the ProteinModification to be copied from.
*/
public Builder(final ProteinModification copyFrom) {
this(copyFrom.getId(), copyFrom.getCategory(), copyFrom.getOccurrenceType(), copyFrom.getCondition());
this.pdbccId = copyFrom.getPdbccId();
this.pdbccName = copyFrom.getPdbccName();
this.residId = copyFrom.getResidId();
this.residName = copyFrom.getResidName();
this.psimodId = copyFrom.getPsimodId();
this.psimodName = copyFrom.getPsimodName();
this.sysName = copyFrom.getSystematicName();
this.formula = copyFrom.getFormula();
this.keywords = new LinkedHashSet<String>(copyFrom.getKeywords());
}
public Builder setCategory(final ModificationCategory cat) {
if (cat == null) throw new IllegalArgumentException("cat == null!");
this.category = cat;
return this;
}
public Builder setOccurrenceType(final ModificationOccurrenceType occType) {
if (occType == null) throw new IllegalArgumentException("occType == null!");
this.occurrenceType =occType;
return this;
}
public Builder setCondition(final ModificationCondition condition) {
if (condition == null) throw new IllegalArgumentException("condition == null!");
this.condition = condition;
return this;
}
/**
* Set the Protein Data Bank Chemical Component ID.
* @param pdbccId Protein Data Bank Chemical Component ID.
* @return the same Builder object so you can chain setters.
*/
public Builder setPdbccId(final String pdbccId) {
this.pdbccId = pdbccId;
return this;
}
/**
* Set the Protein Data Bank Chemical Component name.
* @param pdbccName Protein Data Bank Chemical Component name.
* @return the same Builder object so you can chain setters.
*/
public Builder setPdbccName(final String pdbccName) {
this.pdbccName = pdbccName;
return this;
}
/**
* Set the RESID ID.
* @param residId RESID ID.
* @return the same Builder object so you can chain setters.
*/
public Builder setResidId(final String residId) {
this.residId = residId;
return this;
}
/**
* Set the RESID name.
* @param residName RESID name.
* @return the same Builder object so you can chain setters.
*/
public Builder setResidName(final String residName) {
this.residName = residName;
return this;
}
/**
* Set the PSI-MOD ID.
* @param psimodId PSI-MOD ID.
* @return the same Builder object so you can chain setters.
*/
public Builder setPsimodId(final String psimodId) {
this.psimodId = psimodId;
return this;
}
/**
* Set the PSI-MOD name.
* @param psimodName PSI-MOD name.
* @return the same Builder object so you can chain setters.
*/
public Builder setPsimodName(final String psimodName) {
this.psimodName = psimodName;
return this;
}
/**
* Set the systematic name.
* @param sysName systematic name.
* @return the same Builder object so you can chain setters.
*/
public Builder setSystematicName(final String sysName) {
this.sysName = sysName;
return this;
}
/**
*
* @param description description of the modification.
* @return the same Builder object so you can chain setters.
*/
public Builder setDescription(final String description) {
// description is created on the fly in getDescription
return this;
}
/**
* Add a keyword associate with the PTM.
* @param keyword a keyword.
* @return the same Builder object so you can chain setters.
* @throws IllegalArgumentException if the keyword is null.
*/
public Builder addKeyword(String keyword) {
if (keyword == null) throw new IllegalArgumentException("Keyword cannot be null.");
keywords.add(keyword);
return this;
}
public Builder addKeywords(Collection<String> keywords) {
if (keywords==null) throw new IllegalArgumentException("Keywords cannot be null.");
for (String keyword : keywords) {
addKeyword(keyword);
}
return this;
}
/**
* Set the residue formula.
* @param formula residue formula.
* @return the same Builder object so you can chain setters.
*/
public Builder setFormula(final String formula) {
this.formula = formula;
return this;
}
/**
*
* @return build ProteinModification.
*/
public ProteinModificationImpl build() {
return new ProteinModificationImpl(this);
}
}
/**
*
*/
private ProteinModificationImpl(Builder builder) {
this.id = builder.id;
this.category = builder.category;
this.occurrenceType = builder.occurrenceType;
this.condition = builder.condition;
this.pdbccId = builder.pdbccId;
this.pdbccName = builder.pdbccName;
this.residId = builder.residId;
this.residName = builder.residName;
this.psimodId = builder.psimodId;
this.psimodName = builder.psimodName;
this.sysName = builder.sysName;
this.formula = builder.formula;
this.keywords = new LinkedHashSet<String>(builder.keywords);
}
@Override
public int compareTo(ProteinModification arg0) {
if ( this.equals(arg0))
return 0;
return this.toString().compareTo(arg0.toString());
}
}