/*
* 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 4, 2010
* Author: Jianjiong Gao
*
*/
package org.biojava.nbio.protmod;
import java.util.*;
/**
* contains information about a certain Component.
* The Component class uses the extensible enum pattern.
* You can't instantiate Component directly, instead
* you have to use one of the {@link register} and {@link of} methods.
*
* @author Jianjiong Gao
* @since 3.0
*/
public final class Component {
private final Set<String> pdbccIds;
private final boolean isNTerminal;
private final boolean isCTerminal;
private static Set<Component> components = null;
private static Map<Set<String>, Component> nonTerminalComps = null;
private static Map<Set<String>, Component> nTerminalAminoAcids = null;
private static Map<Set<String>, Component> cTerminalAminoAcids = null;
/**
* Lazy initialization of the static variables.
*/
private static void lazyInit() {
if (components==null) {
components = new HashSet<Component>();
nonTerminalComps = new HashMap<Set<String>, Component>();
nTerminalAminoAcids = new HashMap<Set<String>, Component>();
cTerminalAminoAcids = new HashMap<Set<String>, Component>();
}
}
/**
* Create a ComponentImpl.
* @param pdbccIds a set of possible Protein Data Bank ID. Cannot be null or empty.
* @param isNTerminal true if occurring at N-terminal. false, otherwise.
* @param isCTerminal true if occurring at C-terminal. false, otherwise.
* @throws IllegalArgumentException if pdbccId or type is null,
* or terminal condition is indicated for non-amino-acid component,
* or both N-terminal and C-terminal are true.
*/
private Component(final Set<String> pdbccIds,
final boolean isNTerminal, final boolean isCTerminal) {
if (pdbccIds==null || pdbccIds.isEmpty()) {
throw new IllegalArgumentException("pdbccId or type cannot be null.");
}
if (isNTerminal&&isCTerminal) {
throw new IllegalArgumentException("An amino acid can be specified at" +
"N-terminal or C-terminal but not both."); //TODO: is this true?
}
this.pdbccIds = pdbccIds;
this.isNTerminal = isNTerminal;
this.isCTerminal = isCTerminal;
}
/**
*
* @return Protein Data Bank ID.
*/
public Set<String> getPdbccIds() {
return pdbccIds;
}
/**
*
* @return true if occurring on N terminal; false, otherwise.
*/
public boolean isNTerminal() {
return isNTerminal;
}
/**
*
* @return true if occurring on C terminal; false, other wise.
*/
public boolean isCTerminal() {
return isCTerminal;
}
/**
* Get a Component that does not have to occur at terminals. If the
* corresponding component has already been registered, return that one.
* @param pdbccIds possible Protein Data Bank ID.
* @return a component.
* @throws IllegalArgumentException if pdbccId or type is null,
* or the pdbccId has been registered as a different type.
*/
public static Component of(final String pdbccId) {
return of(pdbccId, false, false);
}
/**
* Get or create a Component.
* @param pdbccId Protein Data Bank ID.
* @param isNTerminal true if occurring at N-terminal. false, otherwise.
* @param isCTerminal true if occurring at C-terminal. false, otherwise.
* @return a component.
* @throws IllegalArgumentException if pdbccId or type is null,
* or the pdbccId has been registered as a different type,
* or terminal condition is indicated for non-amino-acid component,
* or both N-terminal and C-terminal are true.
*/
public static Component of(final String pdbccId,
final boolean isNTerminal, final boolean isCTerminal) {
return of (Collections.singleton(pdbccId), isNTerminal, isCTerminal);
}
/**
* Get a Component that does not have to occur at terminals. If the
* corresponding component has already been registered, return that one.
* @param pdbccIds a set of possible Protein Data Bank ID.
* @return a component.
* @throws IllegalArgumentException if pdbccId or type is null,
* or the pdbccId has been registered as a different type.
*/
public static Component of(final Set<String> pdbccIds) {
return of(pdbccIds, false, false);
}
/**
* Get or create a Component.
* @param pdbccIds a set of possible Protein Data Bank ID.
* @param isNTerminal true if occurring at N-terminal. false, otherwise.
* @param isCTerminal true if occurring at C-terminal. false, otherwise.
* @return a component.
* @throws IllegalArgumentException if pdbccId or type is null,
* or the pdbccId has been registered as a different type,
* or terminal condition is indicated for non-amino-acid component,
* or both N-terminal and C-terminal are true.
*/
public static Component of(final Set<String> pdbccIds,
final boolean isNTerminal, final boolean isCTerminal) {
if (isNTerminal && isCTerminal) {
throw new IllegalArgumentException("An amino acid can be at" +
"N-terminal or C-terminal but not both."); //TODO: is this true?
}
lazyInit();
Component comp;
if (isNTerminal) {
comp = nTerminalAminoAcids.get(pdbccIds);
if (comp == null) {
comp = new Component(pdbccIds, isNTerminal, isCTerminal);
nTerminalAminoAcids.put(pdbccIds, comp);
}
} else if (isCTerminal) {
comp = cTerminalAminoAcids.get(pdbccIds);
if (comp == null) {
comp = new Component(pdbccIds, isNTerminal, isCTerminal);
cTerminalAminoAcids.put(pdbccIds, comp);
}
} else {
comp = nonTerminalComps.get(pdbccIds);
if (comp == null) {
comp = new Component(pdbccIds, isNTerminal, isCTerminal);
nonTerminalComps.put(pdbccIds, comp);
}
}
components.add(comp);
return comp;
}
public static Set<Component> allComponents() {
return Collections.unmodifiableSet(components);
}
/**
*
* @return informative description.
*/
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append(getPdbccIds());
if (isCTerminal()) {
sb.append("(C)");
} else if (isNTerminal()) {
sb.append("(N)");
}
return sb.toString();
}
}