/*
* EuroCarbDB, a framework for carbohydrate bioinformatics
*
* Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
* indicated by the @author tags or express copyright attribution
* statements applied by the authors.
*
* This copyrighted material is made available to anyone wishing to use, modify,
* copy, or redistribute it subject to the terms and conditions of the GNU
* Lesser General Public License, as published by the Free Software Foundation.
* A copy of this license accompanies this distribution in the file LICENSE.txt.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
* for more details.
*
* Last commit: $Rev: 1210 $ by $Author: glycoslave $ on $Date:: 2009-06-12 #$
*/
package org.eurocarbdb.MolecularFramework.sugar;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorException;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorNodeType;
public class Sugar implements GlycoGraph
{
private ArrayList<UnderdeterminedSubTree> m_aSpezialTrees = new ArrayList<UnderdeterminedSubTree>();
private ArrayList<GlycoNode> m_aResidues = new ArrayList<GlycoNode>();
/**
* Delivers all Residues that does not have a parent residue.
* @throws GlycoconjugateException if the structure contain a cyclic part or if the sugar contain no residue with a parent
* @see de.glycosciences.glycoconjugate.GlycoGraph#getRootResiduesForNonCyclicSugars()
*/
public ArrayList<GlycoNode> getRootNodes() throws GlycoconjugateException
{
ArrayList<GlycoNode> t_aResult = new ArrayList<GlycoNode>();
GlycoNode t_objResidue;
// for all residues of the sugar
Iterator<GlycoNode> t_iterResidue = this.getNodeIterator();
while (t_iterResidue.hasNext())
{
t_objResidue = t_iterResidue.next();
GlycoEdge t_objParents = t_objResidue.getParentEdge();
if ( t_objParents == null )
{
t_aResult.add(t_objResidue);
}
}
if ( t_aResult.size() < 1 )
{
throw new GlycoconjugateException("Sugar seems not to have at least one root residue");
}
return t_aResult;
}
/**
* @see de.glycosciences.glycoconjugate.GlycoGraph#getResidueIterator()
*/
public Iterator<GlycoNode> getNodeIterator()
{
return this.m_aResidues.iterator();
}
/**
* @see de.glycosciences.MolecularFrameWork.sugar.GlycoGraph#isConnected()
*/
public boolean isConnected() throws GlycoconjugateException
{
ArrayList<GlycoNode> t_objRoots = this.getRootNodes();
if ( t_objRoots.size() > 1 )
{
return false;
}
return true;
}
public boolean removeNode(GlycoNode a_objResidue) throws GlycoconjugateException
{
GlycoEdge t_objLinkage;
GlycoNode t_objResidue;
if ( a_objResidue == null )
{
throw new GlycoconjugateException("Invalide residue.");
}
if ( a_objResidue.getClass() != SugarUnitCyclic.class )
{
this.searchCyclicForDeleting(a_objResidue);
}
t_objLinkage = a_objResidue.getParentEdge();
if ( t_objLinkage != null )
{
t_objResidue = t_objLinkage.getParent();
if ( t_objResidue == null )
{
throw new GlycoconjugateException("A linkage with a null parent exists.");
}
t_objResidue.removeChildEdge(t_objLinkage);
}
for (Iterator<GlycoEdge> t_iterEdges = a_objResidue.getChildEdges().iterator(); t_iterEdges.hasNext();)
{
t_objLinkage = t_iterEdges.next();
t_objResidue = t_objLinkage.getChild();
if ( t_objResidue == null )
{
throw new GlycoconjugateException("A linkage with a null child exists.");
}
t_objResidue.removeParentEdge(t_objLinkage);
}
return this.m_aResidues.remove(a_objResidue);
}
public ArrayList<GlycoNode> getNodes()
{
return this.m_aResidues;
}
/**
* @see org.eurocarbdb.MolecularFramework.sugar.GlycoGraph#addNode(org.eurocarbdb.MolecularFramework.sugar.GlycoNode)
*/
public boolean addNode(GlycoNode a_objResidue) throws GlycoconjugateException
{
if ( a_objResidue == null )
{
throw new GlycoconjugateException("Invalide residue.");
}
if ( a_objResidue.getClass() == SugarUnitCyclic.class )
{
throw new GlycoconjugateException("Not possible to add cyclic unit that way : use addCyclic().");
}
if ( !this.m_aResidues.contains(a_objResidue) )
{
a_objResidue.removeAllEdges();
return this.m_aResidues.add(a_objResidue);
}
return false;
}
/**
* @see org.eurocarbdb.MolecularFramework.sugar.GlycoGraph#addNode(org.eurocarbdb.MolecularFramework.sugar.GlycoNode, org.eurocarbdb.MolecularFramework.sugar.GlycoEdge, org.eurocarbdb.MolecularFramework.sugar.GlycoNode)
*/
public boolean addNode(GlycoNode a_objParent, GlycoEdge a_objLinkage, GlycoNode a_objChild) throws GlycoconjugateException
{
if ( a_objParent == null || a_objChild == null )
{
throw new GlycoconjugateException("Invalide residue.");
}
if ( a_objLinkage == null )
{
throw new GlycoconjugateException("Invalide linkage.");
}
if ( a_objChild.getParentEdge() != null )
{
throw new GlycoconjugateException("The child residue has a parent residue.");
}
if ( a_objChild.getClass() == SugarUnitCyclic.class )
{
throw new GlycoconjugateException("Not possible to add cyclic unit that way : use addCyclic().");
}
if ( !this.m_aResidues.contains(a_objParent) )
{
a_objParent.removeAllEdges();
this.m_aResidues.add(a_objParent);
}
if ( !this.m_aResidues.contains(a_objChild) )
{
a_objChild.removeAllEdges();
this.m_aResidues.add(a_objChild);
}
if ( this.m_aResidues.contains(a_objChild) && this.m_aResidues.contains(a_objChild) )
{
// test for indirect cyclic structures
if ( this.isParent(a_objChild,a_objParent) || a_objChild == a_objParent )
{
return this.addCyclic(a_objParent,a_objLinkage,a_objChild);
}
}
else
{
throw new GlycoconjugateException("Critical error imposible to add residue.");
}
a_objChild.setParentEdge(a_objLinkage);
a_objParent.addChildEdge(a_objLinkage);
a_objLinkage.setChild(a_objChild);
a_objLinkage.setParent(a_objParent);
return true;
}
public boolean addCyclic(GlycoNode a_objParent, GlycoEdge a_objLinkage, GlycoNode a_objCyclicResidue) throws GlycoconjugateException
{
if ( !this.m_aResidues.contains(a_objParent) )
{
throw new GlycoconjugateException("Parent of the cyclic linkage is not part of the sugar.");
}
if ( !this.m_aResidues.contains(a_objCyclicResidue) )
{
throw new GlycoconjugateException("Cyclic residue of the cyclic linkage is not part of the sugar.");
}
if ( this.isParent(a_objCyclicResidue,a_objParent) || a_objCyclicResidue == a_objParent )
{
SugarUnitCyclic t_objCyclic = new SugarUnitCyclic(a_objCyclicResidue);
t_objCyclic.setParentEdge(a_objLinkage);
a_objParent.addChildEdge(a_objLinkage);
a_objLinkage.setChild(t_objCyclic);
a_objLinkage.setParent(a_objParent);
return this.m_aResidues.add(t_objCyclic);
}
else
{
throw new GlycoconjugateException("The cyclic residue must be a parent residue of the residue.");
}
}
/**
* @see org.eurocarbdb.MolecularFramework.sugar.GlycoGraph#addEdge(org.eurocarbdb.MolecularFramework.sugar.GlycoNode, org.eurocarbdb.MolecularFramework.sugar.GlycoNode, org.eurocarbdb.MolecularFramework.sugar.GlycoEdge)
*/
public boolean addEdge(GlycoNode a_objParent, GlycoNode a_objChild, GlycoEdge a_objLinkage) throws GlycoconjugateException
{
return this.addNode(a_objParent,a_objLinkage,a_objChild);
}
/**
* @see org.eurocarbdb.MolecularFramework.sugar.GlycoGraph#containsNode(org.eurocarbdb.MolecularFramework.sugar.GlycoNode)
*/
public boolean containsNode(GlycoNode a_objNode)
{
return this.m_aResidues.contains(a_objNode);
}
/**
* @param residue
* @throws GlycoconjugateException
*/
private void searchCyclicForDeleting(GlycoNode a_objResidue) throws GlycoconjugateException
{
for (Iterator<GlycoNode> t_iterNodes = this.m_aResidues.iterator(); t_iterNodes.hasNext(); )
{
GlycoNode t_objElement = t_iterNodes.next();
if ( t_objElement.getClass() == SugarUnitCyclic.class )
{
SugarUnitCyclic t_objCyclic = (SugarUnitCyclic) t_objElement;
if ( t_objCyclic.getCyclicStart() == a_objResidue )
{
this.removeNode(t_objElement);
}
}
}
}
/**Recursive check if query node has specified parent
* @param child
* @param parent
* @return
*/
public boolean isParent(GlycoNode a_objParent, GlycoNode a_objNode)
{
GlycoNode t_objParent = a_objNode.getParentNode();
if ( t_objParent == null )
{
return false;
}
if ( t_objParent == a_objParent )
{
return true;
}
return this.isParent(a_objParent,t_objParent);
}
/**
* @see org.eurocarbdb.MolecularFramework.sugar.GlycoGraph#removeEdge(org.eurocarbdb.MolecularFramework.sugar.GlycoEdge)
*/
public boolean removeEdge(GlycoEdge a_objEdge) throws GlycoconjugateException
{
if ( a_objEdge == null )
{
return false;
}
GlycoNode t_objChild = a_objEdge.getChild();
GlycoNode t_objParent = a_objEdge.getParent();
if ( t_objChild == null || t_objParent == null )
{
throw new GlycoconjugateException("The edge contains null values.");
}
if ( t_objChild.getParentEdge() != a_objEdge )
{
throw new GlycoconjugateException("The child attachment is not correct");
}
ArrayList<GlycoEdge> t_aEdges = t_objParent.getChildEdges();
if ( !t_aEdges.contains(a_objEdge) )
{
throw new GlycoconjugateException("The parent attachment is not correct");
}
// test for cyclic chain
if ( this.containsCyclicBelow(a_objEdge) )
{
throw new GlycoconjugateException("You try to remove a edge in a cyclic chain. Remove SugarUnitCyclic first.");
}
t_objChild.removeParentEdge(a_objEdge);
t_objParent.removeChildEdge(a_objEdge);
return true;
}
public Sugar copy() throws GlycoconjugateException
{
ArrayList<SugarUnitAlternative> t_aAlternative = new ArrayList<SugarUnitAlternative>();
HashMap<GlycoNode,GlycoNode> t_hashResidues = new HashMap<GlycoNode,GlycoNode>();
Sugar t_objCopy = new Sugar();
GlycoNode t_objNodeOne;
GlycoNode t_objNodeTwo;
GlycoEdge t_objLinkOriginal;
GlycoEdge t_objLinkCopy;
ArrayList<GlycoEdge> t_aLinkages;
GlycoVisitorNodeType t_visNodeType = new GlycoVisitorNodeType();
// copy all nodes
for (Iterator<GlycoNode> t_iterNode = this.m_aResidues.iterator(); t_iterNode.hasNext();)
{
t_objNodeOne = t_iterNode.next();
try
{
if ( !t_visNodeType.isSugarUnitCyclic(t_objNodeOne) )
{
if ( t_visNodeType.isSugarUnitAlternative(t_objNodeOne) )
{
throw new GlycoconjugateException("Unable to copy alternative residues.");
}
else
{
t_objNodeTwo = t_objNodeOne.copy();
t_hashResidues.put(t_objNodeOne,t_objNodeTwo);
t_objCopy.addNode(t_objNodeTwo);
}
}
}
catch (GlycoVisitorException e)
{
throw new GlycoconjugateException(e.getMessage(),e);
}
}
// copy linkages
for (Iterator<GlycoNode> t_iterNode = this.m_aResidues.iterator(); t_iterNode.hasNext();)
{
t_objNodeOne = t_iterNode.next();
t_aLinkages = t_objNodeOne.getChildEdges();
for (Iterator<GlycoEdge> t_iterLinkages = t_aLinkages.iterator(); t_iterLinkages.hasNext();)
{
t_objLinkOriginal = t_iterLinkages.next();
t_objLinkCopy = t_objLinkOriginal.copy();
t_objNodeOne = t_hashResidues.get(t_objLinkOriginal.getParent());
t_objNodeTwo = t_hashResidues.get(t_objLinkOriginal.getChild());
if ( t_objNodeOne == null )
{
throw new GlycoconjugateException("Impossible to copy sugar. Null values in copy.");
}
if ( t_objNodeTwo == null )
{
// my be cyclic unit
try
{
if ( t_visNodeType.isSugarUnitCyclic(t_objLinkOriginal.getChild()) )
{
SugarUnitCyclic t_objCyclic = t_visNodeType.getSugarUnitCyclic(t_objLinkOriginal.getChild());
// copy cyclic linkage
t_objNodeTwo = t_hashResidues.get(t_objCyclic.getCyclicStart());
if ( t_objNodeTwo == null )
{
throw new GlycoconjugateException("Error coping cyclic unit.");
}
t_objCopy.addCyclic(t_objNodeOne,t_objLinkCopy,t_objNodeTwo);
}
else
{
throw new GlycoconjugateException("Impossible to copy sugar. Null values in copy.");
}
}
catch (GlycoVisitorException e)
{
throw new GlycoconjugateException(e.getMessage(),e);
}
}
else
{
t_objCopy.addEdge( t_objNodeOne, t_objNodeTwo, t_objLinkCopy);
}
}
}
// correct alternative attache positions
for (Iterator<SugarUnitAlternative> t_iterAlternatives = t_aAlternative.iterator(); t_iterAlternatives.hasNext();)
{
SugarUnitAlternative t_objAlternative = t_iterAlternatives.next();
GlycoGraphAlternative t_objAltGraph;
GlycoNode t_objKeyNode;
GlycoNode t_objKeyNodeNew;
HashMap<GlycoNode,GlycoNode> t_objMapNew = new HashMap<GlycoNode,GlycoNode>();
HashMap<GlycoNode,GlycoNode> t_objMapOld;
for (Iterator<GlycoGraphAlternative> t_iterAltGraph = t_objAlternative.getAlternatives().iterator(); t_iterAltGraph.hasNext();)
{
t_objAltGraph = t_iterAltGraph.next();
t_objMapNew.clear();
t_objMapOld = t_objAltGraph.getLeadOutNodeToNode();
for (Iterator<GlycoNode> t_iterPositions = t_objMapOld.keySet().iterator(); t_iterPositions.hasNext();)
{
t_objKeyNode = t_iterPositions.next();
t_objKeyNodeNew = t_hashResidues.get(t_objKeyNode);
if ( t_objKeyNodeNew == null )
{
throw new GlycoconjugateException("Error child attache position of alternative graph was not translated.");
}
t_objMapNew.put(t_objKeyNodeNew, t_objMapOld.get(t_objKeyNode));
}
t_objAlternative.setLeadOutNodeToNode(t_objMapNew,t_objAltGraph);
}
}
// copie special units
UnderdeterminedSubTree t_objTreeOriginal;
UnderdeterminedSubTree t_objTreeCopy;
for (Iterator<UnderdeterminedSubTree> t_iterTree = this.m_aSpezialTrees.iterator(); t_iterTree.hasNext();)
{
t_objTreeOriginal = t_iterTree.next();
t_objTreeCopy = t_objTreeOriginal.copy();
t_objCopy.addUndeterminedSubTree(t_objTreeCopy);
// copy parent information
for (Iterator<GlycoNode> t_iterParents = t_objTreeOriginal.getParents().iterator(); t_iterParents.hasNext();)
{
t_objNodeOne = t_iterParents.next();
t_objNodeTwo = t_hashResidues.get(t_objNodeOne);
if ( t_objNodeTwo == null )
{
throw new GlycoconjugateException("Impossible to copy sugar. Null values in copy.");
}
t_objTreeCopy.addParent( t_objNodeTwo );
}
}
return t_objCopy;
}
public void setUndeterminedSubTrees(ArrayList<UnderdeterminedSubTree> a_aSubTree) throws GlycoconjugateException
{
if ( a_aSubTree == null )
{
throw new GlycoconjugateException("null is not a valide set of special subtrees.");
}
this.m_aSpezialTrees.clear();
for (Iterator<UnderdeterminedSubTree> t_iterTree = a_aSubTree.iterator(); t_iterTree.hasNext();)
{
this.addUndeterminedSubTree(t_iterTree.next());
}
}
public ArrayList<UnderdeterminedSubTree> getUndeterminedSubTrees()
{
return this.m_aSpezialTrees;
}
public boolean addUndeterminedSubTreeParent(UnderdeterminedSubTree a_objTree, GlycoNode a_objParent ) throws GlycoconjugateException
{
if ( !this.m_aResidues.contains(a_objParent) )
{
throw new GlycoconjugateException("Parent is not part of the sugar.");
}
if ( !this.m_aSpezialTrees.contains(a_objTree) )
{
throw new GlycoconjugateException("UnderdeterminedSubTree is not part of the sugar.");
}
return a_objTree.addParent(a_objParent);
}
public boolean addUndeterminedSubTree(UnderdeterminedSubTree a_objTree) throws GlycoconjugateException
{
if ( a_objTree == null )
{
throw new GlycoconjugateException("null is not valide for special subtree.");
}
if ( !this.m_aSpezialTrees.contains(a_objTree) )
{
return this.m_aSpezialTrees.add(a_objTree);
}
return false;
}
private boolean containsCyclicBelow(GlycoEdge a_objEdge) throws GlycoconjugateException
{
GlycoNode t_objNode = a_objEdge.getChild();
if ( t_objNode == null )
{
throw new GlycoconjugateException("Critical error in the sugar, one edge contains a null child.");
}
if ( t_objNode.getClass() == SugarUnitCyclic.class )
{
return true;
}
for (Iterator<GlycoEdge> t_iterEdges = t_objNode.getChildEdges().iterator(); t_iterEdges.hasNext();)
{
if ( this.containsCyclicBelow(t_iterEdges.next()) )
{
return true;
}
}
return false;
}
}