/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2007 Miguel Rojasch <miguelrojasch@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* 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.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
* */
package org.openscience.cdk.tools.manipulator;
import java.util.Iterator;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.formula.MolecularFormulaRange;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IMolecularFormulaSet;
/**
* Class with convenience methods that provide methods to manipulate
* MolecularFormulaSet's. For example:
* <pre>
* IMolecularFormula molecularFormula = MolecularManipulatorSet.getMaxOccurrenceElements(molecularFormulaSet);
* </pre>
* .
*
* @cdk.module formula
* @author miguelrojasch
* @cdk.created 2007-11-20
*/
@TestClass("org.openscience.cdk.formula.MolecularFormulaSetManipulatorTest")
public class MolecularFormulaSetManipulator {
/**
* Extract from a set of MolecularFormula the maximum occurrence of each element found and
* put the element and occurrence in a new IMolecularFormula.
*
* @param mfSet The set of molecularFormules to inspect
* @return A IMolecularFormula containing the maximum occurrence of the elements
* @see #getMinOccurrenceElements(IMolecularFormulaSet)
*/
@TestMethod("testGetMaxOccurrenceElements_IMolecularFormulaSet")
public static IMolecularFormula getMaxOccurrenceElements(IMolecularFormulaSet mfSet){
IMolecularFormula molecularFormula = mfSet.getBuilder().newMolecularFormula();
for(IMolecularFormula mf: mfSet.molecularFormulas()){
for (IIsotope isotope : mf.isotopes()) {
IElement element = mfSet.getBuilder().newElement(isotope);
int occur_new = MolecularFormulaManipulator.getElementCount(mf, element);
if (!MolecularFormulaManipulator.containsElement(molecularFormula, element)) {
molecularFormula.addIsotope(mfSet.getBuilder().newIsotope(element), occur_new);
} else {
int occur_old = MolecularFormulaManipulator.getElementCount(molecularFormula, element);
if (occur_new > occur_old) {
MolecularFormulaManipulator.removeElement(molecularFormula, element);
molecularFormula.addIsotope(mfSet.getBuilder().newIsotope(element), occur_new);
}
}
}
}
return molecularFormula;
}
/**
* Extract from a set of MolecularFormula the minimal occurrence of each element found and
* put the element and occurrence in a new IMolecularFormula.
*
* @param mfSet The set of molecularFormules to inspect
* @return A IMolecularFormula containing the minimal occurrence of the elements
* @see #getMaxOccurrenceElements(IMolecularFormulaSet)
*/
@TestMethod("testGetMinOccurrenceElements_IMolecularFormulaSet")
public static IMolecularFormula getMinOccurrenceElements(IMolecularFormulaSet mfSet){
IMolecularFormula molecularFormula = mfSet.getBuilder().newMolecularFormula();
for(IMolecularFormula mf: mfSet.molecularFormulas()){
for (IIsotope isotope : mf.isotopes()) {
IElement element = mfSet.getBuilder().newElement(isotope);
int occur_new = MolecularFormulaManipulator.getElementCount(mf, element);
if (!MolecularFormulaManipulator.containsElement(molecularFormula, element)) {
molecularFormula.addIsotope(mfSet.getBuilder().newIsotope(element), occur_new);
} else {
int occur_old = MolecularFormulaManipulator.getElementCount(molecularFormula, element);
if (occur_new < occur_old) {
MolecularFormulaManipulator.removeElement(molecularFormula, element);
molecularFormula.addIsotope(mfSet.getBuilder().newIsotope(element), occur_new);
}
}
}
}
return molecularFormula;
}
/**
* Remove all those IMolecularFormula which are not fit theirs IElement
* occurrence into a limits. The limits are given from formulaMax and formulaMin.
* In the minimal IMolecularFormula must contain all those IElement found in the
* minimal IMolecularFormula.
*
* @param formulaSet IMolecularFormulaSet to look for
* @param formulaMax A IMolecularFormula which contains the maximal representation of the Elements
* @param formulaMin A IMolecularFormula which contains the minimal representation of the Elements
* @return A IMolecularFormulaSet with only the IMolecularFormula which the IElements
* are into the correct occurrence
*/
@TestMethod("testRemove_IMolecularFormulaSet_IMolecularFormula_IMolecularFormula")
public static IMolecularFormulaSet remove(IMolecularFormulaSet formulaSet,
IMolecularFormula formulaMin, IMolecularFormula formulaMax){
// prove the correlation between maximum and minimum molecularFormula
if(!validCorrelation(formulaMin, formulaMax))
return null;
IMolecularFormulaSet newFormulaSet = formulaSet.getBuilder().newMolecularFormulaSet();
for(IMolecularFormula formula: formulaSet.molecularFormulas()){
boolean flagPass = true;
// the formula must contain all element found into the formulaMin
if(!validCorrelation(formula,formulaMin))
continue;
for (IElement element : MolecularFormulaManipulator.elements(formulaMin)) {
int occur = MolecularFormulaManipulator.getElementCount(formula, element);
int occurMax = MolecularFormulaManipulator.getElementCount(formulaMax, element);
int occurMin = MolecularFormulaManipulator.getElementCount(formulaMin, element);
if (!(occurMin <= occur) || !(occur <= occurMax)) {
flagPass = false;
break;
}
}
if(flagPass) // stored if each IElement occurrence is into the limits
newFormulaSet.addMolecularFormula(formula);
}
return newFormulaSet;
}
/**
* In the minimal IMolecularFormula must contain all those IElement found in the
* minimal IMolecularFormula.
*
* @param formulaMax A IMolecularFormula which contains the maximal representation of the Elements
* @param formulaMin A IMolecularFormula which contains the minimal representation of the Elements
* @return True, if the correlation is valid
*/
private static boolean validCorrelation(IMolecularFormula formulaMin, IMolecularFormula formulamax){
for (IElement element : MolecularFormulaManipulator.elements(formulaMin)) {
if (!MolecularFormulaManipulator.containsElement(formulamax, element))
return false;
}
return true;
}
/**
* True, if the IMolecularFormulaSet contains the given IMolecularFormula but not
* as object. It compare according contains the same number and type of Isotopes.
* It is not based on compare objects.
*
* @param formulaSet The IMolecularFormulaSet
* @param formula The IMolecularFormula this IMolecularFormulaSet is searched for
* @return True, if the IMolecularFormulaSet contains the given formula
*
* @see IMolecularFormulaSet#contains(IMolecularFormula)
*/
@TestMethod("testContains_IMolecularFormulaSet_IMolecularFormula")
public static boolean contains(IMolecularFormulaSet formulaSet, IMolecularFormula formula){
for(IMolecularFormula fm: formulaSet.molecularFormulas()){
if(MolecularFormulaManipulator.compare(fm, formula)){
return true;
}
}
return false;
}
/**
* Remove all those IMolecularFormula which are not fit theirs IElement
* occurrence into a limits. The limits are given from formulaMax and formulaMin.
* In the minimal IMolecularFormula must contain all those IElement found in the
* minimal IMolecularFormula.
*
* @param formulaSet IMolecularFormulaSet to look for
* @param formulaRange A IMolecularFormulaRange which contains the range representation of the IIsotope
*/
@TestMethod("testRemove_IMolecularFormulaSet_MolecularFormulaRange")
public static IMolecularFormulaSet remove(IMolecularFormulaSet formulaSet,
MolecularFormulaRange formulaRange){
IMolecularFormulaSet newFormulaSet = formulaSet.getBuilder().newMolecularFormulaSet();
for(IMolecularFormula formula: formulaSet.molecularFormulas()){
boolean flagCorrect = true;
Iterator<IIsotope> itEle = formulaRange.isotopes().iterator();
for (IIsotope isotope : formulaRange.isotopes()) {
if (formula.getIsotopeCount(isotope) != 0) {
if ((formula.getIsotopeCount(isotope) < formulaRange.getIsotopeCountMin(isotope))
|| (formula.getIsotopeCount(isotope) > formulaRange.getIsotopeCountMax(isotope))) {
flagCorrect = false;
break;
}
} else if (formulaRange.getIsotopeCountMin(isotope) != 0) {
flagCorrect = false;
break;
}
}
itEle = formula.isotopes().iterator();
while(itEle.hasNext()){
IIsotope isotope = itEle.next();
if(!formulaRange.contains(isotope)){
flagCorrect = false;
break;
}
}
if(flagCorrect) // stored if each IElement occurrence is into the limits
newFormulaSet.addMolecularFormula(formula);
}
return newFormulaSet;
}
}