From: <eg...@us...> - 2007-11-16 21:22:36
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Revision: 9448 http://cdk.svn.sourceforge.net/cdk/?rev=9448&view=rev Author: egonw Date: 2007-11-16 13:22:35 -0800 (Fri, 16 Nov 2007) Log Message: ----------- Renamed blaElement() to blaIsotope(), cleaned IAdductFormula interface (by cherry picking only those methods from IMolecularFormula which are appropriate) and update the two implementing classes Modified Paths: -------------- branches/miguelrojasch/mf/src/org/openscience/cdk/formula/AdductFormula.java branches/miguelrojasch/mf/src/org/openscience/cdk/formula/IAdductFormula.java branches/miguelrojasch/mf/src/org/openscience/cdk/formula/IMolecularFormula.java branches/miguelrojasch/mf/src/org/openscience/cdk/formula/MolecularFormula.java branches/miguelrojasch/mf/src/org/openscience/cdk/tools/MFAnalyser.java Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/formula/AdductFormula.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/formula/AdductFormula.java 2007-11-16 21:05:03 UTC (rev 9447) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/formula/AdductFormula.java 2007-11-16 21:22:35 UTC (rev 9448) @@ -32,16 +32,16 @@ return charge; } - public int getCount(IIsotope isotope) { + public int getIsotopeCount(IIsotope isotope) { int count = 0; Iterator<IMolecularFormula> componentIterator = components.iterator(); while (componentIterator.hasNext()) { - count += componentIterator.next().getCount(isotope); + count += componentIterator.next().getIsotopeCount(isotope); } return count; } - public int getCount() { + public int getIsotopeCount() { return isotopesList().size(); } @@ -95,4 +95,24 @@ return components.size(); } + public boolean contains(IMolecularFormula molecularFormula) { + return components.contains(molecularFormula); + } + + public void getMolecularFormula(int position) { + components.get(position); + } + + public void removeAllMolecularFormulas() { + components.clear(); + } + + public void removeMolecularFormula(IMolecularFormula formula) { + components.remove(formula); + } + + public void removeMolecularFormula(int position) { + components.remove(position); + } + } Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/formula/IAdductFormula.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/formula/IAdductFormula.java 2007-11-16 21:05:03 UTC (rev 9447) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/formula/IAdductFormula.java 2007-11-16 21:22:35 UTC (rev 9448) @@ -1,5 +1,9 @@ package org.openscience.cdk.formula; +import java.util.Iterator; + +import org.openscience.cdk.interfaces.IIsotope; + /** * Examples: * <ul> @@ -8,6 +12,16 @@ * * @author miguelrojasch */ -public interface IAdductFormula extends IMolecularFormula, IMolecularFormulaSet { +public interface IAdductFormula extends IMolecularFormulaSet { + public int getIsotopeCount(IIsotope isotope); + + public Iterator<IIsotope> isotopes(); + + public int getIsotopeCount(); + + public boolean contains(IIsotope isotope); + + public Double getCharge(); + } Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/formula/IMolecularFormula.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/formula/IMolecularFormula.java 2007-11-16 21:05:03 UTC (rev 9447) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/formula/IMolecularFormula.java 2007-11-16 21:22:35 UTC (rev 9448) @@ -16,24 +16,22 @@ */ public interface IMolecularFormula { - public IMolecularFormula addElement(IIsotope isotope); + public IMolecularFormula addIsotope(IIsotope isotope); - public IMolecularFormula addElement(IIsotope isotope, int count); + public IMolecularFormula addIsotope(IIsotope isotope, int count); - public int getElementCount(IIsotope isotope); + public int getIsotopeCount(IIsotope isotope); public Iterator<IIsotope> isotopes(); - public int getElementCount(); + public int getIsotopeCount(); public boolean contains(IIsotope isotope); - public void removeElement(IIsotope isotope); + public void removeIsotope(IIsotope isotope); - public void removeElement(int position); + public void removeAllIsotopes(); - public void removeAllElement(); - public void setCharge(Double charge) ; public Double getCharge(); Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/formula/MolecularFormula.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/formula/MolecularFormula.java 2007-11-16 21:05:03 UTC (rev 9447) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/formula/MolecularFormula.java 2007-11-16 21:22:35 UTC (rev 9448) @@ -17,15 +17,15 @@ public IMolecularFormula add(IMolecularFormula molecularFormula) { Iterator<IIsotope> isotopes = molecularFormula.isotopes(); - while (isotopes.hasNext()) this.addElement(isotopes.next()); + while (isotopes.hasNext()) this.addIsotope(isotopes.next()); return this; } - public IMolecularFormula addElement(IIsotope isotope) { - return this.addElement(isotope, 1); + public IMolecularFormula addIsotope(IIsotope isotope) { + return this.addIsotope(isotope, 1); } - public IMolecularFormula addElement(IIsotope isotope, int count) { + public IMolecularFormula addIsotope(IIsotope isotope, int count) { if (isotopes.containsKey(isotope)) { isotopes.put(isotope, isotopes.get(isotope) + count); } else { @@ -42,11 +42,11 @@ return charge; } - public int getCount(IIsotope isotope) { + public int getIsotopeCount(IIsotope isotope) { return !contains(isotope) ? 0 : isotopes.get(isotope); } - public int getCount() { + public int getIsotopeCount() { return isotopes.size(); } @@ -58,4 +58,12 @@ this.charge = charge; } + public void removeAllIsotopes() { + isotopes.clear(); + } + + public void removeIsotope(IIsotope isotope) { + isotopes.remove(isotope); + } + } Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/tools/MFAnalyser.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/tools/MFAnalyser.java 2007-11-16 21:05:03 UTC (rev 9447) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/tools/MFAnalyser.java 2007-11-16 21:22:35 UTC (rev 9448) @@ -71,24 +71,24 @@ * formula string. The string is immediatly analysed and a set of Nodes * is built based on this analysis * - * @param MF Description of the Parameter + * @param stringMF Description of the Parameter * @param target TODO */ public MFAnalyser(IMolecularFormula molecularFormula, IAtomContainer target) { - this.moleclarFormula = molecularFormula; - this.atomContainer = analyseMF(MF, target); + this.molecularFormula = molecularFormula; + this.atomContainer = analyseMF(stringMF, target); } /** * Construct an instance of MFAnalyser, initialized with a molecular * formula string. The string is immediatly analysed and a set of Nodes * is built based on this analysis * - * @param MF Description of the Parameter + * @param stringMF Description of the Parameter * @param target TODO */ public MFAnalyser(String stringMF, IAtomContainer target) { this.stringMF = stringMF; - this.atomContainer = analyseMF(MF, target); + this.atomContainer = analyseMF(stringMF, target); } @@ -114,7 +114,7 @@ public MFAnalyser(IAtomContainer ac, boolean useboth) { this.useboth=useboth; this.atomContainer = ac; - this.MF = analyseAtomContainer(ac); + this.stringMF = analyseAtomContainer(ac); } @@ -137,7 +137,7 @@ * @see #getHTMLMolecularFormula() */ public String getMolecularFormula() { - return MF; + return stringMF; } @@ -151,7 +151,7 @@ public String getHTMLMolecularFormula() { boolean lastCharacterWasDigit = false; boolean currentCharacterIsDigit; - StringBuffer htmlString = new StringBuffer(MF); + StringBuffer htmlString = new StringBuffer(stringMF); for (int characterCounter = 0; characterCounter <= htmlString.length(); characterCounter++) { try { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |