New and faster method to generate the isotope pattern from a molecula…

…r formula.

git-svn-id: https://cdk.svn.sourceforge.net/svnroot/cdk/cdk/branches/cdk-1.2.x@13221 eb4e18e3-b210-0410-a6ab-dec725e4b171

src/main/org/openscience/cdk/formula/IsotopeContainer.java

@@ -0,0 +1,125 @@
+package org.openscience.cdk.formula;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
+import org.openscience.cdk.interfaces.IMolecularFormula;
+import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
+
+
+/**
+ * This class defines a isotope container. It contains in principle a
+ * IMolecularFormula, a mass and intensity/abundance value.
+ * 
+ * @author Miguel Rojas Cherto
+ * 
+ * @cdk.module  formula
+ */
+@TestClass("org.openscience.cdk.formula.IsotopeContainerTest")
+public class IsotopeContainer{
+	private IMolecularFormula form;
+	private double masOs;
+	private double inte;
+
+	/**
+	 * Constructor of the IsotopeContainer object.
+	 */
+	public IsotopeContainer(){
+
+	}
+	/**
+	 * Constructor of the IsotopeContainer object setting a IMolecularFormula
+	 * object and intensity value.
+	 * 
+	 * @param formula        The formula of this container
+	 * @param intensity      The intensity of this container
+	 */
+	@TestMethod("testIsotopeContainer_IMolecularFormula_double")
+	public IsotopeContainer(IMolecularFormula formula, double intensity){
+		form = formula;
+		if(formula != null)
+			masOs = MolecularFormulaManipulator.getTotalExactMass(formula);
+		inte = intensity;
+	}
+	/**
+	 * Constructor of the IsotopeContainer object setting a mass
+	 *  and intensity value.
+	 * 
+	 * @param mass           The mass of this container
+	 * @param intensity      The intensity of this container
+	 */
+	@TestMethod("testIsotopeContainer_double_double")
+	public IsotopeContainer(double mass, double intensity){
+		masOs = mass;
+		inte = intensity;
+	}
+	/**
+	 * Set IMolecularFormula object of this container.
+	 * 
+	 * @param formula The IMolecularFormula of the this container
+	 */
+	@TestMethod("testSetFormula_IMolecularFormula")
+	public void setFormula(IMolecularFormula formula){
+		form = formula;
+	}
+	/**
+	 * Set the mass value of this container.
+	 * 
+	 * @param mass The mass of the this container
+	 */
+	@TestMethod("testSetMass_double")
+	public void setMass(double mass){
+		masOs = mass;
+	}
+
+	/**
+	 * Set the intensity value of this container.
+	 * 
+	 * @param intensity The intensity of the this container
+	 */
+	@TestMethod("testSetIntensity_double")
+	public void setIntensity(double intensity){
+		inte = intensity;
+	}
+	/**
+	 * Get the IMolecularFormula object of this container.
+	 * 
+	 * @return The IMolecularformula of the this container
+	 */
+	@TestMethod("testGetFormula")
+	public IMolecularFormula getFormula(){
+		return form;
+	}
+	/**
+	 * Get the mass value of this container.
+	 * 
+	 * @return The mass of the this container
+	 */
+	@TestMethod("testGetMass")
+	public double getMass(){
+		return masOs;
+	}
+
+	/**
+	 * Get the intensity value of this container.
+	 * 
+	 * @return The intensity of the this container
+	 */
+	@TestMethod("testGetIntensity")
+	public double getIntensity(){
+		return inte;
+	}
+	/**
+	 * Clones this IsotopeContainer object and its content. 
+	 *
+	 * @return    The cloned object
+	 */
+	@TestMethod("testClone")
+	public Object clone() throws CloneNotSupportedException {
+		IsotopeContainer isoClone = new IsotopeContainer();
+		isoClone.setFormula(getFormula());
+		isoClone.setIntensity(getIntensity());
+		isoClone.setMass(getMass());
+		return isoClone;
+	}
+
+}

src/main/org/openscience/cdk/formula/IsotopePattern.java

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+package org.openscience.cdk.formula;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
+
+
+
+/**
+ * This class defines the properties of a deisotoped
+ * pattern distribution. A isotope pattern is a set of 
+ * compounds with different set of isotopes.
+ * 
+ * @author Miguel Rojas Cherto
+ * 
+ * @cdk.module formula
+ */
+@TestClass("org.openscience.cdk.formula.IsotopePatternTest")
+public class IsotopePattern {
+
+	private List<IsotopeContainer> isotopeCList = new ArrayList<IsotopeContainer>();
+
+	private int monoIsotopePosition;
+
+	private double chargI=0;
+
+	/**
+	 * Constructor of the IsotopePattern object.
+	 */
+	public IsotopePattern(){
+
+	}
+	/**
+	 * Set the mono isotope object.
+	 * 
+	 *  @param isoContainer   The IsotopeContainer object
+	 */
+	@TestMethod("testSetMonoIsotope_IsotopeContainer")
+	public void setMonoIsotope(IsotopeContainer isoContainer){
+		isotopeCList.add(isoContainer);
+		monoIsotopePosition = isotopeCList.indexOf(isoContainer);
+	}
+	/**
+	 * Add an isotope object.
+	 * 
+	 *  @param isoContainer   The IsotopeContainer object
+	 */
+	@TestMethod("testAddIsotope_IsotopeContainer")
+	public void addIsotope(IsotopeContainer isoContainer){
+		isotopeCList.add(isoContainer);
+	}
+	/**
+     * Returns the mono-isotope peak that form this isotope pattern.
+     * 
+     * @return The IsotopeContainer acting as mono-isotope
+     */
+	@TestMethod("testGetMonoIsotope")
+    public IsotopeContainer getMonoIsotope(){
+    	return isotopeCList.get(monoIsotopePosition);
+    }
+
+    /**
+     * Returns the all isotopes that form this isotope pattern.
+     * 
+     * @return The IsotopeContainer acting as mono-isotope
+     */
+	@TestMethod("testGetIsotopes")
+    public List<IsotopeContainer > getIsotopes(){
+    	return isotopeCList;
+    }
+    /**
+     * Returns the a isotopes given a specific position.
+     * 
+     * @param  The position
+     * @return The isotope
+     */
+	@TestMethod("testGetIsotope_int")
+    public IsotopeContainer getIsotope(int position){
+    	return isotopeCList.get(position);
+    }
+    /**
+     * Returns the number of isotopes in this pattern.
+     * 
+     * @return The number of isotopes
+     */
+	@TestMethod("testGetNumberOfIsotopes")
+    public int getNumberOfIsotopes(){
+    	return isotopeCList.size();
+    }
+
+    /**
+     * Set the charge in this pattern.
+     * 
+     * @param charge The charge value
+     */
+	@TestMethod("testSetCharge_double")
+	public void setCharge(double charge) {
+		chargI = charge;
+
+	}
+
+    /**
+     * Get the charge in this pattern.
+     * 
+     * @return The charge value
+     */
+	@TestMethod("testGetCharge")
+	public double getCharge() {
+		return chargI;
+
+	}
+    /**
+	 * Clones this IsotopePattern object and its content. 
+	 *
+	 * @return    The cloned object
+	 */
+	@TestMethod("testClone")
+	public Object clone() throws CloneNotSupportedException {
+    	IsotopePattern isoClone = new IsotopePattern();
+    	IsotopeContainer isoHighest = getMonoIsotope();
+    	for(IsotopeContainer isoContainer: isotopeCList){
+    		if(isoHighest.equals(isoContainer))
+    			isoClone.setMonoIsotope((IsotopeContainer) isoContainer.clone());
+    		else
+    			isoClone.addIsotope((IsotopeContainer) isoContainer.clone());
+    	}
+    	isoClone.setCharge(getCharge());
+    	return isoClone;
+    }
+}