From: <mig...@us...> - 2007-11-07 10:23:20
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Revision: 9392 http://cdk.svn.sourceforge.net/cdk/?rev=9392&view=rev Author: miguelrojasch Date: 2007-11-07 02:23:18 -0800 (Wed, 07 Nov 2007) Log Message: ----------- Clean up JavaDocs Modified Paths: -------------- branches/miguelrojasch/mf/src/org/openscience/cdk/MolecularFormula.java branches/miguelrojasch/mf/src/org/openscience/cdk/MolecularFormulaSet.java branches/miguelrojasch/mf/src/org/openscience/cdk/debug/DebugMolecularFormula.java branches/miguelrojasch/mf/src/org/openscience/cdk/interfaces/IMolecularFormula.java branches/miguelrojasch/mf/src/org/openscience/cdk/interfaces/IMolecularFormulaSet.java Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/MolecularFormula.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/MolecularFormula.java 2007-11-07 10:07:30 UTC (rev 9391) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/MolecularFormula.java 2007-11-07 10:23:18 UTC (rev 9392) @@ -27,7 +27,6 @@ import java.util.Hashtable; import java.util.Iterator; -import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IElement; @@ -41,7 +40,7 @@ * * @cdk.module data * - * @author Miguel Rojas + * @author rojasm * @cdk.created 2007-11-02 */ public class MolecularFormula extends ChemObject Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/MolecularFormulaSet.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/MolecularFormulaSet.java 2007-11-07 10:07:30 UTC (rev 9391) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/MolecularFormulaSet.java 2007-11-07 10:23:18 UTC (rev 9392) @@ -32,15 +32,15 @@ import org.openscience.cdk.interfaces.IMolecularFormulaSet; /** - * A set of molecularFormulas, for example those gererated from + * A set of molecularFormulas, for example those generated from * a exact mass. * * To retrieve the molecularFormula from the set, there are two options: * * <pre> - * Iterator<IMolecularFormula> iter = molecularFormulaSet.molecularFormules(); - * while(iter.hasNext()){ - * IMolecularFormula mf = mfs.next(); + * Iterator<IMolecularFormula> iterations = molecularFormulaSet.molecularFormules(); + * while(iterations.hasNext()){ + * IMolecularFormula molecularFormula = iterations.next(); * } * </pre> * @@ -52,8 +52,9 @@ * } * </pre> * - * @author rojasm + * @author rojasm * @cdk.module data + * @cdk.created 2007-11-02 * @cdk.keyword molecular formula */ public class MolecularFormulaSet extends ChemObject implements Serializable, IMolecularFormulaSet, IChemObjectListener, Cloneable { @@ -261,7 +262,12 @@ - + /** + * Returns a one line string representation of this MolecularFormulaSet. This method is + * conform RFC #9. + * + * @return The string representation of this MolecularFormulaSet + */ public String toString() { StringBuffer buffer = new StringBuffer(); buffer.append("MolecularFormulaSet("); @@ -276,7 +282,7 @@ * @return the cloned Object */ public Object clone() throws CloneNotSupportedException { - MolecularFormulaSet clone = (MolecularFormulaSet)super.clone(); + IMolecularFormulaSet clone = (IMolecularFormulaSet)super.clone(); for (int i = 0; i < molecularFormulaCount; i++) { clone.addMolecularFormula((IMolecularFormula)molecularFormulas[i].clone()); } @@ -300,7 +306,7 @@ */ protected void growMolecularFormulaArray() { growArraySize = molecularFormulas.length; - MolecularFormula[] newMolecularFormulas = new MolecularFormula[molecularFormulas.length + growArraySize]; + IMolecularFormula[] newMolecularFormulas = new MolecularFormula[molecularFormulas.length + growArraySize]; System.arraycopy(molecularFormulas, 0, newMolecularFormulas, 0, molecularFormulas.length); molecularFormulas = newMolecularFormulas; double[] newMultipliers = new double[multipliers.length + growArraySize]; Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/debug/DebugMolecularFormula.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/debug/DebugMolecularFormula.java 2007-11-07 10:07:30 UTC (rev 9391) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/debug/DebugMolecularFormula.java 2007-11-07 10:23:18 UTC (rev 9392) @@ -53,7 +53,7 @@ super(molecularFormula); } - public void add(MolecularFormula molecularFormula) { + public void add(IMolecularFormula molecularFormula) { logger.debug("Adding molecular formula: ", molecularFormula); super.add(molecularFormula); } @@ -118,7 +118,7 @@ return super.getLastElement(); } - public void remove(MolecularFormula molecularFormula) { + public void remove(IMolecularFormula molecularFormula) { logger.debug("Removing molecular Formula: ", molecularFormula); super.remove(molecularFormula); } Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/interfaces/IMolecularFormula.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/interfaces/IMolecularFormula.java 2007-11-07 10:07:30 UTC (rev 9391) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/interfaces/IMolecularFormula.java 2007-11-07 10:23:18 UTC (rev 9392) @@ -25,10 +25,18 @@ import java.util.Iterator; -import org.openscience.cdk.MolecularFormula; - /** - * Represents a set of MolecularFormula. + * Base class for all molecular formulas that maintain a list of Elements + * <p> + * + * Looping over all <code>IElement</code>s in the <code>IMolecularFormula</code> + * is typically done like: + * <pre> + * Iterator elements = molecularFormula.elements(); + * while (elements.hasNext()) { + * IElement element = elements.next(); + * } + * </pre> * * @cdk.module interfaces * @author rojasm @@ -37,11 +45,11 @@ public interface IMolecularFormula extends IChemObject { /** - * Adds a molecular formula to this MolecularFormula. + * Adds a molecular formula to this IMolecularFormula. * - *@param atomContainer The molecular formula to be added + *@param molecularFormula The molecular formula to be added */ - public void add(MolecularFormula molecularFormula); + public void add(IMolecularFormula molecularFormula); /** * add an Element @@ -52,11 +60,11 @@ public void addElement(IElement element); /** - * Adds an element to this MolecularFormula indicating the number of occurence of + * Adds an element to this MolecularFormula indicating the number of occurrence of * this element must be in the MolecularFormula. * * @param element The element to be added to this MolecularFormula - * @param occur The number of occurence of this element + * @param occur The number of occurrence of this element */ public void addElement(IElement element, int occur); @@ -80,7 +88,7 @@ /** * Returns the element at position 0 in the container. * - *@return The atom at position 0 . + *@return The atom at position 0 */ public IElement getFirstElement(); @@ -116,11 +124,11 @@ /** - * Checks a set of Nodes for the occurence of a particular + * Checks a set of Nodes for the occurrence of a particular * element. It returns -1 if the element does not exist. * - *@param The IElement - *@return The occurence of this element in this molecular formula + *@param element The IElement + *@return The occurrence of this element in this molecular formula */ public int getAtomCount(IElement element); @@ -149,7 +157,7 @@ * *@param molecularformula The molecular formula to be removed */ - public void remove(MolecularFormula molecularFormula); + public void remove(IMolecularFormula molecularFormula); /** * Removes the element at the given position from the MolecularFormula. Modified: branches/miguelrojasch/mf/src/org/openscience/cdk/interfaces/IMolecularFormulaSet.java =================================================================== --- branches/miguelrojasch/mf/src/org/openscience/cdk/interfaces/IMolecularFormulaSet.java 2007-11-07 10:07:30 UTC (rev 9391) +++ branches/miguelrojasch/mf/src/org/openscience/cdk/interfaces/IMolecularFormulaSet.java 2007-11-07 10:23:18 UTC (rev 9392) @@ -24,18 +24,8 @@ /** - * Base class for all chemical objects that maintain a list of Atoms and - * ElectronContainers. <p> + * A set of MolecularFormulas. * - * Looping over all <code>IBond</code>s in the <code>IAtomContainer</code> - * is typically done like: - * <pre> - * Iterator bonds = atomContainer.bonds(); - * while (bonds.hasNext()) { - * IBond b = (IBond)bonds.next(); - * } - * </pre> - * * @cdk.module interfaces * @author rojasm */ @@ -101,9 +91,9 @@ /** * Removes an MolecularFormula from this chemObject. * - * @param atomContainer The MolecularFormula to be removed from this chemObject + * @param molecularFormula The MolecularFormula to be removed from this chemObject */ - public void removeMolecularFormula(IMolecularFormula atomContainer); + public void removeMolecularFormula(IMolecularFormula molecularFormula); /** * Removes all MolecularFormula from this chemObject. @@ -177,7 +167,7 @@ /** * Returns the multiplier of the given MolecularFormula. * - * @param container The MolecularFormula for which the multiplier is given + * @param molecularFormula The MolecularFormula for which the multiplier is given * @return -1, if the given molecular formula is not a container in this set * @see #setMultiplier(molecularFormula, double) */ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |