[Cdk-commits] CVS: cdk/src/org/openscience/cdk/tools IsotopeFactory.java,1.8,1.9

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/tools
In directory sc8-pr-cvs1:/tmp/cvs-serv1928/src/org/openscience/cdk/tools

Modified Files:
	IsotopeFactory.java 
Log Message:
Changed getMajorIsotope methods to also deal with abundancies defined as
percentages.


Index: IsotopeFactory.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/IsotopeFactory.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -r1.8 -r1.9
*** IsotopeFactory.java	26 Nov 2002 12:45:23 -0000	1.8
--- IsotopeFactory.java	26 Nov 2002 14:01:57 -0000	1.9
***************
*** 56,59 ****
--- 56,60 ----
  	private static IsotopeFactory ifac = null;
  	private Vector isotopes = null;
+     private Hashtable majorIsotopes = null;
  
      private org.openscience.cdk.tools.LoggingTool logger;
***************
*** 91,97 ****
  		for (int f = 0; f < isotopes.size(); f++) {
              Isotope isotope = (Isotope)isotopes.elementAt(f);
!             logger.debug("Setting up: " + isotope);
  			setup(isotope);
  		}
  	}
  
--- 92,100 ----
  		for (int f = 0; f < isotopes.size(); f++) {
              Isotope isotope = (Isotope)isotopes.elementAt(f);
!             // logger.debug("Setting up: " + isotope);
  			setup(isotope);
  		}
+         
+         majorIsotopes = new Hashtable();
  	}
  
***************
*** 126,153 ****
  	}
  
- 
- 	/**
- 	 *  Returns the most abundant (major) isotope whose symbol equals element.
- 	 *
- 	 *@param  symbol  Description of the Parameter
- 	 *@return         The Major Isotope value
- 	 */
- 	public Isotope getMajorIsotope(String symbol)
- 	{
- 		for (int f = 0; f < isotopes.size(); f++)
- 		{
- 			if (((Isotope) isotopes.elementAt(f)).getSymbol().equals(symbol))
- 			{
- 				if ((((Isotope) isotopes.elementAt(f))).getNaturalAbundance() == ((double) 100))
- 				{
- 					return (Isotope) ((Isotope) isotopes.elementAt(f)).clone();
- 				}
- 			}
- 		}
-         logger.error("Could not find major isotope for: " + symbol);
- 		return null;
- 	}
- 
- 
  	/**
  	 *  Get an array of all isotoptes known to the IsotopeFactory for the given
--- 129,132 ----
***************
*** 173,196 ****
  
  	/**
! 	 *  Returns the major isotope with a given atomic number
! 	 *
! 	 *@param  atomicNumber  The atomicNumber for which an isotope is to be returned
! 	 *@return               The isotope corresponding to the given atomic number
! 	 */
! 	public Isotope getMajorIsotope(int atomicNumber)
! 	{
! 		for (int f = 0; f < isotopes.size(); f++)
! 		{
! 			if (((Isotope) isotopes.elementAt(f)).getAtomicNumber() == atomicNumber)
! 			{
! 				if ((((Isotope) isotopes.elementAt(f))).getNaturalAbundance() == ((double) 100))
! 				{
! 					return (Isotope) ((Isotope) isotopes.elementAt(f)).clone();
! 				}
! 			}
! 		}
! 		return null;
! 	}
! 
  
  	/**
--- 152,216 ----
  
  	/**
! 	 * Returns the most abundant (major) isotope with a given atomic number.
!      *
!      * <p>The isotope's abundancy is for atoms with atomic number 60 and smaller
!      * defined as a number that is proportional to the 100 of the most abundant
!      * isotope. For atoms with higher atomic numbers, the abundancy is defined
!      * as a percentage.
! 	 *
! 	 * @param  atomicNumber  The atomicNumber for which an isotope is to be returned
! 	 * @return               The isotope corresponding to the given atomic number
!      *
!      * @see getMajorIsotope(String symbol)
!      */
!     public Isotope getMajorIsotope(int atomicNumber) {
!         Isotope major = null;
!         for (int f = 0; f < isotopes.size(); f++) {
!             Isotope current = (Isotope) isotopes.elementAt(f);
!             if (current.getAtomicNumber() == atomicNumber) {
!                 if (major == null) {
!                     major = (Isotope)current.clone();
!                 } else {
!                     if (current.getNaturalAbundance() > major.getNaturalAbundance()) {
!                         major = (Isotope)current.clone();
!                     }
!                 }
!             }
!         }
!         if (major == null) logger.error("Could not find major isotope for: " + atomicNumber);
!         return major;
!     }
! 
!     /**
!      *  Returns the most abundant (major) isotope whose symbol equals element.
!      *
!      *@param  symbol  Description of the Parameter
!      *@return         The Major Isotope value
!      */
!     public Isotope getMajorIsotope(String symbol) {
!         Isotope major = null;
!         if (majorIsotopes.contains(symbol)) {
!             major = (Isotope)majorIsotopes.get(symbol);
!         } else {
!             for (int f = 0; f < isotopes.size(); f++) {
!                 Isotope current = (Isotope) isotopes.elementAt(f);
!                 if (current.getSymbol().equals(symbol)) {
!                     if (major == null) {
!                         major = (Isotope)current.clone();
!                     } else {
!                         if (current.getNaturalAbundance() > major.getNaturalAbundance()) {
!                             major = (Isotope)current.clone();
!                         }
!                     }
!                 }
!             }
!             if (major == null) {
!                 logger.error("Could not find major isotope for: " + symbol);
!             } else {
!                 majorIsotopes.put(symbol, major);
!             }
!         }
!         return major;
!     }
  
  	/**