From: <eg...@us...> - 2006-05-01 11:51:47
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Revision: 6103 Author: egonw Date: 2006-05-01 04:51:39 -0700 (Mon, 01 May 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6103&view=rev Log Message: ----------- Added missing JavaDoc. Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/CDKConstants.java trunk/cdk/src/org/openscience/cdk/config/AtomTypeFactory.java Modified: trunk/cdk/src/org/openscience/cdk/CDKConstants.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/CDKConstants.java 2006-05-01 11:13:44 UTC (rev 6102) +++ trunk/cdk/src/org/openscience/cdk/CDKConstants.java 2006-05-01 11:51:39 UTC (rev 6103) @@ -45,7 +45,8 @@ /** A bond of degree 1.0. */ public final static double BONDORDER_SINGLE = 1.0; - /** A bond of degree 1.5. */ + /** A bond of degree 1.5. To indicate aromaticity, the flag ISAROMATIC should be used instead. + * This constant is used for specific file formats only, and should generally not be used. */ public final static double BONDORDER_AROMATIC = 1.5; /** A bond of degree 2.0. */ @@ -170,7 +171,9 @@ */ public final static int MAPPED = 5; + /** Set to true if the atom is an hydrogen bond donor. */ public final static int IS_HYDROGENBOND_DONOR = 6; + /** Set to true if the atom is an hydrogen bond acceptor. */ public final static int IS_HYDROGENBOND_ACCEPTOR = 7; /** Flag is set if a chemobject has reactive center. @@ -267,10 +270,13 @@ * AtomTypes * ****************************************/ + /** Used as property key for indicating the ring size of a certain atom type. */ public static final String PART_OF_RING_OF_SIZE = "Part of ring of size"; + /** Used as property key for indicating the chemical group of a certain atom type. */ public static final String CHEMICAL_GROUP_CONSTANT = "Chemical Group"; + /** Used as property key for indicating the HOSE code for a certain atom type. */ public static final String SPHERICAL_MATCHER = "HOSE code spherical matcher"; } Modified: trunk/cdk/src/org/openscience/cdk/config/AtomTypeFactory.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/config/AtomTypeFactory.java 2006-05-01 11:13:44 UTC (rev 6102) +++ trunk/cdk/src/org/openscience/cdk/config/AtomTypeFactory.java 2006-05-01 11:51:39 UTC (rev 6103) @@ -27,7 +27,6 @@ import java.io.FileInputStream; import java.io.IOException; import java.io.InputStream; -import java.io.OptionalDataException; import java.util.Hashtable; import java.util.Vector; @@ -100,10 +99,9 @@ * Private constructor for the AtomTypeFactory singleton. * * @exception IOException Thrown if something goes wrong with reading the config - * @exception OptionalDataException What ever that may be * @exception ClassNotFoundException Thrown if a class was not found :-) */ - private AtomTypeFactory(String configFile, IChemObjectBuilder builder) throws IOException, OptionalDataException, ClassNotFoundException { + private AtomTypeFactory(String configFile, IChemObjectBuilder builder) throws IOException, ClassNotFoundException { if (logger == null) { logger = new LoggingTool(this); } @@ -115,10 +113,9 @@ * Private constructor for the AtomTypeFactory singleton. * * @exception IOException Thrown if something goes wrong with reading the config - * @exception OptionalDataException What ever that may be * @exception ClassNotFoundException Thrown if a class was not found :-) */ - private AtomTypeFactory(InputStream ins, String format, IChemObjectBuilder builder) throws IOException, OptionalDataException, ClassNotFoundException { + private AtomTypeFactory(InputStream ins, String format, IChemObjectBuilder builder) throws IOException, ClassNotFoundException { if (logger == null) { logger = new LoggingTool(this); } @@ -133,12 +130,12 @@ * @see #getInstance(String) * @param ins InputStream containing the data * @param format String representing the possible formats ('xml' and 'txt') + * @param builder IChemObjectBuilder used to make IChemObject instances * @return The AtomTypeFactory for the given data file * @throws IOException when the file cannot be read - * @throws OptionalDataException ??? * @throws ClassNotFoundException when the AtomTypeFactory cannot be found */ - public static AtomTypeFactory getInstance(InputStream ins, String format, IChemObjectBuilder builder) throws IOException, OptionalDataException, ClassNotFoundException { + public static AtomTypeFactory getInstance(InputStream ins, String format, IChemObjectBuilder builder) throws IOException, ClassNotFoundException { return new AtomTypeFactory(ins, format, builder); } @@ -146,12 +143,12 @@ * Method to create a default AtomTypeFactory, using the structgen atom type list. * * @see #getInstance(String) + * @param builder IChemObjectBuilder used to make IChemObject instances * @return The AtomTypeFactory for the given data file * @throws IOException when the file cannot be read - * @throws OptionalDataException ??? * @throws ClassNotFoundException when the AtomTypeFactory cannot be found */ - public static AtomTypeFactory getInstance(IChemObjectBuilder builder) throws IOException, OptionalDataException, ClassNotFoundException { + public static AtomTypeFactory getInstance(IChemObjectBuilder builder) throws IOException, ClassNotFoundException { return getInstance("org/openscience/cdk/config/data/structgen_atomtypes.xml", builder); } @@ -167,12 +164,12 @@ * </ul> * * @param configFile String the name of the data file + * @param builder IChemObjectBuilder used to make IChemObject instances * @return The AtomTypeFactory for the given data file * @throws IOException when the file cannot be read - * @throws OptionalDataException ??? * @throws ClassNotFoundException when the AtomTypeFactory cannot be found */ - public static AtomTypeFactory getInstance(String configFile, IChemObjectBuilder builder) throws IOException, OptionalDataException, ClassNotFoundException { + public static AtomTypeFactory getInstance(String configFile, IChemObjectBuilder builder) throws IOException, ClassNotFoundException { if (tables == null) { tables = new Hashtable(); } @@ -186,6 +183,7 @@ * Read the config from a text file. * * @param configFile name of the config file + * @param builder IChemObjectBuilder used to make IChemObject instances */ private void readConfiguration(String fileName, IChemObjectBuilder builder) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |