edu.mssm.crover.imports
Class ExtendedSwissProtReader

java.lang.Object
  |
  +--edu.mssm.crover.imports.SwissProtReader
        |
        +--edu.mssm.crover.imports.ExtendedSwissProtReader
All Implemented Interfaces:
SequenceReader

public class ExtendedSwissProtReader
extends SwissProtReader

An extended version of the SwissProtReader. It rejects files with UnsupportedFileFormatException() when the required fields cannot be found in the InputStream. See the information attached to SwissProtReaderType for an up-to date list of fields.


Field Summary
 
Fields inherited from class edu.mssm.crover.imports.SwissProtReader
ORIGIN, SWISSPROT
 
Constructor Summary
ExtendedSwissProtReader(java.io.File seqFile, java.io.File iprFile)
           
 
Method Summary
 java.util.Hashtable getFamilyConcordance()
           
 java.util.Collection getWildTypeProteins()
          getWildTypeProteins returns a Collection of WildTypeProteins that have been read from the SwissProt format sequence file.
static void main(java.lang.String[] args)
           
 
Methods inherited from class edu.mssm.crover.imports.SwissProtReader
findID, findLine, getSupportedType, parseAC, parseAnnotation, parseFT_DISULFID, parseFT_DOMAIN, parseFT_HELIX, parseFT_STRAND, parseFT_TRANSMEM, parseFT_TURN, parseSecondaryStructure, readAnnotations, readFile, readResidues, secStructFromSeq
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ExtendedSwissProtReader

public ExtendedSwissProtReader(java.io.File seqFile,
                               java.io.File iprFile)
                        throws java.io.FileNotFoundException,
                               java.io.IOException
Method Detail

getWildTypeProteins

public java.util.Collection getWildTypeProteins()
                                         throws java.io.IOException
getWildTypeProteins returns a Collection of WildTypeProteins that have been read from the SwissProt format sequence file.

java.io.IOException

getFamilyConcordance

public java.util.Hashtable getFamilyConcordance()
                                         throws java.io.FileNotFoundException,
                                                java.lang.NullPointerException,
                                                java.io.IOException
java.io.FileNotFoundException
java.lang.NullPointerException
java.io.IOException

main

public static void main(java.lang.String[] args)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.