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)