edu.mayo.informatics.resourcereader.obo
Class OBOResourceReaderHelper

java.lang.Object
  extended by edu.mayo.informatics.resourcereader.core.impl.Resource
      extended by edu.mayo.informatics.resourcereader.obo.OBO
          extended by edu.mayo.informatics.resourcereader.obo.OBOResourceReaderHelper
All Implemented Interfaces:
TopResource

public class OBOResourceReaderHelper
extends OBO

This class reads the OBO file and stores the information into a ResourceHeader and ResourceContents object.

Version:
subversion $Revision: $ checked in on $Date: $
Author:
Deepak Sharma, Pradip Kanjamala

Field Summary
 boolean showDeprecatedMessage
           
 
Fields inherited from class edu.mayo.informatics.resourcereader.obo.OBO
logger
 
Constructor Summary
OBOResourceReaderHelper(java.io.BufferedReader inputFileReader, CachingMessageDirectorIF rLogger)
           
OBOResourceReaderHelper(CachingMessageDirectorIF rLogger)
           
OBOResourceReaderHelper(java.net.URI inputFile, CachingMessageDirectorIF rLogger)
           
OBOResourceReaderHelper(java.net.URL inputFileURL, CachingMessageDirectorIF rLogger)
           
 
Method Summary
 java.io.BufferedReader getStream()
           
static void main(java.lang.String[] arg)
           
static java.lang.String parseAsSimpleKeyValue(java.lang.String source, java.lang.String keyString)
           
static java.lang.String parseAsSimpleKeyValueWithLimit(java.lang.String source, java.lang.String keyString, int max_length)
           
 java.util.ArrayList<java.lang.String> parseLineWithXRefs(java.lang.String line)
           
 void readAndMergeContents(OBOContents existingContents, OBOHeader header)
           
 ResourceHeader readHeader()
           
static java.lang.String removeComments(java.lang.String str)
           
static java.lang.String removeEscapes(java.lang.String input)
           
 void setStream(java.io.BufferedReader inputFileReader)
           
 void setStream(java.net.URI inputFile)
           
 void setStream(java.net.URL inputFileURL)
           
 
Methods inherited from class edu.mayo.informatics.resourcereader.core.impl.Resource
getLogger, setLogger
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

showDeprecatedMessage

public boolean showDeprecatedMessage
Constructor Detail

OBOResourceReaderHelper

public OBOResourceReaderHelper(CachingMessageDirectorIF rLogger)

OBOResourceReaderHelper

public OBOResourceReaderHelper(java.net.URI inputFile,
                               CachingMessageDirectorIF rLogger)

OBOResourceReaderHelper

public OBOResourceReaderHelper(java.io.BufferedReader inputFileReader,
                               CachingMessageDirectorIF rLogger)

OBOResourceReaderHelper

public OBOResourceReaderHelper(java.net.URL inputFileURL,
                               CachingMessageDirectorIF rLogger)
Method Detail

setStream

public void setStream(java.net.URI inputFile)

setStream

public void setStream(java.io.BufferedReader inputFileReader)

setStream

public void setStream(java.net.URL inputFileURL)

getStream

public java.io.BufferedReader getStream()

readHeader

public ResourceHeader readHeader()

readAndMergeContents

public void readAndMergeContents(OBOContents existingContents,
                                 OBOHeader header)

parseAsSimpleKeyValueWithLimit

public static java.lang.String parseAsSimpleKeyValueWithLimit(java.lang.String source,
                                                              java.lang.String keyString,
                                                              int max_length)

parseAsSimpleKeyValue

public static java.lang.String parseAsSimpleKeyValue(java.lang.String source,
                                                     java.lang.String keyString)

removeEscapes

public static java.lang.String removeEscapes(java.lang.String input)

removeComments

public static java.lang.String removeComments(java.lang.String str)

parseLineWithXRefs

public java.util.ArrayList<java.lang.String> parseLineWithXRefs(java.lang.String line)

main

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

Copyright: (c) 2004-2006 Mayo Foundation for Medical Education and Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the triple-shield Mayo logo are trademarks and service marks of MFMER.