edu.mayo.informatics.resourcereader.obo
Class OBOResourceReaderHelper
java.lang.Object
edu.mayo.informatics.resourcereader.core.impl.Resource
edu.mayo.informatics.resourcereader.obo.OBO
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
Fields inherited from class edu.mayo.informatics.resourcereader.obo.OBO |
logger |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
showDeprecatedMessage
public boolean showDeprecatedMessage
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)
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)