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Packages that use ParserException | |
org.biojava.bio.program.gff | GFF manipulation. |
org.biojava.bio.program.indexdb | A flat-file ascii index of ascii flat files as per the OBDA specification. |
org.biojava.bio.program.tagvalue | Process files as streams of records, each with tags with values. |
org.biojava.bio.program.unigene | Objects for representing Unigene clusters. |
Uses of ParserException in org.biojava.bio.program.gff |
Methods in org.biojava.bio.program.gff that throw ParserException | |
void |
GFFParser.parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler)
Informs handler of each line of gff read from bReader. |
void |
GFFParser.parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler,
java.lang.String locator)
Informs handler of each line of GFF read from bReader |
protected GFFRecord |
GFFParser.createRecord(GFFDocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment)
Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler. |
static GFFEntrySet |
GFFTools.readGFF(java.lang.String fileName)
Reads a GFFEntrySet from a file with no filtering |
static GFFEntrySet |
GFFTools.readGFF(java.lang.String fileName,
GFFRecordFilter recFilt)
Reads a GFFEntrySet from a file with the specified filter |
static GFFEntrySet |
GFFTools.readGFF(java.io.BufferedReader gffIn)
|
static GFFEntrySet |
GFFTools.readGFF(java.io.BufferedReader gffIn,
GFFRecordFilter recFilt)
|
int |
GFFErrorHandler.invalidStart(java.lang.String token)
The `start' field of the GFF entry was not a valid value. |
int |
GFFErrorHandler.invalidEnd(java.lang.String token)
The `end' field of the GFF entry was not a valid value. |
double |
GFFErrorHandler.invalidScore(java.lang.String token)
The `score' field of the GFF entry was not a valid value. |
int |
GFFErrorHandler.invalidFrame(java.lang.String token)
The `frame' field of the GFF entry was not a valid value. |
StrandedFeature.Strand |
GFFErrorHandler.invalidStrand(java.lang.String token)
The `strand' field of the GFF entry was not a valid value. |
int |
GFFErrorHandler.AbortErrorHandler.invalidStart(java.lang.String token)
|
int |
GFFErrorHandler.AbortErrorHandler.invalidEnd(java.lang.String token)
|
double |
GFFErrorHandler.AbortErrorHandler.invalidScore(java.lang.String token)
|
int |
GFFErrorHandler.AbortErrorHandler.invalidFrame(java.lang.String token)
|
StrandedFeature.Strand |
GFFErrorHandler.AbortErrorHandler.invalidStrand(java.lang.String token)
|
Uses of ParserException in org.biojava.bio.program.indexdb |
Methods in org.biojava.bio.program.indexdb that throw ParserException | |
static void |
IndexTools.indexFasta(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexFasta indexes DNA, RNA or protein Fasta
format sequence files on primary identifier. |
static void |
IndexTools.indexEmbl(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexEmbl indexes DNA, RNA or protein EMBL format
sequence files on ID as primary identifier and AC as secondary. |
static void |
IndexTools.indexGenbank(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexGenbank indexes DNA, RNA or protein Genbank
format sequence files on LOCUS as primary identifier and
ACCESSION as secondary. |
static void |
IndexTools.indexSwissprot(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles)
indexSwissprot indexes Swissprot format protein
sequence files on ID as primary identifier. |
Uses of ParserException in org.biojava.bio.program.tagvalue |
Methods in org.biojava.bio.program.tagvalue that throw ParserException | |
void |
RegexFieldFinder.startTag(java.lang.Object tag)
|
void |
RegexFieldFinder.endTag()
|
void |
RegexFieldFinder.value(TagValueContext ctxt,
java.lang.Object val)
|
TagValue |
RegexParser.parse(java.lang.Object o)
|
java.lang.Object |
RegexChanger.change(java.lang.Object value)
|
void |
TagValueListener.startRecord()
A new record is about to start. |
void |
TagValueListener.endRecord()
The current record has ended. |
void |
TagValueListener.startTag(java.lang.Object tag)
Start a new tag. |
void |
TagValueListener.endTag()
End the current tag. |
void |
TagValueListener.value(TagValueContext ctxt,
java.lang.Object value)
A value has been seen. |
void |
TagDropper.startTag(java.lang.Object tag)
|
void |
TagDropper.endTag()
|
void |
TagDropper.value(TagValueContext ctxt,
java.lang.Object value)
|
void |
TagValueWrapper.startRecord()
|
void |
TagValueWrapper.endRecord()
|
void |
TagValueWrapper.startTag(java.lang.Object tag)
|
void |
TagValueWrapper.endTag()
|
void |
TagValueWrapper.value(TagValueContext ctxt,
java.lang.Object value)
|
void |
Indexer2.endRecord()
|
void |
ValueChanger.startTag(java.lang.Object tag)
|
void |
ValueChanger.value(TagValueContext ctxt,
java.lang.Object value)
|
void |
TagRenamer.startTag(java.lang.Object tag)
|
TagValue |
TagValueParser.parse(java.lang.Object record)
|
void |
TagDelegator.startTag(java.lang.Object tag)
|
void |
TagDelegator.endTag()
|
void |
TagDelegator.value(TagValueContext tvc,
java.lang.Object value)
|
java.lang.Object |
ChangeTable.change(java.lang.Object tag,
java.lang.Object value)
|
java.lang.Object |
ChangeTable.Changer.change(java.lang.Object value)
Produce a modified value from an old value. |
java.util.List |
ChangeTable.Splitter.split(java.lang.Object value)
Produce a list of values from an old value. |
java.lang.Object |
ChangeTable.ChainedChanger.change(java.lang.Object value)
|
void |
Indexer.endRecord()
|
boolean |
Parser.read(java.io.BufferedReader reader,
TagValueParser parser,
TagValueListener listener)
|
Uses of ParserException in org.biojava.bio.program.unigene |
Methods in org.biojava.bio.program.unigene that throw ParserException | |
static ParserListener |
UnigeneTools.buildDataParser(TagValueListener listener)
Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener. |
static ParserListener |
UnigeneTools.buildLibInfoParser(TagValueListener listener)
Generate a tag-value parser for the library info unigene files. |
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