Package | Description |
---|---|
org.biojava.bio.annodb |
Databases of generic structured data (annotation) objects.
|
org.biojava.bio.program.gff |
GFF manipulation.
|
org.biojava.bio.program.gff3 |
Support for reading and writing GFF3.
|
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.
|
Constructor and Description |
---|
IndexedAnnotationDB(java.lang.String dbName,
java.io.File storeLoc,
Index2Model model,
java.util.List toIndex,
int maxKeyLen,
AnnotationType schema,
IndexedAnnotationDB.ParserListenerFactory plFactory)
Create a new IndexedAnnotationDB.
|
Modifier and Type | Method and Description |
---|---|
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.
|
int |
GFFErrorHandler.invalidEnd(java.lang.String token)
The `end' field of the GFF entry was not a valid value.
|
int |
GFFErrorHandler.AbortErrorHandler.invalidEnd(java.lang.String token) |
int |
GFFErrorHandler.invalidFrame(java.lang.String token)
The `frame' field of the GFF entry was not a valid value.
|
int |
GFFErrorHandler.AbortErrorHandler.invalidFrame(java.lang.String token) |
double |
GFFErrorHandler.invalidScore(java.lang.String token)
The `score' field of the GFF entry was not a valid value.
|
double |
GFFErrorHandler.AbortErrorHandler.invalidScore(java.lang.String token) |
int |
GFFErrorHandler.invalidStart(java.lang.String token)
The `start' field of the GFF entry was not a valid value.
|
int |
GFFErrorHandler.AbortErrorHandler.invalidStart(java.lang.String token) |
StrandedFeature.Strand |
GFFErrorHandler.invalidStrand(java.lang.String token)
The `strand' field of the GFF entry was not a valid value.
|
StrandedFeature.Strand |
GFFErrorHandler.AbortErrorHandler.invalidStrand(java.lang.String token) |
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
|
static GFFEntrySet |
GFFTools.readGFF(java.io.BufferedReader gffIn)
Read all GFF entries from a buffered reader.
|
static GFFEntrySet |
GFFTools.readGFF(java.io.BufferedReader gffIn,
GFFRecordFilter recFilt)
Read all GFF entries matching a filter from a buffered reader.
|
static GFFEntrySet |
GFFTools.readGFF(java.io.File inFile)
Reads a
GFFEntrySet from a file with no filtering. |
static GFFEntrySet |
GFFTools.readGFF(java.io.File inFile,
GFFRecordFilter recFilt)
Reads a GFFEntrySet from a file with the specified filter.
|
static GFFEntrySet |
GFFTools.readGFF(java.lang.String fileName)
Deprecated.
use: readGff(File)
|
static GFFEntrySet |
GFFTools.readGFF(java.lang.String fileName,
GFFRecordFilter recFilt)
Deprecated.
use: readGff(File,GFFRecordFilter)
|
Modifier and Type | Method and Description |
---|---|
protected GFF3Record |
GFF3Parser.createRecord(GFF3DocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment,
Ontology ontology,
Ontology fallBack)
Actually turns a list of tokens, some value string and a comment into a
GFF3Record and informs
handler.
|
void |
GFF3Parser.parse(java.io.BufferedReader bReader,
GFF3DocumentHandler handler,
Ontology ontology)
Informs handler of each line of
gff read from bReader.
|
void |
GFF3Parser.parse(java.io.BufferedReader bReader,
GFF3DocumentHandler handler,
Ontology ontology,
java.lang.String locator)
Informs handler of each line of
GFF read from bReader
|
Modifier and Type | Method and Description |
---|---|
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.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.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. |
Modifier and Type | Method and Description |
---|---|
java.lang.Object |
ChangeTable.Changer.change(java.lang.Object value)
Produce a modified value from an old value.
|
java.lang.Object |
ChangeTable.ChainedChanger.change(java.lang.Object value) |
java.lang.Object |
RegexChanger.change(java.lang.Object value) |
java.lang.Object |
ChangeTable.change(java.lang.Object tag,
java.lang.Object value) |
void |
StateMachine.endRecord() |
void |
StateMachine.SimpleStateListener.endRecord() |
void |
Indexer.endRecord() |
void |
TagValueListener.endRecord()
The current record has ended.
|
void |
Indexer2.endRecord() |
void |
AbstractWrapper.endRecord() |
void |
SimpleTagValueWrapper.endRecord() |
void |
StateMachine.endTag() |
void |
StateMachine.SimpleStateListener.endTag() |
void |
TagValueListener.endTag()
End the current tag.
|
void |
TagDropper.endTag() |
void |
Aggregator.endTag() |
void |
TagDelegator.endTag() |
void |
MultiTagger.endTag() |
void |
RegexFieldFinder.endTag() |
void |
AbstractWrapper.endTag() |
void |
SimpleTagValueWrapper.endTag() |
void |
StateMachine.ExitNotification.notifyExit() |
TagValue |
TagValueParser.parse(java.lang.Object record) |
TagValue |
RegexParser.parse(java.lang.Object o) |
void |
StateMachine.TransitionTable.put(java.lang.Object tag,
StateMachine.Transition transition)
set a Transition within this TransitionTable (2-argument form)
|
boolean |
Parser.read(java.io.BufferedReader reader,
TagValueParser parser,
TagValueListener listener) |
void |
StateMachine.BasicState.setTransition(java.lang.Object tag,
StateMachine.State destination)
set a Transition for this State setting notifyOnExit to false.
|
void |
StateMachine.TransitionTable.setTransition(java.lang.Object tag,
StateMachine.State destination,
boolean notifyOnExit)
set a Transition within this TransitionTable (3-argument form)
|
void |
StateMachine.BasicState.setTransition(java.lang.Object tag,
StateMachine.State destination,
boolean notifyOnExit)
set a Transition for this State
|
java.util.List |
ChangeTable.Splitter.split(java.lang.Object value)
Produce a list of values from an old value.
|
void |
StateMachine.startRecord() |
void |
StateMachine.SimpleStateListener.startRecord() |
void |
TagValueListener.startRecord()
A new record is about to start.
|
void |
AbstractWrapper.startRecord() |
void |
SimpleTagValueWrapper.startRecord() |
void |
StateMachine.startTag(java.lang.Object tag)
TagValueListener interface
|
void |
StateMachine.SimpleStateListener.startTag(java.lang.Object tag) |
void |
TagValueListener.startTag(java.lang.Object tag)
Start a new tag.
|
void |
TagDropper.startTag(java.lang.Object tag) |
void |
Aggregator.startTag(java.lang.Object tag) |
void |
ValueChanger.startTag(java.lang.Object tag) |
void |
TagDelegator.startTag(java.lang.Object tag) |
void |
MultiTagger.startTag(java.lang.Object tag) |
void |
RegexFieldFinder.startTag(java.lang.Object tag) |
void |
TagRenamer.startTag(java.lang.Object tag) |
void |
AbstractWrapper.startTag(java.lang.Object tag) |
void |
SimpleTagValueWrapper.startTag(java.lang.Object tag) |
void |
StateMachine.State.transit(java.lang.Object tag) |
void |
StateMachine.BasicState.transit(java.lang.Object tag)
Find the destination State when the specified tag
is encountered.
|
void |
StateMachine.value(TagValueContext ctxt,
java.lang.Object value) |
void |
StateMachine.SimpleStateListener.value(TagValueContext ctxt,
java.lang.Object value) |
void |
TagValueListener.value(TagValueContext ctxt,
java.lang.Object value)
A value has been seen.
|
void |
TagDropper.value(TagValueContext ctxt,
java.lang.Object value) |
void |
Aggregator.value(TagValueContext ctxt,
java.lang.Object value) |
void |
ValueChanger.value(TagValueContext ctxt,
java.lang.Object value) |
void |
TagDelegator.value(TagValueContext tvc,
java.lang.Object value) |
void |
MultiTagger.value(TagValueContext ctxt,
java.lang.Object value) |
void |
RegexFieldFinder.value(TagValueContext ctxt,
java.lang.Object val) |
void |
AbstractWrapper.value(TagValueContext ctxt,
java.lang.Object value) |
void |
SimpleTagValueWrapper.value(TagValueContext ctxt,
java.lang.Object value) |
Modifier and Type | Method and Description |
---|---|
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.
|