apollo.dataadapter.gff3
Class GFF3Adapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.gff3.GFF3Adapter

All Implemented Interfaces:

ApolloDataAdapterI, org.bdgp.io.DataAdapter, org.bdgp.io.VisualDataAdapter

public class GFF3Adapter
extends AbstractApolloAdapter

Field Summary

protected static org.apache.log4j.Logger

logger

Fields inherited from class apollo.dataadapter.AbstractApolloAdapter

curation_set, region, style

Fields inherited from class org.bdgp.io.AbstractDataAdapter

listeners

Fields inherited from interface apollo.dataadapter.ApolloDataAdapterI

OP_APPEND_DATA, OP_READ_DATA, OP_READ_RAW_ANALYSIS, OP_READ_SEQUENCE, OP_WRITE_DATA

Constructor Summary

GFF3Adapter()
Constructor

Method Summary

java.lang.Boolean	addToCurationSet() Add GFF3 data to currently existing CurationSet
void	commitChanges(CurationSet curation) Commit data
CurationSet	getCurationSet() Parse and return the CurationSet
java.lang.String	getGffFilename() Get the GFF filename
java.lang.String	getSeqFilename() Get the sequence filename
org.bdgp.io.IOOperation[]	getSupportedOperations() Get supported operations (read / write)
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) Get the UI for the data adapter
void	init() Initialize the adapter
boolean	isFastaFromGff() Checks whether to parse FASTA from GFF or external FASTA file
void	setDataInput(DataInput di) Sets the input for this adapter
void	setFastaFromGff(boolean fastaFromGff) Sets whether to parse FASTA from GFF or external FASTA file
void	setGffFilename(java.lang.String gffFilename) Set the GFF filename
void	setSeqFilename(java.lang.String seqFilename) Set the sequence filename
void	write(java.lang.Object values) Write data

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

cacheUI, canWriteData, clearOldData, clearStateInformation, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getInput, getInputType, getName, getNameAdapter, getNumberOfChildAdapters, getRawAnalysisResults, getSequence, getSequence, getSequence, getSequences, getSequences, getSpecies, getStateInformation, getStyle, getType, hasLinkData, isComposite, loadNewSpeciesFromLink, operationIsSupported, rollbackAnnotations, rollbackAnnotations, setCuration, setCurationNumber, setCurationState, setDatabase, setDataLoadListener, setInput, setInputType, setLocation, setName, setPadLeft, setPadRight, setRegion, setSpecies, setStateInformation, setStyle

Methods inherited from class org.bdgp.io.AbstractDataAdapter

addProgressListener, fireProgressEvent, removeProgressListener, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.bdgp.io.VisualDataAdapter

addProgressListener, fireProgressEvent, removeProgressListener

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

GFF3Adapter

public GFF3Adapter()

Constructor

Method Detail

setFastaFromGff

public void setFastaFromGff(boolean fastaFromGff)

Sets whether to parse FASTA from GFF or external FASTA file

isFastaFromGff

public boolean isFastaFromGff()

Checks whether to parse FASTA from GFF or external FASTA file

getSupportedOperations

public org.bdgp.io.IOOperation[] getSupportedOperations()

Get supported operations (read / write)

getUI

public org.bdgp.io.DataAdapterUI getUI(org.bdgp.io.IOOperation op)

Get the UI for the data adapter

init

public void init()

Initialize the adapter

Specified by:

init in interface org.bdgp.io.DataAdapter

Overrides:

init in class AbstractApolloAdapter

getGffFilename

public java.lang.String getGffFilename()

Get the GFF filename

setGffFilename

public void setGffFilename(java.lang.String gffFilename)

Set the GFF filename

getSeqFilename

public java.lang.String getSeqFilename()

Get the sequence filename

setSeqFilename

public void setSeqFilename(java.lang.String seqFilename)

Set the sequence filename

setDataInput

public void setDataInput(DataInput di)

Sets the input for this adapter

Specified by:

setDataInput in interface ApolloDataAdapterI

Overrides:

setDataInput in class AbstractApolloAdapter

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

Parse and return the CurationSet

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

addToCurationSet

public java.lang.Boolean addToCurationSet()
                                   throws ApolloAdapterException

Add GFF3 data to currently existing CurationSet

Specified by:

addToCurationSet in interface ApolloDataAdapterI

Overrides:

addToCurationSet in class AbstractApolloAdapter

Parameters:

values - - ApolloDataI object that contains CurationSet

Throws:

ApolloAdapterException - if there is an error in parsing the data

commitChanges

public void commitChanges(CurationSet curation)
                   throws ApolloAdapterException

Commit data

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

Throws:

ApolloAdapterException

write

public void write(java.lang.Object values)
           throws ApolloAdapterException

Write data

Throws:

ApolloAdapterException