apollo.dataadapter.genbank
Class GenbankAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.genbank.GenbankAdapter

All Implemented Interfaces:

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

public class GenbankAdapter
extends AbstractApolloAdapter

Field Summary

protected static org.apache.log4j.Logger

logger

Fields inherited from class apollo.dataadapter.AbstractApolloAdapter

curation_set, 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

GenbankAdapter()

GenbankAdapter(DataInputType inputType, java.lang.String input)

GenbankAdapter(DataInputType inputType, java.lang.String input, boolean noGUI)

Method Summary

void	commitAccessions(boolean commit_acc)
void	commitChanges(CurationSet curation, boolean wantTabular) Write GenBank report in tabular or human-readable format, as requested
static java.lang.String	get3primeStop(AnnotatedFeatureI sf)
static java.lang.String	get5primeStart(AnnotatedFeatureI sf)
CurationSet	getCurationSet() from ApolloDataAdapterI interface.
static java.lang.String	getDbXref(SequenceI seq)
protected static java.lang.String	getGenbankType(java.lang.String type)
protected java.lang.String	getGeneProduct(AnnotatedFeatureI gene, Transcript transcript, java.lang.String CDS_start, java.lang.String CDS_stop, java.lang.String except, int na_except_pos)
protected java.lang.String	getIds(AnnotatedFeatureI gene, Transcript transcript)
protected java.lang.String	getLocus(AnnotatedFeatureI gene, java.lang.String tag) Change the flag that is passed if Genbank decides that some feature does/doesn't get the locus_tag field
static java.lang.String	getProteinDesc(AnnotatedFeatureI gene, Transcript transcript)
java.lang.String	getRawAnalysisResults(java.lang.String id)
SequenceI	getSequence(DbXref dbxref)
SequenceI	getSequence(DbXref dbxref, int start, int end)
SequenceI	getSequence(java.lang.String id) Strings for input types
static java.lang.String	getSequenceName(AnnotatedFeatureI gene, SequenceI seq, Transcript transcript)
java.util.Vector	getSequences(DbXref[] dbxref)
java.util.Vector	getSequences(DbXref[] dbxref, int[] start, int[] end)
java.util.Properties	getStateInformation() State info Properties carries all the info needed for the adapter to do its query This is an alternative to setDataInput.
org.bdgp.io.IOOperation[]	getSupportedOperations() Returns a list of all operations supported by this data adapter
java.lang.String	getType() Doesn't seem to be used
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) Returns a user interface for the requested IOOperation.
void	init() From org.bdgp.io.DataAdapter interface.
protected boolean	knownToGenbank(Transcript transcript)
void	setInput(java.lang.String input) Input string that corresponds with the input type (e.g.
void	setRegion(SequenceI seq)
void	setRegion(java.lang.String region) This region doesnt seem to be used anywhere?
void	setStateInformation(java.util.Properties props) DataLoader calls this
void	setValidationFile(java.lang.String valid_filename)
protected java.lang.String	writeAccession(FeatureSetI fs)
protected java.lang.String	writeFasta(CurationSet curation)
protected java.lang.String	writeGene(AnnotatedFeatureI gene, java.util.Vector omit)
protected java.lang.String	writePeptide(AnnotatedFeatureI gene, java.io.File dir, java.util.Vector omit)
protected java.lang.String	writeTranscript(AnnotatedFeatureI gene, java.io.File dir, java.util.Vector omit)

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

addToCurationSet, cacheUI, canWriteData, clearOldData, clearStateInformation, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getInput, getInputType, getName, getNameAdapter, getNumberOfChildAdapters, getSpecies, getStyle, hasLinkData, isComposite, loadNewSpeciesFromLink, operationIsSupported, rollbackAnnotations, rollbackAnnotations, setCuration, setCurationNumber, setCurationState, setDatabase, setDataInput, setDataLoadListener, setInputType, setLocation, setName, setPadLeft, setPadRight, setSpecies, 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

GenbankAdapter

public GenbankAdapter()

GenbankAdapter

public GenbankAdapter(DataInputType inputType,
                      java.lang.String input)

GenbankAdapter

public GenbankAdapter(DataInputType inputType,
                      java.lang.String input,
                      boolean noGUI)

Method Detail

init

public void init()

Description copied from class: AbstractApolloAdapter

From org.bdgp.io.DataAdapter interface. no-op default implementation. A data adapter should override this if it needs to do some initialization.

Specified by:

init in interface org.bdgp.io.DataAdapter

Overrides:

init in class AbstractApolloAdapter

getType

public java.lang.String getType()

Doesn't seem to be used

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType in class AbstractApolloAdapter

getSupportedOperations

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

Description copied from interface: org.bdgp.io.DataAdapter

Returns a list of all operations supported by this data adapter

getUI

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

Description copied from interface: org.bdgp.io.VisualDataAdapter

Returns a user interface for the requested IOOperation. Most VisualDataAdapters will return a different user interface for each supported IOOperation.

setInput

public void setInput(java.lang.String input)

Input string that corresponds with the input type (e.g. gene name for gene input type)

Specified by:

setInput in interface ApolloDataAdapterI

Overrides:

setInput in class AbstractApolloAdapter

commitAccessions

public void commitAccessions(boolean commit_acc)

setValidationFile

public void setValidationFile(java.lang.String valid_filename)

getStateInformation

public java.util.Properties getStateInformation()

Description copied from interface: ApolloDataAdapterI

State info Properties carries all the info needed for the adapter to do its query This is an alternative to setDataInput. For most cases setDataInput should be sufficient. This should return StateInformation

Specified by:

getStateInformation in interface ApolloDataAdapterI

Overrides:

getStateInformation in class AbstractApolloAdapter

setStateInformation

public void setStateInformation(java.util.Properties props)

DataLoader calls this

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class AbstractApolloAdapter

getSequence

public SequenceI getSequence(java.lang.String id)
                      throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

Strings for input types

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(DbXref dbxref)
                      throws ApolloAdapterException

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(DbXref dbxref,
                             int start,
                             int end)
                      throws ApolloAdapterException

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequences

public java.util.Vector getSequences(DbXref[] dbxref)
                              throws ApolloAdapterException

Specified by:

getSequences in interface ApolloDataAdapterI

Overrides:

getSequences in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequences

public java.util.Vector getSequences(DbXref[] dbxref,
                                     int[] start,
                                     int[] end)
                              throws ApolloAdapterException

Specified by:

getSequences in interface ApolloDataAdapterI

Overrides:

getSequences in class AbstractApolloAdapter

Throws:

ApolloAdapterException

setRegion

public void setRegion(SequenceI seq)
               throws ApolloAdapterException

Throws:

ApolloAdapterException

setRegion

public void setRegion(java.lang.String region)
               throws ApolloAdapterException

Description copied from class: AbstractApolloAdapter

This region doesnt seem to be used anywhere?

Specified by:

setRegion in interface ApolloDataAdapterI

Overrides:

setRegion in class AbstractApolloAdapter

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CurationSet curation,
                          boolean wantTabular)

Write GenBank report in tabular or human-readable format, as requested

writeFasta

protected java.lang.String writeFasta(CurationSet curation)

getGenbankType

protected static java.lang.String getGenbankType(java.lang.String type)

getIds

protected java.lang.String getIds(AnnotatedFeatureI gene,
                                  Transcript transcript)

getGeneProduct

protected java.lang.String getGeneProduct(AnnotatedFeatureI gene,
                                          Transcript transcript,
                                          java.lang.String CDS_start,
                                          java.lang.String CDS_stop,
                                          java.lang.String except,
                                          int na_except_pos)

getLocus

protected java.lang.String getLocus(AnnotatedFeatureI gene,
                                    java.lang.String tag)

Change the flag that is passed if Genbank decides that some feature does/doesn't get the locus_tag field

writeGene

protected java.lang.String writeGene(AnnotatedFeatureI gene,
                                     java.util.Vector omit)

writeTranscript

protected java.lang.String writeTranscript(AnnotatedFeatureI gene,
                                           java.io.File dir,
                                           java.util.Vector omit)

writePeptide

protected java.lang.String writePeptide(AnnotatedFeatureI gene,
                                        java.io.File dir,
                                        java.util.Vector omit)

writeAccession

protected java.lang.String writeAccession(FeatureSetI fs)

get5primeStart

public static java.lang.String get5primeStart(AnnotatedFeatureI sf)

get3primeStop

public static java.lang.String get3primeStop(AnnotatedFeatureI sf)

getDbXref

public static java.lang.String getDbXref(SequenceI seq)

getProteinDesc

public static java.lang.String getProteinDesc(AnnotatedFeatureI gene,
                                              Transcript transcript)

getSequenceName

public static java.lang.String getSequenceName(AnnotatedFeatureI gene,
                                               SequenceI seq,
                                               Transcript transcript)

knownToGenbank

protected boolean knownToGenbank(Transcript transcript)

getRawAnalysisResults

public java.lang.String getRawAnalysisResults(java.lang.String id)
                                       throws ApolloAdapterException

Specified by:

getRawAnalysisResults in interface ApolloDataAdapterI

Overrides:

getRawAnalysisResults in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

from ApolloDataAdapterI interface. input type and input should be set previous to this

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException