apollo.dataadapter
Class BaseGFFAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.BaseGFFAdapter

All Implemented Interfaces:

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

Direct Known Subclasses:

GFFAdapter

public class BaseGFFAdapter
extends AbstractApolloAdapter

I'm a variant of a GFFAdapter that does NO translation of the features I read into sets of features (ie no post-processing of the data). That is, I will read features (or feature pairs) and place them into a StrandedFeatureSet, place those into a curation set, and hand out the curation set.

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

BaseGFFAdapter()

BaseGFFAdapter(java.lang.String filename)

Method Summary

void	clearStateInformation() This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.
void	commitChanges(CurationSet curation) writes the changes from a featureChangeLog to a writeable datasource.
protected java.lang.String	findFile(java.lang.String name)
StrandedFeatureSetI	getAnalysisRegion()
FeatureSetI	getAnnotatedRegion()
StrandedFeatureSetI	getAnnotRegion()
CurationSet	getCurationSet() returns a saved CurationSet.
java.lang.String	getFilename() Returns null if not file
protected GFFFile	getGFFFile()
java.lang.String	getInput() Returns the input String passed to the DataAdapter, the input is of course associated with the input type Should this go into org.bdgp.io.DataAdapter?
DataInputType	getInputType() Returns the type of input data (gene,file,band...)
java.lang.String	getRawAnalysisResults(java.lang.String id)
Sequence	getSequence()
SequenceI	getSequence(DbXref dbxref)
SequenceI	getSequence(DbXref dbxref, int start, int end)
SequenceI	getSequence(java.lang.String id) Strings for input types
java.lang.String	getSequenceFilename()
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() From org.bdgp.io.DataAdapter.
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.
static void	main(java.lang.String[] args)
void	readSequence(java.lang.String file, CurationSet curation)
void	saveSequence(SequenceI seq)
void	setDataInput(DataInput dataInput) This should replace setInput.
void	setFilename(java.lang.String filename) determines whether the entered 'filename' is in fact a url.If it is then retrieves the GFF file via HTTP, to a temp file, and sets fileName to this temp file.
void	setSequenceFilename(java.lang.String seqfile)
void	setStateInformation(java.util.Properties props) This should set StateInformation object! see StateInformation for Strings to use for keys.
java.lang.String	writeAnalyses(CurationSet curation)
java.lang.String	writeAnalysis(FeatureSetI sf)
java.lang.String	writeAnnotation(AnnotatedFeatureI sf)
java.lang.String	writeAnnotations(CurationSet curation)
void	writeGFF(CurationSet curation, java.io.OutputStream os)
java.lang.String	writeTranscript(Transcript trans, boolean isa_gene)

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

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

BaseGFFAdapter

public BaseGFFAdapter(java.lang.String filename)

BaseGFFAdapter

public BaseGFFAdapter()

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()

Description copied from class: AbstractApolloAdapter

From org.bdgp.io.DataAdapter. Default implementation returns "". Override this to return a string describing the data adapter. The reason for the default implementation is that as far as I can tell getType is not used by apollo nor org.bdgp, so seems silly to require it. Am i missing something?

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType in class AbstractApolloAdapter

getInputType

public DataInputType getInputType()

Description copied from class: AbstractApolloAdapter

Returns the type of input data (gene,file,band...)

Specified by:

getInputType in interface ApolloDataAdapterI

Overrides:

getInputType in class AbstractApolloAdapter

See Also:

Should this go into org.bdgp.io.DataAdapter?

getInput

public java.lang.String getInput()

Description copied from class: AbstractApolloAdapter

Returns the input String passed to the DataAdapter, the input is of course associated with the input type Should this go into org.bdgp.io.DataAdapter?

Specified by:

getInput in interface ApolloDataAdapterI

Overrides:

getInput 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.

setFilename

public void setFilename(java.lang.String filename)
                 throws ApolloAdapterException

determines whether the entered 'filename' is in fact a url.If it is then retrieves the GFF file via HTTP, to a temp file, and sets fileName to this temp file. Otherwise, simply sets fileName to the entered filename

Throws:

ApolloAdapterException

getFilename

public java.lang.String getFilename()

Description copied from class: AbstractApolloAdapter

Returns null if not file

Overrides:

getFilename in class AbstractApolloAdapter

setDataInput

public void setDataInput(DataInput dataInput)

Description copied from interface: ApolloDataAdapterI

This should replace setInput. setInput is limited to just a String which is awkward for locations where you have to jam several fields into one String. DataInput deals with locations much better. DataInput can complement stateInfo (hopefully?)

Specified by:

setDataInput in interface ApolloDataAdapterI

Overrides:

setDataInput in class AbstractApolloAdapter

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)

Description copied from interface: ApolloDataAdapterI

This should set StateInformation object! see StateInformation for Strings to use for keys.

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class AbstractApolloAdapter

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

returns a saved CurationSet.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getGFFFile

protected GFFFile getGFFFile()
                      throws org.bdgp.io.DataAdapterException

Throws:

org.bdgp.io.DataAdapterException

findFile

protected java.lang.String findFile(java.lang.String name)
                             throws org.bdgp.io.DataAdapterException

Throws:

org.bdgp.io.DataAdapterException

getAnalysisRegion

public StrandedFeatureSetI getAnalysisRegion()
                                      throws org.bdgp.io.DataAdapterException

Throws:

org.bdgp.io.DataAdapterException

getAnnotRegion

public StrandedFeatureSetI getAnnotRegion()

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Throws:

java.lang.Exception

getAnnotatedRegion

public FeatureSetI getAnnotatedRegion()
                               throws org.bdgp.io.DataAdapterException

Throws:

org.bdgp.io.DataAdapterException

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

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

commitChanges

public void commitChanges(CurationSet curation)
                   throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

writes the changes from a featureChangeLog to a writeable datasource. Not just a featureChangeLog - this writes out the whole curationSet

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

Throws:

ApolloAdapterException

writeGFF

public void writeGFF(CurationSet curation,
                     java.io.OutputStream os)

writeAnnotations

public java.lang.String writeAnnotations(CurationSet curation)

writeAnnotation

public java.lang.String writeAnnotation(AnnotatedFeatureI sf)

writeTranscript

public java.lang.String writeTranscript(Transcript trans,
                                        boolean isa_gene)

writeAnalyses

public java.lang.String writeAnalyses(CurationSet curation)

writeAnalysis

public java.lang.String writeAnalysis(FeatureSetI sf)

getSequence

public Sequence getSequence()

readSequence

public void readSequence(java.lang.String file,
                         CurationSet curation)
                  throws org.bdgp.io.DataAdapterException

Throws:

org.bdgp.io.DataAdapterException

setSequenceFilename

public void setSequenceFilename(java.lang.String seqfile)

getSequenceFilename

public java.lang.String getSequenceFilename()

saveSequence

public void saveSequence(SequenceI seq)
                  throws org.bdgp.io.DataAdapterException

Throws:

org.bdgp.io.DataAdapterException

clearStateInformation

public void clearStateInformation()

Description copied from class: AbstractApolloAdapter

This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.

Overrides:

clearStateInformation in class AbstractApolloAdapter