apollo.dataadapter
Class SyntenyGFFAdapter

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

All Implemented Interfaces:

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

public class SyntenyGFFAdapter
extends GFFAdapter
implements ApolloDataAdapterI

Field Summary

Fields inherited from class apollo.dataadapter.BaseGFFAdapter

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

SyntenyGFFAdapter()

SyntenyGFFAdapter(java.lang.String filename, java.lang.String org1, java.lang.String org2)

Method Summary

StrandedFeatureSetI	getAnalysisRegion()
Chromosome	getChromosome1()
CurationSet	getCurationSet() returns a saved CurationSet.
KaryotypeAdapter	getKaryotypeAdapter()
java.lang.String	getName() Name label for use in Data Adapter Chooser.
org.bdgp.io.IOOperation[]	getSupportedOperations() Returns a list of all operations supported by this data adapter
java.util.Vector	getSyntenyRegions()
java.util.Vector	getSyntenyRegionsByChromosome(java.lang.String chr)
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.

Methods inherited from class apollo.dataadapter.BaseGFFAdapter

clearStateInformation, commitChanges, findFile, getAnnotatedRegion, getAnnotRegion, getFilename, getGFFFile, getInput, getInputType, getRawAnalysisResults, getSequence, getSequence, getSequence, getSequence, getSequenceFilename, getSequences, getSequences, getStateInformation, main, readSequence, saveSequence, setDataInput, setFilename, setSequenceFilename, setStateInformation, writeAnalyses, writeAnalysis, writeAnnotation, writeAnnotations, writeGFF, writeTranscript

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

addToCurationSet, cacheUI, canWriteData, clearOldData, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, 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 apollo.dataadapter.ApolloDataAdapterI

addToCurationSet, canWriteData, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getChildAdapter, getChildAdapter, getCurationState, getInput, getInputType, getNumberOfChildAdapters, getRawAnalysisResults, getSequence, getSequence, getSequence, getSequences, getSequences, getSpecies, getStateInformation, getStyle, hasLinkData, isComposite, loadNewSpeciesFromLink, rollbackAnnotations, setCuration, setDatabase, setDataInput, setDataLoadListener, setInput, setInputType, setPadLeft, setPadRight, setRegion, setStateInformation, setStyle

Methods inherited from interface org.bdgp.io.VisualDataAdapter

addProgressListener, fireProgressEvent, removeProgressListener

Constructor Detail

SyntenyGFFAdapter

public SyntenyGFFAdapter(java.lang.String filename,
                         java.lang.String org1,
                         java.lang.String org2)

SyntenyGFFAdapter

public SyntenyGFFAdapter()

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 BaseGFFAdapter

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 BaseGFFAdapter

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

Specified by:

getSupportedOperations in interface org.bdgp.io.DataAdapter

Overrides:

getSupportedOperations in class BaseGFFAdapter

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.

Specified by:

getUI in interface org.bdgp.io.VisualDataAdapter

Overrides:

getUI in class BaseGFFAdapter

getName

public java.lang.String getName()

Description copied from class: AbstractApolloAdapter

Name label for use in Data Adapter Chooser. Don't override this method--call setName from your constructor.

Specified by:

getName in interface org.bdgp.io.DataAdapter

Overrides:

getName in class AbstractApolloAdapter

getKaryotypeAdapter

public KaryotypeAdapter getKaryotypeAdapter()

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 BaseGFFAdapter

Throws:

ApolloAdapterException

getAnalysisRegion

public StrandedFeatureSetI getAnalysisRegion()
                                      throws ApolloAdapterException

Overrides:

getAnalysisRegion in class GFFAdapter

Throws:

ApolloAdapterException

getSyntenyRegions

public java.util.Vector getSyntenyRegions()

getSyntenyRegionsByChromosome

public java.util.Vector getSyntenyRegionsByChromosome(java.lang.String chr)

getChromosome1

public Chromosome getChromosome1()