apollo.dataadapter
Class GFFAdapter

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

All Implemented Interfaces:

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

Direct Known Subclasses:

SyntenyGFFAdapter

public class GFFAdapter
extends BaseGFFAdapter

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

GFFAdapter()

Method Summary

StrandedFeatureSetI

getAnalysisRegion()

Methods inherited from class apollo.dataadapter.BaseGFFAdapter

clearStateInformation, commitChanges, findFile, getAnnotatedRegion, getAnnotRegion, getCurationSet, getFilename, getGFFFile, getInput, getInputType, getRawAnalysisResults, getSequence, getSequence, getSequence, getSequence, getSequenceFilename, getSequences, getSequences, getStateInformation, getSupportedOperations, getType, getUI, init, 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, 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

Constructor Detail

GFFAdapter

public GFFAdapter()

Method Detail

getAnalysisRegion

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

Overrides:

getAnalysisRegion in class BaseGFFAdapter

Throws:

org.bdgp.io.DataAdapterException