apollo.dataadapter.flychadoxml
Class FlyChadoXmlAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.chadoxml.ChadoXmlAdapter
              apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter

All Implemented Interfaces:

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

public class FlyChadoXmlAdapter
extends ChadoXmlAdapter

A FlyBase-specific reader for Chado XML files. Currently handles only unmacroized Chado XML.

Field Summary

protected static org.apache.log4j.Logger

logger

Fields inherited from class apollo.dataadapter.chadoxml.ChadoXmlAdapter

FIELD_LABEL

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

FlyChadoXmlAdapter()
Must have empty constructor to work with org.bdgp.io.DataAdapterRegistry instance creation from config string

Method Summary

java.lang.String	fillInDatabase(java.lang.String urlString) Replace %DATABASE% field with selected database.
CurationSet	getCurationSet() This is the main method for reading the data.
java.lang.String	getDatabase()
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) From org.bdgp.io.VisualDataAdapter interface
java.net.URL	getURLForBand(java.lang.String band)
java.net.URL	getURLForGene(java.lang.String gene)
java.net.URL	getURLForRange(Region region) parse range string "Chr 2L 10000 20000" -> "2L:10000:20000"
java.net.URL	getURLForScaffold(java.lang.String scaffold)
java.net.URL	makeUrlFromString(java.lang.String urlString) make URL from urlString, replace %DATABASE% with selected database

Methods inherited from class apollo.dataadapter.chadoxml.ChadoXmlAdapter

addToCurationSet, appearsToBeChadoXML, commitChanges, commitChanges, getCurationSetFromInputStream, getInput, getStateInformation, getSupportedOperations, getType, setDataInput, setInput, setOriginalFilename, setStateInformation

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

cacheUI, canWriteData, clearOldData, clearStateInformation, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDataInput, getDefaultStyle, getFilename, getInputType, getName, getNameAdapter, getNumberOfChildAdapters, getRawAnalysisResults, getSequence, getSequence, getSequence, getSequences, getSequences, getSpecies, getStyle, hasLinkData, init, isComposite, loadNewSpeciesFromLink, operationIsSupported, rollbackAnnotations, rollbackAnnotations, setCuration, setCurationNumber, setCurationState, setDatabase, setDataLoadListener, 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

FlyChadoXmlAdapter

public FlyChadoXmlAdapter()

Must have empty constructor to work with org.bdgp.io.DataAdapterRegistry instance creation from config string

Method Detail

getUI

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

From org.bdgp.io.VisualDataAdapter interface

Specified by:

getUI in interface org.bdgp.io.VisualDataAdapter

Overrides:

getUI in class ChadoXmlAdapter

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

This is the main method for reading the data.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class ChadoXmlAdapter

Throws:

ApolloAdapterException

makeUrlFromString

public java.net.URL makeUrlFromString(java.lang.String urlString)

make URL from urlString, replace %DATABASE% with selected database

fillInDatabase

public java.lang.String fillInDatabase(java.lang.String urlString)

Replace %DATABASE% field with selected database. Note: some of this is FlyBase-specific!

getDatabase

public java.lang.String getDatabase()

Overrides:

getDatabase in class AbstractApolloAdapter

getURLForScaffold

public java.net.URL getURLForScaffold(java.lang.String scaffold)

getURLForGene

public java.net.URL getURLForGene(java.lang.String gene)

getURLForBand

public java.net.URL getURLForBand(java.lang.String band)

getURLForRange

public java.net.URL getURLForRange(Region region)

parse range string "Chr 2L 10000 20000" -> "2L:10000:20000"