apollo.dataadapter.chadoxml
Class ChadoXmlAdapter

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

All Implemented Interfaces:

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

Direct Known Subclasses:

FlyChadoXmlAdapter

public class ChadoXmlAdapter
extends AbstractApolloAdapter

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

Field Summary

static java.lang.String	FIELD_LABEL For labeling flat fields (which are stored as properties) so they can be written out properly.
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

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

Method Summary

java.lang.Boolean	addToCurationSet() Like getCurationSet--used for layering new data.
boolean	appearsToBeChadoXML(java.lang.String filename, java.io.BufferedReader in) Check whether the input appears to be chadoXML by looking for the line
void	commitChanges(CurationSet curation) Main method for writing ChadoXML file
void	commitChanges(CurationSet curation, boolean saveAnnots, boolean saveResults) Main method for writing ChadoXML file
CurationSet	getCurationSet() This is the main method for reading the data.
CurationSet	getCurationSetFromInputStream(java.io.InputStream xml_stream)
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?
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() From org.bdgp.io.DataAdapter interface
java.lang.String	getType() Used by GenericFileAdapterGUI
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) From org.bdgp.io.VisualDataAdapter interface
void	setDataInput(DataInput dataInput) This should replace setInput.
void	setInput(java.lang.String inputfile) Input string that corresponds with the input type (eg gene name for gene input type)
void	setOriginalFilename(java.lang.String file) Save original file name so that if we save the data we can access the header info from the original file; and also so we can save the file name as a comment.
void	setStateInformation(java.util.Properties props) DataLoader calls this.

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

cacheUI, canWriteData, clearOldData, clearStateInformation, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, 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

FIELD_LABEL

public static java.lang.String FIELD_LABEL

For labeling flat fields (which are stored as properties) so they can be written out properly. (Should this go somewhere global so that other adapters can see it?)

Constructor Detail

ChadoXmlAdapter

public ChadoXmlAdapter()

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

getSupportedOperations

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

From org.bdgp.io.DataAdapter interface

getType

public java.lang.String getType()

Used by GenericFileAdapterGUI

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType in class AbstractApolloAdapter

setInput

public void setInput(java.lang.String inputfile)

Description copied from class: AbstractApolloAdapter

Input string that corresponds with the input type (eg gene name for gene input type)

Specified by:

setInput in interface ApolloDataAdapterI

Overrides:

setInput in class AbstractApolloAdapter

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

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

setOriginalFilename

public void setOriginalFilename(java.lang.String file)

Save original file name so that if we save the data we can access the header info from the original file; and also so we can save the file name as a comment.

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

This is the main method for reading the data. The filename should already have been set.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getCurationSetFromInputStream

public CurationSet getCurationSetFromInputStream(java.io.InputStream xml_stream)
                                          throws ApolloAdapterException

Throws:

ApolloAdapterException

addToCurationSet

public java.lang.Boolean addToCurationSet()
                                   throws ApolloAdapterException

Like getCurationSet--used for layering new data.

Specified by:

addToCurationSet in interface ApolloDataAdapterI

Overrides:

addToCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CurationSet curation)

Main method for writing ChadoXML file

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

commitChanges

public void commitChanges(CurationSet curation,
                          boolean saveAnnots,
                          boolean saveResults)

Main method for writing ChadoXML file

Overrides:

commitChanges in class AbstractApolloAdapter

appearsToBeChadoXML

public boolean appearsToBeChadoXML(java.lang.String filename,
                                   java.io.BufferedReader in)
                            throws ApolloAdapterException

Check whether the input appears to be chadoXML by looking for the line

Throws:

ApolloAdapterException

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. input, inputType and optionally database set here. MovementPanel(nav bar) sets db to default db (it has no db chooser)

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class AbstractApolloAdapter