apollo.dataadapter.otter
Class OtterXMLAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.otter.OtterXMLAdapter

All Implemented Interfaces:

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

public class OtterXMLAdapter
extends AbstractApolloAdapter

Field Summary

Fields inherited from class apollo.dataadapter.AbstractApolloAdapter

curation_set, logger, 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

OtterXMLAdapter()

Method Summary

void	commitChanges(CurationSet curationSet) writes the changes from a featureChangeLog to a writeable datasource.
CurationSet	getCurationSet() returns a saved CurationSet.
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.io.InputStream	getInputStream()
DataInputType	getInputType() Returns the type of input data (gene,file,band...)
java.lang.String	getName() Name label for use in Data Adapter Chooser.
java.io.OutputStream	getOutputStream()
java.lang.String	getRawAnalysisResults(java.lang.String id)
SequenceI	getSequence(DbXref dbxref)
SequenceI	getSequence(DbXref dbxref, int start, int end)
SequenceI	getSequence(java.lang.String id) Strings for input types
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.
void	setGFFFilename(java.lang.String gfffile)
void	setInputStream(java.io.InputStream newValue)
void	setOutputStream(java.io.OutputStream newValue)
void	setRegion(java.lang.String region) This region doesnt seem to be used anywhere?
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.

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

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

OtterXMLAdapter

public OtterXMLAdapter()

Method Detail

getInputStream

public java.io.InputStream getInputStream()

setInputStream

public void setInputStream(java.io.InputStream newValue)

getOutputStream

public java.io.OutputStream getOutputStream()

setOutputStream

public void setOutputStream(java.io.OutputStream newValue)

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

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.

setRegion

public void setRegion(java.lang.String region)
               throws ApolloAdapterException

Description copied from class: AbstractApolloAdapter

This region doesnt seem to be used anywhere?

Specified by:

setRegion in interface ApolloDataAdapterI

Overrides:

setRegion in class AbstractApolloAdapter

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)

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

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

commitChanges

public void commitChanges(CurationSet curationSet)
                   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

setSequenceFilename

public void setSequenceFilename(java.lang.String seqfile)

setGFFFilename

public void setGFFFilename(java.lang.String gfffile)

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

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