apollo.dataadapter.gamexml
Class GAMEAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.gamexml.GAMEAdapter

All Implemented Interfaces:

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

Direct Known Subclasses:

FlyGAMEAdapter

public class GAMEAdapter
extends AbstractApolloAdapter

Reader for GAME XML files. WARNING -- AElfred (and other SAX drivers) _may_ break large stretches of unmarked content into smaller chunks and call characters() for each smaller chunk CURRENT IMPLEMENTATION DOES NOT DEAL WITH THIS COULD CAUSE PROBLEM WHEN READING IN SEQUENCE RESIDUES haven't seen a problem yet though -- GAH 6-15-98 GAMEAdapter is presently not a singleton. There is separate instances for synteny and non-synteny/one-species. This may change in future.

Field Summary

protected static org.apache.log4j.Logger	logger
protected boolean	NO_GUI

Fields inherited from class apollo.dataadapter.AbstractApolloAdapter

curation_set, 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

GAMEAdapter()

GAMEAdapter(DataInputType inputType, java.lang.String input)

GAMEAdapter(DataInputType inputType, java.lang.String input, boolean noGUI)

Method Summary

java.lang.Boolean	addToCurationSet() Called if user is layering additional GAME data on top of whatever's already been loaded
void	commitChanges(CurationSet curation) writes the changes from a featureChangeLog to a writeable datasource.
void	commitChanges(CurationSet curation, boolean saveAnnots, boolean saveResults) Writes XML If the input type is not FILE, prompts user for a file to save to.
java.lang.String	fillInDatabase(java.lang.String urlString) Replace %DATABASE% field with selected database.
java.lang.String	fillInPadding(java.lang.String urlString) Replace %PadLeft/Right% with pad ints
CurationSet	getCurationSet() from ApolloDataAdapterI interface.
java.lang.String	getDatabase()
DataInput	getDataInput() if file starts with http: then its really an url so correct the type bug fix for being able to load urls from file adapter and with -x
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() org.bdgp.io.DataAdapter method
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) Returns a user interface for the requested IOOperation.
boolean	hasLinkData() Returns true as game data contains link data that can be used by synteny
void	init() From org.bdgp.io.DataAdapter interface.
static void	main(java.lang.String[] args) Tests all the input types - can enter filename as arg
java.net.URL	makeUrlFromString(java.lang.String urlString) make URL from urlString, replace %DATABASE% with selected database
void	setName(java.lang.String nameForReading)
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	setPadLeft(int padLeft) Request to "pad" the input padLeft basepairs to the left(5' forward strand) - Could do this in AbstractApolloAdapter but only game adapter needs this now
void	setPadRight(int padRight) Request to "pad" the input padRight basepairs to the right(3' forward strand)
void	setRegion(SequenceI seq)
static void	setSeqDescription(SequenceI seq, java.lang.String description, java.lang.String seq_id) Given a FASTA-style header line, set the sequence's description and extract the date.
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, getDefaultStyle, getFilename, getInput, getInputType, getName, getNameAdapter, getNumberOfChildAdapters, getRawAnalysisResults, getSequence, getSequence, getSequence, getSequences, getSequences, getSpecies, getStyle, isComposite, loadNewSpeciesFromLink, operationIsSupported, rollbackAnnotations, rollbackAnnotations, setCuration, setCurationNumber, setCurationState, setDatabase, setDataInput, setDataLoadListener, setInput, setInputType, setLocation, 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

NO_GUI

protected boolean NO_GUI

Constructor Detail

GAMEAdapter

public GAMEAdapter()

GAMEAdapter

public GAMEAdapter(DataInputType inputType,
                   java.lang.String input)

GAMEAdapter

public GAMEAdapter(DataInputType inputType,
                   java.lang.String input,
                   boolean noGUI)

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 AbstractApolloAdapter

getType

public java.lang.String getType()

org.bdgp.io.DataAdapter method

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType 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

setName

public void setName(java.lang.String nameForReading)

Overrides:

setName in class AbstractApolloAdapter

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.

setPadLeft

public void setPadLeft(int padLeft)

Request to "pad" the input padLeft basepairs to the left(5' forward strand) - Could do this in AbstractApolloAdapter but only game adapter needs this now

Specified by:

setPadLeft in interface ApolloDataAdapterI

Overrides:

setPadLeft in class AbstractApolloAdapter

setPadRight

public void setPadRight(int padRight)

Request to "pad" the input padRight basepairs to the right(3' forward strand)

Specified by:

setPadRight in interface ApolloDataAdapterI

Overrides:

setPadRight in class AbstractApolloAdapter

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

setRegion

public void setRegion(SequenceI seq)
               throws ApolloAdapterException

Throws:

ApolloAdapterException

hasLinkData

public boolean hasLinkData()

Returns true as game data contains link data that can be used by synteny

Specified by:

hasLinkData in interface ApolloDataAdapterI

Overrides:

hasLinkData 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.

main

public static void main(java.lang.String[] args)
                 throws ApolloAdapterException

Tests all the input types - can enter filename as arg

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CurationSet curation)

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

commitChanges

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

Writes XML If the input type is not FILE, prompts user for a file to save to.

Overrides:

commitChanges in class AbstractApolloAdapter

getDataInput

public DataInput getDataInput()

if file starts with http: then its really an url so correct the type bug fix for being able to load urls from file adapter and with -x

Overrides:

getDataInput in class AbstractApolloAdapter

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

from ApolloDataAdapterI interface. dataInput should be set previous to this

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

addToCurationSet

public java.lang.Boolean addToCurationSet()
                                   throws ApolloAdapterException

Called if user is layering additional GAME data on top of whatever's already been loaded

Specified by:

addToCurationSet in interface ApolloDataAdapterI

Overrides:

addToCurationSet in class AbstractApolloAdapter

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

fillInPadding

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

Replace %PadLeft/Right% with pad ints

setSeqDescription

public static void setSeqDescription(SequenceI seq,
                                     java.lang.String description,
                                     java.lang.String seq_id)

Given a FASTA-style header line, set the sequence's description and extract the date. For fly sequences, the expected format of the header line is >gi||gb|AB003910|AB003910 Fruitfly DNA for 88F actin, complete cds. (08-JUN-1999) Date is that thing at the end, obviously. Another format we see sometimes is RE70410.5prime BI486922 [similar by BLASTN (3.2e-110) to l(3)82Fd "FBan0010199 GO:[] located on: 3R 82F8-82F10;" 05/17/2001] Using the expected dateFormat (defined in DateUtil) parse the date string and return it as a Date object.