apollo.analysis
Class SeqAnalysisLocal

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.analysis.SeqAnalysisBase
          apollo.analysis.SeqAnalysisLocal

All Implemented Interfaces:

AnalysisDataAdapterI, SeqAnalysisI, org.bdgp.io.DataAdapter, org.bdgp.io.VisualDataAdapter

public class SeqAnalysisLocal
extends SeqAnalysisBase

Field Summary

protected static org.apache.log4j.Logger	logger
protected java.lang.String	seqFile

Fields inherited from class apollo.analysis.SeqAnalysisBase

curationSet, rawResults, sequence

Fields inherited from class org.bdgp.io.AbstractDataAdapter

listeners

Fields inherited from interface apollo.analysis.AnalysisDataAdapterI

OP_ANALYZE_DATA

Constructor Summary

SeqAnalysisLocal()

SeqAnalysisLocal(java.util.Hashtable inproperties)

Method Summary

java.lang.String	getName() Returns the name of this data adapter
protected java.lang.String	getProgramDirectory()
protected java.lang.String	getProgramPath() programPath = programDirectory / programName
protected java.lang.String	getProgramShellCommand() programShellCommand = programPath programArgs
java.util.Vector	getRawResultVector() all the raw results - usually Vector of main output and error (if any) as Strings these Strings should *NOT* be parsed; it is up to the SeqAnalysisI implementation object to do any parsing and return the results as a CurationSet or similar object
protected java.lang.String	getSeqFile() writes input sequence as a fasta file
java.lang.String	getType() Returns the type of data handled by this data adapter
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) Returns a user interface for the requested IOOperation.
void	init() For initialization, like opening files or database connections.
void	initSeqAnalysisLocal()
boolean	launch() Once you have configured the SeqAnalysis properties, call this method to run the analysis.
protected void	run()

Methods inherited from class apollo.analysis.SeqAnalysisBase

addProperty, getAllowedProperties, getAllowedValues, getAllRawResults, getCurationSet, getDesc, getFeatureSet, getInputSequence, getInputSequenceCount, getInputSequences, getProgramName, getProgramParams, getProperties, getProperty, getPropertyDescription, getPropertyType, getRawResultHashtable, getSupportedOperations, hasResults, initSeqAnalysis, isAsynchronous, isFinished, isStarted, setAllowedProperties, setAllowedValues, setAllowedValues, setDesc, setInputSequence, setInputSequence, setName, setPropertyDescription, setPropertyType, setRawResultHashtable

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

seqFile

protected java.lang.String seqFile

Constructor Detail

SeqAnalysisLocal

public SeqAnalysisLocal()

SeqAnalysisLocal

public SeqAnalysisLocal(java.util.Hashtable inproperties)

Method Detail

init

public void init()

Description copied from interface: org.bdgp.io.DataAdapter

For initialization, like opening files or database connections.

Specified by:

init in interface org.bdgp.io.DataAdapter

Overrides:

init in class SeqAnalysisBase

initSeqAnalysisLocal

public void initSeqAnalysisLocal()

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.

getName

public java.lang.String getName()

Description copied from interface: org.bdgp.io.DataAdapter

Returns the name of this data adapter

Specified by:

getName in interface SeqAnalysisI

Specified by:

getName in interface org.bdgp.io.DataAdapter

Overrides:

getName in class SeqAnalysisBase

Returns:

the analysis name

getType

public java.lang.String getType()

Description copied from interface: org.bdgp.io.DataAdapter

Returns the type of data handled by this data adapter

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType in class SeqAnalysisBase

launch

public boolean launch()

Description copied from interface: SeqAnalysisI

Once you have configured the SeqAnalysis properties, call this method to run the analysis. The

Specified by:

launch in interface SeqAnalysisI

Overrides:

launch in class SeqAnalysisBase

getSeqFile

protected java.lang.String getSeqFile()

writes input sequence as a fasta file

getRawResultVector

public java.util.Vector getRawResultVector()

Description copied from interface: SeqAnalysisI

all the raw results - usually Vector of main output and error (if any) as Strings these Strings should *NOT* be parsed; it is up to the SeqAnalysisI implementation object to do any parsing and return the results as a CurationSet or similar object

Specified by:

getRawResultVector in interface SeqAnalysisI

Overrides:

getRawResultVector in class SeqAnalysisBase

getProgramShellCommand

protected java.lang.String getProgramShellCommand()

programShellCommand = programPath programArgs

getProgramPath

protected java.lang.String getProgramPath()

programPath = programDirectory / programName

getProgramDirectory

protected java.lang.String getProgramDirectory()

run

protected void run()