apollo.analysis
Class SeqAnalysisBase

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

All Implemented Interfaces:

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

Direct Known Subclasses:

SeqAnalysisLocal, SeqAnalysisRemote

public abstract class SeqAnalysisBase
extends org.bdgp.io.AbstractDataAdapter
implements SeqAnalysisI, AnalysisDataAdapterI

Field Summary

protected CurationSet	curationSet
protected java.util.Hashtable	rawResults
protected SequenceI	sequence

Fields inherited from class org.bdgp.io.AbstractDataAdapter

listeners

Fields inherited from interface apollo.analysis.AnalysisDataAdapterI

OP_ANALYZE_DATA

Constructor Summary

SeqAnalysisBase()

SeqAnalysisBase(java.util.Hashtable ht)
initialize with a properties hash

Method Summary

void	addProperty(java.lang.String name, java.lang.String value) set the value of a property
java.util.Vector	getAllowedProperties() all the known property names (in the order they should be shown in a GUI)
java.util.Vector	getAllowedValues(java.lang.String name) allowed/recommended Vector of values for a property
java.lang.String	getAllRawResults()
CurationSet	getCurationSet()
java.lang.String	getDesc()
FeatureSet	getFeatureSet()
SequenceI	getInputSequence() Retrieve the SequenceI that this analysis builds a CurationSet from
int	getInputSequenceCount() usually returns 1, but some programs (eg clustalw) require >1 input sequence
java.util.Vector	getInputSequences() Retrieve the SequenceI list that this builds a curation set from
java.lang.String	getName() Returns the name of this data adapter
java.lang.String	getProgramName()
protected java.lang.String	getProgramParams()
java.util.Hashtable	getProperties() all set properties (should this be public????)
java.lang.String	getProperty(java.lang.String name) get the value of a property
java.lang.String	getPropertyDescription(java.lang.String name) get the description of a property; this gives metadata to the GUI/front end
java.lang.String	getPropertyType(java.lang.String name) get the type of a property (optional).
java.util.Hashtable	getRawResultHashtable()
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
org.bdgp.io.IOOperation[]	getSupportedOperations() Returns a list of all operations supported by this data adapter
java.lang.String	getType() Returns the type of data handled by this data adapter
boolean	hasResults() does the analysis have any results to read yet? note: an analysis implementation may choose to give results incrementally, so it need not be finished before returning results
void	init() For initialization, like opening files or database connections.
protected void	initSeqAnalysis()
boolean	isAsynchronous() is the analysis asynchronous? (ie will launching the analysis cause the program to block?)
boolean	isFinished() has the analysis finished?
boolean	isStarted() has the analysis been launched?
boolean	launch() Once you have configured the SeqAnalysis properties, call this method to run the analysis.
protected void	setAllowedProperties(java.util.Vector in)
protected void	setAllowedValues(java.util.Hashtable in)
protected void	setAllowedValues(java.lang.String name, java.util.Vector in)
void	setDesc(java.lang.String desc)
void	setInputSequence(SequenceI inseq)
void	setInputSequence(java.util.Vector sequences)
void	setName(java.lang.String name)
protected void	setPropertyDescription(java.lang.String name, java.lang.String desc)
protected void	setPropertyType(java.lang.String name, java.lang.String type)
protected void	setRawResultHashtable(java.util.Hashtable in)

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, getUI, removeProgressListener

Field Detail

sequence

protected SequenceI sequence

curationSet

protected CurationSet curationSet

rawResults

protected java.util.Hashtable rawResults

Constructor Detail

SeqAnalysisBase

public SeqAnalysisBase()

SeqAnalysisBase

public SeqAnalysisBase(java.util.Hashtable ht)

initialize with a properties hash

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

initSeqAnalysis

protected void initSeqAnalysis()

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

Specified by:

getSupportedOperations in interface org.bdgp.io.DataAdapter

addProperty

public void addProperty(java.lang.String name,
                        java.lang.String value)

Description copied from interface: SeqAnalysisI

set the value of a property

Specified by:

addProperty in interface SeqAnalysisI

getProperty

public java.lang.String getProperty(java.lang.String name)

Description copied from interface: SeqAnalysisI

get the value of a property

Specified by:

getProperty in interface SeqAnalysisI

getProperties

public java.util.Hashtable getProperties()

Description copied from interface: SeqAnalysisI

all set properties (should this be public????)

Specified by:

getProperties in interface SeqAnalysisI

getAllowedProperties

public java.util.Vector getAllowedProperties()

Description copied from interface: SeqAnalysisI

all the known property names (in the order they should be shown in a GUI)

Specified by:

getAllowedProperties in interface SeqAnalysisI

setAllowedProperties

protected void setAllowedProperties(java.util.Vector in)

getPropertyDescription

public java.lang.String getPropertyDescription(java.lang.String name)

Description copied from interface: SeqAnalysisI

get the description of a property; this gives metadata to the GUI/front end

Specified by:

getPropertyDescription in interface SeqAnalysisI

setPropertyDescription

protected void setPropertyDescription(java.lang.String name,
                                      java.lang.String desc)

getPropertyType

public java.lang.String getPropertyType(java.lang.String name)

Description copied from interface: SeqAnalysisI

get the type of a property (optional). more metadata to help the GUI construct sensible interfaces

Specified by:

getPropertyType in interface SeqAnalysisI

setPropertyType

protected void setPropertyType(java.lang.String name,
                               java.lang.String type)

getAllowedValues

public java.util.Vector getAllowedValues(java.lang.String name)

Description copied from interface: SeqAnalysisI

allowed/recommended Vector of values for a property

Specified by:

getAllowedValues in interface SeqAnalysisI

setAllowedValues

protected void setAllowedValues(java.util.Hashtable in)

setAllowedValues

protected void setAllowedValues(java.lang.String name,
                                java.util.Vector in)

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

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

setName

public void setName(java.lang.String name)

Specified by:

setName in interface SeqAnalysisI

getDesc

public java.lang.String getDesc()

Specified by:

getDesc in interface SeqAnalysisI

Returns:

a human readable String

setDesc

public void setDesc(java.lang.String desc)

Specified by:

setDesc in interface SeqAnalysisI

getProgramName

public java.lang.String getProgramName()

Specified by:

getProgramName in interface SeqAnalysisI

getProgramParams

protected java.lang.String getProgramParams()

getInputSequence

public SequenceI getInputSequence()

Description copied from interface: SeqAnalysisI

Retrieve the SequenceI that this analysis builds a CurationSet from

Specified by:

getInputSequence in interface SeqAnalysisI

Returns:

the input SequenceI

setInputSequence

public void setInputSequence(SequenceI inseq)

Specified by:

setInputSequence in interface SeqAnalysisI

getInputSequences

public java.util.Vector getInputSequences()

Description copied from interface: SeqAnalysisI

Retrieve the SequenceI list that this builds a curation set from

Specified by:

getInputSequences in interface SeqAnalysisI

Returns:

a Vector of SequenceI objects

setInputSequence

public void setInputSequence(java.util.Vector sequences)

Specified by:

setInputSequence in interface SeqAnalysisI

getInputSequenceCount

public int getInputSequenceCount()

Description copied from interface: SeqAnalysisI

usually returns 1, but some programs (eg clustalw) require >1 input sequence

Specified by:

getInputSequenceCount in interface SeqAnalysisI

isAsynchronous

public boolean isAsynchronous()

is the analysis asynchronous? (ie will launching the analysis cause the program to block?)

Specified by:

isAsynchronous in interface SeqAnalysisI

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

isStarted

public boolean isStarted()

Description copied from interface: SeqAnalysisI

has the analysis been launched?

Specified by:

isStarted in interface SeqAnalysisI

isFinished

public boolean isFinished()

Description copied from interface: SeqAnalysisI

has the analysis finished?

Specified by:

isFinished in interface SeqAnalysisI

hasResults

public boolean hasResults()

Description copied from interface: SeqAnalysisI

does the analysis have any results to read yet? note: an analysis implementation may choose to give results incrementally, so it need not be finished before returning results

Specified by:

hasResults in interface SeqAnalysisI

getCurationSet

public CurationSet getCurationSet()

Specified by:

getCurationSet in interface SeqAnalysisI

Returns:

CurationSet representing the analysis results

getFeatureSet

public FeatureSet getFeatureSet()

Specified by:

getFeatureSet in interface SeqAnalysisI

Returns:

FeatureSetI representing the analysis results

getAllRawResults

public java.lang.String getAllRawResults()

Specified by:

getAllRawResults in interface SeqAnalysisI

Returns:

String representing all the results as a single string. If an analysis returns two outputs, say the main output plus an error/warnings file, then the implementation may choose to return just the main output, or the main output with the error file glommed onto the end. this String 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

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

getRawResultHashtable

public java.util.Hashtable getRawResultHashtable()

Specified by:

getRawResultHashtable in interface SeqAnalysisI

setRawResultHashtable

protected void setRawResultHashtable(java.util.Hashtable in)