apollo.analysis
Interface SeqAnalysisI

All Known Implementing Classes:

SeqAnalysisBase, SeqAnalysisBDGP, SeqAnalysisLocal, SeqAnalysisNCBI, SeqAnalysisRemote

public interface SeqAnalysisI

Method Summary

void	addProperty(java.lang.String name, java.lang.String property) 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()
java.lang.String	getProgramName()
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
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
boolean	isAsynchronous() is the analysis asynchronous (ie will launching the analysis cause the program to block?) hmmm, this should probably be a property...
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.
void	setDesc(java.lang.String name)
void	setInputSequence(SequenceI sequence)
void	setInputSequence(java.util.Vector sequences)
void	setName(java.lang.String name)

Method Detail

addProperty

void addProperty(java.lang.String name,
                 java.lang.String property)

set the value of a property

getProperty

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

get the value of a property

getPropertyDescription

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

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

getPropertyType

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

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

getProperties

java.util.Hashtable getProperties()

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

getAllowedProperties

java.util.Vector getAllowedProperties()

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

getAllowedValues

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

allowed/recommended Vector of values for a property

getName

java.lang.String getName()

Returns:

the analysis name

setName

void setName(java.lang.String name)

getDesc

java.lang.String getDesc()

Returns:

a human readable String

setDesc

void setDesc(java.lang.String name)

getProgramName

java.lang.String getProgramName()

getInputSequence

SequenceI getInputSequence()

Retrieve the SequenceI that this analysis builds a CurationSet from

Returns:

the input SequenceI

setInputSequence

void setInputSequence(SequenceI sequence)

getInputSequences

java.util.Vector getInputSequences()

Retrieve the SequenceI list that this builds a curation set from

Returns:

a Vector of SequenceI objects

setInputSequence

void setInputSequence(java.util.Vector sequences)

getInputSequenceCount

int getInputSequenceCount()

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

launch

boolean launch()

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

isAsynchronous

boolean isAsynchronous()

is the analysis asynchronous (ie will launching the analysis cause the program to block?) hmmm, this should probably be a property...

isStarted

boolean isStarted()

has the analysis been launched?

hasResults

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

isFinished

boolean isFinished()

has the analysis finished?

getCurationSet

CurationSet getCurationSet()

Returns:

CurationSet representing the analysis results

getFeatureSet

FeatureSet getFeatureSet()

Returns:

FeatureSetI representing the analysis results

getAllRawResults

java.lang.String getAllRawResults()

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

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

getRawResultHashtable

java.util.Hashtable getRawResultHashtable()