biolockj.module.getData.sra

Class SequenceReadArchive

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.getData.sra.SequenceReadArchive

All Implemented Interfaces:

BioModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

SraDownload, SraMetaData, SraMetaDB, SrpSrrConverter

public abstract class SequenceReadArchive
extends ScriptModuleImpl

Field Summary

Fields

Modifier and Type	Field and Description
static String	DB_DIR
protected static String	DB_DIR_DESC
protected static String	DB_NAME
static String	SRA_ACC_LIST
protected static String	SRA_ACC_LIST_DESC
static String	SRP
protected static String	SRP_DESC

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
SequenceReadArchive()

Method Summary

Modifier and Type	Method and Description
Boolean	isValidProp(String property)

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScript, buildScriptForPairedReads, checkDependencies, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, getWorkerScriptFunctions, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getDockerImageOwner, getDockerImageTag, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.BioModule

cleanUp, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version

Field Detail

DB_NAME

protected static final String DB_NAME

See Also:

Constant Field Values

DB_DIR

public static final String DB_DIR

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Constant Field Values

DB_DIR_DESC

protected static final String DB_DIR_DESC

See Also:

Constant Field Values

SRA_ACC_LIST

public static final String SRA_ACC_LIST

See Also:

Constant Field Values

SRA_ACC_LIST_DESC

protected static final String SRA_ACC_LIST_DESC

See Also:

Constant Field Values

SRP

public static final String SRP

See Also:

Constant Field Values

SRP_DESC

protected static final String SRP_DESC

See Also:

Constant Field Values

Constructor Detail

SequenceReadArchive

public SequenceReadArchive()

Method Detail

isValidProp

public Boolean isValidProp(String property)
                    throws Exception

Overrides:

isValidProp in class ScriptModuleImpl

Throws:

Exception