Constant Field Values

Contents

• compbio.data.*
• compbio.engine.*
• compbio.metadata.*
• compbio.runner.*
• compbio.ws.*

compbio.data.*

compbio.data.msa.Category

public static final String	CATEGORY_ALIGNMENT	"Alignment"
public static final String	CATEGORY_CONSERVATION	"Conservation"
public static final String	CATEGORY_DISORDER	"Protein Disorder"

compbio.data.msa.JABAService

public static final String	SERVICE_NAMESPACE	"http://msa.data.compbio/01/01/2010/"
public static final String	V2_SERVICE_NAMESPACE	"http://msa.data.compbio/01/12/2010/"

compbio.data.sequence.ClustalAlignmentUtil

public static final char

gapchar

45

compbio.data.sequence.ScoreManager

public static final String

SINGLE_ENTRY_KEY

"Alignment"

compbio.data.sequence.SMERFSConstraints

public static final double	DEFAULT_GAP_THRESHOLD	0.1
public static final int	DEFAULT_WINDOW_SIZE	7

compbio.engine.*

compbio.engine.client.ConfExecutable<T>

public static final String

CLUSTER_TASK_ID_PREFIX

"@"

compbio.engine.client.EnvVariableProcessor

public static final String

PATH

"PATH"

compbio.engine.client.RunConfiguration

public static final String

rconfigFile

"RunnerConfig.xml"

compbio.engine.client.SkeletalExecutable<T>

public static final String	ERROR	"error.txt"
public static final String	INPUT	"input.txt"
public static final String	OUTPUT	"result.txt"

compbio.engine.cluster.drmaa.ClusterSession

public static final String

JOBID

"JOBID"

compbio.engine.conf._Key

public static final String

DELIM

"#"

compbio.engine.conf.DirectoryManager

public static final String

DELIM

"#"

compbio.engine.local.ExecutableWrapper

public static final String	PROC_ERR_FILE	"procError.txt"
public static final String	PROC_OUT_FILE	"procOutput.txt"

compbio.metadata.*

compbio.metadata.PresetManager<T>

public static final String

LOCAL_ENGINE_LIMIT_PRESET

"# LocalEngineExecutionLimit #"

compbio.runner.*

compbio.runner.Util

public static final String

SPACE

" "

compbio.runner.conservation.AACon

public static final String	KEY_VALUE_SEPARATOR	"="
public static final String	STAT_FILE	"stat.txt"

compbio.runner.disorder.Disembl

public final double	COILS_EXPECTATION_THRESHOLD	0.43
public static final String	KEY_VALUE_SEPARATOR	" "
public final double	LOOPS_EXPECTATION_THRESHOLD	0.086
public final double	REM_EXPECTATION_THRESHOLD	0.5

compbio.runner.disorder.GlobPlot

public static final String

KEY_VALUE_SEPARATOR

" "

compbio.runner.disorder.Jronn

public static final String	KEY_VALUE_SEPARATOR	" "
public static final String	STAT_FILE	"stat.txt"

compbio.runner.msa.ClustalO

public static final String

KEY_VALUE_SEPARATOR

"="

compbio.runner.msa.ClustalW

public static final String

KEY_VALUE_SEPARATOR

"="

compbio.runner.msa.Mafft

public static final String

KEY_VALUE_SEPARATOR

" "

compbio.runner.msa.Muscle

public static final String

KEY_VALUE_SEPARATOR

" "

compbio.runner.msa.Probcons

public static final String

KEY_VALUE_SEPARATOR

" "

compbio.runner.msa.Tcoffee

public static final String

KEY_VALUE_SEPARATOR

"="

compbio.ws.*

compbio.ws.client.WSTester

public static final String	fastaAlignment	">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n>Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
public static final String	fastaInput	">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n>Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"