Constant Field Values

Contents

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

compbio.data.*

compbio.data.msa.Category

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

compbio.data.msa.JABAService

public static final java.lang.String	SERVICE_NAMESPACE	"http://msa.data.compbio/01/01/2010/"
public static final java.lang.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 java.lang.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 java.lang.String

CLUSTER_TASK_ID_PREFIX

"@"

compbio.engine.client.EnvVariableProcessor

public static final java.lang.String

PATH

"PATH"

compbio.engine.client.RunConfiguration

public static final java.lang.String

rconfigFile

"RunnerConfig.xml"

compbio.engine.client.SkeletalExecutable<T>

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

compbio.engine.cluster.drmaa.ClusterSession

public static final java.lang.String

JOBID

"JOBID"

compbio.engine.conf.DirectoryManager

public static final java.lang.String

DELIM

"#"

compbio.engine.local.ExecutableWrapper

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

compbio.metadata.*

compbio.metadata.PresetManager<T>

public static final java.lang.String

LOCAL_ENGINE_LIMIT_PRESET

"# LocalEngineExecutionLimit #"

compbio.runner.*

compbio.runner.Util

public static final java.lang.String

SPACE

" "

compbio.runner.conservation.AACon

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

compbio.runner.disorder.Disembl

public final double	COILS_EXPECTATION_THRESHOLD	0.43
public static final java.lang.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 java.lang.String

KEY_VALUE_SEPARATOR

" "

compbio.runner.disorder.Jronn

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

compbio.runner.msa.ClustalO

public static final java.lang.String

KEY_VALUE_SEPARATOR

"="

compbio.runner.msa.ClustalW

public static final java.lang.String

KEY_VALUE_SEPARATOR

"="

compbio.runner.msa.Mafft

public static final java.lang.String

KEY_VALUE_SEPARATOR

" "

compbio.runner.msa.Muscle

public static final java.lang.String

KEY_VALUE_SEPARATOR

" "

compbio.runner.msa.Probcons

public static final java.lang.String

KEY_VALUE_SEPARATOR

" "

compbio.runner.msa.Tcoffee

public static final java.lang.String

KEY_VALUE_SEPARATOR

"="

compbio.ws.*

compbio.ws.client.WSTester

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