Constant Field Values

Contents

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

compbio.data.*

compbio.data.msa.Category

Modifier and Type	Constant Field	Value
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"
public static final java.lang.String	CATEGORY_PREDICTION	"Prediction"

compbio.data.msa.JABAService

Modifier and Type	Constant Field	Value
public static final java.lang.String	JABAWS_VERSION	"2.1"
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/"
public static final java.lang.String	V3_SERVICE_NAMESPACE	"http://msa.data.compbio/01/12/2013/"

compbio.data.sequence.ClustalAlignmentUtil

Modifier and Type	Constant Field	Value
public static final char	gapchar	45
private static final int	maxNameLength	30
private static final int	minNameHolderLength	10
private static final int	oneLineAlignmentLength	60
private static final java.lang.String	spacer	" "

compbio.data.sequence.FastaReader

Modifier and Type	Constant Field	Value
private final java.lang.String	DELIM	">"

compbio.data.sequence.ScoreManager

Modifier and Type	Constant Field	Value
public static final java.lang.String	SINGLE_ENTRY_KEY	"Alignment"

compbio.data.sequence.SequenceUtil

Modifier and Type	Constant Field	Value
private static final java.lang.String	JRONN_WRONG_FORMAT_MESSAGE	"Jronn file must be in the following format:\n>sequence_name\n M\tV\tS\n0.43\t0.22\t0.65\nWhere first line is the sequence name,\nsecond line is the tab delimited sequence,\nthird line contains tab delimited disorder prediction values.\nNo lines are allowed between these three. Additionally, the number of sequence residues must be equal to the number of the disorder values."

compbio.data.sequence.SMERFSConstraints

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_GAP_THRESHOLD	0.1
public static final int	DEFAULT_WINDOW_SIZE	7

compbio.data.sequence.UnknownFileFormatException

Modifier and Type	Constant Field	Value
private static final long	serialVersionUID	196629543695636854L

compbio.engine.*

compbio.engine.client.compbio.engine.client.CommandBuilder.Parameter

Modifier and Type	Constant Field	Value
private static final int	FIRST	-200
private static final int	LAST	-100

compbio.engine.client.ConfExecutable<T>

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLUSTER_TASK_ID_PREFIX	"@"

compbio.engine.client.EnvVariableProcessor

Modifier and Type	Constant Field	Value
private static final java.lang.String	fasta4mafft	"FASTA_4_MAFFT"
private static final java.lang.String	iupred_path	"IUPred_PATH"
private static final java.lang.String	mafft_binaries	"MAFFT_BINARIES"
private static final java.lang.String	NEXT_ENV_PROPERTY_DELIMITER	";"
public static final java.lang.String	PATH	"PATH"
private static final java.lang.String	PROP_NAME_VALUE_SEPARATOR	"#"

compbio.engine.client.RunConfiguration

Modifier and Type	Constant Field	Value
public static final java.lang.String	rconfigFile	"RunnerConfig.xml"

compbio.engine.client.SkeletalExecutable<T>

Modifier and Type	Constant Field	Value
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

Modifier and Type	Constant Field	Value
public static final java.lang.String	JOBID	"JOBID"

compbio.engine.conf.DirectoryManager

Modifier and Type	Constant Field	Value
public static final java.lang.String	DELIM	"#"

compbio.engine.local.ExecutableWrapper

Modifier and Type	Constant Field	Value
public static final java.lang.String	PROC_ERR_FILE	"procError.txt"
public static final java.lang.String	PROC_IN_FILE	"procInput.txt"
public static final java.lang.String	PROC_OUT_FILE	"procOutput.txt"

compbio.engine.local.LocalExecutorService

Modifier and Type	Constant Field	Value
private static final java.lang.String	threadNumPropName	"engine.local.thread.number"

compbio.metadata.*

compbio.metadata.JobExecutionException

Modifier and Type	Constant Field	Value
private static final long	serialVersionUID	-5477751361755778769L

compbio.metadata.JobSubmissionException

Modifier and Type	Constant Field	Value
private static final long	serialVersionUID	607986894357895572L

compbio.metadata.LimitExceededException

Modifier and Type	Constant Field	Value
private static final long	serialVersionUID	15066952180013505L

compbio.metadata.Preset<T>

Modifier and Type	Constant Field	Value
private static final java.lang.String	SPACE	" "

compbio.metadata.PresetManager<T>

Modifier and Type	Constant Field	Value
public static final java.lang.String	LOCAL_ENGINE_LIMIT_PRESET	"# LocalEngineExecutionLimit #"

compbio.metadata.ResultNotAvailableException

Modifier and Type	Constant Field	Value
private static final long	serialVersionUID	-5475613614578761L

compbio.metadata.UnsupportedRuntimeException

Modifier and Type	Constant Field	Value
private static final long	serialVersionUID	-86624836785110293L

compbio.metadata.WrongParameterException

Modifier and Type	Constant Field	Value
private static final long	serialVersionUID	-547775417557345769L

compbio.runner.*

compbio.runner.OptionCombinator

Modifier and Type	Constant Field	Value
private static final java.lang.String	MAXVALUE	"100"
private static final java.lang.String	MINVALUE	"-100"

compbio.runner.Util

Modifier and Type	Constant Field	Value
public static final java.lang.String	SPACE	" "

compbio.runner.conservation.AACon

Modifier and Type	Constant Field	Value
public static final java.lang.String	KEY_VALUE_SEPARATOR	"="
private final java.lang.String	ncorePrm	"-t="
public static final java.lang.String	STAT_FILE	"stat.txt"

compbio.runner.disorder.Disembl

Modifier and Type	Constant Field	Value
public final double	COILS_EXPECTATION_THRESHOLD	0.43
public final double	LOOPS_EXPECTATION_THRESHOLD	0.086
public final double	REM_EXPECTATION_THRESHOLD	0.5

compbio.runner.disorder.IUPred

Modifier and Type	Constant Field	Value
private static final java.lang.String	GLOB_OUTPUT	"out.glob"
private static final java.lang.String	LONG_OUTPUT	"out.long"
private static final java.lang.String	SHORT_OUTPUT	"out.short"

compbio.runner.disorder.Jronn

Modifier and Type	Constant Field	Value
private final java.lang.String	ncorePrm	"-n="
public static final java.lang.String	STAT_FILE	"stat.txt"

compbio.runner.msa.ClustalO

Modifier and Type	Constant Field	Value
private static final java.lang.String	EXEC_STAT_FILE	"stat.log"
public static final java.lang.String	KEY_VALUE_SEPARATOR	"="
private static final java.lang.String	ncorePrm	"--threads"

compbio.runner.msa.ClustalW

Modifier and Type	Constant Field	Value
private static final java.lang.String	EXEC_STAT_FILE	"stat.log"
public static final java.lang.String	KEY_VALUE_SEPARATOR	"="
private static final java.lang.String	TREE_FILE_EXT	".dnd"

compbio.runner.msa.GLprobs

Modifier and Type	Constant Field	Value
private static final java.lang.String	ANNOTATION	"annotation.txt"
public static final java.lang.String	KEY_VALUE_SEPARATOR	" "

compbio.runner.msa.Mafft

Modifier and Type	Constant Field	Value
public static final java.lang.String	KEY_VALUE_SEPARATOR	" "
private final java.lang.String	MATRIX_PAR_NAME	"--aamatrix"

compbio.runner.msa.MSAprobs

Modifier and Type	Constant Field	Value
private static final java.lang.String	ANNOTATION	"annotation.txt"
public static final java.lang.String	KEY_VALUE_SEPARATOR	" "

compbio.runner.msa.Muscle

Modifier and Type	Constant Field	Value
private static final java.lang.String	EXEC_STAT_FILE	"stat.log"
public static final java.lang.String	KEY_VALUE_SEPARATOR	" "

compbio.runner.msa.Probcons

Modifier and Type	Constant Field	Value
private static final java.lang.String	ANNOTATION	"annotation.txt"
public static final java.lang.String	KEY_VALUE_SEPARATOR	" "

compbio.runner.msa.Tcoffee

Modifier and Type	Constant Field	Value
public static final java.lang.String	KEY_VALUE_SEPARATOR	"="
private static final java.lang.String	ncorePrm	"-n_core"

compbio.runner.structure.RNAalifold

Modifier and Type	Constant Field	Value
public static final java.lang.String	KEY_VALUE_SEPARATOR	" "

compbio.stat.*

compbio.stat.collector.DirCleaner

Modifier and Type	Constant Field	Value
static final int	UNDEFINED	-1

compbio.stat.collector.ExecutionStatCollector

Modifier and Type	Constant Field	Value
static final int	UNDEFINED	-1

compbio.stat.collector.JobDirectory

Modifier and Type	Constant Field	Value
static final int	UNDEFINED	-1

compbio.stat.collector.StatDB

Modifier and Type	Constant Field	Value
private static final java.lang.String	driver	"org.apache.derby.jdbc.EmbeddedDriver"
private static final java.lang.String	protocol	"jdbc:derby:"
private static final java.lang.String	statDBName	"ExecutionStatistic"

compbio.stat.servlet.Joblist

Modifier and Type	Constant Field	Value
static final java.lang.String	JT_ABANDONED	"abandoned"
static final java.lang.String	JT_ALL	"all"
static final java.lang.String	JT_CANCELLED	"cancelled"
static final java.lang.String	JT_FAILED	"failed"
static final java.lang.String	JT_INCOMPLETE	"incomplete"

compbio.ws.*

compbio.ws.client.AAConClient

Modifier and Type	Constant Field	Value
static final java.lang.String	hostname	"http://www.compbio.dundee.ac.uk/aacon"
static final java.lang.String	QUALIFIED_SERVICE_NAME	"http://msa.data.compbio/01/12/2010/"
static final java.lang.String	serviceName	"AAConWS"

compbio.ws.client.compbio.ws.client.Constraints

Modifier and Type	Constant Field	Value
static final java.lang.String	help_text	"\r\nUsage: java -jar <JAR file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n\r\n -h=<host_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws\r\n -s=<ServiceName> - a name of servise (the full list can be obtain with the option -list)\r\n <serviceName> is required for all ACTIONS except -list\r\n\r\nACTIONS: \r\n -i=<inputFile> - defines an input file. For most services this is a FASTA file with initial sequences\r\n -list - lists all available web services\r\n -test - tests functioning of <ServiceName> \r\n -parameters - lists parameters supported by <ServiceName>\r\n -presets - lists presets supported by <ServiceName>\r\n -limits - lists limits of <ServiceName>\r\n\r\nN.B. If an input file is specified with -i other actions are ignored!\r\n\r\nOPTIONS (used with the -i action only):\r\n -r=<presetName> - name of the preset to use\r\n -o=<outputFile> - file with output results\r\n -f=<paramFile> - file with the list of parameters to use.\r\n\r\nPlease note that -r and -f options cannot be used together. \r\nAlignment/Prediction is done with either preset or a parameters from the file, but not both!\r\n\r\nEXAMPLES: \r\n<THECLIENT> is java -jar <JAR file name>\r\n\r\n1) List all available services on the host:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -list\r\n\r\n2) Test Clustal web service:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n\r\n3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n into the output.txt:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n\r\n4) Calculate disorder with Disembl take input from input.txt with output results\r\n to be printed out to the standard output:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n\r\n5) List all parameters available for AAconWS service:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n\r\n6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n from input.txt and report the scores to the standard output:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n\r\n Where the content of prm.txt file is -m=LANDGRAF\r\nN.B. The list of the supported parameters can be obtained as shown in the example 5.\r\n"
static final java.lang.String	hostkey	"-h"
static final java.lang.String	inputkey	"-i"
static final java.lang.String	limitList	"-limits"
static final java.lang.String	listServices	"-list"
static final java.lang.String	listServicesOld	"-list_services"
static final java.lang.String	outputkey	"-o"
static final java.lang.String	parameterkey	"-p"
static final java.lang.String	paramFile	"-f"
static final java.lang.String	paramList	"-parameters"
static final java.lang.String	presetkey	"-r"
static final java.lang.String	presetList	"-presets"
static final java.lang.String	pseparator	"="
static final java.lang.String	servicekey	"-s"
static final java.lang.String	testKey	"-test"

compbio.ws.client.compbio.ws.client.Services.ServiceInfo

Modifier and Type	Constant Field	Value
static final java.lang.String	line_delimiter	"\n"

compbio.ws.client.WSTester

Modifier and Type	Constant Field	Value
public static final java.lang.String	clustalRNAAlignment	"CLUSTAL\nFoo C-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGA\nBar G-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGA\nFoo UGGUUG----GCAAC\nBar U-UACGAUUAACCAC"
private static final java.lang.String	FAILED	"FAILED"
public static final java.lang.String	fastaAlignment	">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n>Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
public static final java.lang.String	fastaInput1record	">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n"
public static final java.lang.String	fastaInput2records	">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n>Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"
public static final java.lang.String	fastaRNAAlignment	">Foo\nC-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n>Bar\nG-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n"
private static final java.lang.String	OK	"OK"
private static final java.lang.String	UNSUPPORTED	"UNSUPPORTED"

compbio.ws.server.GAUtils

Modifier and Type	Constant Field	Value
static final java.lang.String	VERSION_TYPE	"WAR"