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" |
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/" |
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 |
" " |
Modifier and Type | Constant Field | Value |
---|---|---|
private final java.lang.String |
DELIM |
">" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
SINGLE_ENTRY_KEY |
"Alignment" |
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." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
DEFAULT_GAP_THRESHOLD |
0.1 |
public static final int |
DEFAULT_WINDOW_SIZE |
7 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
196629543695636854L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
FIRST |
-200 |
private static final int |
LAST |
-100 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
CLUSTER_TASK_ID_PREFIX |
"@" |
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 |
"#" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
rconfigFile |
"RunnerConfig.xml" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
JOBID |
"JOBID" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DELIM |
"#" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
threadNumPropName |
"engine.local.thread.number" |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
-5477751361755778769L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
607986894357895572L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
15066952180013505L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
SPACE |
" " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
LOCAL_ENGINE_LIMIT_PRESET |
"# LocalEngineExecutionLimit #" |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
-5475613614578761L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
-86624836785110293L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
-547775417557345769L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
MAXVALUE |
"100" |
private static final java.lang.String |
MINVALUE |
"-100" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
SPACE |
" " |
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" |
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 |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
private final java.lang.String |
ncorePrm |
"-n=" |
public static final java.lang.String |
STAT_FILE |
"stat.txt" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
ANNOTATION |
"annotation.txt" |
public static final java.lang.String |
KEY_VALUE_SEPARATOR |
" " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
KEY_VALUE_SEPARATOR |
" " |
private final java.lang.String |
MATRIX_PAR_NAME |
"--aamatrix" |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
ANNOTATION |
"annotation.txt" |
public static final java.lang.String |
KEY_VALUE_SEPARATOR |
" " |
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 |
" " |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
ANNOTATION |
"annotation.txt" |
public static final java.lang.String |
KEY_VALUE_SEPARATOR |
" " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
KEY_VALUE_SEPARATOR |
"=" |
private static final java.lang.String |
ncorePrm |
"-n_core" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
KEY_VALUE_SEPARATOR |
" " |
Modifier and Type | Constant Field | Value |
---|---|---|
static final int |
UNDEFINED |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
static final int |
UNDEFINED |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
static final int |
UNDEFINED |
-1 |
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" |
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" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
static final java.lang.String |
line_delimiter |
"\n" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
static final java.lang.String |
VERSION_TYPE |
"WAR" |