X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fconstant-values.html;fp=website%2Ffull_javadoc%2Fconstant-values.html;h=0a2e8bff7a7cc1e7225aad28dd2c36bff1ad60f3;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/constant-values.html b/website/full_javadoc/constant-values.html new file mode 100644 index 0000000..0a2e8bf --- /dev/null +++ b/website/full_javadoc/constant-values.html @@ -0,0 +1,742 @@ + + + + + + +Constant Field Values + + + + + + + + + + + + +

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+Constant Field Values

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+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.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.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.ClustalAlignmentUtil
+`public static final char`	`gapchar`	`45`

+ +

+ + + + + + + + + + + + +
compbio.data.sequence.ScoreManager
+public static final String SINGLE_ENTRY_KEY "Alignment"
+ +

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.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.ConfExecutable<T>
+`public static final String`	`CLUSTER_TASK_ID_PREFIX`	`"@"`

+ +

+ + + + + + + + + + + + +
compbio.engine.client.EnvVariableProcessor
+public static final String PATH "PATH"
+ +

compbio.engine.client.EnvVariableProcessor
+`public static final String`	`PATH`	`"PATH"`

+ +

+ + + + + + + + + + + + +
compbio.engine.client.RunConfiguration
+public static final String rconfigFile "RunnerConfig.xml"
+ +

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.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.cluster.drmaa.ClusterSession
+`public static final String`	`JOBID`	`"JOBID"`

+ +

+ + + + + + + + + + + + +
compbio.engine.conf._Key
+public static final String DELIM "#"
+ +

compbio.engine.conf._Key
+`public static final String`	`DELIM`	`"#"`

+ +

+ + + + + + + + + + + + +
compbio.engine.conf.DirectoryManager
+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.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.metadata.PresetManager<T>
+`public static final String`	`LOCAL_ENGINE_LIMIT_PRESET`	`"# LocalEngineExecutionLimit #"`

+ +

+ + + + + +
+compbio.runner.*
+ +

+ + + + + + + + + + + + +
compbio.runner.Util
+public static final String SPACE " "
+ +

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.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.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.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.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.ClustalO
+`public static final String`	`KEY_VALUE_SEPARATOR`	`"="`

+ +

+ + + + + + + + + + + + +
compbio.runner.msa.ClustalW
+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.Mafft
+`public static final String`	`KEY_VALUE_SEPARATOR`	`" "`

+ +

+ + + + + + + + + + + + +
compbio.runner.msa.Muscle
+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.Probcons
+`public static final String`	`KEY_VALUE_SEPARATOR`	`" "`

+ +

+ + + + + + + + + + + + +
compbio.runner.msa.Tcoffee
+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"
+ +

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"`

+ +