X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fdisorder%2FJronn.html;fp=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fdisorder%2FJronn.html;h=0000000000000000000000000000000000000000;hb=0bbebf27d045b1345bc042bdf24ef2e6808df251;hp=9a0b602d28cc84ceaa831816c8f0f835eabb671e;hpb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/disorder/Jronn.html b/website/full_javadoc/compbio/runner/disorder/Jronn.html deleted file mode 100644 index 9a0b602..0000000 --- a/website/full_javadoc/compbio/runner/disorder/Jronn.html +++ /dev/null @@ -1,514 +0,0 @@ - - - - - - -Jronn - - - - - - - - - - - - -
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Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
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- -compbio.runner.disorder -
-Class Jronn

-
-java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Jronn>
-      extended by compbio.runner.disorder.Jronn
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All Implemented Interfaces:
Executable<Jronn>
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public class Jronn
extends SkeletalExecutable<Jronn>
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-Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out -

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Author:
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pvtroshin
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-Nested Class Summary
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Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
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-Field Summary
-static StringKEY_VALUE_SEPARATOR - -
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-static StringSTAT_FILE - -
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Fields inherited from class compbio.engine.client.SkeletalExecutable
ERROR, INPUT, OUTPUT
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-Constructor Summary
Jronn() - -
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-Method Summary
- List<String>getCreatedFiles() - -
-          This method cannot really tell whether the files has actually been - created or not.
- CommandBuilder<Jronn>getParameters(Executable.ExecProvider provider) - -
-           
- ScoreManagergetResults(String workDirectory) - -
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-static StringgetStatFile() - -
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- Class<Jronn>getType() - -
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- JronnsetInput(String inFile) - -
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- voidsetNCore(int ncoreNumber) - -
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- JronnsetOutput(String outFile) - -
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Methods inherited from class compbio.engine.client.SkeletalExecutable
addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setParameter, toString
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Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
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-Field Detail
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-KEY_VALUE_SEPARATOR

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-public static final String KEY_VALUE_SEPARATOR
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See Also:
Constant Field Values
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-STAT_FILE

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-public static final String STAT_FILE
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See Also:
Constant Field Values
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-Constructor Detail
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-Jronn

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-public Jronn()
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-Method Detail
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-getResults

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-public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
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Throws: -
ResultNotAvailableException
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-getCreatedFiles

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-public List<String> getCreatedFiles()
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Description copied from class: SkeletalExecutable
-
This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

-

-
Specified by:
getCreatedFiles in interface Executable<Jronn>
Overrides:
getCreatedFiles in class SkeletalExecutable<Jronn>
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See Also:
Executable.getCreatedFiles()
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-setInput

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-public Jronn setInput(String inFile)
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Overrides:
setInput in class SkeletalExecutable<Jronn>
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-setOutput

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-public Jronn setOutput(String outFile)
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Overrides:
setOutput in class SkeletalExecutable<Jronn>
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-getType

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-public Class<Jronn> getType()
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Specified by:
getType in class SkeletalExecutable<Jronn>
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Returns:
subclasses must return their type
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-getStatFile

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-public static String getStatFile()
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-setNCore

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-public void setNCore(int ncoreNumber)
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-getParameters

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-public CommandBuilder<Jronn> getParameters(Executable.ExecProvider provider)
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Specified by:
getParameters in interface Executable<Jronn>
Overrides:
getParameters in class SkeletalExecutable<Jronn>
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- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - -