X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fconservation%2FAACon.html;fp=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fconservation%2FAACon.html;h=8bf0ab25b2c66646eacc3ded0e43c583c44cafb4;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/conservation/AACon.html b/website/full_javadoc/compbio/runner/conservation/AACon.html new file mode 100644 index 0000000..8bf0ab2 --- /dev/null +++ b/website/full_javadoc/compbio/runner/conservation/AACon.html @@ -0,0 +1,514 @@ + + + + + + +AACon + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.runner.conservation +
+Class AACon

+
+java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<AACon>
+      extended by compbio.runner.conservation.AACon
+
+
+
All Implemented Interfaces:
Executable<AACon>
+
+
+
+
public class AACon
extends SkeletalExecutable<AACon>
+ + +

+Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out +

+ +

+

+
Author:
+
pvtroshin
+
+
+ +

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

+ + + + + + + + +
+Field Detail
+ +

+KEY_VALUE_SEPARATOR

+
+public static final String KEY_VALUE_SEPARATOR
+
+
+
See Also:
Constant Field Values
+
+
+ +

+STAT_FILE

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

+AACon

+
+public AACon()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getResults

+
+public ScoreManager getResults(String workDirectory)
+                        throws ResultNotAvailableException
+
+
+ +
Throws: +
ResultNotAvailableException
+
+
+
+ +

+getCreatedFiles

+
+public List<String> getCreatedFiles()
+
+
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<AACon>
Overrides:
getCreatedFiles in class SkeletalExecutable<AACon>
+
+
+
See Also:
Executable.getCreatedFiles()
+
+
+
+ +

+setInput

+
+public AACon setInput(String inFile)
+
+
+
Overrides:
setInput in class SkeletalExecutable<AACon>
+
+
+
+
+
+
+ +

+setOutput

+
+public AACon setOutput(String outFile)
+
+
+
Overrides:
setOutput in class SkeletalExecutable<AACon>
+
+
+
+
+
+
+ +

+getType

+
+public Class<AACon> getType()
+
+
+
Specified by:
getType in class SkeletalExecutable<AACon>
+
+
+ +
Returns:
subclasses must return their type
+
+
+
+ +

+getStatFile

+
+public static String getStatFile()
+
+
+
+
+
+
+ +

+setNCore

+
+public void setNCore(int ncoreNumber)
+
+
+
+
+
+
+ +

+getParameters

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