X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fengine%2Fclient%2FSkeletalExecutable.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fengine%2Fclient%2FSkeletalExecutable.html;h=0000000000000000000000000000000000000000;hb=0bbebf27d045b1345bc042bdf24ef2e6808df251;hp=c8ac24302eb454d2a466f8ed661f28ef0c1511a4;hpb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;p=jabaws.git diff --git a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html deleted file mode 100644 index c8ac243..0000000 --- a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html +++ /dev/null @@ -1,782 +0,0 @@ - - - - - - -SkeletalExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Class SkeletalExecutable<T>

-
-java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<T>
-
-
-
All Implemented Interfaces:
Executable<T>
-
-
-
Direct Known Subclasses:
AACon, ClustalO, ClustalW, Disembl, GlobPlot, IUPred, Jronn, Mafft, Muscle, Probcons, Tcoffee
-
-
-
-
public abstract class SkeletalExecutable<T>
extends Object
implements Executable<T>
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static StringERROR - -
-           
-static StringINPUT - -
-           
-static StringOUTPUT - -
-           
-  - - - - - - - - - - - - - -
-Constructor Summary
SkeletalExecutable() - -
-           
SkeletalExecutable(String parameterKeyValueDelimiter) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Executable<T>addParameters(List<String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- booleanequals(Object obj) - -
-           
-static intgetClusterCpuNum(Class<? extends Executable<?>> type) - -
-           
- StringgetClusterJobSettings() - -
-           
- List<String>getCreatedFiles() - -
-          This method cannot really tell whether the files has actually been - created or not.
- StringgetError() - -
-           
- StringgetInput() - -
-           
- Limit<T>getLimit(String presetName) - -
-           
- LimitsManager<T>getLimits() - -
-           
- StringgetOutput() - -
-           
- CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
-           
-abstract  Class<T>getType() - -
-           
- inthashCode() - -
-           
- Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
-           
- SkeletalExecutable<T>setError(String errFile) - -
-           
- SkeletalExecutable<T>setInput(String inFile) - -
-           
- SkeletalExecutable<T>setOutput(String outFile) - -
-           
- Executable<T>setParameter(String parameter) - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  - - - - - - - -
Methods inherited from interface compbio.engine.client.Executable
getResults
-  -

- - - - - - - - -
-Field Detail
- -

-INPUT

-
-public static final String INPUT
-
-
-
See Also:
Constant Field Values
-
-
- -

-OUTPUT

-
-public static final String OUTPUT
-
-
-
See Also:
Constant Field Values
-
-
- -

-ERROR

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

-SkeletalExecutable

-
-public SkeletalExecutable()
-
-
-
- -

-SkeletalExecutable

-
-public SkeletalExecutable(String parameterKeyValueDelimiter)
-
-
- - - - - - - - -
-Method Detail
- -

-setInput

-
-public SkeletalExecutable<T> setInput(String inFile)
-
-
-
-
-
-
-
-
-
- -

-setOutput

-
-public SkeletalExecutable<T> setOutput(String outFile)
-
-
-
-
-
-
-
-
-
- -

-setError

-
-public SkeletalExecutable<T> setError(String errFile)
-
-
-
-
-
-
-
-
-
- -

-getParameters

-
-public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
-
-
-
Specified by:
getParameters in interface Executable<T>
-
-
-
-
-
-
- -

-addParameters

-
-public Executable<T> addParameters(List<String> parameters)
-
-
Description copied from interface: Executable
-
Adds parameter to the list of parameters for a native executable -

-

-
Specified by:
addParameters in interface Executable<T>
-
-
- -
Returns:
this Executable
-
-
-
- -

-setParameter

-
-public Executable<T> setParameter(String parameter)
-
-
-
-
-
-
-
-
-
- -

-getCreatedFiles

-
-public List<String> getCreatedFiles()
-
-
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<T>
-
-
-
See Also:
Executable.getCreatedFiles()
-
-
-
- -

-getInput

-
-public String getInput()
-
-
-
Specified by:
getInput in interface Executable<T>
-
-
-
-
-
-
- -

-getOutput

-
-public String getOutput()
-
-
-
Specified by:
getOutput in interface Executable<T>
-
-
-
-
-
-
- -

-getError

-
-public String getError()
-
-
-
Specified by:
getError in interface Executable<T>
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-loadRunConfiguration

-
-public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
-
-
-
Specified by:
loadRunConfiguration in interface Executable<T>
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-getClusterJobSettings

-
-public String getClusterJobSettings()
-
-
-
Specified by:
getClusterJobSettings in interface Executable<T>
-
-
-
-
-
-
- -

-getClusterCpuNum

-
-public static int getClusterCpuNum(Class<? extends Executable<?>> type)
-
-
-
-
-
- -
Returns:
number of cpus to use on the cluster or 0 if the value is - undefined
-
-
-
- -

-getLimit

-
-public Limit<T> getLimit(String presetName)
-
-
-
Specified by:
getLimit in interface Executable<T>
-
-
-
-
-
-
- -

-getLimits

-
-public LimitsManager<T> getLimits()
-
-
-
Specified by:
getLimits in interface Executable<T>
-
-
-
-
-
-
- -

-getType

-
-public abstract Class<T> getType()
-
-
-
-
-
- -
Returns:
subclasses must return their type
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - -