X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2F_SkeletalCommandBuilder.html;fp=website%2Ffull_javadoc%2Fcompbio%2Frunner%2F_SkeletalCommandBuilder.html;h=e1f1135c9d855f7033599bb371157ffbec5a48e0;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html new file mode 100644 index 0000000..e1f1135 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html @@ -0,0 +1,611 @@ + + + + + + +_SkeletalCommandBuilder + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
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+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.runner +
+Class _SkeletalCommandBuilder

+
+java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+
+
+
All Implemented Interfaces:
Executable<_SkeletalCommandBuilder>
+
+
+
Direct Known Subclasses:
BlastAll, Mcl, OB, PSIBlast, Ronn, RPSBlast
+
+
+Deprecated. +

+

+
@Deprecated
+public abstract class _SkeletalCommandBuilder
extends Object
implements Executable<_SkeletalCommandBuilder>
+ + +

+

+ +

+ + + + + + + +
+Nested Class Summary
+  + + + + + + + +
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
+  + + + + + + + + + + + +
+Constructor Summary
_SkeletalCommandBuilder() + +
+          Deprecated.  
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ _SkeletalCommandBuilderaddParameter(String parameter) + +
+          Deprecated.  
+ _SkeletalCommandBuilderaddParameters(List<String> parameters) + +
+          Deprecated. Adds parameter to the list of parameters for a native executable
+ _SkeletalCommandBuilderaddParameters(String[] parameters) + +
+          Deprecated.  
+ StringgetClusterJobSettings() + +
+          Deprecated.  
+ StringgetEmail() + +
+          Deprecated.  
+ StringgetError() + +
+          Deprecated.  
+ Limit<_SkeletalCommandBuilder>getLimit(String presetName) + +
+          Deprecated.  
+ LimitsManager<_SkeletalCommandBuilder>getLimits() + +
+          Deprecated.  
+ StringgetName() + +
+          Deprecated.  
+ StringgetOutput() + +
+          Deprecated.  
+ CommandBuilder<_SkeletalCommandBuilder>getParameters(Executable.ExecProvider provider) + +
+          Deprecated.  
+ + + + + +
+<V> V
+		getResults(String directory) + +
+          Deprecated.  
+ Executable<?>loadRunConfiguration(RunConfiguration rconfig) + +
+          Deprecated.  
+ _SkeletalCommandBuildersetEmail(String email) + +
+          Deprecated.  
+ _SkeletalCommandBuildersetName(String name) + +
+          Deprecated.  
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  + + + + + + + +
Methods inherited from interface compbio.engine.client.Executable
getCreatedFiles, getInput
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+_SkeletalCommandBuilder

+
+public _SkeletalCommandBuilder()
+
+
Deprecated. 
+ + + + + + + + +
+Method Detail
+ +

+setEmail

+
+public _SkeletalCommandBuilder setEmail(String email)
+
+
Deprecated. 
+
+
+
+
+
+
+
+ +

+setName

+
+public _SkeletalCommandBuilder setName(String name)
+
+
Deprecated. 
+
+
+
+
+
+
+
+ +

+getName

+
+public String getName()
+
+
Deprecated. 
+
+
+
+
+
+
+
+ +

+getEmail

+
+public String getEmail()
+
+
Deprecated. 
+
+
+
+
+
+
+
+ +

+addParameters

+
+public _SkeletalCommandBuilder addParameters(String[] parameters)
+
+
Deprecated. 
+
+
+
+
+
+
+
+ +

+addParameters

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

+

+
Specified by:
addParameters in interface Executable<_SkeletalCommandBuilder>
+
+
+ +
Returns:
this Executable
+
+
+
+ +

+getParameters

+
+public CommandBuilder<_SkeletalCommandBuilder> getParameters(Executable.ExecProvider provider)
+
+
Deprecated. 
+
Specified by:
getParameters in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+
+
+ +

+addParameter

+
+public _SkeletalCommandBuilder addParameter(String parameter)
+
+
Deprecated. 
+
+
+
+
+
+
+
+ +

+getResults

+
+public <V> V getResults(String directory)
+
+
Deprecated. 
+
Specified by:
getResults in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+
+
+ +

+loadRunConfiguration

+
+public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
+
+
Deprecated. 
+
Specified by:
loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+
+
+ +

+getOutput

+
+public String getOutput()
+
+
Deprecated. 
+
Specified by:
getOutput in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+
+
+ +

+getError

+
+public String getError()
+
+
Deprecated. 
+
Specified by:
getError in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+
+
+ +

+getLimit

+
+public Limit<_SkeletalCommandBuilder> getLimit(String presetName)
+
+
Deprecated. 
+
Specified by:
getLimit in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+
+
+ +

+getLimits

+
+public LimitsManager<_SkeletalCommandBuilder> getLimits()
+
+
Deprecated. 
+
Specified by:
getLimits in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+
+
+ +

+getClusterJobSettings

+
+public String getClusterJobSettings()
+
+
Deprecated. 
+
Specified by:
getClusterJobSettings in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + +