X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fengine%2Fclient%2FConfExecutable.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fengine%2Fclient%2FConfExecutable.html;h=297f34160f85ea1667f56632f9f6879194673efc;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/engine/client/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/ConfExecutable.html new file mode 100644 index 0000000..297f341 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/ConfExecutable.html @@ -0,0 +1,1022 @@ + + + + + + +ConfExecutable + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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 ConfExecutable<T>

+
+java.lang.Object
+  extended by compbio.engine.client.ConfExecutable<T>
+
+
+
All Implemented Interfaces:
ConfiguredExecutable<T>, Executable<T>, PipedExecutable<T>
+
+
+
+
public class ConfExecutable<T>
extends Object
implements ConfiguredExecutable<T>
+ + +

+

+ +

+ + + + + + + +
+Nested Class Summary
+  + + + + + + + +
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
+  + + + + + + + + + + + +
+Field Summary
+static StringCLUSTER_TASK_ID_PREFIX + +
+           
+  + + + + + + + + + + +
+Constructor Summary
ConfExecutable(Executable<T> executable, + String taskDirectory) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Executable<T>addParameters(List<String> parameters) + +
+          Adds parameter to the list of parameters for a native executable
+ StringgetClusterJobSettings() + +
+           
+ StringgetCommand(Executable.ExecProvider provider) + +
+           
+ List<String>getCreatedFiles() + +
+           
+ Map<String,String>getEnvironment() + +
+           
+ StringgetError() + +
+           
+ Executable.ExecProvidergetExecProvider() + +
+           
+ Executable<T>getExecutable() + +
+           
+ StringgetInput() + +
+          Not all input paths are relative! Input path could be absolute!
+ Limit<T>getLimit(String presetName) + +
+           
+ LimitsManager<T>getLimits() + +
+           
+ StringgetOutput() + +
+           
+ CommandBuilder<T>getParameters() + +
+           
+ CommandBuilder<T>getParameters(Executable.ExecProvider provider) + +
+           
+ + + + + +
+<V> V
+		getResults() + +
+           
+ + + + + +
+<V> V
+		getResults(String directory) + +
+           
+ RunConfigurationgetRunConfiguration() + +
+           
+static + + + + +
+<V> LimitsManager<V>
+		getRunnerLimits(Class<V> clazz) + +
+          This method should be executed once and result of its execution reused.
+static + + + + +
+<V> RunnerConfig<V>
+		getRunnerOptions(Class<? extends Executable<V>> clazz) + +
+           
+static + + + + +
+<V> PresetManager<V>
+		getRunnerPresets(Class<? extends Executable<V>> clazz) + +
+           
+ Executable.ExecProvidergetSupportedRuntimes() + +
+           
+ StringgetTaskId() + +
+           
+ StringgetWorkDirectory() + +
+           
+ ConfiguredExecutable<?>loadRunConfiguration(InputStream input) + +
+           
+ ConfiguredExecutable<?>loadRunConfiguration(RunConfiguration rconf) + +
+           
+static ConfiguredExecutable<?>newConfExecutable(RunConfiguration rconf) + +
+           
+ booleansaveRunConfiguration() + +
+           
+ voidsetExecProvider(Executable.ExecProvider provider) + +
+           
+ voidsetWorkDirectory(String workDirectory) + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

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

+CLUSTER_TASK_ID_PREFIX

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

+ConfExecutable

+
+public ConfExecutable(Executable<T> executable,
+                      String taskDirectory)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getExecProvider

+
+public Executable.ExecProvider getExecProvider()
+
+
+
Specified by:
getExecProvider in interface ConfiguredExecutable<T>
+
+
+
+
+
+
+ +

+setExecProvider

+
+public void setExecProvider(Executable.ExecProvider provider)
+
+
+
+
+
+
+
+
+
+ +

+getCommand

+
+public String getCommand(Executable.ExecProvider provider)
+                  throws UnsupportedRuntimeException
+
+
+
Specified by:
getCommand in interface ConfiguredExecutable<T>
+
+
+ +
Throws: +
UnsupportedRuntimeException
+
+
+
+ +

+getSupportedRuntimes

+
+public Executable.ExecProvider getSupportedRuntimes()
+
+
+
Specified by:
getSupportedRuntimes in interface ConfiguredExecutable<T>
+
+
+
+
+
+
+ +

+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>
+
+
+
+
+
+
+ +

+getTaskId

+
+public String getTaskId()
+
+
+
Specified by:
getTaskId in interface ConfiguredExecutable<T>
+
+
+
+
+
+
+ +

+setWorkDirectory

+
+public void setWorkDirectory(String workDirectory)
+
+
+
Specified by:
setWorkDirectory in interface ConfiguredExecutable<T>
+
+
+
+
+
+
+ +

+getWorkDirectory

+
+public String getWorkDirectory()
+
+
+
Specified by:
getWorkDirectory in interface ConfiguredExecutable<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
+
+
+
+ +

+getOutput

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

+getError

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

+getCreatedFiles

+
+public List<String> getCreatedFiles()
+
+
+
Specified by:
getCreatedFiles in interface Executable<T>
+
+
+
+
+
+
+ +

+getInput

+
+public String getInput()
+
+
Not all input paths are relative! Input path could be absolute! +

+

+
Specified by:
getInput in interface Executable<T>
+
+
+
See Also:
compbio.engine.client.Executable#getInputFiles()
+
+
+
+ +

+getParameters

+
+public CommandBuilder<T> getParameters()
+
+
+
Specified by:
getParameters in interface ConfiguredExecutable<T>
+
+
+
+
+
+
+ +

+getParameters

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

+getExecutable

+
+public Executable<T> getExecutable()
+
+
+
Specified by:
getExecutable in interface ConfiguredExecutable<T>
+
+
+
+
+
+
+ +

+getResults

+
+public <V> V getResults()
+             throws ResultNotAvailableException
+
+
+
Specified by:
getResults in interface ConfiguredExecutable<T>
+
+
+ +
Throws: +
ResultNotAvailableException
+
+
+
+ +

+getResults

+
+public <V> V getResults(String directory)
+             throws ResultNotAvailableException
+
+
+
Specified by:
getResults in interface Executable<T>
+
+
+ +
Throws: +
ResultNotAvailableException
+
+
+
+ +

+getRunnerOptions

+
+public static <V> RunnerConfig<V> getRunnerOptions(Class<? extends Executable<V>> clazz)
+                                        throws IOException
+
+
+
+
+
+ +
Throws: +
IOException
+
+
+
+ +

+getRunnerPresets

+
+public static <V> PresetManager<V> getRunnerPresets(Class<? extends Executable<V>> clazz)
+                                         throws IOException
+
+
+
+
+
+ +
Throws: +
IOException
+
+
+
+ +

+getRunnerLimits

+
+public static <V> LimitsManager<V> getRunnerLimits(Class<V> clazz)
+                                        throws IOException
+
+
This method should be executed once and result of its execution reused. + If not used carefully it could slow down the system! +

+

+
+
+
+
Type Parameters:
V -
Parameters:
clazz - +
Returns:
LimitsManager instance +
Throws: +
IOException
+
+
+
+ +

+getEnvironment

+
+public Map<String,String> getEnvironment()
+
+
+
Specified by:
getEnvironment in interface ConfiguredExecutable<T>
+
+
+
+
+
+
+ +

+loadRunConfiguration

+
+public ConfiguredExecutable<?> loadRunConfiguration(RunConfiguration rconf)
+
+
+
Specified by:
loadRunConfiguration in interface Executable<T>
+
+
+
+
+
+
+ +

+newConfExecutable

+
+public static ConfiguredExecutable<?> newConfExecutable(RunConfiguration rconf)
+
+
+
+
+
+
+
+
+
+ +

+saveRunConfiguration

+
+public boolean saveRunConfiguration()
+                             throws IOException
+
+
+
Specified by:
saveRunConfiguration in interface ConfiguredExecutable<T>
+
+
+ +
Throws: +
IOException
+
+
+
+ +

+getRunConfiguration

+
+public RunConfiguration getRunConfiguration()
+
+
+
+
+
+
+
+
+
+ +

+loadRunConfiguration

+
+public ConfiguredExecutable<?> loadRunConfiguration(InputStream input)
+                                             throws IOException
+
+
+
Specified by:
loadRunConfiguration in interface ConfiguredExecutable<T>
+
+
+ +
Throws: +
IOException
+
+
+
+ +

+toString

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

+getClusterJobSettings

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