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java.lang.Objectstartup.FunSiPWorkflow
public class FunSiPWorkflow
This class represents the different actions etc. defined in a single configuration file. After being parsed, all these actions are launched by the workflow parameters also defined in the configuration file.
Nested Class Summary | |
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static class |
FunSiPWorkflow.MULTITHREADING
The different types of available multithreading: a) NO_MULTITHREADING : no multithreading at all b) SINGLE_PC_MULTITHREADING : launches each different ClassificationAction in a seperate thread, and waits until they're all finished; c) CLUSTER_MULTITHREADING : attempts to launch each ClassificationAction in a seperate job for the cluster (standard qsub-command). |
Constructor Summary | |
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FunSiPWorkflow(org.apache.log4j.Logger logger,
java.lang.String fileName)
Constructor, does nothing really but assigning the provided method parameters to local variables. |
Method Summary | |
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void |
addClassificationAction(ClassificationAction ca)
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void |
addInputMergeFiles(java.util.List<java.lang.String> inputMerge)
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void |
addOutputMergeFile(java.lang.String outputMerge)
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void |
convertToGenomeViewOutput(java.io.File file)
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java.util.List<ClassificationAction> |
getClassificationActions()
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java.lang.String |
getFileName()
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java.util.List<java.util.List<java.lang.String>> |
getInputMergeFiles()
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java.lang.String |
getLoggingStyle()
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int |
getOptimizer_step()
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int[] |
getOptimizerData()
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java.util.List<java.lang.String> |
getOutputMergeFile()
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FunSiPWorkflow.MULTITHREADING |
getThreading()
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boolean |
isMergeResults()
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boolean |
isOptimizer()
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void |
run()
Inherited because the workflow must be run as a thread. |
void |
setClassificationActions(java.util.List<ClassificationAction> caList)
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void |
setExplicitFiles(java.io.File[] files)
This method is used when additional fastafiles that need to be evaluated are provided on the commandline by the user. |
void |
setFileName(java.lang.String s)
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void |
setInputMergeFiles(java.util.List<java.util.List<java.lang.String>> inputMergeFiles)
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void |
setMergeResults(boolean mergeResults)
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void |
setOptimizer_steps(int optimizer_start,
int optimizer_stop,
int optimizer_step)
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void |
setOptimizer(boolean optimizer)
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void |
setOutputMergeFile(java.util.List<java.lang.String> outputMergeFile)
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boolean |
setThreading(java.lang.String threading_style)
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java.util.List<startup.FunSiPWorkflow.OptimizationScore> |
sortScores(java.util.List<startup.FunSiPWorkflow.OptimizationScore> list)
Dummy bubblesort algorithm (normally list only consists of 2-10 items) for the OptimizationScore type. |
void |
waitForSync()
This method is used for synchronization purposes between the different spawned threads. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public FunSiPWorkflow(org.apache.log4j.Logger logger, java.lang.String fileName)
logger
- The logging facilityfileName
- The name of the configurationfile by which this workflow
is created. Can be null if this method is invoked by other means.Method Detail |
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public void setExplicitFiles(java.io.File[] files)
files
- The files that need to be evaluated.public void run()
run
in interface java.lang.Runnable
public void convertToGenomeViewOutput(java.io.File file)
public void waitForSync() throws java.lang.InterruptedException
java.lang.InterruptedException
public java.util.List<startup.FunSiPWorkflow.OptimizationScore> sortScores(java.util.List<startup.FunSiPWorkflow.OptimizationScore> list)
list
- List that needs to be sorted (descending order)
public void addClassificationAction(ClassificationAction ca)
public java.util.List<ClassificationAction> getClassificationActions()
public void setClassificationActions(java.util.List<ClassificationAction> caList)
public boolean setThreading(java.lang.String threading_style)
public java.lang.String getLoggingStyle()
public FunSiPWorkflow.MULTITHREADING getThreading()
public java.util.List<java.util.List<java.lang.String>> getInputMergeFiles()
public void setInputMergeFiles(java.util.List<java.util.List<java.lang.String>> inputMergeFiles)
public boolean isMergeResults()
public void setMergeResults(boolean mergeResults)
public java.util.List<java.lang.String> getOutputMergeFile()
public void setOutputMergeFile(java.util.List<java.lang.String> outputMergeFile)
public void addInputMergeFiles(java.util.List<java.lang.String> inputMerge)
public void addOutputMergeFile(java.lang.String outputMerge)
public boolean isOptimizer()
public void setOptimizer(boolean optimizer)
public int getOptimizer_step()
public void setOptimizer_steps(int optimizer_start, int optimizer_stop, int optimizer_step)
public int[] getOptimizerData()
public void setFileName(java.lang.String s)
public java.lang.String getFileName()
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