ModuleUtil

java.lang.Object
- biolockj.util.ModuleUtil

```
public class ModuleUtil
extends Object
```
This utility holds general methods useful for BioModule interaction and management.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static String`	`displayID(BioModule module)` Return the module ID as a 2 digit display number (add leading zero if needed).
`static ClassifierModule`	`getClassifier(BioModule module, boolean checkAhead)` Get a classifier module Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
`static String`	`getDefaultDemultiplexer()` Get the Java Class name for the default Demultiplexer module
`static String`	`getDefaultFastaConverter()` Get the Java Class name for the default Fasta converter module
`static String`	`getDefaultMergePairedReadsConverter()` Get the Java Class name for the default Merge paired read module
`static String`	`getDefaultStatsModule()` Return the class name of the default R statistics BioModule
`static BioModule`	`getModule(BioModule module, String className, boolean checkAhead)` Get a module with given className unless a classifier module is found 1st. Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
`static BioModule`	`getModule(String className)` Construct a BioModule based on its className.
`static List<BioModule>`	`getModules(BioModule module, Boolean checkAhead)` Return pipeline modules after the given module if checkAhead = TRUE Otherwise return pipeline modules before the given module. If returning the prior modules, return the pipeline modules in reverse order, so the 1st item in the list is the module immediately preceding the given module.
`static BioModule`	`getNextModule(BioModule module)` BioModules are run in the order configured. Return the module configured to run after the given module.
`static BioModule`	`getPreviousModule(BioModule module)` BioModules are run in the order configured. Return the module configured to run before the given module.
`static boolean`	`hasExecuted(BioModule module)` Return TRUE if module has executed.
`static boolean`	`isComplete(BioModule module)` Return TRUE if module completed successfully.
`static boolean`	`isFirstRModule(BioModule module)` Test if module is the first `R_Module` configured in the pipeline.
`static boolean`	`isIncomplete(BioModule module)` Return TRUE if module started execution but is not complete.
`static boolean`	`isMetadataModule(BioModule module)` Method determines if the given module is a metadata-module (which does not use/modify sequence data.
`static void`	`markComplete(BioModule module)` Method creates a file named "biolockjComplete" in module root directory to document module has completed successfully.
`static void`	`markStarted(BioModule module)` Method creates a file named "biolockjStarted" in module root directory to document module has completed successfully.
`static boolean`	`moduleExists(String className)` Check if a module was in the pipeline at least once.
`static File`	`requireSubDir(BioModule module, String subDirName)` Get BioModule subdirectory File object with given name.
`static boolean`	`subDirExists(BioModule module, String subDirName)` Return TRUE if BioModule sub-directory exists

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Method Detail
  - displayID
```
public static String displayID(BioModule module)
```
    Return the module ID as a 2 digit display number (add leading zero if needed).
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    ID display value
  - getClassifier
```
public static ClassifierModule getClassifier(BioModule module,
                                             boolean checkAhead)
```
    Get a classifier module
    Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
    
    Parameters:
    
    module - Calling BioModule
    
    checkAhead - Boolean TRUE to check for NEXT, set FALSE to check BEHIND
    
    Returns:
    
    BioModule
  - getDefaultDemultiplexer
```
public static String getDefaultDemultiplexer()
```
    Get the Java Class name for the default Demultiplexer module
    
    Returns:
    
    Demultiplexer module Java class name
  - getDefaultFastaConverter
```
public static String getDefaultFastaConverter()
```
    Get the Java Class name for the default Fasta converter module
    
    Returns:
    
    Fasta converter module Java class name
  - getDefaultMergePairedReadsConverter
```
public static String getDefaultMergePairedReadsConverter()
```
    Get the Java Class name for the default Merge paired read module
    
    Returns:
    
    Merge paired read module Java class name
  - getDefaultStatsModule
```
public static String getDefaultStatsModule()
```
    Return the class name of the default R statistics BioModule
    
    Returns:
    
    default stats module
  - getModule
```
public static BioModule getModule(BioModule module,
                                  String className,
                                  boolean checkAhead)
                           throws Exception
```
    Get a module with given className unless a classifier module is found 1st.
    Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
    
    Parameters:
    
    module - Calling BioModule
    
    className - Target BioModule class name
    
    checkAhead - Boolean TRUE to check for NEXT, set FALSE to check BEHIND
    
    Returns:
    
    BioModule
    
    Throws:
    
    Exception - if errors occur
  - getModule
```
public static BioModule getModule(String className)
                           throws Exception
```
    Construct a BioModule based on its className.
    
    Parameters:
    
    className - BioModule class name
    
    Returns:
    
    BioModule module
    
    Throws:
    
    Exception - if errors occur
  - getModules
```
public static List<BioModule> getModules(BioModule module,
                                         Boolean checkAhead)
```
    Return pipeline modules after the given module if checkAhead = TRUE
    Otherwise return pipeline modules before the given module.
    If returning the prior modules, return the pipeline modules in reverse order, so the 1st item in the list is the module immediately preceding the given module.
    
    Parameters:
    
    module - Reference BioModule
    
    checkAhead - Set TRUE to return modules after the given reference module
    
    Returns:
    
    List of BioModules before/after the current module, as determined by checkAhead parameter
  - getNextModule
```
public static BioModule getNextModule(BioModule module)
```
    BioModules are run in the order configured.
    Return the module configured to run after the given module.
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    Next BioModule
  - getPreviousModule
```
public static BioModule getPreviousModule(BioModule module)
```
    BioModules are run in the order configured.
    Return the module configured to run before the given module.
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    Previous BioModule
  - hasExecuted
```
public static boolean hasExecuted(BioModule module)
```
    Return TRUE if module has executed.
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    TRUE if module has executed
  - isComplete
```
public static boolean isComplete(BioModule module)
```
    Return TRUE if module completed successfully.
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    TRUE if module has completed successfully.
  - isFirstRModule
```
public static boolean isFirstRModule(BioModule module)
```
    Test if module is the first R_Module configured in the pipeline.
    
    Parameters:
    
    module - BioModule to test
    
    Returns:
    
    TRUE if module is 1st R_Module in this branch
  - isIncomplete
```
public static boolean isIncomplete(BioModule module)
```
    Return TRUE if module started execution but is not complete.
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    TRUE if module started execution but is not complete
  - isMetadataModule
```
public static boolean isMetadataModule(BioModule module)
```
    Method determines if the given module is a metadata-module (which does not use/modify sequence data.
    
    Parameters:
    
    module - BioModule in question
    
    Returns:
    
    TRUE if module produced exactly 1 file (metadata file)
  - markComplete
```
public static void markComplete(BioModule module)
                         throws Exception
```
    Method creates a file named "biolockjComplete" in module root directory to document module has completed successfully. Also clean up by removing file "biolockjStarted".
    
    Parameters:
    
    module - BioModule
    
    Throws:
    
    Exception - if unable to create "biolockjComplete" file
  - markStarted
```
public static void markStarted(BioModule module)
                        throws Exception
```
    Method creates a file named "biolockjStarted" in module root directory to document module has completed successfully. Also sets the start time and caches module name to list of executed modules so we can check later if it ran during this pipeline execution (as opposed to a previous failed run).
    
    Parameters:
    
    module - module
    
    Throws:
    
    Exception - if unable to create "biolockjStarted" file
  - moduleExists
```
public static boolean moduleExists(String className)
```
    Check if a module was in the pipeline at least once.
    
    Parameters:
    
    className - module simple name
    
    Returns:
    
    boolean
  - requireSubDir
```
public static File requireSubDir(BioModule module,
                                 String subDirName)
```
    Get BioModule subdirectory File object with given name. If directory doesn't exist, create it.
    
    Parameters:
    
    module - BioModule
    
    subDirName - BioModule sub-directory name
    
    Returns:
    
    BioModule sub-directory File object
  - subDirExists
```
public static boolean subDirExists(BioModule module,
                                   String subDirName)
```
    Return TRUE if BioModule sub-directory exists
    
    Parameters:
    
    module - BioModule
    
    subDirName - BioModule sub-directory name
    
    Returns:
    
    TRUE if BioModule sub-directory exists

Class ModuleUtil

Method Summary

Methods inherited from class java.lang.Object

Method Detail

displayID

getClassifier

getDefaultDemultiplexer

getDefaultFastaConverter

getDefaultMergePairedReadsConverter

getDefaultStatsModule

getModule

getModule

getModules

getNextModule

getPreviousModule

hasExecuted

isComplete

isFirstRModule

isIncomplete

isMetadataModule

markComplete

markStarted

moduleExists

requireSubDir

subDirExists