BioLockJUtil

java.lang.Object
- biolockj.util.BioLockJUtil

```
public class BioLockJUtil
extends Object
```
Simple utility containing String manipulation and formatting functions.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`INTERNAL_PIPELINE_INPUT_TYPES` Internal `Config` String property: "internal.pipelineInputTypes" This value is set after parsing the input files from `Config` property: "input.dirPaths" in the method: `getPipelineInputFiles()`.
`static String`	`PIPELINE_HUMANN2_COUNT_TABLE_INPUT_TYPE` Pipeline input file type indicating the file is Humann2 generated
`static String`	`PIPELINE_LOG_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE` Internal `Config` String property: "taxa_count_log_norm" Set as the value of "internal.pipelineInputTypes" for log-normalized taxa count files that meet the file requirements to pass `TaxaUtil.isLogNormalizedTaxaFile(File)`.
`static String`	`PIPELINE_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE` Internal `Config` String property: "taxa_count_norm" Set as the value of "internal.pipelineInputTypes" for normalized taxa count files that meet the file requirements to pass `TaxaUtil.isNormalizedTaxaFile(File)`.
`static String`	`PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE` Internal `Config` String property: "otu_count" Set as the value of "internal.pipelineInputTypes" for OTU count files that meet the file requirements to pass `OtuUtil.isOtuFile(File)`.
`static String`	`PIPELINE_PAIRED_READS_INPUT_TYPE` Internal `Config` String property: "paired" Set as the value of "internal.pipelineInputTypes" for paired sequence input files.
`static String`	`PIPELINE_PARSER_INPUT_TYPE` Internal `Config` String property: "classifier_output" Set as the value of "internal.pipelineInputTypes" for classifier output files.
`static String`	`PIPELINE_R_INPUT_TYPE` Internal `Config` String property: "R" Set as the value of "internal.pipelineInputTypes" if input files are some type of count table merged with the metadata such as those output by `AddMetadataToTaxaTables`.
`static String`	`PIPELINE_SEQ_INPUT_TYPE` Internal `Config` String property: "seq" Set as the value of "internal.pipelineInputTypes" for sequence input files.
`static String`	`PIPELINE_STATS_TABLE_INPUT_TYPE` Internal `Config` String property: "stats" Set as the value of "internal.pipelineInputTypes" if input files are tables of statistics such as those output by `R_CalculateStats`.
`static String`	`PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE` Internal `Config` String property: "taxa_count" Set as the value of "internal.pipelineInputTypes" for taxa count files that meet the file requirements to pass `TaxaUtil.isTaxaFile(File)`.
`static String`	`RETURN` Return character constant backslash-n

Constructor Summary

Constructors
Constructor and Description

BioLockJUtil()

Constructors
Constructor and Description
`BioLockJUtil()`

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`static String`	`addLeadingSpaces(String val, int length)` Add leading spaces until the val is padded to given length
`static String`	`addTrailingSpaces(String val, int length)` Add trailing spaces until the val is padded to given length
`static void`	`checkVersion()`
`static boolean`	`copyInputFiles()` Copy input files into an internal folder within the pipeline root direction named "input"
`static File`	`createFile(String path)` Used to save status files for modules and the pipeline.
`static String`	`fileExt(File file)` Return the file extension - but ignore ".gz".
`static String`	`formatDigits(Integer input, Integer numDigits)` This method formats the input number to have a length of at least numDigits. Simply add leading zeros until numDigits is reached.
`static String`	`formatNumericOutput(Long input, boolean addCommas)` This method formats the input number by adding commas.
`static String`	`formatPercentage(long num, long denom)` Build the percentage display string for the num/denom ratio as "##.##%"
`static File`	`getBljDir()` Get the program source (either the jar path or main class biolockj.BioLockJ);
`static List<String>`	`getClassNames(Collection<?> objs)` Return an ordered list of the class names from the input collection.
`static String`	`getCollectionAsString(Collection<?> data)` Concatenate data and return as a comma separated String.
`static File`	`getCommonParent(File f1, File f2)` Compare files to return a common parent directory (if any)
`static String`	`getDateString()` Get todays date represented as YEARmonDA.
`static List<String>`	`getFilePaths(Collection<File> files)` Return an ordered list of absolute file paths from the input collection.
`static BufferedReader`	`getFileReader(File file)` Get a `BufferedReader` for standard text file or `GZIPInputStream` for gzipped files ending in ".gz"
`static List<File>`	`getInputDirs()` Get the list of input directories for the pipeline.
`static List<InputDataModule>`	`getInputModules()`
`static Collection<File>`	`getPipelineInputFiles()` Basic input files may be sequences, or any other file type acceptable in a pipeline module.
`static File`	`getSource()` Get the source of the java runtime classes ( /bin directory or JAR file ).
`static File`	`getUserProfile()` Deprecated.
`static String`	`getVersion()` Method returns the current version of BioLockJ without Git build info
`static String`	`getVersion(boolean getBuildId)` Method returns the current version of BioLockJ - or undefined message.
`static boolean`	`hasNullOrEmptyVal(Collection<Object> vals)` Check collection vals for null or empty toString() values
`static void`	`ignoreFile(File file)` Method used to add a file to the ignore file list property.
`static void`	`initPipelineInput()` Basic input files may be sequences, or any other file type acceptable in a pipeline module.
`static boolean`	`isDirectMode()` Return TRUE if runtime parameters indicate attempt to run in direct mode
`static String`	`join(Collection<?> collection)` Merge the collection into a String with 1 space between each element.toString() value.
`static int`	`millisToMinutes(long milliseconds)` Convert milliseconds to minutes - useful to convert Java millisecond output rounded to the nearest minute.
`static long`	`minutesToMillis(int minutes)` Convert minutes to milliseconds - useful to convert Config props measure in minutes to milliseconds since many Java functions have milliseconds args.
`static List<List<String>>`	`parseCountTable(File file)` Read in BioLockJ count table, each inner lists represents 1 line from the file. Each cell in the tab delimited file is stored as 1 element in the inner lists.
`static boolean`	`pipelineInputType(String type)` Convenience method to check pipeline input file type.
`static File`	`pipelineInternalInputDir()` Return the pipeline input directory
`static String`	`printLongFormList(Collection<?> data)` Print collection one item per line.
`static List<File>`	`removeIgnoredAndEmptyFiles(Collection<File> files)` Remove ignored and empty files from the input files.
`static String`	`removeOuterQuotes(String value)` Remove the outer single or double quotes of the given value. Quotes are only removed if quotes are found as very 1st and last characters.
`static String`	`removeQuotes(String value)` Remove all single and double quotation marks found in value.
`static void`	`showInfo(String[] args)` Print basic version or help info if requested. Called by 1st line BioLockJ.java main() method

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

- Field Detail
  - INTERNAL_PIPELINE_INPUT_TYPES
```
public static final String INTERNAL_PIPELINE_INPUT_TYPES
```
    Internal Config String property: "internal.pipelineInputTypes"
    This value is set after parsing the input files from Config property: "input.dirPaths" in the method: getPipelineInputFiles(). The primary purpose of storing this value is to determine if BioModule.getPreRequisiteModules() are appropriate to add during pipeline initialization.
    
    BioModule.getPreRequisiteModules() are add dependent modules if missing from the Config. This ensures the current module will have the correct input files and is a convenient way to manage the size and readability of Config files. Prerequisite modules are always appropriate for full pipelines with sequence input file, however if the output from a prerequisite module is used as the input for a new pipeline via "input.dirPaths", adding the prerequisite module will cause FATAL pipeline errors.
    
    New pipelines can be run starting with any module, so BioLockJ must be prepared to accept the input files required for any module. All BioModules require input files from one of the following 6 categories:
    In rare cases, such as running R plot modules, the input directories must contain multiple data types.
    For example:
    With this input a user can run a pipeline with only 2 modules:
    1. JsonReport
    2. R_PlotOtus
    See Also:
    
    Constant Field Values
  - PIPELINE_HUMANN2_COUNT_TABLE_INPUT_TYPE
```
public static final String PIPELINE_HUMANN2_COUNT_TABLE_INPUT_TYPE
```
    Pipeline input file type indicating the file is Humann2 generated
    
    See Also:
    
    Constant Field Values
  - PIPELINE_LOG_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE
```
public static final String PIPELINE_LOG_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE
```
    Internal Config String property: "taxa_count_log_norm"
    Set as the value of "internal.pipelineInputTypes" for log-normalized taxa count files that meet the file requirements to pass TaxaUtil.isLogNormalizedTaxaFile(File).
    
    See Also:
    
    Constant Field Values
  - PIPELINE_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE
```
public static final String PIPELINE_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE
```
    Internal Config String property: "taxa_count_norm"
    Set as the value of "internal.pipelineInputTypes" for normalized taxa count files that meet the file requirements to pass TaxaUtil.isNormalizedTaxaFile(File).
    
    See Also:
    
    Constant Field Values
  - PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE
```
public static final String PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE
```
    Internal Config String property: "otu_count"
    Set as the value of "internal.pipelineInputTypes" for OTU count files that meet the file requirements to pass OtuUtil.isOtuFile(File).
    
    See Also:
    
    Constant Field Values
  - PIPELINE_PARSER_INPUT_TYPE
```
public static final String PIPELINE_PARSER_INPUT_TYPE
```
    Internal Config String property: "classifier_output"
    Set as the value of "internal.pipelineInputTypes" for classifier output files.
    
    See Also:
    
    Constant Field Values
  - PIPELINE_R_INPUT_TYPE
```
public static final String PIPELINE_R_INPUT_TYPE
```
    Internal Config String property: "R"
    Set as the value of "internal.pipelineInputTypes" if input files are some type of count table merged with the metadata such as those output by AddMetadataToTaxaTables. These files can be input into any R_Module.
    
    See Also:
    
    Constant Field Values
  - PIPELINE_SEQ_INPUT_TYPE
```
public static final String PIPELINE_SEQ_INPUT_TYPE
```
    Internal Config String property: "seq"
    Set as the value of "internal.pipelineInputTypes" for sequence input files.
    
    See Also:
    
    Constant Field Values
  - PIPELINE_PAIRED_READS_INPUT_TYPE
```
public static final String PIPELINE_PAIRED_READS_INPUT_TYPE
```
    Internal Config String property: "paired"
    Set as the value of "internal.pipelineInputTypes" for paired sequence input files.
    
    See Also:
    
    Constant Field Values
  - PIPELINE_STATS_TABLE_INPUT_TYPE
```
public static final String PIPELINE_STATS_TABLE_INPUT_TYPE
```
    Internal Config String property: "stats"
    Set as the value of "internal.pipelineInputTypes" if input files are tables of statistics such as those output by R_CalculateStats.
    
    See Also:
    
    Constant Field Values
  - PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE
```
public static final String PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE
```
    Internal Config String property: "taxa_count"
    Set as the value of "internal.pipelineInputTypes" for taxa count files that meet the file requirements to pass TaxaUtil.isTaxaFile(File).
    
    See Also:
    
    Constant Field Values
  - RETURN
```
public static final String RETURN
```
    Return character constant *backslash-n*
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - BioLockJUtil
```
public BioLockJUtil()
```
- Method Detail
  - addLeadingSpaces
```
public static String addLeadingSpaces(String val,
                                      int length)
```
    Add leading spaces until the val is padded to given length
    
    Parameters:
    
    val - Value to add spaces
    
    length - Total length of val with spaces
    
    Returns:
    
    Padded value
  - addTrailingSpaces
```
public static String addTrailingSpaces(String val,
                                       int length)
```
    Add trailing spaces until the val is padded to given length
    
    Parameters:
    
    val - Value to add spaces
    
    length - Total length of val with spaces
    
    Returns:
    
    Padded value
  - copyInputFiles
```
public static boolean copyInputFiles()
                              throws ConfigNotFoundException,
                                     ConfigFormatException
```
    Copy input files into an internal folder within the pipeline root direction named "input"
    
    Returns:
    
    Internal pipeline input dir
    
    Throws:
    
    ConfigNotFoundException - if "input.dirPaths" or "pipeline.copyInput" property is undefined
    
    ConfigFormatException - if "pipeline.copyInput" does not have a boolean "Y" or "N" value
  - createFile
```
public static File createFile(String path)
                       throws BioLockJStatusException,
                              IOException
```
    Used to save status files for modules and the pipeline.
    
    Parameters:
    
    path - Target dir path
    
    Returns:
    
    File Created file
    
    Throws:
    
    BioLockJStatusException
    
    IOException
    
    Exception - if errors occur attempting to save the file
  - fileExt
```
public static String fileExt(File file)
```
    Return the file extension - but ignore ".gz".
    
    Parameters:
    
    file - File
    
    Returns:
    
    File extension
  - formatDigits
```
public static String formatDigits(Integer input,
                                  Integer numDigits)
```
    This method formats the input number to have a length of at least numDigits.
    Simply add leading zeros until numDigits is reached.
    
    Parameters:
    
    input - Integer value
    
    numDigits - Number of digits return value should contain
    
    Returns:
    
    number as String with leading zeros.
  - formatNumericOutput
```
public static String formatNumericOutput(Long input,
                                         boolean addCommas)
```
    This method formats the input number by adding commas.
    
    Parameters:
    
    input - Long value
    
    addCommas - boolean if numeric output should be displayed using commas
    
    Returns:
    
    number as String with commas
  - formatPercentage
```
public static String formatPercentage(long num,
                                      long denom)
```
    Build the percentage display string for the num/denom ratio as "##.##%"
    
    Parameters:
    
    num - Numerator
    
    denom - Denominator
    
    Returns:
    
    ratio
  - getBljDir
```
public static File getBljDir()
                      throws ConfigPathException
```
    Get the program source (either the jar path or main class biolockj.BioLockJ);
    
    Returns:
    
    java source parameter (either Jar or main class with classpath)
    
    Throws:
    
    ConfigPathException - if unable to determine $BLJ source
  - getClassNames
```
public static List<String> getClassNames(Collection<?> objs)
```
    Return an ordered list of the class names from the input collection.
    
    Parameters:
    
    objs - Objects
    
    Returns:
    
    List of class names
  - getCollectionAsString
```
public static String getCollectionAsString(Collection<?> data)
```
    Concatenate data and return as a comma separated String.
    
    Parameters:
    
    data - Collection of data
    
    Returns:
    
    Collection data as a String
  - getCommonParent
```
public static File getCommonParent(File f1,
                                   File f2)
```
    Compare files to return a common parent directory (if any)
    
    Parameters:
    
    f1 - File 1
    
    f2 - File 2
    
    Returns:
    
    Directory path share by f1 and f2
  - getFilePaths
```
public static List<String> getFilePaths(Collection<File> files)
```
    Return an ordered list of absolute file paths from the input collection.
    
    Parameters:
    
    files - Files
    
    Returns:
    
    List of file paths
  - getFileReader
```
public static BufferedReader getFileReader(File file)
                                    throws FileNotFoundException,
                                           IOException
```
    Get a BufferedReader for standard text file or GZIPInputStream for gzipped files ending in ".gz"
    
    Parameters:
    
    file - to be read
    
    Returns:
    
    BufferedReader or GZIPInputStream if file is gzipped
    
    Throws:
    
    FileNotFoundException - if file does not exist
    
    IOException - if unable to read or write the file
  - getInputDirs
```
public static List<File> getInputDirs()
                               throws Exception
```
    Get the list of input directories for the pipeline.
    
    Returns:
    
    List of system directory file paths
    
    Throws:
    
    Exception
  - getPipelineInputFiles
```
public static Collection<File> getPipelineInputFiles()
```
    Basic input files may be sequences, or any other file type acceptable in a pipeline module.
    
    Returns:
    
    Collection of pipeline input files
  - getSource
```
public static File getSource()
                      throws URISyntaxException
```
    Get the source of the java runtime classes ( /bin directory or JAR file ).
    
    Returns:
    
    File object
    
    Throws:
    
    URISyntaxException - if unable to locate the Java source
  - getUserProfile
```
@Deprecated
public static File getUserProfile()
```
    Deprecated.
    
    Return the user shell profile
    
    Returns:
    
    Shell profile
  - getVersion
```
public static String getVersion()
```
    Method returns the current version of BioLockJ without Git build info
    
    Returns:
    
    BioLockJ version
  - getVersion
```
public static String getVersion(boolean getBuildId)
```
    Method returns the current version of BioLockJ - or undefined message.
    
    Parameters:
    
    getBuildId - boolean - If enabled, print git revision hash
    
    Returns:
    
    BioLockJ version
  - checkVersion
```
public static void checkVersion()
```
  - hasNullOrEmptyVal
```
public static boolean hasNullOrEmptyVal(Collection<Object> vals)
```
    Check collection vals for null or empty toString() values
    
    Parameters:
    
    vals - Collection of objects
    
    Returns:
    
    Boolean TRUE if all at least 1 value is null or empty
  - ignoreFile
```
public static void ignoreFile(File file)
                       throws DockerVolCreationException
```
    Method used to add a file to the ignore file list property.
    
    Parameters:
    
    file - File to ignore
    
    Throws:
    
    DockerVolCreationException
  - initPipelineInput
```
public static void initPipelineInput()
                              throws Exception
```
    Basic input files may be sequences, or any other file type acceptable in a pipeline module.
    
    Throws:
    
    Exception
  - getInputModules
```
public static List<InputDataModule> getInputModules()
                                             throws Exception
```
    Throws:
    
    Exception
  - isDirectMode
```
public static boolean isDirectMode()
```
    Return TRUE if runtime parameters indicate attempt to run in direct mode
    
    Returns:
    
    boolean
  - join
```
public static String join(Collection<?> collection)
```
    Merge the collection into a String with 1 space between each element.toString() value.
    
    Parameters:
    
    collection - Collection of objects
    
    Returns:
    
    Joined values
  - millisToMinutes
```
public static int millisToMinutes(long milliseconds)
```
    Convert milliseconds to minutes - useful to convert Java millisecond output rounded to the nearest minute.
    
    Parameters:
    
    milliseconds - number of milliseconds
    
    Returns:
    
    same amount of time as minutes
  - minutesToMillis
```
public static long minutesToMillis(int minutes)
```
    Convert minutes to milliseconds - useful to convert Config props measure in minutes to milliseconds since many Java functions have milliseconds args.
    
    Parameters:
    
    minutes - number of minutes
    
    Returns:
    
    same amount of time as milliseconds
  - parseCountTable
```
public static List<List<String>> parseCountTable(File file)
                                          throws FileNotFoundException,
                                                 IOException
```
    Read in BioLockJ count table, each inner lists represents 1 line from the file.
    Each cell in the tab delimited file is stored as 1 element in the inner lists.
    
    Parameters:
    
    file - Path abundance file
    
    Returns:
    
    List of Lists - each inner list 1 line
    
    Throws:
    
    IOException - if errors occur reading path abundance file
    
    FileNotFoundException - if path abundance file not found
  - pipelineInputType
```
public static boolean pipelineInputType(String type)
                                 throws ConfigNotFoundException
```
    Convenience method to check pipeline input file type.
    
    Parameters:
    
    type - Pipeline input file type
    
    Returns:
    
    TRUE if type = Config."internal.pipelineInputTypes"
    
    Throws:
    
    ConfigNotFoundException - if "internal.pipelineInputTypes" is undefined
  - getDateString
```
public static String getDateString()
```
    Get todays date represented as YEARmonDA.
    
    Returns:
  - pipelineInternalInputDir
```
public static File pipelineInternalInputDir()
```
    Return the pipeline input directory
    
    Returns:
    
    Input dir
  - printLongFormList
```
public static String printLongFormList(Collection<?> data)
```
    Print collection one item per line.
    
    Parameters:
    
    data - Collection of data
    
    Returns:
    
    Collection data as a String
  - removeIgnoredAndEmptyFiles
```
public static List<File> removeIgnoredAndEmptyFiles(Collection<File> files)
```
    Remove ignored and empty files from the input files.
    
    Parameters:
    
    files - Collection of files
    
    Returns:
    
    valid files
  - removeOuterQuotes
```
public static String removeOuterQuotes(String value)
```
    Remove the outer single or double quotes of the given value.
    Quotes are only removed if quotes are found as very 1st and last characters.
    
    Parameters:
    
    value - Possibly quoted value
    
    Returns:
    
    value without outer quotes
  - removeQuotes
```
public static String removeQuotes(String value)
```
    Remove all single and double quotation marks found in value.
    
    Parameters:
    
    value - Possibly quoted value
    
    Returns:
    
    value with no quotes
  - showInfo
```
public static void showInfo(String[] args)
```
    Print basic version or help info if requested.
    Called by 1st line BioLockJ.java main() method
    
    Parameters:
    
    args - BioLockJ.java main() runtime args

Class BioLockJUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

INTERNAL_PIPELINE_INPUT_TYPES

PIPELINE_HUMANN2_COUNT_TABLE_INPUT_TYPE

PIPELINE_LOG_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE

PIPELINE_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE

PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE

PIPELINE_PARSER_INPUT_TYPE

PIPELINE_R_INPUT_TYPE

PIPELINE_SEQ_INPUT_TYPE

PIPELINE_PAIRED_READS_INPUT_TYPE

PIPELINE_STATS_TABLE_INPUT_TYPE

PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE

RETURN

Constructor Detail

BioLockJUtil

Method Detail

addLeadingSpaces

addTrailingSpaces

copyInputFiles

createFile

fileExt

formatDigits

formatNumericOutput

formatPercentage

getBljDir

getClassNames

getCollectionAsString

getCommonParent

getFilePaths

getFileReader

getInputDirs

getPipelineInputFiles

getSource

getUserProfile

getVersion

getVersion

checkVersion

hasNullOrEmptyVal

ignoreFile

initPipelineInput

getInputModules

isDirectMode

join

millisToMinutes

minutesToMillis

parseCountTable

pipelineInputType

getDateString

pipelineInternalInputDir

printLongFormList

removeIgnoredAndEmptyFiles

removeOuterQuotes

removeQuotes

showInfo