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_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)`.

Constructor Summary

Constructors
Constructor and Description

BioLockJUtil()

Constructors
Constructor and Description
`BioLockJUtil()`

Method Summary

All Methods Static Methods Concrete 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 boolean`	`deleteWithRetry(File file, int numTries)` Delete file or directory with retry.
`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 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 File`	`getLocalDir(String path)` Return directory for path after modifying if running in a Docker container and/or interpreting bash env vars.
`static File`	`getLocalFile(String path)` Return file for path after modifying if running in a Docker container and/or interpreting bash env vars.
`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 String`	`getVersion()` Method returns the current version of BioLockJ.
`static void`	`ignoreFile(File file)` Method used to add a file to the ignore file list property.
`static String`	`join(Collection<?> collection)` Merge the collection into a String with 1 space between each element.toString() value.
`static boolean`	`noNullOrEmptyVals(Collection<Object> vals)` Verify all items in collection are not null and do not have empty toString() values.
`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 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`	`setPipelineInputFiles(List<File> files)` Setter for pipeline input files.

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_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
- 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
  - deleteWithRetry
```
public static boolean deleteWithRetry(File file,
                                      int numTries)
                               throws Exception
```
    Delete file or directory with retry. Wait 3 seconds between each try - waiting for resource to release lock if .
    
    Parameters:
    
    file - File or directory
    
    numTries - Number of attempts
    
    Returns:
    
    boolean status
    
    Throws:
    
    Exception - if errors occur
  - 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 - if errors occur
  - getLocalDir
```
public static File getLocalDir(String path)
                        throws ConfigPathException
```
    Return directory for path after modifying if running in a Docker container and/or interpreting bash env vars.
    
    Parameters:
    
    path - Directory path
    
    Returns:
    
    Local Directory
    
    Throws:
    
    ConfigPathException - if the local path is not found
  - getLocalFile
```
public static File getLocalFile(String path)
                         throws ConfigPathException
```
    Return file for path after modifying if running in a Docker container and/or interpreting bash env vars.
    
    Parameters:
    
    path - File path
    
    Returns:
    
    Local File
    
    Throws:
    
    ConfigPathException - if the local path is not found
  - getPipelineInputFiles
```
public static Collection<File> getPipelineInputFiles()
                                              throws Exception
```
    Basic input files may be sequences, or any other file type acceptable in a pipeline module.
    
    Returns:
    
    Collection of pipeline input files
    
    Throws:
    
    Exception - if errors occur
  - 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
  - getVersion
```
public static String getVersion()
                         throws Exception
```
    Method returns the current version of BioLockJ.
    
    Returns:
    
    BioLockJ version
    
    Throws:
    
    Exception - if errors occur
  - ignoreFile
```
public static void ignoreFile(File file)
```
    Method used to add a file to the ignore file list property.
    
    Parameters:
    
    file - File to ignore
  - 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
  - noNullOrEmptyVals
```
public static boolean noNullOrEmptyVals(Collection<Object> vals)
```
    Verify all items in collection are not null and do not have empty toString() values.
    
    Parameters:
    
    vals - Collection of objects
    
    Returns:
    
    Boolean TRUE if all vals exist and are not empty
  - parseCountTable
```
public static List<List<String>> parseCountTable(File file)
                                          throws Exception
```
    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:
    
    Exception - if errors occur
  - 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
  - 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
  - setPipelineInputFiles
```
public static void setPipelineInputFiles(List<File> files)
```
    Setter for pipeline input files.
    
    Parameters:
    
    files - List of input files

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_STATS_TABLE_INPUT_TYPE

PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE

Constructor Detail

BioLockJUtil

Method Detail

addLeadingSpaces

addTrailingSpaces

deleteWithRetry

fileExt

formatDigits

formatNumericOutput

formatPercentage

getBljDir

getClassNames

getCollectionAsString

getCommonParent

getFilePaths

getFileReader

getInputDirs

getLocalDir

getLocalFile

getPipelineInputFiles

getSource

getVersion

ignoreFile

join

noNullOrEmptyVals

parseCountTable

pipelineInputType

printLongFormList

removeIgnoredAndEmptyFiles

removeOuterQuotes

removeQuotes

setPipelineInputFiles