TaxaUtil

java.lang.Object
- biolockj.util.TaxaUtil

```
public class TaxaUtil
extends Object
```
This utility helps work individual Taxa names, not full OTU path files which need OtuUtil.
Taxa files containing sample taxa counts for a given taxonomy level as output by BuildTaxaTables.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`FILE_EXT`
`static String`	`NORMALIZED` File suffix appended to normalized taxa count tables: "norm"
`protected static String`	`TAXA_TABLE` Included in the file name of each file output.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static List<String>`	`allTaxonomyLevels()` Returns a list of all taxonomy levels, not only the levels configured via `Config`."report.taxonomyLevels".
`static String`	`bottomTaxaLevel()` Return the bottom configured taxonomy level from `Config`."report.taxonomyLevels"
`static TreeSet<String>`	`findUniqueTaxa(TreeSet<String> otus, String level)` Extract taxonomy names at the given level from all given OTUs.
`static String`	`getLeafLevel(String otu)` Return OTU taxonomy level for the leaf edge of the OTU
`static Integer`	`getLevelNum(String level)` Return the absolute taxonomy level for the given level.
`static TreeMap<String,TreeMap<String,Long>>`	`getLevelTaxaCounts(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts, String level)` Return TreeMap keyed on Sample ID, each sample maps to an inner map(taxa, count). Input param sampleOtuCounts contains OTUs for which many can share the same level taxonomy assignment. For example if sample42 contained the following 3 OTU values: phylum__Actinobacteria\|class__Actinobacteria\|order__Actinomycetales\|family__Actinomycetaceae\|genus__Actinomyces 1000 phylum__Bacteroidetes\|class__Bacteroidia\|order__Bacteroidales\|family__Porphyromonadaceae\|genus__Barnesiella 500 phylum__Bacteroidetes\|class__Bacteroidia\|order__Bacteroidales\|family__Porphyromonadaceae\|genus__Parabacteroides 77 The phylum level output would contain entries: TreeMap(sample42, TreeMap( Actinobacteria=1000, Bacteroidetes=577 ) )
`static TreeMap<String,String>`	`getTaxaByLevel(String otu)` Return a map of the given otu parameter split by level.
`static List<String>`	`getTaxaLevels()` Method ensures taxonomy levels are returned in descending order from top to bottom.
`static List<String>`	`getTaxaLevelSpan()` Return taxa levels from top to bottom level, including in-between levels not configured as part of
`static String`	`getTaxaName(String otu, String level)` Extract a taxonomy name at the given level from the given OTU.
`static File`	`getTaxonomyTableFile(File dir, String level, String suffix)` Create File object of a taxonomy table at the given level, with the given suffix, in the given directory dir.
`static String`	`getTaxonomyTableLevel(File file)` Extract the table taxonomy level from an existing taxonomy table file.
`static String`	`getUnclassifiedTaxa(String taxa, String level)` Build the name of an unclassified taxa using the given "taxa" parameter. Returns a name like Unclassified (taxa name) Taxa
`static List<String>`	`initTaxaLevels()` Set taxonomy levels ordered by level, from highest to lowest.
`static boolean`	`isLogNormalizedTaxaFile(File file)` Check the file name to determine if it is a Log normalized taxonomy table file.
`static boolean`	`isNormalizedTaxaFile(File file)` Check the file name to determine if it is a normalized taxonomy table file.
`static boolean`	`isTaxaFile(File file)` Check the file name to determine if it is a taxonomy table file.
`static String`	`parentTaxaLevel(String level)` Get parent level name of the given level parameter.
`static TaxaLevelTable`	`readTaxaTable(File taxaTable)` Read a table of counts, formatted with samples as rows (ids in first column) and taxa as columns (ids in header).
`static String`	`topTaxaLevel()` Return the top configured taxonomy level from `Config`."report.taxonomyLevels"
`static void`	`writeDataToFile(File outFile, List<String> sampleNames, List<String> taxaNames, TaxaLevelTable taxaCounts)` Write transformed data to file
`static void`	`writeDataToFile(File outFile, TaxaLevelTable taxaCounts)`

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

- Field Detail
  - NORMALIZED
```
public static final String NORMALIZED
```
    File suffix appended to normalized taxa count tables: "norm"
    
    See Also:
    
    Constant Field Values
  - TAXA_TABLE
```
protected static final String TAXA_TABLE
```
    Included in the file name of each file output. One file per sample is output by the ParserModule.
    
    See Also:
    
    Constant Field Values
  - FILE_EXT
```
public static final String FILE_EXT
```
    See Also:
    
    Constant Field Values
- Method Detail
  - allTaxonomyLevels
```
public static List<String> allTaxonomyLevels()
```
    Returns a list of all taxonomy levels, not only the levels configured via Config."report.taxonomyLevels".
    
    Returns:
    
    Ordered List of all possible taxonomy levels
  - bottomTaxaLevel
```
public static String bottomTaxaLevel()
```
    Return the bottom configured taxonomy level from Config."report.taxonomyLevels"
    
    Returns:
    
    Taxonomy level
  - findUniqueTaxa
```
public static TreeSet<String> findUniqueTaxa(TreeSet<String> otus,
                                             String level)
```
    Extract taxonomy names at the given level from all given OTUs.
    
    Parameters:
    
    otus - TreeSet of OTUs in ParserModule format
    
    level - Config."report.taxonomyLevels"
    
    Returns:
    
    Ordered TreeSet of unique taxonomy names
  - getLeafLevel
```
public static String getLeafLevel(String otu)
```
    Return OTU taxonomy level for the leaf edge of the OTU
    
    Parameters:
    
    otu - OTU
    
    Returns:
    
    Leaf taxonomy level
  - getLevelNum
```
public static Integer getLevelNum(String level)
```
    Return the absolute taxonomy level for the given level. Constants.DOMAIN, Constants.PHYLUM, Constants.CLASS, Constants.ORDER, Constants.FAMILY, Constants.GENUS, Constants.SPECIES
    Parameters:
    
    level - Taxonomy level
    
    Returns:
    
    Integer level number
  - getLevelTaxaCounts
```
public static TreeMap<String,TreeMap<String,Long>> getLevelTaxaCounts(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts,
                                                                      String level)
```
    Return TreeMap keyed on Sample ID, each sample maps to an inner map(taxa, count).
    Input param sampleOtuCounts contains OTUs for which many can share the same level taxonomy assignment.
    For example if sample42 contained the following 3 OTU values:
    - phylum__Actinobacteria|class__Actinobacteria|order__Actinomycetales|family__Actinomycetaceae|genus__Actinomyces 1000
    - phylum__Bacteroidetes|class__Bacteroidia|order__Bacteroidales|family__Porphyromonadaceae|genus__Barnesiella 500
    - phylum__Bacteroidetes|class__Bacteroidia|order__Bacteroidales|family__Porphyromonadaceae|genus__Parabacteroides 77
    The phylum level output would contain entries:
    1. TreeMap(sample42, TreeMap( Actinobacteria=1000, Bacteroidetes=577 ) )
    Parameters:
    
    sampleOtuCounts - TreeMap(sampleId, TreeMap(OTU, count)) OTU counts for every sample
    
    level - Config."report.taxonomyLevels"
    
    Returns:
    
    TreeMap(sampleId, TreeMap(taxa, count))
  - getTaxaByLevel
```
public static TreeMap<String,String> getTaxaByLevel(String otu)
```
    Return a map of the given otu parameter split by level.
    
    Parameters:
    
    otu - OTU path value
    
    Returns:
    
    TreeMap(level, taxa)
  - getTaxaLevels
```
public static List<String> getTaxaLevels()
```
    Method ensures taxonomy levels are returned in descending order from top to bottom.
    
    Returns:
    
    configLevels
  - getTaxaLevelSpan
```
public static List<String> getTaxaLevelSpan()
```
    Return taxa levels from top to bottom level, including in-between levels not configured as part of
    
    Returns:
    
    List of taxonomy levels
  - getTaxaName
```
public static String getTaxaName(String otu,
                                 String level)
```
    Extract a taxonomy name at the given level from the given OTU.
    
    Parameters:
    
    otu - OTU name in ParserModule format
    
    level - Config."report.taxonomyLevels"
    
    Returns:
    
    Taxonomy name
  - getTaxonomyTableFile
```
public static File getTaxonomyTableFile(File dir,
                                        String level,
                                        String suffix)
                                 throws BioLockJException
```
    Create File object of a taxonomy table at the given level, with the given suffix, in the given directory dir.
    
    Parameters:
    
    dir - Target directory
    
    level - Taxonomy level
    
    suffix - File suffix
    
    Returns:
    
    Taxonomy Table File
    
    Throws:
    
    BioLockJException - if level is null
  - getTaxonomyTableLevel
```
public static String getTaxonomyTableLevel(File file)
```
    Extract the table taxonomy level from an existing taxonomy table file.
    
    Parameters:
    
    file - File Taxonomy Table
    
    Returns:
    
    Taxonomy level
  - getUnclassifiedTaxa
```
public static String getUnclassifiedTaxa(String taxa,
                                         String level)
```
    Build the name of an unclassified taxa using the given "taxa" parameter.
    Returns a name like Unclassified (taxa name) Taxa
    
    Parameters:
    
    taxa - Taxa parent name
    
    level - Taxa parent level
    
    Returns:
    
    Unclassified Taxa name
  - initTaxaLevels
```
public static List<String> initTaxaLevels()
                                   throws ConfigNotFoundException,
                                          ConfigFormatException,
                                          DockerVolCreationException
```
    Set taxonomy levels ordered by level, from highest to lowest. Require property. Accepts only valid options: , , , , , ,
    
    Returns:
    
    List of ordered taxonomy levels
    
    Throws:
    
    ConfigNotFoundException - if is undefined
    
    ConfigFormatException - if is defined, but does not contain any valid taxonomy levels
    
    DockerVolCreationException
  - isLogNormalizedTaxaFile
```
public static boolean isLogNormalizedTaxaFile(File file)
```
    Check the file name to determine if it is a Log normalized taxonomy table file.
    
    Parameters:
    
    file - File to test
    
    Returns:
    
    boolean TRUE if file is a normalized taxonomy count file
  - isNormalizedTaxaFile
```
public static boolean isNormalizedTaxaFile(File file)
```
    Check the file name to determine if it is a normalized taxonomy table file.
    
    Parameters:
    
    file - File to test
    
    Returns:
    
    boolean TRUE if file is a normalized taxonomy count file
  - isTaxaFile
```
public static boolean isTaxaFile(File file)
```
    Check the file name to determine if it is a taxonomy table file.
    
    Parameters:
    
    file - File to test
    
    Returns:
    
    boolean TRUE if file is a taxonomy count file
  - parentTaxaLevel
```
public static String parentTaxaLevel(String level)
```
    Get parent level name of the given level parameter.
    
    Parameters:
    
    level - Taxonomy level
    
    Returns:
    
    Parent taxonomy level
  - topTaxaLevel
```
public static String topTaxaLevel()
```
    Return the top configured taxonomy level from Config."report.taxonomyLevels"
    
    Returns:
    
    Taxonomy level
  - readTaxaTable
```
public static TaxaLevelTable readTaxaTable(File taxaTable)
                                    throws FileNotFoundException,
                                           IOException,
                                           BioLockJException
```
    Read a table of counts, formatted with samples as rows (ids in first column) and taxa as columns (ids in header).
    
    Parameters:
    
    taxaTable -
    
    Returns:
    
    Map linking sample name to map that links taxa IDs to value.
    
    Throws:
    
    FileNotFoundException
    
    IOException
    
    BioLockJException
  - writeDataToFile
```
public static void writeDataToFile(File outFile,
                                   List<String> sampleNames,
                                   List<String> taxaNames,
                                   TaxaLevelTable taxaCounts)
                            throws Exception
```
    Write transformed data to file
    
    Parameters:
    
    outFile - File to write to
    
    sampleNames - Sample names to include
    
    taxaNames - Taxa names to include
    
    taxaCounts - transformed Taxa counts
    
    Throws:
    
    Exception - if errors occur
  - writeDataToFile
```
public static void writeDataToFile(File outFile,
                                   TaxaLevelTable taxaCounts)
                            throws Exception
```
    Throws:
    
    Exception

Class TaxaUtil

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NORMALIZED

TAXA_TABLE

FILE_EXT

Method Detail

allTaxonomyLevels

bottomTaxaLevel

findUniqueTaxa

getLeafLevel

getLevelNum

getLevelTaxaCounts

getTaxaByLevel

getTaxaLevels

getTaxaLevelSpan

getTaxaName

getTaxonomyTableFile

getTaxonomyTableLevel

getUnclassifiedTaxa

initTaxaLevels

isLogNormalizedTaxaFile

isNormalizedTaxaFile

isTaxaFile

parentTaxaLevel

topTaxaLevel

readTaxaTable

writeDataToFile

writeDataToFile