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`	`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 String`	`buildUnclassifiedTaxa(String taxa)` Build the name of an unclassified taxa using the given "taxa" parameter. Returns a name like Unclassified (taxa name) Taxa
`static TreeSet<String>`	`findUniqueTaxa(TreeSet<String> otus, String level)` Extract taxonomy names at the given level from all given OTUs.
`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 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 String`	`topTaxaLevel()` Return the top configured taxonomy level from `Config`."report.taxonomyLevels"

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
- 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
  - buildUnclassifiedTaxa
```
public static String buildUnclassifiedTaxa(String taxa)
```
    Build the name of an unclassified taxa using the given "taxa" parameter.
    Returns a name like Unclassified (taxa name) Taxa
    
    Parameters:
    
    taxa - Taxa name
    
    Returns:
    
    Unclassified Taxa name
  - 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
  - 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 Exception
```
    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:
    
    Exception - if errors occur
  - 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
  - initTaxaLevels
```
public static List<String> initTaxaLevels()
                                   throws ConfigNotFoundException,
                                          ConfigFormatException
```
    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
  - 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

Class TaxaUtil

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NORMALIZED

TAXA_TABLE

Method Detail

allTaxonomyLevels

bottomTaxaLevel

buildUnclassifiedTaxa

findUniqueTaxa

getLevelTaxaCounts

getTaxaByLevel

getTaxaLevels

getTaxaLevelSpan

getTaxaName

getTaxonomyTableFile

getTaxonomyTableLevel

initTaxaLevels

isLogNormalizedTaxaFile

isNormalizedTaxaFile

isTaxaFile

parentTaxaLevel

topTaxaLevel