Package org.snpeff.snpEffect
Class Config
- java.lang.Object
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- org.snpeff.snpEffect.Config
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Iterable<java.lang.String>
public class Config extends java.lang.Object implements java.io.Serializable, java.lang.Iterable<java.lang.String>
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
DEFAULT_CONFIG_FILE
static java.lang.String
DEFAULT_COORDINATES
static java.lang.String
DEFAULT_DATA_DIR
static java.lang.String
GENOMES_DIR
static java.lang.String
KEY_BUNDLE_SUFIX
static java.lang.String
KEY_CODON_PREFIX
static java.lang.String
KEY_CODONTABLE_SUFIX
static java.lang.String
KEY_COORDINATES
static java.lang.String
KEY_DATA_DIR
static java.lang.String
KEY_DATABASE_LOCAL
static java.lang.String
KEY_DATABASE_REPOSITORY
static java.lang.String
KEY_DBNSFP_FIELDS
static java.lang.String
KEY_GENOME_SUFIX
static java.lang.String
KEY_LOF_DELETE_PROTEIN_CODING_BASES
static java.lang.String
KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
static java.lang.String
KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
static java.lang.String
KEY_REFERENCE_SUFIX
static java.lang.String
KEY_VERSIONS_URL
static int
MAX_WARNING_COUNT
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Constructor Summary
Constructors Constructor Description Config(java.lang.String genomeVersion)
Create a config (uses DEFAULT_CONFIG_FILE)Config(java.lang.String genomeVersion, java.lang.String configFileName)
Create a configuration from 'configFileName'Config(java.lang.String genomeVersion, java.lang.String configFileName, java.lang.String dataDir, java.util.Map<java.lang.String,java.lang.String> override)
Create a configuration from 'configFileName'Config(java.lang.String genomeVersion, java.lang.String configFileName, java.lang.String dataDir, java.util.Map<java.lang.String,java.lang.String> override, boolean verbose)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.net.URL
downloadUrl(java.lang.String genomeVer)
Build the URL for downloading a database file Format : DatabaseRepository / v VERSION / snpEff_v VERSION _ genomeVersion .zip Example : http://downloads.sourceforge.net/project/snpeff/databases/v2_0_3/snpEff_v2_0_3_EF3.64.zipstatic Config
get()
java.lang.String
getBaseFileNameGenes()
Genes file path (no extension)java.lang.String
getBaseFileNameMotif()
java.lang.String
getBaseFileNameRegulation()
Regulation file (GFF format)java.lang.String
getBaseFileNameSequence()
java.lang.String
getBundleName(java.lang.String genomeVer)
Is this genome packed in a bundle?java.lang.String
getConfigFileName()
java.lang.String
getCoordinates()
java.lang.String
getDatabaseLocal(java.lang.String dbName)
Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.java.lang.String
getDatabaseLocalKey(java.lang.String dbName)
java.lang.String
getDatabaseRepository()
java.lang.String
getDatabaseRepository(java.lang.String dbName)
Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.java.net.URL
getDatabaseRepositoryUrl(java.lang.String dbName)
java.lang.String
getDbNsfpFields()
java.lang.String
getDirData()
Main data directoryjava.lang.String
getDirDataGenomeVersion()
Data dir for a specific genome version (i.e.java.lang.String
getDirMain()
Main dirjava.lang.String
getDirRegulationBed()
Directory where regulation 'BED' files aredouble
getDouble(java.lang.String propertyName, double defaultValue)
Get a property as a doublejava.util.List<java.lang.String>
getFileListGenomeFasta()
Filenames for reference sequence (fasta files)java.lang.String
getFileNameCds()
java.lang.String
getFileNameGenomeFasta()
Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that existsjava.lang.String
getFileNameProteins()
java.lang.String
getFileNameSequence()
java.lang.String
getFileNameSequence(java.lang.String chr)
java.lang.String
getFileSnpEffectPredictor()
Genome
getGenome()
Genome
getGenome(java.lang.String genomeId)
java.lang.String
getGenomeVersion()
double
getLofDeleteProteinCodingBases()
double
getLofIgnoreProteinCodingAfter()
double
getLofIgnoreProteinCodingBefore()
long
getLong(java.lang.String propertyName, long defaultValue)
Get a property as a longjava.lang.String
getName(java.lang.String genomeVersion)
java.lang.String
getReference(java.lang.String genomeVersion)
SnpEffectPredictor
getSnpEffectPredictor()
java.lang.String
getString(java.lang.String propertyName)
Get a property as a stringjava.lang.String
getString(java.lang.String propertyName, java.lang.String defaultValue)
Get a property as a stringjava.lang.String
getVersionsUrl()
boolean
isDebug()
boolean
isErrorChromoHit()
boolean
isErrorOnMissingChromo()
boolean
isExpandIub()
boolean
isHgvs()
boolean
isHgvs1LetterAA()
boolean
isHgvsOld()
boolean
isHgvsShift()
boolean
isHgvsTrId()
boolean
isOnlyRegulation()
boolean
isTreatAllAsProteinCoding()
boolean
isVerbose()
java.util.Iterator<java.lang.String>
iterator()
java.util.List<java.lang.String>
keys()
SnpEffectPredictor
loadSnpEffectPredictor()
Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)static Config
reset()
void
setDebug(boolean debug)
void
setErrorChromoHit(boolean errorChromoHit)
void
setErrorOnMissingChromo(boolean errorOnMissingChromo)
void
setExpandIub(boolean expandIub)
void
setHgvsOld(boolean hgvsDnaOld)
void
setHgvsOneLetterAA(boolean hgvsOneLetterAa)
void
setHgvsShift(boolean hgvsShift)
void
setHgvsTrId(boolean hgvsTrId)
void
setOnlyRegulation(boolean onlyRegulation)
void
setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)
void
setString(java.lang.String propertyName, java.lang.String value)
void
setTreatAllAsProteinCoding(boolean treatAllAsProteinCoding)
void
setUseHgvs(boolean useHgvs)
void
setVerbose(boolean verbose)
java.lang.String
toString()
void
warning(java.lang.String warningType, java.lang.String details)
Show a warning message and exit
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Field Detail
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DEFAULT_CONFIG_FILE
public static final java.lang.String DEFAULT_CONFIG_FILE
- See Also:
- Constant Field Values
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DEFAULT_DATA_DIR
public static final java.lang.String DEFAULT_DATA_DIR
- See Also:
- Constant Field Values
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GENOMES_DIR
public static java.lang.String GENOMES_DIR
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MAX_WARNING_COUNT
public static int MAX_WARNING_COUNT
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DEFAULT_COORDINATES
public static java.lang.String DEFAULT_COORDINATES
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KEY_BUNDLE_SUFIX
public static final java.lang.String KEY_BUNDLE_SUFIX
- See Also:
- Constant Field Values
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KEY_CODON_PREFIX
public static final java.lang.String KEY_CODON_PREFIX
- See Also:
- Constant Field Values
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KEY_CODONTABLE_SUFIX
public static final java.lang.String KEY_CODONTABLE_SUFIX
- See Also:
- Constant Field Values
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KEY_COORDINATES
public static final java.lang.String KEY_COORDINATES
- See Also:
- Constant Field Values
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KEY_DATA_DIR
public static final java.lang.String KEY_DATA_DIR
- See Also:
- Constant Field Values
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KEY_DATABASE_LOCAL
public static final java.lang.String KEY_DATABASE_LOCAL
- See Also:
- Constant Field Values
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KEY_DATABASE_REPOSITORY
public static final java.lang.String KEY_DATABASE_REPOSITORY
- See Also:
- Constant Field Values
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KEY_DBNSFP_FIELDS
public static final java.lang.String KEY_DBNSFP_FIELDS
- See Also:
- Constant Field Values
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KEY_GENOME_SUFIX
public static final java.lang.String KEY_GENOME_SUFIX
- See Also:
- Constant Field Values
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KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
public static final java.lang.String KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
- See Also:
- Constant Field Values
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KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
public static final java.lang.String KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
- See Also:
- Constant Field Values
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KEY_LOF_DELETE_PROTEIN_CODING_BASES
public static final java.lang.String KEY_LOF_DELETE_PROTEIN_CODING_BASES
- See Also:
- Constant Field Values
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KEY_REFERENCE_SUFIX
public static final java.lang.String KEY_REFERENCE_SUFIX
- See Also:
- Constant Field Values
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KEY_VERSIONS_URL
public static final java.lang.String KEY_VERSIONS_URL
- See Also:
- Constant Field Values
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Constructor Detail
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Config
public Config(java.lang.String genomeVersion)
Create a config (uses DEFAULT_CONFIG_FILE)
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Config
public Config(java.lang.String genomeVersion, java.lang.String configFileName)
Create a configuration from 'configFileName'
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Config
public Config(java.lang.String genomeVersion, java.lang.String configFileName, java.lang.String dataDir, java.util.Map<java.lang.String,java.lang.String> override)
Create a configuration from 'configFileName'
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Config
public Config(java.lang.String genomeVersion, java.lang.String configFileName, java.lang.String dataDir, java.util.Map<java.lang.String,java.lang.String> override, boolean verbose)
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Method Detail
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get
public static Config get()
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reset
public static Config reset()
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downloadUrl
public java.net.URL downloadUrl(java.lang.String genomeVer)
Build the URL for downloading a database file Format : DatabaseRepository / v VERSION / snpEff_v VERSION _ genomeVersion .zip Example : http://downloads.sourceforge.net/project/snpeff/databases/v2_0_3/snpEff_v2_0_3_EF3.64.zip
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getBaseFileNameGenes
public java.lang.String getBaseFileNameGenes()
Genes file path (no extension)
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getBaseFileNameMotif
public java.lang.String getBaseFileNameMotif()
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getBaseFileNameRegulation
public java.lang.String getBaseFileNameRegulation()
Regulation file (GFF format)
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getBaseFileNameSequence
public java.lang.String getBaseFileNameSequence()
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getBundleName
public java.lang.String getBundleName(java.lang.String genomeVer)
Is this genome packed in a bundle?
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getConfigFileName
public java.lang.String getConfigFileName()
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getCoordinates
public java.lang.String getCoordinates()
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getDatabaseLocal
public java.lang.String getDatabaseLocal(java.lang.String dbName)
Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.
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getDatabaseLocalKey
public java.lang.String getDatabaseLocalKey(java.lang.String dbName)
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getDatabaseRepository
public java.lang.String getDatabaseRepository()
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getDatabaseRepository
public java.lang.String getDatabaseRepository(java.lang.String dbName)
Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.
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getDatabaseRepositoryUrl
public java.net.URL getDatabaseRepositoryUrl(java.lang.String dbName)
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getDbNsfpFields
public java.lang.String getDbNsfpFields()
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getDirData
public java.lang.String getDirData()
Main data directory
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getDirDataGenomeVersion
public java.lang.String getDirDataGenomeVersion()
Data dir for a specific genome version (i.e. where the database is)
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getDirMain
public java.lang.String getDirMain()
Main dir
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getDirRegulationBed
public java.lang.String getDirRegulationBed()
Directory where regulation 'BED' files are
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getDouble
public double getDouble(java.lang.String propertyName, double defaultValue)
Get a property as a double
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getFileListGenomeFasta
public java.util.List<java.lang.String> getFileListGenomeFasta()
Filenames for reference sequence (fasta files)
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getFileNameCds
public java.lang.String getFileNameCds()
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getFileNameGenomeFasta
public java.lang.String getFileNameGenomeFasta()
Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that exists
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getFileNameProteins
public java.lang.String getFileNameProteins()
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getFileNameSequence
public java.lang.String getFileNameSequence()
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getFileNameSequence
public java.lang.String getFileNameSequence(java.lang.String chr)
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getFileSnpEffectPredictor
public java.lang.String getFileSnpEffectPredictor()
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getGenome
public Genome getGenome()
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getGenome
public Genome getGenome(java.lang.String genomeId)
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getGenomeVersion
public java.lang.String getGenomeVersion()
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getLofDeleteProteinCodingBases
public double getLofDeleteProteinCodingBases()
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getLofIgnoreProteinCodingAfter
public double getLofIgnoreProteinCodingAfter()
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getLofIgnoreProteinCodingBefore
public double getLofIgnoreProteinCodingBefore()
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getLong
public long getLong(java.lang.String propertyName, long defaultValue)
Get a property as a long
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getName
public java.lang.String getName(java.lang.String genomeVersion)
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getReference
public java.lang.String getReference(java.lang.String genomeVersion)
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getSnpEffectPredictor
public SnpEffectPredictor getSnpEffectPredictor()
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getString
public java.lang.String getString(java.lang.String propertyName)
Get a property as a string
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getString
public java.lang.String getString(java.lang.String propertyName, java.lang.String defaultValue)
Get a property as a string
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getVersionsUrl
public java.lang.String getVersionsUrl()
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isDebug
public boolean isDebug()
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isErrorChromoHit
public boolean isErrorChromoHit()
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isErrorOnMissingChromo
public boolean isErrorOnMissingChromo()
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isExpandIub
public boolean isExpandIub()
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isHgvs
public boolean isHgvs()
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isHgvs1LetterAA
public boolean isHgvs1LetterAA()
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isHgvsOld
public boolean isHgvsOld()
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isHgvsShift
public boolean isHgvsShift()
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isHgvsTrId
public boolean isHgvsTrId()
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isOnlyRegulation
public boolean isOnlyRegulation()
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isTreatAllAsProteinCoding
public boolean isTreatAllAsProteinCoding()
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isVerbose
public boolean isVerbose()
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iterator
public java.util.Iterator<java.lang.String> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<java.lang.String>
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keys
public java.util.List<java.lang.String> keys()
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loadSnpEffectPredictor
public SnpEffectPredictor loadSnpEffectPredictor()
Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)
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setDebug
public void setDebug(boolean debug)
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setErrorChromoHit
public void setErrorChromoHit(boolean errorChromoHit)
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setErrorOnMissingChromo
public void setErrorOnMissingChromo(boolean errorOnMissingChromo)
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setExpandIub
public void setExpandIub(boolean expandIub)
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setHgvsOld
public void setHgvsOld(boolean hgvsDnaOld)
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setHgvsOneLetterAA
public void setHgvsOneLetterAA(boolean hgvsOneLetterAa)
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setHgvsShift
public void setHgvsShift(boolean hgvsShift)
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setHgvsTrId
public void setHgvsTrId(boolean hgvsTrId)
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setOnlyRegulation
public void setOnlyRegulation(boolean onlyRegulation)
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setSnpEffectPredictor
public void setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)
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setString
public void setString(java.lang.String propertyName, java.lang.String value)
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setTreatAllAsProteinCoding
public void setTreatAllAsProteinCoding(boolean treatAllAsProteinCoding)
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setUseHgvs
public void setUseHgvs(boolean useHgvs)
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setVerbose
public void setVerbose(boolean verbose)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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warning
public void warning(java.lang.String warningType, java.lang.String details)
Show a warning message and exit
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