Class Config

  • 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
    • Field Detail

      • DEFAULT_CONFIG_FILE

        public static final java.lang.String DEFAULT_CONFIG_FILE
        See Also:
        Constant Field Values
      • DEFAULT_DATA_DIR

        public static final java.lang.String DEFAULT_DATA_DIR
        See Also:
        Constant Field Values
      • GENOMES_DIR

        public static java.lang.String GENOMES_DIR
      • MAX_WARNING_COUNT

        public static int MAX_WARNING_COUNT
      • DEFAULT_COORDINATES

        public static java.lang.String DEFAULT_COORDINATES
      • KEY_BUNDLE_SUFIX

        public static final java.lang.String KEY_BUNDLE_SUFIX
        See Also:
        Constant Field Values
      • KEY_CODON_PREFIX

        public static final java.lang.String KEY_CODON_PREFIX
        See Also:
        Constant Field Values
      • KEY_CODONTABLE_SUFIX

        public static final java.lang.String KEY_CODONTABLE_SUFIX
        See Also:
        Constant Field Values
      • KEY_DATABASE_LOCAL

        public static final java.lang.String KEY_DATABASE_LOCAL
        See Also:
        Constant Field Values
      • KEY_DATABASE_REPOSITORY

        public static final java.lang.String KEY_DATABASE_REPOSITORY
        See Also:
        Constant Field Values
      • KEY_DBNSFP_FIELDS

        public static final java.lang.String KEY_DBNSFP_FIELDS
        See Also:
        Constant Field Values
      • KEY_GENOME_SUFIX

        public static final java.lang.String KEY_GENOME_SUFIX
        See Also:
        Constant Field Values
      • KEY_LOF_IGNORE_PROTEIN_CODING_AFTER

        public static final java.lang.String KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
        See Also:
        Constant Field Values
      • KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE

        public static final java.lang.String KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
        See Also:
        Constant Field Values
      • KEY_LOF_DELETE_PROTEIN_CODING_BASES

        public static final java.lang.String KEY_LOF_DELETE_PROTEIN_CODING_BASES
        See Also:
        Constant Field Values
      • KEY_REFERENCE_SUFIX

        public static final java.lang.String KEY_REFERENCE_SUFIX
        See Also:
        Constant Field Values
      • KEY_VERSIONS_URL

        public static final java.lang.String KEY_VERSIONS_URL
        See Also:
        Constant Field Values
    • Constructor Detail

      • Config

        public Config​(java.lang.String genomeVersion)
        Create a config (uses DEFAULT_CONFIG_FILE)
      • Config

        public Config​(java.lang.String genomeVersion,
                      java.lang.String configFileName)
        Create a configuration from 'configFileName'
      • 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'
      • 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)
    • Method Detail

      • get

        public static Config get()
      • reset

        public static Config reset()
      • 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
      • getBaseFileNameGenes

        public java.lang.String getBaseFileNameGenes()
        Genes file path (no extension)
      • getBaseFileNameMotif

        public java.lang.String getBaseFileNameMotif()
      • getBaseFileNameRegulation

        public java.lang.String getBaseFileNameRegulation()
        Regulation file (GFF format)
      • getBaseFileNameSequence

        public java.lang.String getBaseFileNameSequence()
      • getBundleName

        public java.lang.String getBundleName​(java.lang.String genomeVer)
        Is this genome packed in a bundle?
      • getConfigFileName

        public java.lang.String getConfigFileName()
      • getCoordinates

        public java.lang.String getCoordinates()
      • getDatabaseLocal

        public java.lang.String getDatabaseLocal​(java.lang.String dbName)
        Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.
      • getDatabaseLocalKey

        public java.lang.String getDatabaseLocalKey​(java.lang.String dbName)
      • getDatabaseRepository

        public java.lang.String getDatabaseRepository()
      • getDatabaseRepository

        public java.lang.String getDatabaseRepository​(java.lang.String dbName)
        Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.
      • getDatabaseRepositoryUrl

        public java.net.URL getDatabaseRepositoryUrl​(java.lang.String dbName)
      • getDbNsfpFields

        public java.lang.String getDbNsfpFields()
      • getDirData

        public java.lang.String getDirData()
        Main data directory
      • getDirDataGenomeVersion

        public java.lang.String getDirDataGenomeVersion()
        Data dir for a specific genome version (i.e. where the database is)
      • getDirMain

        public java.lang.String getDirMain()
        Main dir
      • getDirRegulationBed

        public java.lang.String getDirRegulationBed()
        Directory where regulation 'BED' files are
      • getDouble

        public double getDouble​(java.lang.String propertyName,
                                double defaultValue)
        Get a property as a double
      • getFileListGenomeFasta

        public java.util.List<java.lang.String> getFileListGenomeFasta()
        Filenames for reference sequence (fasta files)
      • getFileNameCds

        public java.lang.String getFileNameCds()
      • 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
      • getFileNameProteins

        public java.lang.String getFileNameProteins()
      • getFileNameSequence

        public java.lang.String getFileNameSequence()
      • getFileNameSequence

        public java.lang.String getFileNameSequence​(java.lang.String chr)
      • getFileSnpEffectPredictor

        public java.lang.String getFileSnpEffectPredictor()
      • getGenome

        public Genome getGenome()
      • getGenome

        public Genome getGenome​(java.lang.String genomeId)
      • getGenomeVersion

        public java.lang.String getGenomeVersion()
      • getLofDeleteProteinCodingBases

        public double getLofDeleteProteinCodingBases()
      • getLofIgnoreProteinCodingAfter

        public double getLofIgnoreProteinCodingAfter()
      • getLofIgnoreProteinCodingBefore

        public double getLofIgnoreProteinCodingBefore()
      • getLong

        public long getLong​(java.lang.String propertyName,
                            long defaultValue)
        Get a property as a long
      • getName

        public java.lang.String getName​(java.lang.String genomeVersion)
      • getReference

        public java.lang.String getReference​(java.lang.String genomeVersion)
      • getString

        public java.lang.String getString​(java.lang.String propertyName)
        Get a property as a string
      • getString

        public java.lang.String getString​(java.lang.String propertyName,
                                          java.lang.String defaultValue)
        Get a property as a string
      • getVersionsUrl

        public java.lang.String getVersionsUrl()
      • isDebug

        public boolean isDebug()
      • isErrorChromoHit

        public boolean isErrorChromoHit()
      • isErrorOnMissingChromo

        public boolean isErrorOnMissingChromo()
      • isExpandIub

        public boolean isExpandIub()
      • isHgvs

        public boolean isHgvs()
      • isHgvs1LetterAA

        public boolean isHgvs1LetterAA()
      • isHgvsOld

        public boolean isHgvsOld()
      • isHgvsShift

        public boolean isHgvsShift()
      • isHgvsTrId

        public boolean isHgvsTrId()
      • isOnlyRegulation

        public boolean isOnlyRegulation()
      • isTreatAllAsProteinCoding

        public boolean isTreatAllAsProteinCoding()
      • isVerbose

        public boolean isVerbose()
      • iterator

        public java.util.Iterator<java.lang.String> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<java.lang.String>
      • keys

        public java.util.List<java.lang.String> keys()
      • loadSnpEffectPredictor

        public SnpEffectPredictor loadSnpEffectPredictor()
        Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)
      • setDebug

        public void setDebug​(boolean debug)
      • setErrorChromoHit

        public void setErrorChromoHit​(boolean errorChromoHit)
      • setErrorOnMissingChromo

        public void setErrorOnMissingChromo​(boolean errorOnMissingChromo)
      • setExpandIub

        public void setExpandIub​(boolean expandIub)
      • setHgvsOld

        public void setHgvsOld​(boolean hgvsDnaOld)
      • setHgvsOneLetterAA

        public void setHgvsOneLetterAA​(boolean hgvsOneLetterAa)
      • setHgvsShift

        public void setHgvsShift​(boolean hgvsShift)
      • setHgvsTrId

        public void setHgvsTrId​(boolean hgvsTrId)
      • setOnlyRegulation

        public void setOnlyRegulation​(boolean onlyRegulation)
      • setSnpEffectPredictor

        public void setSnpEffectPredictor​(SnpEffectPredictor snpEffectPredictor)
      • setString

        public void setString​(java.lang.String propertyName,
                              java.lang.String value)
      • setTreatAllAsProteinCoding

        public void setTreatAllAsProteinCoding​(boolean treatAllAsProteinCoding)
      • setUseHgvs

        public void setUseHgvs​(boolean useHgvs)
      • setVerbose

        public void setVerbose​(boolean verbose)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • warning

        public void warning​(java.lang.String warningType,
                            java.lang.String details)
        Show a warning message and exit