Package org.snpeff.genBank
Class Embl
- java.lang.Object
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- org.snpeff.genBank.Features
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- org.snpeff.genBank.Embl
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Field Summary
Fields Modifier and Type Field Description static int
FEATURE_KEY_LEN
static int
FEATURE_NAME_LEN
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Fields inherited from class org.snpeff.genBank.Features
COMPLEMENT, debug, JOIN, MAX_LEN_TO_SHOW, ORDER
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Constructor Summary
Constructors Constructor Description Embl(java.lang.String fileName)
Create a Genbank record from a 'GB' fileEmbl(LineFileIterator lineFileIterator)
Create a Genbank record from a 'GB' file
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
isNewFeature(java.lang.String line)
Has this line a new feature?protected void
parseFieldLine(java.lang.String fkey, java.lang.String valueOri, int fieldLineNum)
Parse a feature line Line types: ID - identification (begins each entry; 1 per entry) AC - accession number (>=1 per entry) PR - project identifier (0 or 1 per entry) DT - date (2 per entry) DE - description (>=1 per entry) KW - keyword (>=1 per entry) OS - organism species (>=1 per entry) OC - organism classification (>=1 per entry) OG - organelle (0 or 1 per entry) RN - reference number (>=1 per entry) RC - reference comment (>=0 per entry) RP - reference positions (>=1 per entry) RX - reference cross-reference (>=0 per entry) RG - reference group (>=0 per entry) RA - reference author(s) (>=0 per entry) RT - reference title (>=1 per entry) RL - reference location (>=1 per entry) DR - database cross-reference (>=0 per entry) CC - comments or notes (>=0 per entry) AH - assembly header (0 or 1 per entry) AS - assembly information (0 or >=1 per entry) FH - feature table header (2 per entry) FT - feature table data (>=2 per entry) XX - spacer line (many per entry) SQ - sequence header (1 per entry) CO - contig/construct line (0 or >=1 per entry) bb - (blanks) sequence data (>=1 per entry) // - termination line (ends each entry; 1 per entry)void
readFile()
Load and parse the contents of a data file-
Methods inherited from class org.snpeff.genBank.Features
getAccession, getDate, getDefinition, getDivision, getFeatures, getKeywords, getLocusName, getMoleculeType, getOrganism, getReferences, getSequence, getSequenceLength, getShape, getSource, getVersion, isEmpty, iterator, open, parseFeatures, toString
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Field Detail
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FEATURE_NAME_LEN
public static final int FEATURE_NAME_LEN
- See Also:
- Constant Field Values
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FEATURE_KEY_LEN
public static final int FEATURE_KEY_LEN
- See Also:
- Constant Field Values
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Constructor Detail
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Embl
public Embl(LineFileIterator lineFileIterator)
Create a Genbank record from a 'GB' file- Parameters:
fileName
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Embl
public Embl(java.lang.String fileName)
Create a Genbank record from a 'GB' file- Parameters:
fileName
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Method Detail
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isNewFeature
protected boolean isNewFeature(java.lang.String line)
Has this line a new feature?- Specified by:
isNewFeature
in classFeatures
- Parameters:
line
-- Returns:
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parseFieldLine
protected void parseFieldLine(java.lang.String fkey, java.lang.String valueOri, int fieldLineNum)
Parse a feature line Line types: ID - identification (begins each entry; 1 per entry) AC - accession number (>=1 per entry) PR - project identifier (0 or 1 per entry) DT - date (2 per entry) DE - description (>=1 per entry) KW - keyword (>=1 per entry) OS - organism species (>=1 per entry) OC - organism classification (>=1 per entry) OG - organelle (0 or 1 per entry) RN - reference number (>=1 per entry) RC - reference comment (>=0 per entry) RP - reference positions (>=1 per entry) RX - reference cross-reference (>=0 per entry) RG - reference group (>=0 per entry) RA - reference author(s) (>=0 per entry) RT - reference title (>=1 per entry) RL - reference location (>=1 per entry) DR - database cross-reference (>=0 per entry) CC - comments or notes (>=0 per entry) AH - assembly header (0 or 1 per entry) AS - assembly information (0 or >=1 per entry) FH - feature table header (2 per entry) FT - feature table data (>=2 per entry) XX - spacer line (many per entry) SQ - sequence header (1 per entry) CO - contig/construct line (0 or >=1 per entry) bb - (blanks) sequence data (>=1 per entry) // - termination line (ends each entry; 1 per entry)
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