Package org.snpeff.genBank
Class Embl
java.lang.Object
org.snpeff.genBank.Features
org.snpeff.genBank.Embl
A class representing the same data as an EMBL file
References: http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
- Author:
- pablocingolani
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
Fields inherited from class org.snpeff.genBank.Features
COMPLEMENT, debug, JOIN, MAX_LEN_TO_SHOW, ORDER
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Constructor Summary
ConstructorsConstructorDescriptionCreate a Genbank record from a 'GB' fileEmbl
(LineFileIterator lineFileIterator) Create a Genbank record from a 'GB' file -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
isNewFeature
(String line) Has this line a new feature?protected void
parseFieldLine
(String fkey, 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 fileMethods 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
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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FEATURE_NAME_LEN
public static final int FEATURE_NAME_LEN- See Also:
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FEATURE_KEY_LEN
public static final int FEATURE_KEY_LEN- See Also:
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Constructor Details
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Embl
Create a Genbank record from a 'GB' file- Parameters:
fileName
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Embl
Create a Genbank record from a 'GB' file- Parameters:
fileName
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Method Details
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isNewFeature
Has this line a new feature?- Specified by:
isNewFeature
in classFeatures
- Parameters:
line
-- Returns:
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parseFieldLine
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) -
readFile
public void readFile()Load and parse the contents of a data file
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