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 intstatic final intFields inherited from class Features
COMPLEMENT, debug, JOIN, MAX_LEN_TO_SHOW, ORDER -
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 booleanisNewFeature(String line) Has this line a new feature?protected voidparseFieldLine(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)voidreadFile()Load and parse the contents of a data fileMethods inherited from class Features
getAccession, getDate, getDefinition, getDivision, getFeatures, getKeywords, getLocusName, getMoleculeType, getOrganism, getReferences, getSequence, getSequenceLength, getShape, getSource, getVersion, isEmpty, iterator, open, parseFeatures, toStringMethods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface 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
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Method Details
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isNewFeature
Has this line a new feature?- Specified by:
isNewFeaturein 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
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