Package org.snpeff.binseq
Class GenomicSequences
- java.lang.Object
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- org.snpeff.binseq.GenomicSequences
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Iterable<MarkerSeq>
public class GenomicSequences extends java.lang.Object implements java.lang.Iterable<MarkerSeq>, java.io.Serializable
This class stores all "relevant" sequences in a genome This class is able to: i) Add all regions of interest ii) Store genomic sequences for those regions of interest iii) Retrieve genomic sequences by interval- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static int
CHR_LEN_SEPARATE_FILE
static int
MAX_ITERATIONS
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Constructor Summary
Constructors Constructor Description GenomicSequences(Genome genome)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addChromosomeSequence(java.lang.String chr, java.lang.String chrSeq)
Create a sequence for the whole chromsome (mostly used in test cases)int
addGeneSequences(java.lang.String chr, java.lang.String chrSeq)
Add sequences for each gene in the genomevoid
build()
Build interval forestvoid
clear()
boolean
hasChromosome(java.lang.String chr)
Do we have sequence information for this chromosome?boolean
isEmpty()
java.util.Iterator<MarkerSeq>
iterator()
boolean
load()
Load sequences for all 'small chromosomes" (from "sequence.bin" file)boolean
load(java.lang.String chr)
Load sequences for a single chromosome (from "sequence.chr.bin" file)boolean
loadOrCreateFromGenome(java.lang.String chr)
Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons.MarkerSeq
queryMarkerSequence(Marker marker)
Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form databasejava.lang.String
querySequence(Marker marker)
Get sequence for a markervoid
reset()
void
save(Config config)
Save genomic sequence into separate files (per chromosome)void
setDisableLoad(boolean disableLoad)
void
setVerbose(boolean verbose)
java.lang.String
toString()
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Field Detail
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MAX_ITERATIONS
public static final int MAX_ITERATIONS
- See Also:
- Constant Field Values
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CHR_LEN_SEPARATE_FILE
public static final int CHR_LEN_SEPARATE_FILE
- See Also:
- Constant Field Values
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Constructor Detail
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GenomicSequences
public GenomicSequences(Genome genome)
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Method Detail
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addChromosomeSequence
public void addChromosomeSequence(java.lang.String chr, java.lang.String chrSeq)
Create a sequence for the whole chromsome (mostly used in test cases)
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addGeneSequences
public int addGeneSequences(java.lang.String chr, java.lang.String chrSeq)
Add sequences for each gene in the genome
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build
public void build()
Build interval forest
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clear
public void clear()
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hasChromosome
public boolean hasChromosome(java.lang.String chr)
Do we have sequence information for this chromosome?
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isEmpty
public boolean isEmpty()
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iterator
public java.util.Iterator<MarkerSeq> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<MarkerSeq>
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load
public boolean load()
Load sequences for all 'small chromosomes" (from "sequence.bin" file)
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load
public boolean load(java.lang.String chr)
Load sequences for a single chromosome (from "sequence.chr.bin" file)
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loadOrCreateFromGenome
public boolean loadOrCreateFromGenome(java.lang.String chr)
Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons.
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queryMarkerSequence
public MarkerSeq queryMarkerSequence(Marker marker)
Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database- Returns:
- A markerSeq containing 'marker' or null if nothing is found
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querySequence
public java.lang.String querySequence(Marker marker)
Get sequence for a marker
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reset
public void reset()
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save
public void save(Config config)
Save genomic sequence into separate files (per chromosome)
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setDisableLoad
public void setDisableLoad(boolean disableLoad)
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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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