java.lang.Object
- org.snpeff.snpEffect.factory.SnpEffPredictorFactory

Direct Known Subclasses:

SnpEffPredictorFactoryFeatures, SnpEffPredictorFactoryGenesFile, SnpEffPredictorFactoryGff, SnpEffPredictorFactoryKnownGene, SnpEffPredictorFactoryRefSeq
```
public abstract class SnpEffPredictorFactory
extends java.lang.Object
```
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration

Author:

pcingola

Field Summary

Fields
Modifier and Type Field Description

static int MARK

static int MIN_TOTAL_FRAME_COUNT

Constructor Summary

Constructors
Constructor Description

SnpEffPredictorFactory(Config config, int inOffset)

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`add(Cds cds)`
`protected void`	`add(Chromosome chromo)`
`protected Exon`	`add(Exon exon)`	Add an exon
`protected void`	`add(Gene gene)`	Add a Gene
`protected void`	`add(Marker marker)`	Add a generic Marker
`protected void`	`add(Transcript tr)`	Add a transcript
`protected void`	`addMarker(Marker marker, boolean unique)`	Add a marker to the collection
`protected void`	`addSequences(java.lang.String chr, java.lang.String chrSeq)`	Add genomic reference sequences
`protected void`	`adjustChromosomes()`	Adjust chromosome length using gene information This is used when the sequence is not available (which makes sense on test-cases and debugging only)
`protected void`	`adjustTranscripts()`	Adjust transcripts: recalculate start, end, strand, etc.
`protected void`	`beforeExonSequences()`	Perform some actions before reading sequences
`protected void`	`codingFromCds()`	Only coding transcripts have CDS: Make sure that transcripts having CDS are protein coding It might not be always "precise" though: $ grep CDS genes.gtf \| cut -f 2 \| ~/snpEff/scripts/uniqCount.pl 113 IG_C_gene 64 IG_D_gene 24 IG_J_gene 366 IG_V_gene 21 TR_C_gene 3 TR_D_gene 82 TR_J_gene 296 TR_V_gene 461 non_stop_decay 63322 nonsense_mediated_decay 905 polymorphic_pseudogene 34 processed_transcript 1340112 protein_coding
`protected void`	`collapseZeroLenIntrons()`	Collapse exons having zero size introns between them
`abstract SnpEffectPredictor`	`create()`
`protected void`	`createRandSequences()`	Create random sequences for exons Note: This is only used for test cases!
`protected void`	`deleteRedundant()`	Consolidate transcripts: If two exons are one right next to the other, join them E.g.
`protected void`	`exonsFromCds()`	Create exons from CDS info
`protected void`	`exonsFromCds(Transcript tr)`	Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this process
`protected Gene`	`findGene(java.lang.String id)`
`protected Gene`	`findGene(java.lang.String geneId, java.lang.String id)`
`protected Marker`	`findMarker(java.lang.String id)`
`protected Transcript`	`findTranscript(java.lang.String id)`
`protected Transcript`	`findTranscript(java.lang.String trId, java.lang.String id)`
`protected Chromosome`	`getOrCreateChromosome(java.lang.String chromoName)`	Get a chromosome.
`java.util.Map<java.lang.String,java.lang.String>`	`getProteinByTrId()`
`protected int`	`parsePosition(java.lang.String posStr)`	Parse a string as a 'position'.
`protected void`	`readExonSequences()`	Read exon sequences from a FASTA file
`protected void`	`replaceTranscript(Transcript trOld, Transcript trNew)`
`void`	`setCircularCorrectLargeGap(boolean circularCorrectLargeGap)`
`void`	`setCreateRandSequences(boolean createRandSequences)`
`void`	`setDebug(boolean debug)`
`void`	`setFastaFile(java.lang.String fastaFile)`
`void`	`setFileName(java.lang.String fileName)`
`void`	`setRandom(java.util.Random random)`
`void`	`setReadSequences(boolean readSequences)`	Read sequences? Note: This is only used for debugging and testing
`void`	`setStoreSequences(boolean storeSequences)`
`void`	`setVerbose(boolean verbose)`
`protected java.lang.String`	`showChromoNamesDifferences()`	Shw differences in chromosome names

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MARK
```
public static final int MARK
```
    See Also:
    
    Constant Field Values
  - MIN_TOTAL_FRAME_COUNT
```
public static int MIN_TOTAL_FRAME_COUNT
```
- Constructor Detail
  - SnpEffPredictorFactory
```
public SnpEffPredictorFactory(Config config,
                              int inOffset)
```
- Method Detail
  - add
```
protected void add(Cds cds)
```
  - add
```
protected void add(Chromosome chromo)
```
  - add
```
protected Exon add(Exon exon)
```
    Add an exon
    
    Parameters:
    
    exon -
    
    Returns:
    
    exon added. Note: If the exon exists with the same ID, return old exon. If exon exists with same ID and same coordiates, add a new exon with different ID.
  - add
```
protected void add(Gene gene)
```
    Add a Gene
  - add
```
protected void add(Marker marker)
```
    Add a generic Marker
  - add
```
protected void add(Transcript tr)
```
    Add a transcript
  - addMarker
```
protected void addMarker(Marker marker,
                         boolean unique)
```
    Add a marker to the collection
  - addSequences
```
protected void addSequences(java.lang.String chr,
                            java.lang.String chrSeq)
```
    Add genomic reference sequences
  - adjustChromosomes
```
protected void adjustChromosomes()
```
    Adjust chromosome length using gene information This is used when the sequence is not available (which makes sense on test-cases and debugging only)
  - adjustTranscripts
```
protected void adjustTranscripts()
```
    Adjust transcripts: recalculate start, end, strand, etc.
  - beforeExonSequences
```
protected void beforeExonSequences()
```
    Perform some actions before reading sequences
  - codingFromCds
```
protected void codingFromCds()
```
    Only coding transcripts have CDS: Make sure that transcripts having CDS are protein coding It might not be always "precise" though: $ grep CDS genes.gtf | cut -f 2 | ~/snpEff/scripts/uniqCount.pl 113 IG_C_gene 64 IG_D_gene 24 IG_J_gene 366 IG_V_gene 21 TR_C_gene 3 TR_D_gene 82 TR_J_gene 296 TR_V_gene 461 non_stop_decay 63322 nonsense_mediated_decay 905 polymorphic_pseudogene 34 processed_transcript 1340112 protein_coding
  - collapseZeroLenIntrons
```
protected void collapseZeroLenIntrons()
```
    Collapse exons having zero size introns between them
  - create
```
public abstract SnpEffectPredictor create()
```
  - createRandSequences
```
protected void createRandSequences()
```
    Create random sequences for exons Note: This is only used for test cases!
  - deleteRedundant
```
protected void deleteRedundant()
```
    Consolidate transcripts: If two exons are one right next to the other, join them E.g. exon1:1234-2345, exon2:2346-2400 => exon:1234-2400 This happens mostly in GTF files, where the stop-codon is specified separated from the exon info.
  - exonsFromCds
```
protected void exonsFromCds()
```
    Create exons from CDS info
  - exonsFromCds
```
protected void exonsFromCds(Transcript tr)
```
    Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this process
    
    Parameters:
    
    tr - : Transcript with CDS info, but no exons
  - findGene
```
protected Gene findGene(java.lang.String id)
```
  - findGene
```
protected Gene findGene(java.lang.String geneId,
                        java.lang.String id)
```
  - findMarker
```
protected Marker findMarker(java.lang.String id)
```
  - findTranscript
```
protected Transcript findTranscript(java.lang.String id)
```
  - findTranscript
```
protected Transcript findTranscript(java.lang.String trId,
                                    java.lang.String id)
```
  - getOrCreateChromosome
```
protected Chromosome getOrCreateChromosome(java.lang.String chromoName)
```
    Get a chromosome. If it doesn't exist, create it
  - getProteinByTrId
```
public java.util.Map<java.lang.String,java.lang.String> getProteinByTrId()
```
  - parsePosition
```
protected int parsePosition(java.lang.String posStr)
```
    Parse a string as a 'position'. Note: It subtracts 'inOffset' so that all coordinates are zero-based
  - readExonSequences
```
protected void readExonSequences()
```
    Read exon sequences from a FASTA file
  - replaceTranscript
```
protected void replaceTranscript(Transcript trOld,
                                 Transcript trNew)
```
  - setCircularCorrectLargeGap
```
public void setCircularCorrectLargeGap(boolean circularCorrectLargeGap)
```
  - setCreateRandSequences
```
public void setCreateRandSequences(boolean createRandSequences)
```
  - setDebug
```
public void setDebug(boolean debug)
```
  - setFastaFile
```
public void setFastaFile(java.lang.String fastaFile)
```
  - setFileName
```
public void setFileName(java.lang.String fileName)
```
  - setRandom
```
public void setRandom(java.util.Random random)
```
  - setReadSequences
```
public void setReadSequences(boolean readSequences)
```
    Read sequences? Note: This is only used for debugging and testing
  - setStoreSequences
```
public void setStoreSequences(boolean storeSequences)
```
  - setVerbose
```
public void setVerbose(boolean verbose)
```
  - showChromoNamesDifferences
```
protected java.lang.String showChromoNamesDifferences()
```
    Shw differences in chromosome names

Class SnpEffPredictorFactory

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MARK

MIN_TOTAL_FRAME_COUNT

Constructor Detail

SnpEffPredictorFactory

Method Detail

add

add

add

add

add

add

addMarker

addSequences

adjustChromosomes

adjustTranscripts

beforeExonSequences

codingFromCds

collapseZeroLenIntrons

create

createRandSequences

deleteRedundant

exonsFromCds

exonsFromCds

findGene

findGene

findMarker

findTranscript

findTranscript

getOrCreateChromosome

getProteinByTrId

parsePosition

readExonSequences

replaceTranscript

setCircularCorrectLargeGap

setCreateRandSequences

setDebug

setFastaFile

setFileName

setRandom

setReadSequences

setStoreSequences

setVerbose

showChromoNamesDifferences