Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdProtein

java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdProtein

All Implemented Interfaces:

CommandLine

public class SnpEffCmdProtein
extends SnpEff

Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.

Author:

pcingola

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.SnpEff

SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat

Field Summary

Fields

Modifier and Type	Field	Description
static double	MAX_ERROR_RATE
static boolean	onlyOneError

Fields inherited from class org.snpeff.SnpEff

args, BUILD, BUILD_DATE, canonical, canonicalFile, command, COMMAND_LINE_WIDTH, config, configOverride, customIntervalFiles, dataDir, debug, DEFAULT_COMMAND, download, expandIub, filterIntervalFiles, genome, genomeVer, help, hgvs, hgvsForce, hgvsOld, hgvsOneLetterAa, hgvsShift, hgvsTrId, interaction, log, maxTranscriptSupportLevel, motif, multiThreaded, nextProt, nextProtKeepAllTrs, noGenome, numWorkers, onlyProtein, onlyRegulation, onlyTranscriptsFile, output, quiet, regulationTracks, REVISION, saveOutput, shiftArgs, snpEffCmd, SOFTWARE_NAME, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, spliceSiteSize, strict, suppressOutput, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT

Constructor Summary

Constructors

Constructor	Description
SnpEffCmdProtein()
SnpEffCmdProtein(java.lang.String genomeVer, java.lang.String configFile, java.lang.String proteinFile)
SnpEffCmdProtein(Config config)
SnpEffCmdProtein(Config config, java.lang.String proteinFile)

Method Summary

Modifier and Type	Method	Description
static int	diffCount(java.lang.String s1, java.lang.String s2)	Count number of differences between strings
static java.lang.String	diffStr(java.lang.String s1, java.lang.String s2)	Show difference between two strings
java.util.HashMap<java.lang.String,SmithWaterman>	getAlignmentByTrId()
int	getTotalErrors()
int	getTotalNotFound()
int	getTotalOk()
int	getTotalWarnings()
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run command
void	setCheckNumOk(boolean checkNumOk)
void	setProteinByTrId(java.util.Map<java.lang.String,java.lang.String> proteinByTrId)
void	setStoreAlignments(boolean storeAlignments)
void	usage(java.lang.String message)	Show usage and exit

Methods inherited from class org.snpeff.SnpEff

addRegulationTrack, canonical, cmd, commandLineStr, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, main, reportValues, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

onlyOneError

public static boolean onlyOneError

MAX_ERROR_RATE

public static double MAX_ERROR_RATE

Constructor Detail

SnpEffCmdProtein

public SnpEffCmdProtein()

SnpEffCmdProtein

public SnpEffCmdProtein(Config config)

SnpEffCmdProtein

public SnpEffCmdProtein(Config config,
                        java.lang.String proteinFile)

SnpEffCmdProtein

public SnpEffCmdProtein(java.lang.String genomeVer,
                        java.lang.String configFile,
                        java.lang.String proteinFile)

Method Detail

diffCount

public static int diffCount(java.lang.String s1,
                            java.lang.String s2)

Count number of differences between strings

diffStr

public static java.lang.String diffStr(java.lang.String s1,
                                       java.lang.String s2)

Show difference between two strings

getAlignmentByTrId

public java.util.HashMap<java.lang.String,SmithWaterman> getAlignmentByTrId()

getTotalErrors

public int getTotalErrors()

getTotalNotFound

public int getTotalNotFound()

getTotalOk

public int getTotalOk()

getTotalWarnings

public int getTotalWarnings()

parseArgs

public void parseArgs(java.lang.String[] args)

Parse command line arguments

Specified by:

parseArgs in interface CommandLine

Overrides:

parseArgs in class SnpEff

run

public boolean run()

Run command

Specified by:

run in interface CommandLine

Overrides:

run in class SnpEff

setCheckNumOk

public void setCheckNumOk(boolean checkNumOk)

setProteinByTrId

public void setProteinByTrId(java.util.Map<java.lang.String,java.lang.String> proteinByTrId)

setStoreAlignments

public void setStoreAlignments(boolean storeAlignments)

usage

public void usage(java.lang.String message)

Show usage and exit

Specified by:

usage in interface CommandLine

Overrides:

usage in class SnpEff