apollo.analysis.filter
Class AnalysisInput

java.lang.Object
  apollo.analysis.filter.AnalysisInput

public class AnalysisInput
extends java.lang.Object

This contains all of the filtering parameters to use on a set of raw output from a computational analysis of the sequence.

Field Summary

protected java.lang.String	analysis_type
protected java.lang.String	autopromote
protected int	coincidence
protected boolean	collapse
protected java.lang.String	database
protected boolean	debug
protected java.lang.String	debug_str
protected java.lang.String	display_type
protected boolean	distinctHSPs
protected boolean	filter
protected boolean	join_EST_ends
protected boolean	keep_polyApredict
protected boolean	keep_promoter
protected int	max_cover
protected int	max_exons
protected double	max_expect
protected int	max_gap
protected int	max_ratio
protected int	min_identity
protected int	min_length
protected int	min_score
static int	NO_LIMIT
protected int	offset
protected boolean	queryIsGenomic The filter panel isn't necessarily the right place to put this checkbox, but it was the easiest way to implement it.
protected boolean	remove_shadows
protected boolean	remove_twilight
protected java.lang.String	revcomp_3prime
protected java.util.Date	run_date
protected boolean	split_dups
protected boolean	split_frames
protected java.lang.String	tier
protected boolean	trim_polyA
protected boolean	use_percentage
protected int	wordsize

Constructor Summary

AnalysisInput()

Method Summary

void	autonomousHSPs(boolean dothis)
boolean	collapseResults()
void	collapseResults(boolean collapse)
boolean	debugFilter(java.lang.String this_str)
void	filterShadows(boolean remove)
java.lang.String	get3PrimeSuffix()
java.lang.String	getAnalysisType()
java.lang.String	getBaptizer()
int	getCoincidence()
java.lang.String	getDatabase()
int	getMaxAlignGap()
int	getMaxCover()
int	getMaxExons()
double	getMaxExpect()
int	getMaxRatio()
int	getMinIdentity()
int	getMinLength()
int	getMinScore()
int	getOffset()
java.util.Date	getRunDate()
java.lang.String	getTier()
int	getTwilightLower()
int	getTwilightUpper()
java.lang.String	getType()
int	getWordSize()
boolean	joinESTends()
void	joinESTends(boolean dothis)
boolean	keepPolyA()
void	keepPolyA(boolean dothis)
boolean	keepPromoter()
void	keepPromoter(boolean dothis)
boolean	limitAlignGap()
boolean	limitCoverage()
boolean	limitMaxExons()
boolean	promoteResults()
void	promoteResults(java.lang.String baptizer)
boolean	queryIsGenomic()
boolean	removeLowContent()
boolean	removeShadows()
boolean	removeTwilights()
boolean	revComp3Prime()
void	revComp3Prime(java.lang.String suffix)
boolean	runFilter()
void	runFilter(boolean filter)
void	seRtunDate(java.util.Date run_date)
void	setAnalysisType(java.lang.String type)
void	setCoincidence(int coincidence)
void	setCoincidence(java.lang.String coincidenceStr)
void	setDatabase(java.lang.String db)
void	setDebug(boolean dothis)
void	setDebug(java.lang.String debug_str)
void	setLengthUnits(boolean is_percent)
void	setMaxAlignGap(int max_gap)
void	setMaxAlignGap(java.lang.String max_gapStr)
void	setMaxCover(int max_cover)
void	setMaxCover(java.lang.String max_coverStr)
void	setMaxExons(int max_exons)
void	setMaxExons(java.lang.String max_exonsStr)
void	setMaxExpect(double max_expect)
void	setMaxExpect(java.lang.String max_expectStr)
void	setMaxRatio(int max_ratio)
void	setMaxRatio(java.lang.String maxratioStr)
void	setMinIdentity(int identity)
void	setMinIdentity(java.lang.String identityStr)
void	setMinLength(int length)
void	setMinLength(java.lang.String lengthStr)
void	setMinScore(int score)
void	setMinScore(java.lang.String scoreStr)
void	setOffset(int offset)
void	setOffset(java.lang.String offsetStr, int genomic_start)
void	setQueryIsGenomic(boolean dothis)
void	setRemoveTwilights(boolean dothis)
void	setRunDate(long processed_time)
void	setSplitFrames(boolean dothis)
void	setSplitTandems(boolean dothis)
void	setTier(java.lang.String tier)
void	setType(java.lang.String type)
void	setWordSize(int wordsize)
void	setWordSize(java.lang.String wordsizeStr)
boolean	splitFrames()
boolean	splitTandems()
boolean	trimPolyA()
void	trimPolyA(boolean dothis)
boolean	useAutonomousHSPs()
boolean	useCoincidence()
boolean	useExpect()
boolean	useIdentity()
boolean	useLength()
boolean	usePercentage()
boolean	useScore()

Methods inherited from class java.lang.Object

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

Field Detail

NO_LIMIT

public static int NO_LIMIT

tier

protected java.lang.String tier

display_type

protected java.lang.String display_type

analysis_type

protected java.lang.String analysis_type

filter

protected boolean filter

min_score

protected int min_score

min_identity

protected int min_identity

min_length

protected int min_length

wordsize

protected int wordsize

max_ratio

protected int max_ratio

max_expect

protected double max_expect

max_cover

protected int max_cover

max_exons

protected int max_exons

max_gap

protected int max_gap

coincidence

protected int coincidence

offset

protected int offset

remove_twilight

protected boolean remove_twilight

remove_shadows

protected boolean remove_shadows

distinctHSPs

protected boolean distinctHSPs

split_frames

protected boolean split_frames

split_dups

protected boolean split_dups

use_percentage

protected boolean use_percentage

join_EST_ends

protected boolean join_EST_ends

trim_polyA

protected boolean trim_polyA

revcomp_3prime

protected java.lang.String revcomp_3prime

debug_str

protected java.lang.String debug_str

debug

protected boolean debug

run_date

protected java.util.Date run_date

database

protected java.lang.String database

collapse

protected boolean collapse

autopromote

protected java.lang.String autopromote

keep_polyApredict

protected boolean keep_polyApredict

keep_promoter

protected boolean keep_promoter

queryIsGenomic

protected boolean queryIsGenomic

The filter panel isn't necessarily the right place to put this checkbox, but it was the easiest way to implement it.

Constructor Detail

AnalysisInput

public AnalysisInput()

Method Detail

setTier

public void setTier(java.lang.String tier)

getTier

public java.lang.String getTier()

setType

public void setType(java.lang.String type)

getType

public java.lang.String getType()

setAnalysisType

public void setAnalysisType(java.lang.String type)

getAnalysisType

public java.lang.String getAnalysisType()

runFilter

public boolean runFilter()

runFilter

public void runFilter(boolean filter)

setMaxRatio

public void setMaxRatio(java.lang.String maxratioStr)

setMaxRatio

public void setMaxRatio(int max_ratio)

getMaxRatio

public int getMaxRatio()

setWordSize

public void setWordSize(java.lang.String wordsizeStr)

setWordSize

public void setWordSize(int wordsize)

getWordSize

public int getWordSize()

removeLowContent

public boolean removeLowContent()

setMaxExpect

public void setMaxExpect(java.lang.String max_expectStr)

setMaxExpect

public void setMaxExpect(double max_expect)

getMaxExpect

public double getMaxExpect()

useExpect

public boolean useExpect()

setMaxCover

public void setMaxCover(java.lang.String max_coverStr)

setMaxCover

public void setMaxCover(int max_cover)

getMaxCover

public int getMaxCover()

limitCoverage

public boolean limitCoverage()

setMaxExons

public void setMaxExons(java.lang.String max_exonsStr)

setMaxExons

public void setMaxExons(int max_exons)

getMaxExons

public int getMaxExons()

limitMaxExons

public boolean limitMaxExons()

setMaxAlignGap

public void setMaxAlignGap(java.lang.String max_gapStr)

setMaxAlignGap

public void setMaxAlignGap(int max_gap)

getMaxAlignGap

public int getMaxAlignGap()

limitAlignGap

public boolean limitAlignGap()

setCoincidence

public void setCoincidence(java.lang.String coincidenceStr)

setCoincidence

public void setCoincidence(int coincidence)

getCoincidence

public int getCoincidence()

useCoincidence

public boolean useCoincidence()

removeShadows

public boolean removeShadows()

filterShadows

public void filterShadows(boolean remove)

getTwilightUpper

public int getTwilightUpper()

getTwilightLower

public int getTwilightLower()

removeTwilights

public boolean removeTwilights()

setRemoveTwilights

public void setRemoveTwilights(boolean dothis)

setMinScore

public void setMinScore(java.lang.String scoreStr)

setMinScore

public void setMinScore(int score)

getMinScore

public int getMinScore()

useScore

public boolean useScore()

setMinIdentity

public void setMinIdentity(java.lang.String identityStr)

setMinIdentity

public void setMinIdentity(int identity)

getMinIdentity

public int getMinIdentity()

useIdentity

public boolean useIdentity()

setMinLength

public void setMinLength(java.lang.String lengthStr)

setMinLength

public void setMinLength(int length)

getMinLength

public int getMinLength()

useLength

public boolean useLength()

setLengthUnits

public void setLengthUnits(boolean is_percent)

usePercentage

public boolean usePercentage()

autonomousHSPs

public void autonomousHSPs(boolean dothis)

useAutonomousHSPs

public boolean useAutonomousHSPs()

setSplitTandems

public void setSplitTandems(boolean dothis)

splitTandems

public boolean splitTandems()

revComp3Prime

public void revComp3Prime(java.lang.String suffix)

revComp3Prime

public boolean revComp3Prime()

get3PrimeSuffix

public java.lang.String get3PrimeSuffix()

joinESTends

public void joinESTends(boolean dothis)

joinESTends

public boolean joinESTends()

trimPolyA

public void trimPolyA(boolean dothis)

trimPolyA

public boolean trimPolyA()

keepPolyA

public void keepPolyA(boolean dothis)

keepPolyA

public boolean keepPolyA()

keepPromoter

public void keepPromoter(boolean dothis)

keepPromoter

public boolean keepPromoter()

setDebug

public void setDebug(java.lang.String debug_str)

setDebug

public void setDebug(boolean dothis)

debugFilter

public boolean debugFilter(java.lang.String this_str)

setSplitFrames

public void setSplitFrames(boolean dothis)

splitFrames

public boolean splitFrames()

setQueryIsGenomic

public void setQueryIsGenomic(boolean dothis)

queryIsGenomic

public boolean queryIsGenomic()

setOffset

public void setOffset(java.lang.String offsetStr,
                      int genomic_start)

setOffset

public void setOffset(int offset)

getOffset

public int getOffset()

getRunDate

public java.util.Date getRunDate()

setRunDate

public void setRunDate(long processed_time)

seRtunDate

public void seRtunDate(java.util.Date run_date)

collapseResults

public void collapseResults(boolean collapse)

collapseResults

public boolean collapseResults()

promoteResults

public void promoteResults(java.lang.String baptizer)

promoteResults

public boolean promoteResults()

getBaptizer

public java.lang.String getBaptizer()

setDatabase

public void setDatabase(java.lang.String db)

getDatabase

public java.lang.String getDatabase()