Package ubic.gemma.core.analysis.sequence

Class ProbeMapperConfig

  • public class ProbeMapperConfig
extends Object
    Holds parameters for how mapping should be done.
    Author:
    paul

    • Field Detail

      • DEFAULT_TRIM_NONCANONICAL_CHROMOSOMES

        public static final boolean DEFAULT_TRIM_NONCANONICAL_CHROMOSOMES
        See Also:
        Constant Field Values

      • DEFAULT_ALLOW_PREDICTED

        public static final boolean DEFAULT_ALLOW_PREDICTED
        See Also:
        Constant Field Values

      • DEFAULT_IDENTITY_THRESHOLD

        public static final double DEFAULT_IDENTITY_THRESHOLD
        Sequence identity below which we throw hits away (expressed as a fraction)
        See Also:
        Constant Field Values

      • DEFAULT_MINIMUM_EXON_OVERLAP_FRACTION

        public static final double DEFAULT_MINIMUM_EXON_OVERLAP_FRACTION
        Fraction of bases which must overlap with an annotated exon. This should probably be higher than zero, to avoid "pure intron" hits, but setting it too high can cause loss of sensitivity.
        See Also:
        Constant Field Values

      • NON_REPEAT_NON_SPECIFIC_SITE_THRESHOLD

        public static final int NON_REPEAT_NON_SPECIFIC_SITE_THRESHOLD
        Sequences which hybridize to this many or more sites in the genome are candidates to be considered non-specific. This is used even if the sequence does not contain a repeat.
        See Also:
        Constant Field Values

      • NON_SPECIFIC_SITE_THRESHOLD

        public static final int NON_SPECIFIC_SITE_THRESHOLD
        Sequences which hybridize to this many or more sites in the genome are candidates to be considered non-specific. This is used in combination with the REPEAT_FRACTION_MAXIMUM. Note that many sequences which contain repeats nonetheless only align to very few sites in the genome. Similarly, there are sequences that map to multiple sites which are _not_ repeats. This value is also not designed to care about whether the alignments are in known genes or not. Thus setting this too low could result in over-stringent filtering.
        See Also:
        Constant Field Values

      • REPEAT_FRACTION_MAXIMUM

        public static final double REPEAT_FRACTION_MAXIMUM
        Sequences which have more than this fraction accounted for by repeats (via repeatmasker) will not be examined if they produce multiple alignments to the genome, regardless of the alignment quality.
        See Also:
        Constant Field Values

    • Constructor Detail

      • ProbeMapperConfig

        public ProbeMapperConfig()

    • Method Detail

      • getBlatScoreThreshold

        public double getBlatScoreThreshold()
        Returns:
        the blatScoreThreshold

      • setBlatScoreThreshold

        public void setBlatScoreThreshold​(double blatScoreThreshold)
        Parameters:
        blatScoreThreshold - the blatScoreThreshold to set

      • getIdentityThreshold

        public double getIdentityThreshold()
        Returns:
        the identityThreshold

      • setIdentityThreshold

        public void setIdentityThreshold​(double identityThreshold)
        Parameters:
        identityThreshold - the identityThreshold to set

      • getMaximumRepeatFraction

        public double getMaximumRepeatFraction()
        Returns:
        the maximumRepeatFraction

      • setMaximumRepeatFraction

        public void setMaximumRepeatFraction​(double maximumRepeatFraction)
        Parameters:
        maximumRepeatFraction - the maximumRepeatFraction to set

      • getMinimumExonOverlapFraction

        public double getMinimumExonOverlapFraction()

      • setMinimumExonOverlapFraction

        public void setMinimumExonOverlapFraction​(double minimumExonOverlapFraction)

      • getNonRepeatNonSpecificSiteCountThreshold

        public double getNonRepeatNonSpecificSiteCountThreshold()

      • setNonRepeatNonSpecificSiteCountThreshold

        public void setNonRepeatNonSpecificSiteCountThreshold​(double nonRepeatNonSpecificSiteCountThreshold)

      • getNonSpecificSiteCountThreshold

        public double getNonSpecificSiteCountThreshold()
        Returns:
        the nonSpecificSiteCountThreshold

      • setNonSpecificSiteCountThreshold

        public void setNonSpecificSiteCountThreshold​(double nonSpecificSiteCountThreshold)
        Parameters:
        nonSpecificSiteCountThreshold - the nonSpecificSiteCountThreshold to set

      • isAllowPredictedGenes

        public boolean isAllowPredictedGenes()

      • setAllowPredictedGenes

        public void setAllowPredictedGenes​(boolean allowPredictedGenes)

      • isTrimNonCanonicalChromosomehits

        public boolean isTrimNonCanonicalChromosomehits()

      • isUseEnsembl

        public boolean isUseEnsembl()
        Returns:
        the useEnsembl

      • setUseEnsembl

        public void setUseEnsembl​(boolean useEnsembl)
        Parameters:
        useEnsembl - the useEnsembl to set

      • isUseEsts

        public boolean isUseEsts()
        Returns:
        the useEsts

      • setUseEsts

        public void setUseEsts​(boolean useEsts)
        Parameters:
        useEsts - the useEsts to set

      • isUseKnownGene

        public boolean isUseKnownGene()
        Returns:
        the useKnownGene

      • setUseKnownGene

        public void setUseKnownGene​(boolean useKnownGene)
        Parameters:
        useKnownGene - the useKnownGene to set

      • isUseMiRNA

        public boolean isUseMiRNA()
        Returns:
        the useMiRNA

      • setUseMiRNA

        public void setUseMiRNA​(boolean useMiRNA)
        Parameters:
        useMiRNA - the useMiRNA to set

      • isUseMrnas

        public boolean isUseMrnas()
        Returns:
        the useMrnas

      • setUseMrnas

        public void setUseMrnas​(boolean useMrnas)
        Parameters:
        useMrnas - the useMrnas to set

      • isUseRefGene

        public boolean isUseRefGene()
        Returns:
        the useRefGene

      • setUseRefGene

        public void setUseRefGene​(boolean useRefGene)
        Parameters:
        useRefGene - the useRefGene to set

      • setAllTracksOff

        public void setAllTracksOff()
        Set to use no tracks. Obviously then nothing will be found, so it is wise to then switch some tracks on.

      • setAllTracksOn

        public void setAllTracksOn()
        Set to use all tracks, including ESTs

      • setTrimNonCanonicalChromosomeHits

        public void setTrimNonCanonicalChromosomeHits​(boolean trimNonCanonicalChromosomeHits)

      • getWarnings

        protected int getWarnings()

      • incrementWarnings

        protected void incrementWarnings()