Package ubic.gemma.core.analysis.sequence

Class ProbeMapperConfig

java.lang.Object
ubic.gemma.core.analysis.sequence.ProbeMapperConfig
public class ProbeMapperConfig extends Object
Holds parameters for how mapping should be done.
Author:
paul

  • Field Details

    • DEFAULT_TRIM_NONCANONICAL_CHROMOSOMES

      public static final boolean DEFAULT_TRIM_NONCANONICAL_CHROMOSOMES
      See Also:

    • DEFAULT_ALLOW_PARS

      public static final boolean DEFAULT_ALLOW_PARS
      See Also:

    • DEFAULT_ALLOW_PREDICTED

      public static final boolean DEFAULT_ALLOW_PREDICTED
      See Also:

    • MAX_WARNINGS

      public static final int MAX_WARNINGS
      See Also:

    • DEFAULT_IDENTITY_THRESHOLD

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

    • 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:

    • DEFAULT_SCORE_THRESHOLD

      public static final double DEFAULT_SCORE_THRESHOLD
      BLAT score threshold below which we do not consider hits. This reflects the fraction of aligned bases.
      See Also:

    • 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:

    • 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:

    • 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:

  • Constructor Details

    • ProbeMapperConfig

      public ProbeMapperConfig()

  • Method Details

    • 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)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getWarnings

      protected int getWarnings()

    • incrementWarnings

      protected void incrementWarnings()