Class MsaCompactor


  • public class MsaCompactor
    extends java.lang.Object
    • Constructor Detail

    • Method Detail

      • calcTree

        public final Phylogeny calcTree()
      • chart

        public final java.util.List<MsaProperties> chart​(int step,
                                                         boolean realign,
                                                         boolean normalize_for_effective_seq_length)
                                                  throws java.io.IOException,
                                                         java.lang.InterruptedException
        Throws:
        java.io.IOException
        java.lang.InterruptedException
      • deleteGapColumns

        public final void deleteGapColumns​(double max_allowed_gap_ratio)
      • displayTree

        public final void displayTree​(Phylogeny phy)
      • getMsa

        public final Msa getMsa()
      • removeSequencesByMinimalLength

        public final void removeSequencesByMinimalLength​(int min_effective_length)
                                                  throws java.io.IOException
        Throws:
        java.io.IOException
      • removeViaGapAverage

        public final java.util.List<MsaProperties> removeViaGapAverage​(double mean_gapiness)
                                                                throws java.io.IOException,
                                                                       java.lang.InterruptedException
        Throws:
        java.io.IOException
        java.lang.InterruptedException
      • removeViaLength

        public java.util.List<MsaProperties> removeViaLength​(int length)
                                                      throws java.io.IOException,
                                                             java.lang.InterruptedException
        Throws:
        java.io.IOException
        java.lang.InterruptedException
      • removeWorstOffenders

        public final java.util.List<MsaProperties> removeWorstOffenders​(int to_remove)
                                                                 throws java.io.IOException,
                                                                        java.lang.InterruptedException
        Throws:
        java.io.IOException
        java.lang.InterruptedException
      • setCalculateNormalizedShannonEntropy

        public final void setCalculateNormalizedShannonEntropy​(boolean calculate_shannon_entropy)
      • setInfileName

        public void setInfileName​(java.lang.String infile_name)
      • setMafftOptions

        public final void setMafftOptions​(java.lang.String maffts_opts)
      • setNorm

        public final void setNorm​(boolean normalize_for_effective_seq_length)
      • setOutFileBase

        public final void setOutFileBase​(java.io.File out_file_base)
      • setOutputFormat

        public final void setOutputFormat​(Msa.MSA_FORMAT output_format)
      • setPathToMafft

        public void setPathToMafft​(java.lang.String path_to_mafft)
      • setPeformPhylogenticInference

        public void setPeformPhylogenticInference​(boolean phylogentic_inference)
      • setRealign

        public final void setRealign​(boolean realign)
      • setRemovedSeqsOutBase

        public final void setRemovedSeqsOutBase​(java.io.File removed_seqs_out_base)
      • setStep

        public final void setStep​(int step)
      • setStepForDiagnostics

        public final void setStepForDiagnostics​(int step_for_diagnostics)
      • writeAndAlignRemovedSeqs

        public final java.lang.String writeAndAlignRemovedSeqs()
                                                        throws java.io.IOException,
                                                               java.lang.InterruptedException
        Throws:
        java.io.IOException
        java.lang.InterruptedException
      • writeMsa

        public final java.lang.String writeMsa​(java.io.File outfile)
                                        throws java.io.IOException
        Throws:
        java.io.IOException
      • guessPathToMafft

        public static final java.lang.String guessPathToMafft()