Constructor Detail

• MsaCompactor

  public MsaCompactor​(DeleteableMsa msa)

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()