Class MsaCompactor

Method Details

• calcTree

  public final Phylogeny calcTree()

• chart

  public final List<MsaProperties> chart(int step, boolean realign, boolean normalize_for_effective_seq_length) throws IOException, InterruptedException

  Throws:

  IOException

  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 IOException

  Throws:

  IOException

• removeViaGapAverage

  public final List<MsaProperties> removeViaGapAverage(double mean_gapiness) throws IOException, InterruptedException

  Throws:

  IOException

  InterruptedException

• removeViaLength

  public List<MsaProperties> removeViaLength(int length) throws IOException, InterruptedException

  Throws:

  IOException

  InterruptedException

• removeWorstOffenders

  public final List<MsaProperties> removeWorstOffenders(int to_remove) throws IOException, InterruptedException

  Throws:

  IOException

  InterruptedException

• setCalculateNormalizedShannonEntropy

  public final void setCalculateNormalizedShannonEntropy(boolean calculate_shannon_entropy)

• setInfileName

  public void setInfileName(String infile_name)

• setMafftOptions

  public final void setMafftOptions(String maffts_opts)

• setNorm

  public final void setNorm(boolean normalize_for_effective_seq_length)

• setOutFileBase

  public final void setOutFileBase(File out_file_base)

• setOutputFormat

  public final void setOutputFormat(Msa.MSA_FORMAT output_format)

• setPathToMafft

  public void setPathToMafft(String path_to_mafft)

• setPeformPhylogenticInference

  public void setPeformPhylogenticInference(boolean phylogentic_inference)

• setRealign

  public final void setRealign(boolean realign)

• setRemovedSeqsOutBase

  public final void setRemovedSeqsOutBase(File removed_seqs_out_base)

• setStep

  public final void setStep(int step)

• setStepForDiagnostics

  public final void setStepForDiagnostics(int step_for_diagnostics)

• writeAndAlignRemovedSeqs

  public final String writeAndAlignRemovedSeqs() throws IOException, InterruptedException

  Throws:

  IOException

  InterruptedException

• writeMsa

  public final String writeMsa(File outfile) throws IOException

  Throws:

  IOException

• guessPathToMafft

  public static final String guessPathToMafft()