public class MsaCompactor
extends java.lang.Object
Constructor and Description |
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MsaCompactor(DeleteableMsa msa) |
Modifier and Type | Method and Description |
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Phylogeny |
calcTree() |
java.util.List<MsaProperties> |
chart(int step,
boolean realign,
boolean normalize_for_effective_seq_length) |
void |
deleteGapColumns(double max_allowed_gap_ratio) |
void |
displayTree(Phylogeny phy) |
Msa |
getMsa() |
static java.lang.String |
guessPathToMafft() |
void |
removeSequencesByMinimalLength(int min_effective_length) |
java.util.List<MsaProperties> |
removeViaGapAverage(double mean_gapiness) |
java.util.List<MsaProperties> |
removeViaLength(int length) |
java.util.List<MsaProperties> |
removeWorstOffenders(int to_remove) |
void |
setCalculateNormalizedShannonEntropy(boolean calculate_shannon_entropy) |
void |
setInfileName(java.lang.String infile_name) |
void |
setMafftOptions(java.lang.String maffts_opts) |
void |
setNorm(boolean normalize_for_effective_seq_length) |
void |
setOutFileBase(java.io.File out_file_base) |
void |
setOutputFormat(Msa.MSA_FORMAT output_format) |
void |
setPathToMafft(java.lang.String path_to_mafft) |
void |
setPeformPhylogenticInference(boolean phylogentic_inference) |
void |
setRealign(boolean realign) |
void |
setRemovedSeqsOutBase(java.io.File removed_seqs_out_base) |
void |
setStep(int step) |
void |
setStepForDiagnostics(int step_for_diagnostics) |
java.lang.String |
writeAndAlignRemovedSeqs() |
java.lang.String |
writeMsa(java.io.File outfile) |
public MsaCompactor(DeleteableMsa msa)
public final Phylogeny calcTree()
public final java.util.List<MsaProperties> chart(int step, boolean realign, boolean normalize_for_effective_seq_length) throws java.io.IOException, java.lang.InterruptedException
java.io.IOException
java.lang.InterruptedException
public final void deleteGapColumns(double max_allowed_gap_ratio)
public final void displayTree(Phylogeny phy)
public final Msa getMsa()
public final void removeSequencesByMinimalLength(int min_effective_length) throws java.io.IOException
java.io.IOException
public final java.util.List<MsaProperties> removeViaGapAverage(double mean_gapiness) throws java.io.IOException, java.lang.InterruptedException
java.io.IOException
java.lang.InterruptedException
public java.util.List<MsaProperties> removeViaLength(int length) throws java.io.IOException, java.lang.InterruptedException
java.io.IOException
java.lang.InterruptedException
public final java.util.List<MsaProperties> removeWorstOffenders(int to_remove) throws java.io.IOException, java.lang.InterruptedException
java.io.IOException
java.lang.InterruptedException
public final void setCalculateNormalizedShannonEntropy(boolean calculate_shannon_entropy)
public void setInfileName(java.lang.String infile_name)
public final void setMafftOptions(java.lang.String maffts_opts)
public final void setNorm(boolean normalize_for_effective_seq_length)
public final void setOutFileBase(java.io.File out_file_base)
public final void setOutputFormat(Msa.MSA_FORMAT output_format)
public void setPathToMafft(java.lang.String path_to_mafft)
public void setPeformPhylogenticInference(boolean phylogentic_inference)
public final void setRealign(boolean realign)
public final void setRemovedSeqsOutBase(java.io.File removed_seqs_out_base)
public final void setStep(int step)
public final void setStepForDiagnostics(int step_for_diagnostics)
public final java.lang.String writeAndAlignRemovedSeqs() throws java.io.IOException, java.lang.InterruptedException
java.io.IOException
java.lang.InterruptedException
public final java.lang.String writeMsa(java.io.File outfile) throws java.io.IOException
java.io.IOException
public static final java.lang.String guessPathToMafft()