Package org.forester.msa_compactor
Class MsaCompactor
- java.lang.Object
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- org.forester.msa_compactor.MsaCompactor
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public class MsaCompactor extends java.lang.Object
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Constructor Summary
Constructors Constructor Description MsaCompactor(DeleteableMsa msa)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description 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)
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Constructor Detail
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MsaCompactor
public MsaCompactor(DeleteableMsa msa)
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Method Detail
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calcTree
public final Phylogeny calcTree()
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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
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deleteGapColumns
public final void deleteGapColumns(double max_allowed_gap_ratio)
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displayTree
public final void displayTree(Phylogeny phy)
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getMsa
public final Msa getMsa()
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removeSequencesByMinimalLength
public final void removeSequencesByMinimalLength(int min_effective_length) throws java.io.IOException
- Throws:
java.io.IOException
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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
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removeViaLength
public java.util.List<MsaProperties> removeViaLength(int length) throws java.io.IOException, java.lang.InterruptedException
- Throws:
java.io.IOException
java.lang.InterruptedException
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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
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setCalculateNormalizedShannonEntropy
public final void setCalculateNormalizedShannonEntropy(boolean calculate_shannon_entropy)
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setInfileName
public void setInfileName(java.lang.String infile_name)
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setMafftOptions
public final void setMafftOptions(java.lang.String maffts_opts)
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setNorm
public final void setNorm(boolean normalize_for_effective_seq_length)
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setOutFileBase
public final void setOutFileBase(java.io.File out_file_base)
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setOutputFormat
public final void setOutputFormat(Msa.MSA_FORMAT output_format)
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setPathToMafft
public void setPathToMafft(java.lang.String path_to_mafft)
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setPeformPhylogenticInference
public void setPeformPhylogenticInference(boolean phylogentic_inference)
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setRealign
public final void setRealign(boolean realign)
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setRemovedSeqsOutBase
public final void setRemovedSeqsOutBase(java.io.File removed_seqs_out_base)
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setStep
public final void setStep(int step)
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setStepForDiagnostics
public final void setStepForDiagnostics(int step_for_diagnostics)
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writeAndAlignRemovedSeqs
public final java.lang.String writeAndAlignRemovedSeqs() throws java.io.IOException, java.lang.InterruptedException
- Throws:
java.io.IOException
java.lang.InterruptedException
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writeMsa
public final java.lang.String writeMsa(java.io.File outfile) throws java.io.IOException
- Throws:
java.io.IOException
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guessPathToMafft
public static final java.lang.String guessPathToMafft()
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