Package org.forester.msa
Class DeleteableMsa
java.lang.Object
org.forester.msa.BasicMsa
org.forester.msa.DeleteableMsa
- All Implemented Interfaces:
Msa
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Nested Class Summary
Nested classes/interfaces inherited from interface org.forester.msa.Msa
Msa.MSA_FORMAT -
Method Summary
Modifier and TypeMethodDescriptionfinal double[]static intcalcGapSumPerColumn(Msa msa, int col) static final DeleteableMsacreateInstance(List<MolecularSequence> seqs) static final DeleteableMsacreateInstance(Msa msa) final voiddeleteGapColumns(double max_allowed_gap_ratio) final voidfinal MolecularSequenceshortfinal StringgetIdentifier(int row) final intfinal intfinal chargetResidueAt(int row, int col) getSequence(int row) final booleanisAllGap(int col) final voidsetIdentifier(int row, String id) final voidsetResidueAt(int row, int col, char residue) Methods inherited from class org.forester.msa.BasicMsa
asSequenceList, getColumnAt, getSequence, getSequenceAsString, getType, isGapAt, toString, write
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Method Details
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calcGappiness
public final double[] calcGappiness() -
calcGapSumPerColumn
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determineMaxIdLength
public short determineMaxIdLength() -
deleteGapColumns
public final void deleteGapColumns(double max_allowed_gap_ratio) -
deleteGapOnlyColumns
public final void deleteGapOnlyColumns() -
deleteRow
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getIdentifier
- Specified by:
getIdentifierin interfaceMsa- Overrides:
getIdentifierin classBasicMsa
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getLength
public final int getLength() -
getNumberOfSequences
public final int getNumberOfSequences()- Specified by:
getNumberOfSequencesin interfaceMsa- Overrides:
getNumberOfSequencesin classBasicMsa
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getResidueAt
public final char getResidueAt(int row, int col) - Specified by:
getResidueAtin interfaceMsa- Overrides:
getResidueAtin classBasicMsa
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getSequence
- Specified by:
getSequencein interfaceMsa- Overrides:
getSequencein classBasicMsa
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isAllGap
public final boolean isAllGap(int col) -
setIdentifier
- Specified by:
setIdentifierin interfaceMsa- Overrides:
setIdentifierin classBasicMsa
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setResidueAt
public final void setResidueAt(int row, int col, char residue) - Specified by:
setResidueAtin interfaceMsa- Overrides:
setResidueAtin classBasicMsa
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createInstance
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createInstance
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