Package org.forester.msa
Class DeleteableMsa
- java.lang.Object
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- org.forester.msa.BasicMsa
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- org.forester.msa.DeleteableMsa
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.forester.msa.Msa
Msa.MSA_FORMAT
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description double[]
calcGappiness()
static int
calcGapSumPerColumn(Msa msa, int col)
static DeleteableMsa
createInstance(java.util.List<MolecularSequence> seqs)
static DeleteableMsa
createInstance(Msa msa)
void
deleteGapColumns(double max_allowed_gap_ratio)
void
deleteGapOnlyColumns()
MolecularSequence
deleteRow(java.lang.String id, boolean return_removed_seq)
short
determineMaxIdLength()
java.lang.String
getIdentifier(int row)
int
getLength()
int
getNumberOfSequences()
char
getResidueAt(int row, int col)
MolecularSequence
getSequence(int row)
boolean
isAllGap(int col)
void
setIdentifier(int row, java.lang.String id)
void
setResidueAt(int row, int col, char residue)
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Methods inherited from class org.forester.msa.BasicMsa
asSequenceList, getColumnAt, getSequence, getSequenceAsString, getType, isGapAt, toString, write
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Method Detail
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calcGappiness
public final double[] calcGappiness()
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calcGapSumPerColumn
public static int calcGapSumPerColumn(Msa msa, int col)
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determineMaxIdLength
public short determineMaxIdLength()
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deleteGapColumns
public final void deleteGapColumns(double max_allowed_gap_ratio)
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deleteGapOnlyColumns
public final void deleteGapOnlyColumns()
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deleteRow
public final MolecularSequence deleteRow(java.lang.String id, boolean return_removed_seq)
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getIdentifier
public final java.lang.String getIdentifier(int row)
- Specified by:
getIdentifier
in interfaceMsa
- Overrides:
getIdentifier
in classBasicMsa
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getLength
public final int getLength()
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getNumberOfSequences
public final int getNumberOfSequences()
- Specified by:
getNumberOfSequences
in interfaceMsa
- Overrides:
getNumberOfSequences
in classBasicMsa
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getResidueAt
public final char getResidueAt(int row, int col)
- Specified by:
getResidueAt
in interfaceMsa
- Overrides:
getResidueAt
in classBasicMsa
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getSequence
public MolecularSequence getSequence(int row)
- Specified by:
getSequence
in interfaceMsa
- Overrides:
getSequence
in classBasicMsa
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isAllGap
public final boolean isAllGap(int col)
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setIdentifier
public final void setIdentifier(int row, java.lang.String id)
- Specified by:
setIdentifier
in interfaceMsa
- Overrides:
setIdentifier
in classBasicMsa
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setResidueAt
public final void setResidueAt(int row, int col, char residue)
- Specified by:
setResidueAt
in interfaceMsa
- Overrides:
setResidueAt
in classBasicMsa
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createInstance
public static final DeleteableMsa createInstance(java.util.List<MolecularSequence> seqs)
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createInstance
public static final DeleteableMsa createInstance(Msa msa)
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