public final class DeleteableMsa
extends BasicMsa

Nested Class Summary
- Nested classes/interfaces inherited from interface org.forester.msa.Msa
  Msa.MSA_FORMAT

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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

public static int calcGapSumPerColumn(Msa msa,
                                      int col)

public final void deleteGapColumns(double max_allowed_gap_ratio)

public final void deleteGapOnlyColumns()

public final MolecularSequence deleteRow(java.lang.String id,
                                         boolean return_removed_seq)

public final boolean isAllGap(int col)

public final void setIdentifier(int row,
                                java.lang.String id)

public final void setResidueAt(int row,
                               int col,
                               char residue)

public static final DeleteableMsa createInstance(java.util.List<MolecularSequence> seqs)

public static final DeleteableMsa createInstance(Msa msa)

Class DeleteableMsa