public class MultipleAlignmentTools
extends java.lang.Object
MultipleAlignment
.
Supported functions:
Constructor and Description |
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MultipleAlignmentTools() |
Modifier and Type | Method and Description |
---|---|
static Atom |
getAtomForSequencePosition(MultipleAlignment multAln,
java.util.List<java.lang.Integer> mapSeqToStruct,
int structure,
int sequencePos)
Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.
|
static Matrix |
getAverageResidueDistances(MultipleAlignment alignment)
The average residue distance Matrix contains the average distance from each residue to all
other residues aligned with it.
|
static int |
getBlockForSequencePosition(MultipleAlignment multAln,
java.util.List<java.lang.Integer> mapSeqToStruct,
int sequencePos)
Returns the block number of a specified position in the sequence alignment.
|
static java.util.List<java.lang.String> |
getBlockSequenceAlignment(MultipleAlignment alignment)
Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
|
static java.util.List<java.lang.String> |
getBlockSequenceAlignment(MultipleAlignment alignment,
java.util.List<java.lang.Integer> mapSeqToStruct)
Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
|
static java.util.List<java.lang.String> |
getSequenceAlignment(MultipleAlignment alignment)
Calculate the sequence alignment Strings for the whole alignment.
|
static java.util.List<java.lang.String> |
getSequenceAlignment(MultipleAlignment alignment,
java.util.List<java.lang.Integer> mapSeqToStruct)
Calculate the sequence alignment Strings for the whole alignment.
|
public static java.util.List<java.lang.String> getSequenceAlignment(MultipleAlignment alignment, java.util.List<java.lang.Integer> mapSeqToStruct)
Blocks are concatenated in the order returned by MultipleAlignment.getBlocks()
,
so sequences may not be sequential. Gaps are represented by '-'. Separation between different
Blocks is indicated by a gap in all positions, meaning that there is a possible discontinuity.
alignment
- input MultipleAlignmentmapSeqToStruct
- provides a link from the sequence alignment position to the structure alignment
position. Specially designed for the GUI. Has to be initialized previously and will be overwritten.public static java.util.List<java.lang.String> getSequenceAlignment(MultipleAlignment alignment)
Blocks are concatenated in the order returned by MultipleAlignment.getBlocks()
,
so sequences may not be sequential. Gaps are represented by '-'. Separation between different
Blocks is indicated by a gap in all positions, meaning that there is a possible discontinuity.
alignment
- input MultipleAlignmentpublic static java.util.List<java.lang.String> getBlockSequenceAlignment(MultipleAlignment alignment, java.util.List<java.lang.Integer> mapSeqToStruct)
getSequenceAlignment(MultipleAlignment)
.
Blocks are concatenated in the order returned by MultipleAlignment.getBlocks()
,
so sequences may not be sequential. Gaps between blocks are omitted,
while gaps within blocks are represented by '-'. Separation between different Blocks is
indicated by a gap in all positions, meaning that there is something unaligned inbetween.
alignment
- input MultipleAlignmentmapSeqToStruct
- provides a link from the sequence alignment position to the structure alignment
position. Specially designed for the GUI. Has to be initialized previously and will be overwritten.public static java.util.List<java.lang.String> getBlockSequenceAlignment(MultipleAlignment alignment)
getSequenceAlignment(MultipleAlignment)
.
Blocks are concatenated in the order returned by MultipleAlignment.getBlocks()
,
so sequences may not be sequential. Gaps between blocks are omitted,
while gaps within blocks are represented by '-'. Separation between different Blocks is
indicated by a gap in all positions, meaning that there is something unaligned inbetween.
alignment
- input MultipleAlignmentpublic static Atom getAtomForSequencePosition(MultipleAlignment multAln, java.util.List<java.lang.Integer> mapSeqToStruct, int structure, int sequencePos)
multAln
- the MultipleAlignment object from where the sequence alignment has been generatedmapSeqToStruct
- the mapping between sequence and structure generated with the sequence alignmentstructure
- the structure index of the alignment (row)sequencePos
- the sequence alignment position (column)public static int getBlockForSequencePosition(MultipleAlignment multAln, java.util.List<java.lang.Integer> mapSeqToStruct, int sequencePos)
multAln
- the MultipleAlignment object from where the sequence alignment has been generatedmapSeqToStruct
- the mapping between sequence and structure generated with the sequence alignmentsequencePos
- the position in the sequence alignment (column)public static Matrix getAverageResidueDistances(MultipleAlignment alignment)
Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.
alignment
- MultipleAlignment