|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.bio.structure.io.StructureSequenceMatcher
public class StructureSequenceMatcher
A utility class with methods for matching ProteinSequences with Structures.
Constructor Summary | |
---|---|
StructureSequenceMatcher()
|
Method Summary | ||
---|---|---|
static ProteinSequence |
getProteinSequenceForStructure(Structure struct,
Map<Integer,Group> groupIndexPosition)
Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups. |
|
static ResidueNumber[] |
matchSequenceToStructure(ProteinSequence seq,
Structure struct)
Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence. |
|
static ProteinSequence |
removeGaps(ProteinSequence gapped)
Removes all gaps ('-') from a protein sequence |
|
static
|
removeGaps(T[][] gapped)
Creates a new list consisting of all columns of gapped where no row contained a null value. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public StructureSequenceMatcher()
Method Detail |
---|
public static ProteinSequence getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition)
struct
- Input structuregroupIndexPosition
- An empty map, which will be populated with
(residue index in returned ProteinSequence) -> (Group within struct)
SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which
does the heavy lifting.
public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Structure struct)
Smith-Waterman alignment is used to match the sequences. Residues in the sequence but not the structure or mismatched between sequence and structure will have a null atom, while residues in the structure but not the sequence are ignored with a warning.
seq
- The protein sequence. Should match the sequence of struct very
closely.struct
- The corresponding protein structure
public static ProteinSequence removeGaps(ProteinSequence gapped)
gapped
-
public static <T> T[][] removeGaps(T[][] gapped)
gapped
- A rectangular matrix containing null to mark gaps
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |