org.biojava.spice.manypanel
Class AlignmentTool

java.lang.Object
  org.biojava.spice.manypanel.AlignmentTool

public class AlignmentTool

extends Object

Constructor Summary

AlignmentTool()

Method Summary

static List	createAlignmentTable(Alignment ali, String queryCode) returns a list of maps relative to one accession code that has the length of the alignment (can include gaps).
static Chain	createChain(Alignment ali, String querySequence, String queryId, String subjectId) creates a chaing that represents the alignment relative to the query.
static String	extractId(Alignment a, String code)
static String	getCigar(Alignment a, String intObjectId)
static List	getTableByCigar(String cigar) returns a list of maps

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlignmentTool

public AlignmentTool()

Method Detail

getCigar

public static String getCigar(Alignment a,
                              String intObjectId)
                       throws Exception

Throws:

Exception

extractId

public static String extractId(Alignment a,
                               String code)

createAlignmentTable

public static List createAlignmentTable(Alignment ali,
                                        String queryCode)

returns a list of maps relative to one accession code that has the length of the alignment (can include gaps). usually this is done for both objects in an alignment, and then the two created lists are being processed. each element of this list is a Map with the following keys: arraypos ... seqpos ... position of the sequence. is null if this sequence position is not aligned

Parameters:

ali - alignment

queryCode - the accessionCode for the object to be the reference.

Returns:

a List of maps objects

getTableByCigar

public static List getTableByCigar(String cigar)

returns a list of maps

Parameters:

cigar -

Returns:

a List of map objects

createChain

public static Chain createChain(Alignment ali,
                                String querySequence,
                                String queryId,
                                String subjectId)

creates a chaing that represents the alignment relative to the query. if a position is alignmed to the subject then that position will have an integer in the PDBCode field. this int is the sequence position in the subject

Parameters:

ali -

querySequence -

queryId -

subjectId -

Returns:

a chain object