org.biojava.spice.das
Class AlignmentTools

java.lang.Object
  org.biojava.spice.das.AlignmentTools

public class AlignmentTools

extends Object

Author:

Andreas Prlic

Constructor Summary

AlignmentTools(RegistryConfiguration conf)

Method Summary

static void	addMatrix(Alignment ali, String intObjectId, Matrix matrix) add a Matrix to an object
static void	addObject(Alignment ali, String accessionCode, String intObjectId, String objectVersion, String type, String dbSource, String dbVersion, String dbCoordSys, List details) add a new object to an alignment
static void	addVector(Alignment ali, String intObjectId, Atom atom) add a shift vector to an alignment
Alignment[]	getAlignments(String code) get alignments for a particular uniprot or pdb code
static Annotation	getObject(String s, Alignment a)
static String	getPDBCodeFromAlignment(Alignment ali)
static String	getUniProtCodeFromAlignment(Alignment ali)

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentTools

public AlignmentTools(RegistryConfiguration conf)

Parameters:

conf - the configuration to be used

Method Detail

addVector

public static void addVector(Alignment ali,
                             String intObjectId,
                             Atom atom)
                      throws DASException

add a shift vector to an alignment

Parameters:

ali -

intObjectId -

atom -

Throws:

DASException

addMatrix

public static void addMatrix(Alignment ali,
                             String intObjectId,
                             Matrix matrix)
                      throws DASException

add a Matrix to an object

Parameters:

ali -

intObjectId -

matrix -

Throws:

DASException

addObject

public static void addObject(Alignment ali,
                             String accessionCode,
                             String intObjectId,
                             String objectVersion,
                             String type,
                             String dbSource,
                             String dbVersion,
                             String dbCoordSys,
                             List details)
                      throws DASException

add a new object to an alignment

Parameters:

ali - the alignment to which the new object should be attached to

accessionCode -

intObjectId -

objectVersion -

type -

dbSource -

dbVersion -

dbCoordSys -

details - a list of detail annotation as created with getObjectDetails. Can be null or size 0.

Throws:

DASException

getObject

public static Annotation getObject(String s,
                                   Alignment a)

getAlignments

public Alignment[] getAlignments(String code)

get alignments for a particular uniprot or pdb code

Parameters:

code -

Returns:

an array of Alignment object

getUniProtCodeFromAlignment

public static String getUniProtCodeFromAlignment(Alignment ali)

getPDBCodeFromAlignment

public static String getPDBCodeFromAlignment(Alignment ali)