PIP.IO.StampPackage
Class Alignments

java.lang.Object
  PIP.IO.StampPackage.Alignments

public class Alignments
extends java.lang.Object

Constructor Summary

Alignments()

Method Summary

static void	addToGroupsFile(java.io.FileWriter fw, java.lang.String sequenceId, java.lang.String sequenceIndex, int startRes, int endRes, java.lang.String colour)
static void	cleanAlignments(java.lang.String nameOfAlignmentFile, java.lang.String directory, int size, java.util.List<Domain> toKeep)
static void	convertStampOutputToJalviewFormat(java.lang.String nameOfAlignmentFile, java.lang.String directory, int size, java.lang.String nameOfJalviewFile) This fucntion takes in a Stamp output and removes all of the stuff that is not required....
static void	createGroupsFiles(java.util.List<InteractionSurface> listOfSimilarInteractionSurfaces, java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentsA, java.lang.String nameOfGroupsFile)
static int	fromAlignmentPositionCalculateResiduePosition(java.util.List<java.lang.Character> alignment, int position)
static int	fromResiduePositionCalculateAlignmentPosition(java.util.List<java.lang.Character> alignment, int position)
static int	getFileWithLargestNumberOfAlignments(java.lang.String nameAlignmentFile, java.lang.String directory)
static java.util.Map<java.lang.String,java.util.List<java.lang.Character>>	readInAlignments(java.lang.String nameAlignmentFile, java.lang.String directory, int size)

Methods inherited from class java.lang.Object

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

Constructor Detail

Alignments

public Alignments()

Method Detail

fromResiduePositionCalculateAlignmentPosition

public static int fromResiduePositionCalculateAlignmentPosition(java.util.List<java.lang.Character> alignment,
                                                                int position)

fromAlignmentPositionCalculateResiduePosition

public static int fromAlignmentPositionCalculateResiduePosition(java.util.List<java.lang.Character> alignment,
                                                                int position)

createGroupsFiles

public static void createGroupsFiles(java.util.List<InteractionSurface> listOfSimilarInteractionSurfaces,
                                     java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentsA,
                                     java.lang.String nameOfGroupsFile)
                              throws java.io.IOException

Throws:

java.io.IOException

convertStampOutputToJalviewFormat

public static void convertStampOutputToJalviewFormat(java.lang.String nameOfAlignmentFile,
                                                     java.lang.String directory,
                                                     int size,
                                                     java.lang.String nameOfJalviewFile)
                                              throws java.io.IOException,
                                                     java.io.UnsupportedEncodingException,
                                                     java.lang.InterruptedException

This fucntion takes in a Stamp output and removes all of the stuff that is not required....

Throws:

java.io.IOException

java.io.UnsupportedEncodingException

java.lang.InterruptedException

addToGroupsFile

public static void addToGroupsFile(java.io.FileWriter fw,
                                   java.lang.String sequenceId,
                                   java.lang.String sequenceIndex,
                                   int startRes,
                                   int endRes,
                                   java.lang.String colour)
                            throws java.io.IOException

Throws:

java.io.IOException

readInAlignments

public static java.util.Map<java.lang.String,java.util.List<java.lang.Character>> readInAlignments(java.lang.String nameAlignmentFile,
                                                                                                   java.lang.String directory,
                                                                                                   int size)
                                                                                            throws java.io.IOException

Throws:

java.io.IOException

getFileWithLargestNumberOfAlignments

public static int getFileWithLargestNumberOfAlignments(java.lang.String nameAlignmentFile,
                                                       java.lang.String directory)

cleanAlignments

public static void cleanAlignments(java.lang.String nameOfAlignmentFile,
                                   java.lang.String directory,
                                   int size,
                                   java.util.List<Domain> toKeep)
                            throws java.io.IOException

Throws:

java.io.IOException