com.compomics.util.experiment.identification.ptm

Class PtmSiteMapping

java.lang.Object

com.compomics.util.experiment.identification.ptm.PtmSiteMapping

public class PtmSiteMapping
extends Object

This class contains convenience methods to map ptms on potential sites.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PtmSiteMapping()

Method Summary

Modifier and Type	Method and Description
static HashMap<Integer,Integer>	align(Collection<Integer> serie1, Collection<Integer> serie2) Aligns two series of integer, minimizing the distance between them and excluding outliers.
static HashMap<Integer,Integer>	alignAll(Collection<Integer> serie1, Collection<Integer> serie2) Aligns two series of integer, minimizing the distance between them.
static HashMap<Integer,Integer>	alignAll(HashMap<Integer,ArrayList<Integer>> input) Aligns a series of integer on possible targets maximizing the number of matched targets.

Methods inherited from class java.lang.Object

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

Constructor Detail

PtmSiteMapping

public PtmSiteMapping()

Method Detail

align

public static HashMap<Integer,Integer> align(Collection<Integer> serie1,
                                             Collection<Integer> serie2)

Aligns two series of integer, minimizing the distance between them and excluding outliers. Example: series1 = {0, 1, 13, 25, 15, 6, 99} series2 = {100, 2, 12, 14, 18, 30, 115, 1000} result = {0>null, 1>2, 6>null, 13>12, 15>14, 25>18, 99>100}

Parameters:

serie1 - first list of integer

serie2 - second list of integer

Returns:

a map of the doublets created.

alignAll

public static HashMap<Integer,Integer> alignAll(Collection<Integer> serie1,
                                                Collection<Integer> serie2)

Aligns two series of integer, minimizing the distance between them. Example: serie1 = {0, 1, 13, 25, 15, 6, 99} serie2 = {100, 2, 12, 14, 18, 30, 115, 1000} result = {0> 115, 1>2, 6>30, 13>12, 15>14, 25>18, 99>100}

Parameters:

serie1 - first list of integer

serie2 - second list of integer

Returns:

a map of the doublets created.

alignAll

public static HashMap<Integer,Integer> alignAll(HashMap<Integer,ArrayList<Integer>> input)

Aligns a series of integer on possible targets maximizing the number of matched targets. Example: input = { 0 > {100, 2, 12, 14, 18, 30, 115, 1000}, 1 > {12}, 2 > {3, 12, 14}, 8 > {12}, 13 > {3, 12, 14}, 25 > {100, 2, 12, 14, 18, 30, 115, 1000}, 15 > {100, 2, 12, 14, 18, 30, 115, 1000}, 6 > {100, 2, 12, 14, 18, 30, 115, 1000}, 99 > {3} } result = {1 > null, 8 > 12, 99 > 3, 13 > 14, 2 > null, 0 > 2, 6 > 100, 15 > 18, 25 > 30}

Parameters:

input - the input map

Returns:

a map of the doublets created.