Class ModificationSiteMapping
java.lang.Object
com.compomics.util.experiment.identification.modification.ModificationSiteMapping
public class ModificationSiteMapping extends Object
This class contains convenience methods to map modifications on potential sites.
- Author:
- Marc Vaudel
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Constructor Summary
Constructors Constructor Description ModificationSiteMapping()
Empty default constructor -
Method Summary
Modifier and Type Method 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.
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Constructor Details
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ModificationSiteMapping
public ModificationSiteMapping()Empty default constructor
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Method Details
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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 integerserie2
- second list of integer- Returns:
- a map of the doublets created.
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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 integerserie2
- second list of integer- Returns:
- a map of the doublets created.
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alignAll
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.
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