org.proteios.io
Class XTandemParameterSetOptionsUtil

java.lang.Object
  org.proteios.io.XTandemParameterSetOptionsUtil

public class XTandemParameterSetOptionsUtil
extends Object

Author:

olle

Constructor Summary

XTandemParameterSetOptionsUtil()
Default constructor.

Method Summary

List<String>	fetchListPathDefaultParametersStringList() Fetches list path default parameters string list with alternating key and value strings.
List<String>	fetchProSpeciesStringList() Fetches Prokaryotes species string list with alternating key and value strings.
List<String>	fetchProteinCleavageSiteStringList() Fetches protein cleavage site string list with alternating key and value strings.
List<String>	fetchRefinePotentialModificationMass1StringList() Fetches refine potential modification mass 1 string list with alternating key and value strings.
List<String>	fetchRefinePotentialModificationMassStringList() Fetches refine potential modification mass string list with alternating key and value strings.
List<String>	fetchResidueModificationMassStringList() Fetches residue modification mass string list with alternating key and value strings.
List<String>	fetchResiduePotentialModificationMassStringList() Fetches residue potential modification mass string list with alternating key and value strings.
List<String>	fetchSpeciesStringList() Fetches Eukaryotes species string list with alternating key and value strings.
void	fetchXTandemSearchProperties() Fetches X!
String	stringListToListString(List<String> stringList, String delimiterString) Converts a list with String elements to a list String with chosen delimiter string between elements.
List<String>	uniqueStringItemList(List<String> stringList) Converts a list with String elements to a list with unique String elements by removing duplicate elements.

Methods inherited from class java.lang.Object

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

Constructor Detail

XTandemParameterSetOptionsUtil

public XTandemParameterSetOptionsUtil()

Default constructor.

Method Detail

fetchXTandemSearchProperties

public void fetchXTandemSearchProperties()

Fetches X!Tandem search constants from Properties file.

fetchListPathDefaultParametersStringList

public List<String> fetchListPathDefaultParametersStringList()

Fetches list path default parameters string list with alternating key and value strings.

fetchSpeciesStringList

public List<String> fetchSpeciesStringList()

Fetches Eukaryotes species string list with alternating key and value strings.

fetchProSpeciesStringList

public List<String> fetchProSpeciesStringList()

Fetches Prokaryotes species string list with alternating key and value strings.

fetchResidueModificationMassStringList

public List<String> fetchResidueModificationMassStringList()

Fetches residue modification mass string list with alternating key and value strings.

fetchResiduePotentialModificationMassStringList

public List<String> fetchResiduePotentialModificationMassStringList()

Fetches residue potential modification mass string list with alternating key and value strings.

fetchRefinePotentialModificationMassStringList

public List<String> fetchRefinePotentialModificationMassStringList()

Fetches refine potential modification mass string list with alternating key and value strings.

fetchRefinePotentialModificationMass1StringList

public List<String> fetchRefinePotentialModificationMass1StringList()

Fetches refine potential modification mass 1 string list with alternating key and value strings.

fetchProteinCleavageSiteStringList

public List<String> fetchProteinCleavageSiteStringList()

Fetches protein cleavage site string list with alternating key and value strings.

uniqueStringItemList

public List<String> uniqueStringItemList(List<String> stringList)

Converts a list with String elements to a list with unique String elements by removing duplicate elements. Example: List with the four String elements "one", "two", "one", and "three" will be converted to a List with three String elements "one", "two", and "three".

Parameters:

stringList - List A list of String elements

Returns:

List A list of unique String elements

stringListToListString

public String stringListToListString(List<String> stringList,
                                     String delimiterString)

Converts a list with String elements to a list String with chosen delimiter string between elements. Element strings equal to null will be ignored, while element strings equal to empty strings will be added. Example: List with the three String elements "one", "two", and "three" will be converted to a List string "one, two, three" using delimiter string ", ".

Parameters:

stringList - List A list of String elements

delimiterString - String A string delimiting elements in list string

Returns:

String A string with a comma-delimited list