org.proteios.io
Class MascotParameterSetOptionsUtil

java.lang.Object
  org.proteios.io.MascotParameterSetOptionsUtil

public class MascotParameterSetOptionsUtil
extends Object

Author:

olle

Constructor Summary

MascotParameterSetOptionsUtil()
Default constructor.

MascotParameterSetOptionsUtil(String searchType)
Constructor with search type argument.

Method Summary

List<String>	fetchDataFormatStringList() Fetches data format string list with alternating key and value strings.
List<String>	fetchEnzymeStringList() Fetches enzyme string list with alternating key and value strings.
List<String>	fetchInstrumentStringList() Fetches instrument string list with alternating key and value strings.
void	fetchMascotSearchProperties() Fetches Mascot search constants from Properties file.
List<String>	fetchMascotStringListFromLocalInstallation(String argument) Fetches Mascot string list with alternating key and value strings from locally installed search engine.
List<String>	fetchMascotStringListFromWebInterface(String selectNameString) Fetches Mascot string list with alternating key and value strings.
List<String>	fetchMassIonTypeStringList() Fetches mass ion type string list with alternating key and value strings.
List<String>	fetchMassTypeStringList() Fetches mass type string list with alternating key and value strings.
List<String>	fetchMissedCleavagesStringList() Fetches missed cleavages string list with alternating key and value strings.
List<String>	fetchModificationStringList() Fetches modification string list with alternating key and value strings.
List<String>	fetchMsMsTolUnitStringList() Fetches MS-MS tolerance unit string list with alternating key and value strings.
List<String>	fetchPeptideChargeStringList() Fetches peptide charge string list with alternating key and value strings.
List<String>	fetchPeptideIsotopeErrorStringList() Fetches peptide isotope error string list with alternating key and value strings.
List<String>	fetchPeptideTolUnitStringList() Fetches peptide tolerance unit string list with alternating key and value strings.
List<String>	fetchQuantitationStringList() Fetches quantitation string list with alternating key and value strings.
List<String>	fetchReportTopStringList() Fetches report top string list with alternating key and value strings.
List<String>	fetchSequenceLibraryStringList() Fetches sequence library (database) string list with alternating key and value strings.
List<String>	fetchSpeciesStringList() Fetches species string list with alternating key and value strings.
boolean	isWebInterfaceUsed() Get webInterfaceUsed flag.
void	setWebInterfaceUsed(boolean webInterfaceUsed) Set webInterfaceUsed flag.
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

MascotParameterSetOptionsUtil

public MascotParameterSetOptionsUtil()

Default constructor.

MascotParameterSetOptionsUtil

public MascotParameterSetOptionsUtil(String searchType)

Constructor with search type argument.

Parameters:

searchType - String The Mascot searchType to use.

Method Detail

isWebInterfaceUsed

public boolean isWebInterfaceUsed()

Get webInterfaceUsed flag.

Returns:

boolean Flag for using web interface.

setWebInterfaceUsed

public void setWebInterfaceUsed(boolean webInterfaceUsed)

Set webInterfaceUsed flag.

Parameters:

webInterfaceUsed - boolean Flag for using web interface.

fetchMascotSearchProperties

public void fetchMascotSearchProperties()

Fetches Mascot search constants from Properties file.

fetchEnzymeStringList

public List<String> fetchEnzymeStringList()

Fetches enzyme string list with alternating key and value strings.

fetchMissedCleavagesStringList

public List<String> fetchMissedCleavagesStringList()

Fetches missed cleavages string list with alternating key and value strings.

fetchSequenceLibraryStringList

public List<String> fetchSequenceLibraryStringList()

Fetches sequence library (database) string list with alternating key and value strings.

fetchSpeciesStringList

public List<String> fetchSpeciesStringList()

Fetches species string list with alternating key and value strings.

fetchModificationStringList

public List<String> fetchModificationStringList()

Fetches modification string list with alternating key and value strings.

fetchQuantitationStringList

public List<String> fetchQuantitationStringList()

Fetches quantitation string list with alternating key and value strings.

fetchPeptideTolUnitStringList

public List<String> fetchPeptideTolUnitStringList()

Fetches peptide tolerance unit string list with alternating key and value strings.

fetchPeptideIsotopeErrorStringList

public List<String> fetchPeptideIsotopeErrorStringList()

Fetches peptide isotope error string list with alternating key and value strings.

fetchMsMsTolUnitStringList

public List<String> fetchMsMsTolUnitStringList()

Fetches MS-MS tolerance unit string list with alternating key and value strings.

fetchPeptideChargeStringList

public List<String> fetchPeptideChargeStringList()

Fetches peptide charge string list with alternating key and value strings.

fetchMassTypeStringList

public List<String> fetchMassTypeStringList()

Fetches mass type string list with alternating key and value strings.

fetchMassIonTypeStringList

public List<String> fetchMassIonTypeStringList()

Fetches mass ion type string list with alternating key and value strings.

fetchDataFormatStringList

public List<String> fetchDataFormatStringList()

Fetches data format string list with alternating key and value strings.

fetchInstrumentStringList

public List<String> fetchInstrumentStringList()

Fetches instrument string list with alternating key and value strings.

fetchReportTopStringList

public List<String> fetchReportTopStringList()

Fetches report top string list with alternating key and value strings.

fetchMascotStringListFromWebInterface

public List<String> fetchMascotStringListFromWebInterface(String selectNameString)

Fetches Mascot string list with alternating key and value strings. The Html ... block contains the trigger _selectNameString_ string in the start tag: .

Parameters:

selectNameString - String The special "name" string to look for

Returns:

List A list with alternating key and value strings

fetchMascotStringListFromLocalInstallation

public List<String> fetchMascotStringListFromLocalInstallation(String argument)

Fetches Mascot string list with alternating key and value strings from locally installed search engine.

Parameters:

argument - String Argument to give to program to print option list

Returns:

List A 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