org.proteios.io
Class OMSSAParameterSetOptionsUtil

java.lang.Object
  org.proteios.io.OMSSAParameterSetOptionsUtil

public class OMSSAParameterSetOptionsUtil
extends Object

Author:

olle

Constructor Summary

OMSSAParameterSetOptionsUtil()
Default constructor.

Method Summary

List<String>	fetchEnzymeStringList() Fetches enzyme string list with alternating key and value strings.
List<String>	fetchFileTypeStringList() Fetches file type string list with alternating key and value strings.
List<String>	fetchIonTypeStringList() Fetches ion type string list with alternating key and value strings.
List<String>	fetchModificationStringList() Fetches modification string list with alternating key and value strings.
void	fetchOMSSASearchProperties() Fetches OMSSA search constants from Properties file.
List<String>	fetchOMSSAStringListFromLocalInstallation(String argument) Fetches OMSSA string list with alternating key and value strings from locally installed search engine.
List<String>	fetchOMSSAStringListFromWebInterface(String selectNameString) Fetches OMSSA 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

OMSSAParameterSetOptionsUtil

public OMSSAParameterSetOptionsUtil()

Default constructor.

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.

fetchOMSSASearchProperties

public void fetchOMSSASearchProperties()

Fetches OMSSA search constants from Properties file.

fetchFileTypeStringList

public List<String> fetchFileTypeStringList()

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

fetchEnzymeStringList

public List<String> fetchEnzymeStringList()

Fetches enzyme 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.

fetchIonTypeStringList

public List<String> fetchIonTypeStringList()

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

fetchOMSSAStringListFromWebInterface

public List<String> fetchOMSSAStringListFromWebInterface(String selectNameString)

Fetches OMSSA 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

fetchOMSSAStringListFromLocalInstallation

public List<String> fetchOMSSAStringListFromLocalInstallation(String argument)

Fetches OMSSA 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