'****************************************************************************
'* Copyright (C) 2004 Peter Mortensen and Matthias Mann *
'* This file is part of MSQuant. *
'* *
'* MSQuant is distributed under the terms of *
'* the GNU General Public License. See src/COPYING.TXT or *
'* <http://www.gnu.org/licenses/gpl.txt> for details. *
'* *
'* MSQuant is free software; you can redistribute it *
'* and/or modify it under the terms of the GNU *
'* General Public License as published by the Free *
'* Software Foundation; either version 2 of the *
'* License, or (at your option) any later version. *
'* *
'* MSQuant is distributed in the hope that it will be *
'* useful, but WITHOUT ANY WARRANTY; without even the *
'* implied warranty of MERCHANTABILITY or FITNESS FOR *
'* A PARTICULAR PURPOSE. See the GNU General Public *
'* License for more details. *
'* *
'* You should have received a copy of the GNU General *
'* Public License along with MSQuant; if not, write to *
'* the Free Software Foundation, Inc., 59 Temple *
'* Place, Suite 330, Boston, MA 02111-1307 USA *
'* *
'* Purpose: old stuff to be removed, including old quantitation modes *
'* stuff *
'* *
'* *
'****************************************************************************
'****************************************************************************
'* CEBI *
'* Software Development Group *
'* Peter Mortensen *
'* E-mail: NUKESPAMMERSdrmortensen@get2netZZZZZZ.dk *
'* WWW: http://www.cebi.sdu.dk/ *
'* *
'* Program for post-processing of result from search in mass *
'* spectrometric data. *
'* *
'* FILENAME: MSQuantCommon_obsolete.vb *
'* TYPE: VISUAL_BASIC *
'* *
'* CREATED: PM 2005-04-19 Vrs 1.0. Moved from somewhere else. *
'* UPDATED: PM 2005-xx-xx *
'* *
'****************************************************************************
'Note: newer class, QuantitationModes_moreGeneral, is (currently)
' somewhere else.
Imports MolecularSharedStructures
Namespace obsolete
'Put in here at a later date: simpleModificationSpecification,
' SortByGUIIndexOrder, QuantitationModes, etc.
End Namespace 'obsolete
'****************************************************************************
'd$ <summary>
'd$ Purpose: namespace general description
'd$ <see cref="T:VBXMLDoc.CVBXMLDoc" />.
'd$ <isUnitTest></isUnitTest>
'd$ <applicationname>test_rawDataFileHandling</applicationname>
'd$ <author>Peter Mortensen</author>
'd$ <seealso>http://www.cebi.sdu.dk/</seealso>
'd$ <codetype>PLATFORM independent / GUI</codetype>
'd$ </summary>
Namespace massSpectrometryBase
'Changed PM_MARKER_DELETE 2007-03-14
' Delete at any time
'
' 'Changed PM_GENERALISED_QUANT_MODE 2003-12-07
' '****************************************************************************
' '* SUBROUTINE NAME: SortByGUIIndexOrder *
' 'd$ <summary> N/A. ...
' 'd$ Note: xyz </summary>
' Class SortByGUIIndexOrder
' Implements System.Collections.Generic.IComparer( _
' Of quantitationModeStructure)
' Function Compare( _
' ByVal aItem1 As quantitationModeStructure, _
' ByVal aItem2 As quantitationModeStructure) _
' As Integer _
' Implements _
' System.Collections.Generic.IComparer( _
' Of quantitationModeStructure).Compare
'
' Dim toReturn As Integer = 0
' If aItem1.xxxGUInameIndex > aItem2.xxxGUInameIndex Then
' toReturn = 1
' Else
' If aItem1.xxxGUInameIndex < aItem2.xxxGUInameIndex Then
' toReturn = -1
' Else
' 'Equal....
' Dim peter9 As Integer = 9
' End If
' End If
' Return toReturn
' End Function 'Compare
' End Class 'SortByGUIIndexOrder
'****************************************************************************
'd$ <summary>
'd$ Purpose: Handles the user defined quantitaion modes.
'd$ It was created because putting it the application object
'd$ would create intolerable dependencies for
'd$ the DTASuperCharge project.
'd$
'd$ <see cref="T:VBXMLDoc.CVBXMLDoc" />.
'd$ <applicationname>test_rawDataFileHandling</applicationname>
'd$ <author>Peter Mortensen</author>
'd$ <seealso>http://www.cebi.sdu.dk/</seealso>
'd$ <codetype>PLATFORM independent / GUI</codetype>
'd$ </summary>
Public NotInheritable Class QuantitationModes
'Changed PM_GENERALISED_QUANT_MODE 2003-12-06
'Dim mQuantSpecList As ArrayList 'Type is quantitationModeStructure
Dim mQuantSpecList2 As Generic.List(Of quantitationModeStructure)
Dim mQuantModList As ArrayList 'Type is quantModification
'****************************************************************************
'* SUBROUTINE NAME: New *
'd$ <summary>Constructor</summary>
Public Sub New()
MyBase.New() 'Is this necessary? Yes!
'InitializeComponent() Is this necessary??
End Sub 'New()
'Changed PM_MARKER_DELETE 2007-03-14
' Delete at any time
'
' 'Changed PM_QUANTMODES_VERSIONING 2004-02-19
' '****************************************************************************
' '* <placeholder for header> *
' '****************************************************************************
' Public Shared Function defaultQuantModefields() _
' As quantitationModeStructure
'
' Dim toReturn As quantitationModeStructure
' toReturn.uniqueID = -1
' toReturn.numberOfMods = 0
' toReturn.firstModID = 0
' toReturn.secondModID = 0
' toReturn.GUIname = "Unknown quantitation mode"
' toReturn.xxxGUInameIndex = -1
' toReturn.baseModification = 0
'
' Return toReturn
' End Function 'defaultQuantModefields
'Changed PM_MARKER_DELETE 2007-03-14
' Delete at any time
'
' 'Changed PM_GENERALISED_QUANT_MODE 2003-12-04
' '****************************************************************************
' '* <placeholder for header> *
' '****************************************************************************
' Public Shared Sub old_addNewQuantMode( _
' ByVal aUniqueID As Integer, ByVal aNumberOfMods As Integer, _
' ByVal aFirstModID As Integer, ByVal aSecondModID As Integer, _
' ByVal aGUIname As String, ByVal aGUInameIndex As Integer, _
' ByVal aBaseModification As Integer, _
' ByRef anInOutQuantSpecList2 As Generic.List(Of quantitationModeStructure))
' 'Old:
' ' ByRef anInOutQuantSpecList As ArrayList
'
' Dim newQuant As quantitationModeStructure = _
' defaultQuantModefields()
' newQuant.uniqueID = aUniqueID
' newQuant.numberOfMods = aNumberOfMods
' newQuant.firstModID = aFirstModID
' newQuant.secondModID = aSecondModID
' newQuant.GUIname = aGUIname
' newQuant.xxxGUInameIndex = aGUInameIndex
'
' newQuant.baseModification = aBaseModification
'
' anInOutQuantSpecList2.Add(newQuant)
' End Sub 'old_addNewQuantMode
'****************************************************************************
'* SUBROUTINE NAME: getFullQuantDefinition *
'd$ <summary> N/A </summary>
Public Sub getFullQuantDefinitions( _
ByRef anOutFullQuantDefinitions As _
fullQuantDefinitionsStructure)
anOutFullQuantDefinitions = _
New fullQuantDefinitionsStructure
anOutFullQuantDefinitions.quantSpecList2 = mQuantSpecList2
anOutFullQuantDefinitions.quantModList = mQuantModList
End Sub 'getFullQuantDefinitions
'****************************************************************************
'* SUBROUTINE NAME: setFullQuantDefinitions *
'd$ <summary> N/A </summary>
Public Sub setFullQuantDefinitions( _
ByRef anInFullQuantDefinitions As _
fullQuantDefinitionsStructure)
mQuantSpecList2 = anInFullQuantDefinitions.quantSpecList2
mQuantModList = anInFullQuantDefinitions.quantModList
End Sub 'setFullQuantDefinitions
'Changed PM_GENERALISED_QUANT_MODE 2003-12-07
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Function isNoQuantitationMode(ByVal aQuantModeCode As Integer) _
As Boolean
Dim toReturn As Boolean = False
Dim found As Boolean = False 'For error checking
Dim quantModeItem As quantitationModeStructure
For Each quantModeItem In mQuantSpecList2
If quantModeItem.uniqueID = aQuantModeCode Then
toReturn = quantModeItem.numberOfMods = 0
found = True
Exit For
End If
Next
Trace.Assert(found, _
"PIL ASSERT. Unknown quantitation code: " & aQuantModeCode)
Return toReturn
End Function 'isNoQuantitationMode
'Changed PM_GENERALISED_QUANT_MODE 2003-12-07
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Function getQuantitationMode( _
ByVal aQuantModeCode As Integer) _
As quantitationModeStructure
Dim toReturn As quantitationModeStructure
toReturn.GUIname = Nothing 'Keep compiler happy.
toReturn.uniqueID = -1 'For error chekcing
Dim quantModeItem As quantitationModeStructure
For Each quantModeItem In mQuantSpecList2
If quantModeItem.uniqueID = aQuantModeCode Then
toReturn = quantModeItem
Exit For
End If
Next
Trace.Assert(toReturn.uniqueID >= 0, _
"PIL ASSERT. Unknown quantitation code: " & aQuantModeCode)
Return toReturn
End Function 'getQuantitationMode
'Is this function needed????
'Changed PM_GENERALISED_QUANT_MODE 2003-12-08
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Function getQuantModification7( _
ByVal aQuantModificationCode As Integer) _
As quantModificationStructure
Dim toReturn As quantModificationStructure = _
massSpectrometryBase.quantitation.QuantitationModes_moreGeneral.blankQuantModification() 'Keep compiler happy.
toReturn.quantModificationID = -1 'For error chekcing
Dim quantModificationItem As quantModificationStructure
For Each quantModificationItem In mQuantModList
If quantModificationItem.quantModificationID = aQuantModificationCode Then
toReturn = quantModificationItem
Exit For
End If
Next
Trace.Assert(toReturn.quantModificationID >= 0, _
"PIL ASSERT. Unknown quantitation modification code: " & _
aQuantModificationCode)
Return toReturn
End Function 'getQuantModification
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Function getQuantModificationsList() _
As ArrayList 'Type is quantModification.
Return mQuantModList
End Function 'getQuantModificationsList
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Function getFirstQuantitationCode() As Integer
Dim toReturn As Integer = -1
Trace.Assert(mQuantSpecList2.Count > 0, "PIL ASSERT. mQuantSpecList is empty!")
Dim firstInList As quantitationModeStructure = mQuantSpecList2(0)
toReturn = firstInList.uniqueID
Return toReturn
End Function 'getFirstQuantitationCode
'Changed PM_QUANTGENERAL_PREPARATION 2006-07-13. Needed?
' '****************************************************************************
' '* <placeholder for header> *
' '* anInList: type is quantModCount *
' '****************************************************************************
' Public Function constructSimpleModificationList2( _
' ByRef anInList As ArrayList) As ArrayList
'
' Dim toReturn As ArrayList = New ArrayList 'Type is simpleModificationSpecification
' If Not anInList Is Nothing Then
' Dim inputItem As modificationCountStructure
' For Each inputItem In anInList
'
' Dim ID As Integer = inputItem.quantModificationID
' Dim quantInfo As quantModificationStructure = _
' getQuantModification(ID)
'
' Dim outItem As massSpectrometryBase.quantitation.simpleModificationSpecification
' outItem.diffFromBase = quantInfo.massDiffFromBase
' outItem.AA = quantInfo.AA
' toReturn.Add(outItem)
' Next
' End If
' Return toReturn
' End Function 'constructSimpleModificationList
End Class 'QuantitationModes
End Namespace 'massSpectrometryBase
Generated by script codePublish.pl at 2009-01-05T15:20:59.