'****************************************************************************
'* 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: <to be filled in>. *
'* *
'****************************************************************************
'****************************************************************************
'* 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: MMConstModule.vb *
'* TYPE: VISUAL_BASIC *
'* *
'* CREATED: PM 2003-??-?? Vrs 1.0. *
'* UPDATED: PM 2004-xx-xx *
'* *
'****************************************************************************
Option Strict On
Option Explicit On
Public Module errDetectModule
Public Const ENUM_OFFSET_QUANTMODE As Integer = 101
Public Const ENUM_OFFSET_RAWFILEMODE As Integer = 229
Public Const ENUM_OFFSET_MSTYPES As Integer = 251
End Module 'errDetectModule
'Changed PM_FINNEGAN_RAWFILEMODE 2003-08-18
Public Enum rawFileModeEnum 'Note: the order of enumerators ís
' independent of the order in the Tools/Options dialog. That
' dependence is expressed in constants LISTINDEX_XYZ, etc.
enumAnalyst = ENUM_OFFSET_RAWFILEMODE
enumFinnegan
enumMicromass
End Enum 'rawFileModeEnum
'Changed PM_SPECTRUMDISPLAY_ZEDGRAPH 2007-09-19
Public Enum displayModeEnum
enumQS = 373
enumXCalibur
enumZedGraph
End Enum 'rawFileModeEnum
'Changed PM_MSTYPES_FOR_QUANT_OPTION 2004-09-13
Public Enum QuantMSTypesEnum 'Note: the order of enumerators ís
' independent of the order in the Tools/Options dialog. That
' dependence is expressed in constants LISTINDEX_XYZ, etc.
enumAllMStypes = ENUM_OFFSET_MSTYPES
enumMS_SIM
enumMSFullScan
End Enum 'QuantMSTypesEnum
Public Structure peptStruct
Dim monoMW As Double
Dim Sequence As String
End Structure 'peptStruct
Public Structure peakStruct
Dim mass As Double
Dim intensity As Double
Dim resolution As Integer
Dim massAcc As Double
Dim massLower As Double
Dim massHigher As Double
Dim isAveMass As Boolean
Dim isMatched As Boolean
Dim visited As Boolean
End Structure 'peakStruct
'Note: currently not used anywhere.
Public Structure entryStruct 'for the collection of protein entries of any peptide
Dim idx As Integer
Dim ID As String
Dim offsetInAASeq As Integer
End Structure 'entryStruct
Public Enum enzymeEnum
enumMmTrypsin = 1
enumMmASP_N = 2
End Enum 'enzymeEnum
'Note: currently not used anywhere.
Public Enum missedCleavEnum
enumZero
enumZeroAndProlineCut
enumZeroPlusWithinTwoAA
enumOne
enumTwo
enumThree
End Enum 'missedCleavEnum
Public Structure proteinStruct
Dim idx As Integer
Dim ID As String
Dim offsetInAASeq As Long
Dim AASeq As String
Dim similSList As SortedList 'Hashtable
'if we had sufficent memory the collection of peptides could also be here
End Structure 'proteinStruct
Public Structure peakSegStruct '
Dim massUpper As Double 'upper limit of this segment
Dim idxUpper As Integer ' index for the first meas peak higher than this segment
'how many measured peaks in this segment after dynamic exclusion
Dim numPeaksInSeg As Integer
End Structure 'peakSegStruct
Public Structure subScoreStruct
Dim segment As Integer
Dim n As Integer 'number of calculated fragments in the segment
Dim k As Integer 'current number of matching peaks
Dim kMax As Integer 'matching peptides at minimum subprobability
Dim subP As Double 'current sub score
Dim p As Double 'p the single probability from bionminal formula
Dim subPMax As Double 'probability as minimum subprobability
Dim segAccMassRange As Double 'mass interval in which calc frags could fall
Dim segDeltaM As Double 'mass interval spanned by the currently counted peaks
Dim segDeltaMMax As Double 'mass interval spanned by the counted peaks at min probab
End Structure 'subScoreStruct
Public Module MMConstModule
Public Const MIN_AA_TO_COUNT_PEPT As Integer = 5
Public Const SMALLEST_OBSERVABLE_PEPTIDE_MASS As Double = 800.0
Public Const LARGEST_OBSERVABLE_PEPTIDE_MASS As Double = 2400.0
Public Const MAX_NUM_FRAGMENTS_FROM_DAT_FILES As Integer = 1000
'Changed PM_INFINITE_FRAGMENTS 2005-08-09
'Public Const MAX_Y_IONS_TO_DISPLAY As Integer = 100
Public Const MAX_NUM_CALC_FRAGMENTS As Integer = 500
'equivalent square box distribution of masses is y[Da] = 0.05 + 0.0002*x[Da]
'to do: check this in more detail
Public Const MASS_DISTR_WIDTH_CO As Double = 0.05
Public Const MASS_DISTR_WIDTH_C1 As Double = 0.0002
Public Const NUM_SEGMENTS As Integer = 6
' Public Const SEG1UPPER As Double = 145.0
' Public Const SEG2UPPER As Double = 350.0
'Public Const SEG3UPPER As Double = 550.0
' Public Const SEG4UPPER As Double = 750.0
'Public Const SEG5UPPER As Double = 1000.0
'Public Const SEG6UPPER As Double = 100000.0
End Module 'errDetectModule
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