# This document lists all the files to be included in the
# standard release of Inspect.  The script Release.py is
# responsible for parsing this file, copying stuff as
# needed, and zipping the release.

####################################
# Inspect source code (to be kept in synch with Makefile):
base64.c
BN.c
BuildMS2DB.c
ChargeState.c
CMemLeak.c
Errors.c
ExonGraphAlign.c
FreeMod.c
main.c
Mods.c
MS2DB.c
ParseInput.c
ParseXML.c
PValue.c
Run.c
Score.c
Scorpion.c
SNP.c
Spectrum.c
Spliced.c
SpliceDB.c
SpliceScan.c
SVM.c
Tagger.c
Trie.c
TagFile.c
Utils.c
base64.h
BN.h
BuildMS2DB.h
ChargeState.h
CMemLeak.h
Errors.h
ExonGraphAlign.h
FreeMod.h
Inspect.h
Mods.h
MS2DB.h
ParseInput.h
ParseXML.h
PValue.h
Run.h
Score.h
Scorpion.h
SNP.h
Spectrum.h
Spliced.h
SpliceDB.h
SpliceScan.h
SVM.h
Tagger.h
Trie.h
TagFile.h
Utils.h
LDA.c
LDA.h
ParentMass.c
ParentMass.h
IonScoring.c
IonScoring.h
TagFile.c
TagFile.h

# Other build-specific files:
Inspect.sln
Inspect.vcproj
Makefile
ReleaseFiles.txt
BuildInspect.py

####################################
# Executables and dlls:
#Inspect.exe
#libexpat.dll

####################################
# PyInspect stuff:
PyInspect.pyd
PyInspect/PyInspect.c
PyInspect/PySpectrum.c
PyInspect/PySpectrum.h
PyInspect/PyUtils.c
PyInspect/PyUtils.h
ReleasePyInspect.py

####################################
# PySVM stuff:
PySVM.pyd
PySVM/PySVM.c
PySVM/PySVM.sln
PySVM/PySVM.vcproj
PySVM/svm-predict.c
PySVM/svm.cpp
PySVM/svm.h
ReleasePySVM.py

####################################
# Inspect data files:
AminoAcidMasses.txt
InVivoModifications.txt
InVitroModifications.txt
CCSVM1.model
CCSVM1.range
CCSVM2.model
CCSVM2.range
Ch2BNPEP.dat
Ch2BNPEPQ.dat
Ch3BNPEP.dat
Ch3BNPEPQ.dat
IsotopePatterns.txt
PMCLDA1.model
PMCLDA2.model
PMCLDA3.model
PRM2.dat
PRM3.dat
PRMQ2.dat
PRMQ3.dat
PTMods.txt
ScoringModel.dat
Database/CommonContaminants.fasta
TagSkewScores.dat
PRM2.bn
PRM3.bn
TAG2.bn
TAG3.bn
MQScoreSVM2.model
MQScoreSVM2.range
MQScoreSVM3.model
MQScoreSVM3.range
MQScoreLDA2.model
MQScoreLDA3.model
PhosCut2.bn
PhosCut3.bn
CCSVM2Phos.model
CCSVM2Phos.range
PMCLDA2Phos.model
PMCLDA3Phos.model

####################################
# Documentation:
docs/Analysis.html
docs/Copyright.html
docs/Database.html
docs/index.html
docs/Installation.html
docs/MS2DB.html
docs/Searching.html
docs/UnrestrictedSearchTutorial.pdf
docs/RunningInspectOnTheFWGrid.pdf
docs/InspectTutorial.pdf
docs/PLSTutorial.pdf

####################################
# Analysis scripts:
BasicStats.py
Global.py
Label.py
LDA.py
Learning.py
MakeImage.py
MSSpectrum.py
PrepDB.py
PLSUtils.py
FDRUtils.py
ResultsParser.py
Score.py
SelectProteins.py
ShuffleDB.py
Summary.py
SystemTest.py
Utils.py
ParseXML.py
InspectToPepXML.py
ProteinGrouper.py
TrieUtils.py
ComputeFScore.py
ComputeFDR.jar
BuildMS2DB.jar
MS2DBShuffler.jar

####################################
# Old PTM analysis scripts:
ExplainPTMs.py
PTMChooserLM.py
PTMDatabase.txt

####################################
# New PTM analysis scripts:
ComputePTMFeatures.py
CombinePTMFeatures.py
BuildMGF.py
PTMSearchBigDB.py
TrainPTMFeatures.py
AdjustPTM.py
BuildConsensusSpectrum.py
PTMAnalysis.py
SpectralSimilarity.py
RunPySVM.py
CompareHEKPTM.py
GetByteOffset.py
StripPTM.py
PhosphateLocalization.py

####################################
# System tests:
SystemTest/TestInput.txt
SystemTest/TestInputMod.txt
SystemTest/TestPMC.txt
SystemTest/TestSpectrum.dta
SystemTest/TestSpectra.pkl
SystemTest/TestInputTag1.txt
SystemTest/TestInputTag3.txt
SystemTest/SimpleChromosome.trie
SystemTest/SimpleGenes.gff
SystemTest/BuildSimpleChromosome.txt
SystemTest/TestMS2.txt
SystemTest/Yeast.ms2
SystemTest/YeastSmall.fasta
Database/TestDatabase.index
Database/TestDatabase.trie
SystemTest/Shew_Short.fasta
SystemTest/TestCDTA.txt
SystemTest/Shew_dta.txt


# Not for production use:
#TestSuite.py
