1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
|
#Specify the version being used as well as the language
cmake_minimum_required(VERSION 3.1)
#Name your project here
project(TopPIC)
SET(CMAKE_VERBOSE_MAKEFILE ON)
SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/../bin)
SET(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/../lib)
SET(CMAKE_INSTALL_PREFIX /usr)
SET(TOPPIC_DATA_DIR ${CMAKE_INSTALL_PREFIX}/share/toppic)
# Now configure the software with the TOPPIC_DATA_DIR variable.
configure_file(${CMAKE_SOURCE_DIR}/cmake/config.h.in
${CMAKE_BINARY_DIR}/config.h)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -std=c++11 -O3 -DWITHOUT_MZ5 -fPIC")
#SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -g -std=c++11 -DWITHOUT_MZ5 -fPIC")
#SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -std=c++11 -O2 -pg -fPIC")
message(STATUS "system name " ${CMAKE_SYSTEM_NAME})
# for Qt
set(CMAKE_AUTOMOC ON)
SET(CMAKE_INCLUDE_CURRENT_DIR ON)
set(CMAKE_AUTOUIC ON)
set(CMAKE_AUTORCC ON)
find_package(Qt5Widgets)
find_package(Qt5Core)
find_package(Qt5Gui)
# Find package PwizLite
find_package(PwizLite REQUIRED)
message(STATUS "PwizLite_INCLUDE_DIRS: ${PwizLite_INCLUDE_DIRS}")
message(STATUS "PwizLite_LIBRARIES: ${PwizLite_LIBRARIES}")
# To find package htslib, we first need to resort to the pkg-config
# program. Find it first.
find_package(PkgConfig REQUIRED)
# Now use it to search htslib (that is the name of the pc file).
pkg_search_module(HtsLib REQUIRED IMPORTED_TARGET htslib libhts)
message(STATUS "HtsLib_INCLUDE_DIRS: ${HtsLib_INCLUDE_DIRS}")
message(STATUS "HtsLib_LIBRARY: ${HtsLib_LIBRARY}")
IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
# Linux specific code
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DTOPPIC_LINUX")
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src
${CMAKE_CURRENT_SOURCE_DIR}/ext
${Qt5Widgets_INCLUDE_DIRS}
${Qt5Core_INCLUDE_DIRS}
${Qt5Gui_INCLUDE_DIRS}
${PwizLite_INCLUDE_DIRS}
${HtsLib_INCLUDE_DIRS}
)
ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
IF(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
# Windows specific code
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DTOPPIC_WINDOWS -DWIN32")
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src
${CMAKE_CURRENT_SOURCE_DIR}/ext
${Qt5Widgets_INCLUDE_DIRS}
${Qt5Core_INCLUDE_DIRS}
${Qt5Gui_INCLUDE_DIRS})
ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
message(STATUS "cmake cxx flags " ${CMAKE_CXX_FLAGS})
# pwiz
# Filippo Rusconi <lopippo@debian.org> Use the system library
# See below the target_link_libraries functions.
#file(GLOB PWIZ_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/utility/minimxml/*.cpp
#${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/utility/misc/*.cpp
#${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/data/common/*.cpp
#${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/data/msdata/*.cpp)
# hts
# Filippo Rusconi <lopippo@debian.org> Use the system library
# See below the target_link_libraries functions.
# file(GLOB HTS_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/ext/htslib/*.c)
# common
file(GLOB_RECURSE COMMON_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/common/*.cpp)
file(GLOB SEQ_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/seq/*.cpp)
file(GLOB SPEC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/ms/spec/*.cpp)
file(GLOB ENV_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/ms/env/*.cpp)
file(GLOB FEATURE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/ms/feature/*.cpp)
file(GLOB PRSM_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/prsm/*.cpp)
# classes for topfd
file(GLOB_RECURSE TOPFD_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/topfd/*.cpp)
# topfd console
file(GLOB TOPFD_CONSOLE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topfd_argument.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topfd.cpp)
# topfd gui
file(GLOB TOPFD_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topfd/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topfd/*.qrc)
# topfd_single console main
file(GLOB TOPFD_SINGLE_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topfd_single_process.cpp)
file(GLOB TOPFD_SINGLE_CONSOLE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topfd_single_argument.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topfd_single.cpp)
# classes for toppic
file(GLOB_RECURSE FILTER_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/filter/*.cpp)
file(GLOB ZERO_PTM_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/zeroptmsearch/*.cpp)
file(GLOB ONE_PTM_SEARCH_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/oneptmsearch/*.cpp)
file(GLOB PTM_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/ptmsearch/*.cpp)
file(GLOB TDGF_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/stat/tdgf/*.cpp)
file(GLOB LOCAL_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/stat/local/*.cpp)
file(GLOB VISUAL_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/visual/*.cpp)
# toppic console main
file(GLOB TOPPIC_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/toppic_process.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/toppic_argument.cpp)
file(GLOB TOPPIC_CONSOLE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/toppic.cpp)
# toppic gui main
file(GLOB TOPPIC_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/toppic/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/toppic/*.qrc)
# classes for topmg
file(GLOB TOPMG_FILTER_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/filter/massmatch/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/filter/oneptm/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/filter/diag/*.cpp)
file(GLOB GRAPH_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/graph/*.cpp)
file(GLOB GRAPH_ALIGN_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/graphalign/*.cpp)
file(GLOB MCMC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/stat/mcmc/*.cpp)
# topmg console main
file(GLOB TOPMG_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topmg_process.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topmg_argument.cpp)
file(GLOB TOPMG_CONSOLE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topmg.cpp)
# topmg gui main
file(GLOB TOPMG_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topmg/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topmg/*.qrc)
# topdiff classes
file(GLOB DIFF_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/merge/*.cpp)
# topdiff console main
file(GLOB TOPDIFF_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topdiff_process.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topdiff_argument.cpp)
file(GLOB TOPDIFF_CONSOLE_SRCS
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topdiff.cpp)
# topdiff gui main
file(GLOB TOPDIFF_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topdiff/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topdiff/*.qrc)
# unit test using catch
file(GLOB UNIT_TEST_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/test/*.cpp)
add_executable(topfd
${TOPFD_CONSOLE_SRCS} ${TOPFD_SRCS} ${SPEC_SRCS} ${ENV_SRCS}
${FEATURE_SRCS} ${PWIZ_SRCS} ${COMMON_SRCS})
#add_executable(topfd_single
# ${TOPFD_SINGLE_CONSOLE_SRCS} ${TOPFD_SINGLE_PROC_SRCS} ${TOPFD_SRCS}
# ${SPEC_SRCS} ${ENV_SRCS} ${PWIZ_SRCS} ${COMMON_SRCS})
add_executable(topfd_gui
${TOPFD_GUI_SRCS} ${TOPFD_SRCS} ${SPEC_SRCS} ${ENV_SRCS}
${FEATURE_SRCS} ${PWIZ_SRCS} ${COMMON_SRCS})
add_executable(toppic
${TOPPIC_CONSOLE_SRCS} ${TOPPIC_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
${SEQ_SRCS} ${SPEC_SRCS} ${ENV_SRCS} ${FEATURE_SRCS} ${PRSM_SRCS} ${FILTER_SRCS}
${ZERO_PTM_SRCS} ${ONE_PTM_SEARCH_SRCS} ${PTM_SRCS}
${TDGF_SRCS} ${LOCAL_SRCS} ${VISUAL_SRCS})
add_executable(toppic_gui
${TOPPIC_GUI_SRCS} ${TOPPIC_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
${SEQ_SRCS} ${SPEC_SRCS} ${ENV_SRCS} ${FEATURE_SRCS} ${PRSM_SRCS} ${FILTER_SRCS}
${ZERO_PTM_SRCS} ${ONE_PTM_SEARCH_SRCS} ${PTM_SRCS}
${TDGF_SRCS} ${LOCAL_SRCS} ${VISUAL_SRCS})
add_executable(topmg
${TOPMG_CONSOLE_SRCS} ${TOPMG_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
${SEQ_SRCS} ${SPEC_SRCS} ${ENV_SRCS} ${FEATURE_SRCS} ${PRSM_SRCS} ${TOPMG_FILTER_SRCS}
${ONE_PTM_SEARCH_SRCS} ${GRAPH_SRCS} ${GRAPH_ALIGN_SRCS} ${TDGF_SRCS}
${MCMC_SRCS} ${VISUAL_SRCS})
add_executable(topmg_gui
${TOPMG_GUI_SRCS} ${TOPMG_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
${SEQ_SRCS} ${SPEC_SRCS} ${ENV_SRCS} ${FEATURE_SRCS} ${PRSM_SRCS}
${TOPMG_FILTER_SRCS} ${ONE_PTM_SEARCH_SRCS}
${GRAPH_SRCS} ${GRAPH_ALIGN_SRCS} ${TDGF_SRCS}
${MCMC_SRCS} ${VISUAL_SRCS})
add_executable(topdiff
${TOPDIFF_CONSOLE_SRCS} ${TOPDIFF_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
${SEQ_SRCS} ${SPEC_SRCS} ${ENV_SRCS} ${FEATURE_SRCS} ${PRSM_SRCS} ${DIFF_SRCS})
add_executable(topdiff_gui ${TOPDIFF_GUI_SRCS} ${TOPDIFF_GUI_QRC}
${TOPDIFF_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
${SEQ_SRCS} ${SPEC_SRCS} ${ENV_SRCS} ${FEATURE_SRCS} ${PRSM_SRCS} ${DIFF_SRCS})
#add_executable(toppic_test
# ${TEST_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
# ${SEQ_SRCS} ${SPEC_SRCS} ${ENV_SRCS} ${FEATURE_SRCS} ${PRSM_SRCS} ${FILTER_SRCS}
# ${ZERO_PTM_SRCS} ${ONE_PTM_SEARCH_SRCS} ${PTM_SRCS}
# ${TDGF_SRCS} ${LOCAL_SRCS} ${VISUAL_SRCS})
#add_executable(toppic_match_peak ${TOPPIC_MATCH_PEAK_SRCS} ${TOPPIC_ARGU_SRCS} ${HTS_SRCS} ${BASE_SRCS} ${SPEC_SRCS} ${PRSM_SRCS} ${PRSM_VIEW_SRCS})
#add_executable(topfd_train ${TOPFD_TRAIN_SRCS} ${TOPFD_ARGU_SRCS} ${HTS_SRCS} ${BASE_SRCS} ${SPEC_SRCS} ${FEATURE_SRCS} ${PWIZ_SRC})
IF(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
target_link_libraries(topfd xerces-c
boost_program_options-mt boost_filesystem-mt
boost_system-mt boost_thread-mt
boost_iostreams-mt boost_chrono-mt pthread z Ws2_32)
# target_link_libraries(topfd_single xerces-c
# boost_program_options-mt boost_filesystem-mt
# boost_system-mt boost_thread-mt
# boost_iostreams-mt boost_chrono-mt pthread z Ws2_32)
target_link_libraries(toppic xerces-c
boost_filesystem-mt boost_system-mt
boost_program_options-mt boost_thread-mt pthread z Ws2_32)
target_link_libraries(topmg xerces-c
boost_filesystem-mt boost_system-mt
boost_program_options-mt boost_thread-mt pthread z Ws2_32)
target_link_libraries(topdiff xerces-c boost_program_options-mt
boost_filesystem-mt boost_system-mt boost_thread-mt pthread z Ws2_32)
# for Qt
SET(QTOPTION -Wl,-subsystem,windows)
target_link_libraries(topfd_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui
xerces-c boost_filesystem-mt boost_system-mt boost_thread-mt
boost_iostreams-mt boost_chrono-mt pthread z Ws2_32)
target_link_libraries(toppic_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui xerces-c
boost_filesystem-mt boost_system-mt
boost_program_options-mt boost_thread-mt pthread z Ws2_32)
target_link_libraries(topmg_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui xerces-c
boost_filesystem-mt boost_system-mt
boost_program_options-mt boost_thread-mt pthread z Ws2_32)
target_link_libraries(topdiff_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui xerces-c
boost_filesystem-mt boost_system-mt
boost_program_options-mt boost_thread-mt pthread z Ws2_32)
ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
# xerces-c boost_system, boost_thread boost_iostreams boost_chrono pthread z are required by
# ProteoWizard
IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
target_link_libraries(topfd xerces-c boost_program_options
boost_filesystem boost_system boost_thread boost_iostreams boost_chrono
PwizLite::PwizLite pthread z)
target_link_libraries(topfd_gui Qt5Widgets Qt5Core Qt5Gui
xerces-c boost_filesystem boost_system boost_thread boost_iostreams
boost_chrono PwizLite::PwizLite pthread z)
#target_link_libraries(topfd_single xerces-c boost_program_options
# boost_filesystem boost_system boost_thread boost_iostreams boost_chrono
# pthread z)
target_link_libraries(toppic xerces-c boost_program_options
boost_filesystem boost_system boost_thread PkgConfig::HtsLib pthread z)
target_link_libraries(toppic_gui Qt5Widgets Qt5Core Qt5Gui xerces-c boost_program_options
boost_filesystem boost_system boost_thread PkgConfig::HtsLib hts pthread z)
target_link_libraries(topmg xerces-c boost_program_options
boost_filesystem boost_system boost_thread PkgConfig::HtsLib pthread z)
target_link_libraries(topmg_gui Qt5Widgets Qt5Core Qt5Gui xerces-c boost_program_options
boost_filesystem boost_system boost_thread PkgConfig::HtsLib pthread z)
target_link_libraries(topdiff xerces-c boost_program_options
boost_filesystem boost_system boost_thread PkgConfig::HtsLib pthread z)
target_link_libraries(topdiff_gui Qt5Widgets Qt5Core Qt5Gui
xerces-c boost_program_options boost_filesystem boost_system boost_thread boost_iostreams
PkgConfig::HtsLib pthread z)
# target_link_libraries(toppic_test xerces-c boost_program_options
# boost_filesystem boost_system boost_thread pthread z)
# target_link_libraries(toppic_match_peak xerces-c boost_program_options
# boost_filesystem boost_system boost_thread pthread z)
# target_link_libraries(topfd_train xerces-c boost_program_options
# boost_filesystem boost_system boost_thread boost_iostreams boost_chrono pthread z)
#file(MAKE_DIRECTORY ${CMAKE_INSTALL_PREFIX}/usr/bin)
install (TARGETS topfd toppic toppic_gui topmg topmg_gui topdiff topdiff_gui DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
install (DIRECTORY toppic_resources/ DESTINATION ${TOPPIC_DATA_DIR})
ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
|
