Next-generation multiplexed targeted proteomics quantifies post-translational modifications in disease and compound-protein interactions with high throughput.

1. // Copyright(c) 2011 - 2018 Thermo Fisher Scientific - LSMS
2. //
3. // Permission is hereby granted, free of charge, to any person obtaining a copy
4. // of this software and associated documentation files (the "Software"), to deal
5. // in the Software without restriction, including without limitation the rights
6. // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
7. // copies of the Software, and to permit persons to whom the Software is
8. // furnished to do so, subject to the following conditions:
9. //
10. // The above copyright notice and this permission notice shall be included in all
11. // copies or substantial portions of the Software.
12. //
13. // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
14. // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
15. // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
16. // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
17. // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
18. // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
19. // SOFTWARE.
20. #include "StdAfx.h"
21. #include "ApiUsageTest.h"
22. #include "HandlerToResetEvent.h"
24. using namespace System::Reflection;
25. using namespace Microsoft::Win32;
27. using namespace Thermo::Interfaces::InstrumentAccess_V1;
28. using namespace Thermo::Interfaces::InstrumentAccess_V1::Control::Acquisition;
29. using namespace Thermo::Interfaces::ExactiveAccess_V1::Control::Acquisition;
31. namespace ManagedCppLoad
32. {
33. ApiUsageTest::ApiUsageTest()
34. {
35. }
36. ApiUsageTest::!ApiUsageTest()
37. {
38. m_instrument = nullptr; // no active destruction here
39. }
40. ApiUsageTest::~ApiUsageTest()
41. {
42. this->!ApiUsageTest();
43. }
45. // Return true if loading the API has been successful
46. bool ApiUsageTest::Load()
47. {
48. Console::Write(L"Loading Exactive Series API...");
49. try
50. {
51. Object^ o = LoadDirect();
52. IInstrumentAccessContainer^ iac = safe_cast<IInstrumentAccessContainer^>(o);
53. m_instrument = safe_cast<IExactiveInstrumentAccess^>(iac->Get(1));
54. }
55. catch (Exception^ e)
56. {
57. Console::WriteLine(L" failed to load API");
58. Console::WriteLine();
59. Console::WriteLine(e->ToString());
60. return false;
61. }
63. Console::WriteLine(L" API Loaded");
64. return true;
65. }
67. // Return true if the instrument is accessible within 10 seconds
68. bool ApiUsageTest::WaitForInstrument()
69. {
70. Console::Write(L"Waiting for instrument to become connected within 10 seconds...");
71. try
72. {
73. IExactiveAcquisition^ ea = m_instrument->Control->Acquisition;
74. if (!ea->WaitFor(TimeSpan::FromSeconds(10), SystemMode::Off, SystemMode::On, SystemMode::Standby))
75. {
76. Console::WriteLine(L" Sorry, system mode remained at {0}", ea->State->SystemMode);
77. return false;
78. }
79. // I cheated, we wait a maximum of 20 secs.
80. if (!ea->WaitFor(TimeSpan::FromSeconds(10), InstrumentState::Off, InstrumentState::StandBy, InstrumentState::ReadyToDownload))
81. {
82. Console::WriteLine(L" Sorry, instrument state remained at {0}", ea->State->SystemState);
83. return false;
84. }
85. }
86. catch (Exception^ e)
87. {
88. Console::WriteLine(L" failed to use the API");
89. Console::WriteLine();
90. Console::WriteLine(e->ToString());
91. return false;
92. }
93. Console::WriteLine(L" Instrument connected");
94. return true;
95. }
97. // Return the scans interface in a way that it is suitable to receive commands
98. IScans^ ApiUsageTest::GetWorkingScansInterface()
99. {
100. Console::Write(L"Placing custom scans and waiting for it to accept commands...");
102. IScans^ s = nullptr;
103. try
104. {
105. s = m_instrument->Control->GetScans(false);
107. // The interface is not usable until parameters are available, create a waiting mutex and wait on it.
108. AutoResetEvent^ waiter = gcnew AutoResetEvent((s->PossibleParameters != nullptr) && (s->PossibleParameters->Length > 0)); // auto-dispose
109. HandlerToResetEvent^ handler = gcnew HandlerToResetEvent(waiter); // auto-dispose
110. s->PossibleParametersChanged += gcnew System::EventHandler(handler, &HandlerToResetEvent::Handler);
111. waiter->WaitOne(1000); // 1 second should really be sufficient because we are already connected. Expect few ms to get this happen
112. s->PossibleParametersChanged -= gcnew System::EventHandler(handler, &HandlerToResetEvent::Handler);
113. if ((s->PossibleParameters == nullptr) || (s->PossibleParameters->Length == 0))
114. {
115. Console::WriteLine(L" Sorry, IScans interface node doesn't supply parameters for unknown reason");
116. return nullptr;
117. }
118. }
119. catch (System::Security::AccessControl::PrivilegeNotHeldException^ priv)
120. {
121. Console::WriteLine(L" cannot get IScans interface, missing privilege '{0}'", priv->PrivilegeName);
122. return nullptr;
123. }
124. catch (Exception^ e)
125. {
126. Console::WriteLine(L" cannot get IScans interface");
127. Console::WriteLine();
128. Console::WriteLine(e->ToString());
129. return nullptr;
130. }
132. // assume "Set" is part of the commands
133. Console::WriteLine(L"Available");
134. return s;
135. }
137. // Place two consecutive scans, one on positive, one in negative mode
138. void ApiUsageTest::PlaceScans(IScans^ scans)
139. {
140. Console::Write(L"Placing custom scans with different polarity...");
142. try
143. {
144. ICustomScan^ cs;
145. for (int i = 0; i < 5; i++)
146. {
147. cs = scans->CreateCustomScan();
148. cs->RunningNumber = 2001;
149. // assume we have one possible values "0" and "1" for polarity
150. cs->Values["Polarity"] = "0";
151. if (!scans->SetCustomScan(cs))
152. {
153. Console::WriteLine(L" cannot place custom scan for unknown reason");
154. return;
155. }
156. cs = scans->CreateCustomScan();
157. cs->RunningNumber = 2002;
158. // assume we have one possible values "0" and "1" for polarity
159. cs->Values["Polarity"] = "1";
160. if (!scans->SetCustomScan(cs))
161. {
162. Console::WriteLine(L" cannot place custom scan for unknown reason");
163. return;
164. }
165. }
166. }
167. catch (Exception^ e)
168. {
169. Console::WriteLine(L" cannot place custom scans");
170. Console::WriteLine();
171. Console::WriteLine(e->ToString());
172. }
173. Console::WriteLine(L" OK");
174. }
176. // New way of linking the API requires knowledge about class/namespace and the implementing API.
177. // Exactive's standard values can be found in the standard Xcalibur registry at
178. // HKLM\Software[\Wow6432Node]\Finnigan\Xcalibur\Devices\Thermo Exactive
179. // under the string values ApiFileName_Clr2_32_V1 and ApiClassName_Clr2_32_V1
180. Object^ ApiUsageTest::LoadDirect()
181. {
182. String^ asmName = nullptr;
183. String^ typeName = nullptr;
185. String^ baseName = String::Format(L"SOFTWARE{0}\\Finnigan\\Xcalibur\\Devices\\Thermo Exactive", (IntPtr::Size > 4) ? L"" : L"\\Wow6432Node");
186. RegistryKey^ key = Registry::LocalMachine->OpenSubKey(baseName);
187. if (key != nullptr)
188. {
189. asmName = safe_cast<String^>(key->GetValue(L"ApiFileName_Clr2_32_V1", nullptr));
190. typeName = safe_cast<String^>(key->GetValue(L"ApiClassName_Clr2_32_V1", nullptr));
191. key->Close();
192. }
193. if (String::IsNullOrEmpty(asmName) || String::IsNullOrEmpty(typeName))
194. {
195. Console::Error->WriteLine("Exactive is not registered or service hasn't been started one time.");
196. Environment::Exit(3);
197. }
199. Assembly^ assm = Assembly::LoadFrom(asmName);
200. Object^ o = assm->CreateInstance(typeName);
201. return o;
202. }
204. // Old way of linking to the API using COM. Disadvantages are strange error messages, late detection
205. // of bitness or CLR errors and too much .NET-magic
206. Object^ ApiUsageTest::LoadPerCom()
207. {
208. Type ^t = Type::GetTypeFromProgID("Thermo Exactive.API_Clr2_32_V1", true);
209. Object ^o = Activator::CreateInstance(t);
210. return o;
211. }
212. }

ApiUsageTest.cpp at commit c246dcc, under MIT · at the source