1. mzR
  2. src
  3. pwiz
  4. data
  5. identdata
  6. IdentDataFile.cpp
Browse code

Updating pwiz to 3_0_21263

Steffen Neumann authored on 23/09/2021 12:34:25
Showing1 changed files
src/pwiz/data/identdata/IdentDataFile.cpp
History View file @72fef926d8
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,212 @@
1 
+//
2 
+// $Id$
3 
+//
4 
+//
5 
+// Original author: Robert Burke <robert.burke@proteowizard.org>
6 
+//
7 
+// Copyright 2009 Spielberg Family Center for Applied Proteomics
8 
+//   University of Southern California, Los Angeles, California  90033
9 
+//
10 
+// Licensed under the Apache License, Version 2.0 (the "License");
11 
+// you may not use this file except in compliance with the License.
12 
+// You may obtain a copy of the License at
13 
+//
14 
+// http://www.apache.org/licenses/LICENSE-2.0
15 
+//
16 
+// Unless required by applicable law or agreed to in writing, software
17 
+// distributed under the License is distributed on an "AS IS" BASIS,
18 
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19 
+// See the License for the specific language governing permissions and
20 
+// limitations under the License.
21 
+//
22 
+
23 
+#define PWIZ_SOURCE
24 
+
25 
+#include "IdentDataFile.hpp"
26 
+#include "TextWriter.hpp"
27 
+#include "Serializer_mzid.hpp"
28 
+#include "Serializer_pepXML.hpp"
29 
+#include "DefaultReaderList.hpp"
30 
+#include "pwiz/utility/misc/Filesystem.hpp"
31 
+#include "pwiz/utility/misc/Std.hpp"
32 
+#include "pwiz/utility/minimxml/XMLWriter.hpp" // for charcounter defn
33 
+#include "boost/iostreams/device/file.hpp"
34 
+#include "boost/iostreams/filtering_stream.hpp"
35 
+#include "boost/iostreams/filter/gzip.hpp"
36 
+
37 
+
38 
+namespace pwiz {
39 
+namespace identdata {
40 
+
41 
+
42 
+using namespace pwiz::util;
43 
+
44 
+
45 
+namespace {
46 
+
47 
+
48 
+void readFile(const string& filename,
49 
+              IdentData& mzid,
50 
+              const Reader& reader,
51 
+              const string& head,
52 
+              const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
53 
+              bool ignoreSequenceCollectionAndAnalysisData)
54 
+{
55 
+    if (!reader.accept(filename, head))
56 
+        throw runtime_error("[IdentDataFile::readFile()] Unsupported file format.");
57 
+
58 
+    Reader::Config config;
59 
+    config.ignoreSequenceCollectionAndAnalysisData = ignoreSequenceCollectionAndAnalysisData;
60 
+    config.iterationListenerRegistry = iterationListenerRegistry;
61 
+    reader.read(filename, head, mzid, config);
62 
+}
63 
+
64 
+
65 
+shared_ptr<DefaultReaderList> defaultReaderList_;
66 
+
67 
+
68 
+} // namespace
69 
+
70 
+
71 
+PWIZ_API_DECL IdentDataFile::IdentDataFile(const string& filename,
72 
+                                           const Reader* reader,
73 
+                                           const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
74 
+                                           bool ignoreSequenceCollectionAndAnalysisData)
75 
+{
76 
+    // peek at head of file
77 
+    string head = read_file_header(filename, 512);
78 
+
79 
+    if (reader)
80 
+    {
81 
+        readFile(filename, *this, *reader, head, iterationListenerRegistry, ignoreSequenceCollectionAndAnalysisData);
82 
+    }
83 
+    else
84 
+    {
85 
+        if (!defaultReaderList_.get())
86 
+            defaultReaderList_ = shared_ptr<DefaultReaderList>(new DefaultReaderList);
87 
+        readFile(filename, *this, *defaultReaderList_, head, iterationListenerRegistry, ignoreSequenceCollectionAndAnalysisData);
88 
+    }
89 
+}
90 
+
91 
+
92 
+PWIZ_API_DECL
93 
+void IdentDataFile::write(const string& filename,
94 
+                          const WriteConfig& config,
95 
+                          const IterationListenerRegistry* iterationListenerRegistry)
96 
+{
97 
+    write(*this, filename, config, iterationListenerRegistry);
98 
+}
99 
+
100 
+
101 
+PWIZ_API_DECL
102 
+void IdentDataFile::write(ostream& os,
103 
+                          const std::string& filename,
104 
+                          const WriteConfig& config,
105 
+                          const IterationListenerRegistry* iterationListenerRegistry)
106 
+{
107 
+    write(*this, filename, os, config, iterationListenerRegistry);
108 
+}
109 
+
110 
+
111 
+namespace {
112 
+
113 
+
114 
+shared_ptr<ostream> openFile(const string& filename)
115 
+{
116 
+    shared_ptr<ostream> result(new ofstream(filename.c_str(), ios::binary));
117 
+
118 
+    if (!result.get() || !*result)
119 
+        throw runtime_error(("[IdentDataFile::openFile()] Unable to open file " + filename).c_str());
120 
+
121 
+    return result;
122 
+}
123 
+
124 
+
125 
+void writeStream(ostream& os, const IdentData& idd, const string& filename,
126 
+                 const IdentDataFile::WriteConfig& config,
127 
+                 const IterationListenerRegistry* iterationListenerRegistry)
128 
+{
129 
+    switch (config.format)
130 
+    {
131 
+        case IdentDataFile::Format_Text:
132 
+        {
133 
+            TextWriter(os,0)(idd);
134 
+            break;
135 
+        }
136 
+
137 
+        case IdentDataFile::Format_MzIdentML:
138 
+        {
139 
+            Serializer_mzIdentML serializer;
140 
+            serializer.write(os, idd, iterationListenerRegistry);
141 
+            break;
142 
+        }
143 
+
144 
+        case IdentDataFile::Format_pepXML:
145 
+        {
146 
+            Serializer_pepXML serializer;
147 
+            serializer.write(os, idd, filename, iterationListenerRegistry);
148 
+            break;
149 
+        }
150 
+
151 
+        default:
152 
+            throw runtime_error("[IdentDataFile::write()] Format not implemented.");
153 
+    }
154 
+}
155 
+
156 
+
157 
+} // namespace
158 
+
159 
+
160 
+PWIZ_API_DECL
161 
+void IdentDataFile::write(const IdentData& idd,
162 
+                          const string& filename,
163 
+                          const WriteConfig& config,
164 
+                          const IterationListenerRegistry* iterationListenerRegistry)
165 
+{
166 
+    shared_ptr<ostream> os = openFile(filename);
167 
+    writeStream(*os, idd, filename, config, iterationListenerRegistry);
168 
+}
169 
+
170 
+
171 
+PWIZ_API_DECL
172 
+void IdentDataFile::write(const IdentData& idd,
173 
+                          const string& filename,
174 
+                          ostream& os,
175 
+                          const WriteConfig& config,
176 
+                          const IterationListenerRegistry* iterationListenerRegistry)
177 
+{
178 
+    WriteConfig config2(config);
179 
+    //config2.gzipped = false;
180 
+    writeStream(os, idd, filename, config2, iterationListenerRegistry);
181 
+}
182 
+
183 
+
184 
+PWIZ_API_DECL ostream& operator<<(ostream& os, IdentDataFile::Format format)
185 
+{
186 
+    switch (format)
187 
+    {
188 
+        case IdentDataFile::Format_Text:
189 
+            os << "Text";
190 
+            return os;
191 
+        case IdentDataFile::Format_MzIdentML:
192 
+            os << "mzIdentML";
193 
+            return os;
194 
+        case IdentDataFile::Format_pepXML:
195 
+            os << "pepXML";
196 
+            return os;
197 
+        default:
198 
+            os << "Unknown";
199 
+            return os;
200 
+    }
201 
+}
202 
+
203 
+
204 
+PWIZ_API_DECL ostream& operator<<(ostream& os, const IdentDataFile::WriteConfig& config)
205 
+{
206 
+    os << config.format;
207 
+    return os;
208 
+}
209 
+
210 
+
211 
+} // namespace identdata
212 
+} // namespace pwiz
Browse code

Removed old pwiz code

Steffen Neumann authored on 22/09/2021 10:40:31
Showing1 changed files
src/pwiz/data/identdata/IdentDataFile.cpp
History View file @d6c9b8db08
1 1 
deleted file mode 100644
... ... 
@@ -1,212 +0,0 @@
1 
-//
2 
-// $Id: IdentDataFile.cpp 2820 2011-06-27 22:51:16Z chambm $
3 
-//
4 
-//
5 
-// Original author: Robert Burke <robert.burke@proteowizard.org>
6 
-//
7 
-// Copyright 2009 Spielberg Family Center for Applied Proteomics
8 
-//   University of Southern California, Los Angeles, California  90033
9 
-//
10 
-// Licensed under the Apache License, Version 2.0 (the "License");
11 
-// you may not use this file except in compliance with the License.
12 
-// You may obtain a copy of the License at
13 
-//
14 
-// http://www.apache.org/licenses/LICENSE-2.0
15 
-//
16 
-// Unless required by applicable law or agreed to in writing, software
17 
-// distributed under the License is distributed on an "AS IS" BASIS,
18 
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19 
-// See the License for the specific language governing permissions and
20 
-// limitations under the License.
21 
-//
22 
-
23 
-#define PWIZ_SOURCE
24 
-
25 
-#include "IdentDataFile.hpp"
26 
-#include "TextWriter.hpp"
27 
-#include "Serializer_mzid.hpp"
28 
-#include "Serializer_pepXML.hpp"
29 
-#include "DefaultReaderList.hpp"
30 
-#include "pwiz/utility/misc/Filesystem.hpp"
31 
-#include "pwiz/utility/misc/Std.hpp"
32 
-#include "pwiz/utility/minimxml/XMLWriter.hpp" // for charcounter defn
33 
-#include "boost/iostreams/device/file.hpp"
34 
-#include "boost/iostreams/filtering_stream.hpp"
35 
-#include "boost/iostreams/filter/gzip.hpp"
36 
-
37 
-
38 
-namespace pwiz {
39 
-namespace identdata {
40 
-
41 
-
42 
-using namespace pwiz::util;
43 
-
44 
-
45 
-namespace {
46 
-
47 
-
48 
-void readFile(const string& filename,
49 
-              IdentData& mzid,
50 
-              const Reader& reader,
51 
-              const string& head,
52 
-              const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
53 
-              bool ignoreSequenceCollectionAndAnalysisData)
54 
-{
55 
-    if (!reader.accept(filename, head))
56 
-        throw runtime_error("[IdentDataFile::readFile()] Unsupported file format.");
57 
-
58 
-    Reader::Config config;
59 
-    config.ignoreSequenceCollectionAndAnalysisData = ignoreSequenceCollectionAndAnalysisData;
60 
-    config.iterationListenerRegistry = iterationListenerRegistry;
61 
-    reader.read(filename, head, mzid, config);
62 
-}
63 
-
64 
-
65 
-shared_ptr<DefaultReaderList> defaultReaderList_;
66 
-
67 
-
68 
-} // namespace
69 
-
70 
-
71 
-PWIZ_API_DECL IdentDataFile::IdentDataFile(const string& filename,
72 
-                                           const Reader* reader,
73 
-                                           const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
74 
-                                           bool ignoreSequenceCollectionAndAnalysisData)
75 
-{
76 
-    // peek at head of file
77 
-    string head = read_file_header(filename, 512);
78 
-
79 
-    if (reader)
80 
-    {
81 
-        readFile(filename, *this, *reader, head, iterationListenerRegistry, ignoreSequenceCollectionAndAnalysisData);
82 
-    }
83 
-    else
84 
-    {
85 
-        if (!defaultReaderList_.get())
86 
-            defaultReaderList_ = shared_ptr<DefaultReaderList>(new DefaultReaderList);
87 
-        readFile(filename, *this, *defaultReaderList_, head, iterationListenerRegistry, ignoreSequenceCollectionAndAnalysisData);
88 
-    }
89 
-}
90 
-
91 
-
92 
-PWIZ_API_DECL
93 
-void IdentDataFile::write(const string& filename,
94 
-                          const WriteConfig& config,
95 
-                          const IterationListenerRegistry* iterationListenerRegistry)
96 
-{
97 
-    write(*this, filename, config, iterationListenerRegistry);
98 
-}
99 
-
100 
-
101 
-PWIZ_API_DECL
102 
-void IdentDataFile::write(ostream& os,
103 
-                          const std::string& filename,
104 
-                          const WriteConfig& config,
105 
-                          const IterationListenerRegistry* iterationListenerRegistry)
106 
-{
107 
-    write(*this, filename, os, config, iterationListenerRegistry);
108 
-}
109 
-
110 
-
111 
-namespace {
112 
-
113 
-
114 
-shared_ptr<ostream> openFile(const string& filename)
115 
-{
116 
-    shared_ptr<ostream> result(new ofstream(filename.c_str(), ios::binary));
117 
-
118 
-    if (!result.get() || !*result)
119 
-        throw runtime_error(("[IdentDataFile::openFile()] Unable to open file " + filename).c_str());
120 
-
121 
-    return result;
122 
-}
123 
-
124 
-
125 
-void writeStream(ostream& os, const IdentData& idd, const string& filename,
126 
-                 const IdentDataFile::WriteConfig& config,
127 
-                 const IterationListenerRegistry* iterationListenerRegistry)
128 
-{
129 
-    switch (config.format)
130 
-    {
131 
-        case IdentDataFile::Format_Text:
132 
-        {
133 
-            TextWriter(os,0)(idd);
134 
-            break;
135 
-        }
136 
-
137 
-        case IdentDataFile::Format_MzIdentML:
138 
-        {
139 
-            Serializer_mzIdentML serializer;
140 
-            serializer.write(os, idd, iterationListenerRegistry);
141 
-            break;
142 
-        }
143 
-
144 
-        case IdentDataFile::Format_pepXML:
145 
-        {
146 
-            Serializer_pepXML serializer;
147 
-            serializer.write(os, idd, filename, iterationListenerRegistry);
148 
-            break;
149 
-        }
150 
-
151 
-        default:
152 
-            throw runtime_error("[IdentDataFile::write()] Format not implemented.");
153 
-    }
154 
-}
155 
-
156 
-
157 
-} // namespace
158 
-
159 
-
160 
-PWIZ_API_DECL
161 
-void IdentDataFile::write(const IdentData& idd,
162 
-                          const string& filename,
163 
-                          const WriteConfig& config,
164 
-                          const IterationListenerRegistry* iterationListenerRegistry)
165 
-{
166 
-    shared_ptr<ostream> os = openFile(filename);
167 
-    writeStream(*os, idd, filename, config, iterationListenerRegistry);
168 
-}
169 
-
170 
-
171 
-PWIZ_API_DECL
172 
-void IdentDataFile::write(const IdentData& idd,
173 
-                          const string& filename,
174 
-                          ostream& os,
175 
-                          const WriteConfig& config,
176 
-                          const IterationListenerRegistry* iterationListenerRegistry)
177 
-{
178 
-    WriteConfig config2(config);
179 
-    //config2.gzipped = false;
180 
-    writeStream(os, idd, filename, config2, iterationListenerRegistry);
181 
-}
182 
-
183 
-
184 
-PWIZ_API_DECL ostream& operator<<(ostream& os, IdentDataFile::Format format)
185 
-{
186 
-    switch (format)
187 
-    {
188 
-        case IdentDataFile::Format_Text:
189 
-            os << "Text";
190 
-            return os;
191 
-        case IdentDataFile::Format_MzIdentML:
192 
-            os << "mzIdentML";
193 
-            return os;
194 
-        case IdentDataFile::Format_pepXML:
195 
-            os << "pepXML";
196 
-            return os;
197 
-        default:
198 
-            os << "Unknown";
199 
-            return os;
200 
-    }
201 
-}
202 
-
203 
-
204 
-PWIZ_API_DECL ostream& operator<<(ostream& os, const IdentDataFile::WriteConfig& config)
205 
-{
206 
-    os << config.format;
207 
-    return os;
208 
-}
209 
-
210 
-
211 
-} // namespace identdata
212 
-} // namespace pwiz
Browse code

upgrade pwiz and close connection for pwiz backend

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@120458 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 26/08/2016 07:40:19
Showing1 changed files
src/pwiz/data/identdata/IdentDataFile.cpp
History View file @d2f3523269
... ... 
@@ -28,7 +28,7 @@
28 28 
 #include "Serializer_pepXML.hpp"
29 29 
 #include "DefaultReaderList.hpp"
30 30 
 #include "pwiz/utility/misc/Filesystem.hpp"
31 
-#include "pwiz/utility/misc/Std.hpp"
31 
+#include "pwiz/utility/misc/Std.hpp"
32 32 
 #include "pwiz/utility/minimxml/XMLWriter.hpp" // for charcounter defn
33 33 
 #include "boost/iostreams/device/file.hpp"
34 34 
 #include "boost/iostreams/filtering_stream.hpp"
... ... 
@@ -48,7 +48,7 @@ namespace {
48 48 
 void readFile(const string& filename,
49 49 
               IdentData& mzid,
50 50 
               const Reader& reader,
51 
-              const string& head,
51 
+              const string& head,
52 52 
               const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
53 53 
               bool ignoreSequenceCollectionAndAnalysisData)
54 54 
 {
... ... 
@@ -69,7 +69,7 @@ shared_ptr<DefaultReaderList> defaultReaderList_;
69 69
70 70
71 71 
 PWIZ_API_DECL IdentDataFile::IdentDataFile(const string& filename,
72 
-                                           const Reader* reader,
72 
+                                           const Reader* reader,
73 73 
                                            const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
74 74 
                                            bool ignoreSequenceCollectionAndAnalysisData)
75 75 
 {
... ... 
@@ -90,21 +90,21 @@ PWIZ_API_DECL IdentDataFile::IdentDataFile(const string& filename,
90 90
91 91
92 92 
 PWIZ_API_DECL
93 
-void IdentDataFile::write(const string& filename,
94 
-                          const WriteConfig& config,
93 
+void IdentDataFile::write(const string& filename,
94 
+                          const WriteConfig& config,
95 95 
                           const IterationListenerRegistry* iterationListenerRegistry)
96 96 
 {
97 97 
     write(*this, filename, config, iterationListenerRegistry);
98 
-}
99 
-
100 
-
101 
-PWIZ_API_DECL
98 
+}
99 
+
100 
+
101 
+PWIZ_API_DECL
102 102 
 void IdentDataFile::write(ostream& os,
103 
-                          const std::string& filename,
104 
-                          const WriteConfig& config,
105 
-                          const IterationListenerRegistry* iterationListenerRegistry)
106 
-{
107 
-    write(*this, filename, os, config, iterationListenerRegistry);
103 
+                          const std::string& filename,
104 
+                          const WriteConfig& config,
105 
+                          const IterationListenerRegistry* iterationListenerRegistry)
106 
+{
107 
+    write(*this, filename, os, config, iterationListenerRegistry);
108 108 
 }
109 109
110 110
... ... 
@@ -123,7 +123,7 @@ shared_ptr<ostream> openFile(const string& filename)
123 123
124 124
125 125 
 void writeStream(ostream& os, const IdentData& idd, const string& filename,
126 
-                 const IdentDataFile::WriteConfig& config,
126 
+                 const IdentDataFile::WriteConfig& config,
127 127 
                  const IterationListenerRegistry* iterationListenerRegistry)
128 128 
 {
129 129 
     switch (config.format)
... ... 
@@ -160,24 +160,24 @@ void writeStream(ostream& os, const IdentData& idd, const string& filename,
160 160 
 PWIZ_API_DECL
161 161 
 void IdentDataFile::write(const IdentData& idd,
162 162 
                           const string& filename,
163 
-                          const WriteConfig& config,
163 
+                          const WriteConfig& config,
164 164 
                           const IterationListenerRegistry* iterationListenerRegistry)
165 165 
 {
166 166 
     shared_ptr<ostream> os = openFile(filename);
167 167 
     writeStream(*os, idd, filename, config, iterationListenerRegistry);
168 
-}
169 
-
170 
-
171 
-PWIZ_API_DECL
172 
-void IdentDataFile::write(const IdentData& idd,
173 
-                          const string& filename,
174 
-                          ostream& os,
175 
-                          const WriteConfig& config,
176 
-                          const IterationListenerRegistry* iterationListenerRegistry)
177 
-{
178 
-    WriteConfig config2(config);
179 
-    //config2.gzipped = false;
180 
-    writeStream(os, idd, filename, config2, iterationListenerRegistry);
168 
+}
169 
+
170 
+
171 
+PWIZ_API_DECL
172 
+void IdentDataFile::write(const IdentData& idd,
173 
+                          const string& filename,
174 
+                          ostream& os,
175 
+                          const WriteConfig& config,
176 
+                          const IterationListenerRegistry* iterationListenerRegistry)
177 
+{
178 
+    WriteConfig config2(config);
179 
+    //config2.gzipped = false;
180 
+    writeStream(os, idd, filename, config2, iterationListenerRegistry);
181 181 
 }
182 182
183 183
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 130 commits.

Commit information:

Commit id: 289dc240065888efcaa22ae75951e81f94fc800f

Fix package description after merge

Committed by: Steffen Neumann
Author Name: Steffen Neumann
Commit date: 2014-09-28 17:21:35 +0200
Author date: 2014-09-28 17:21:35 +0200

Commit id: 88248e8d6d86bb54dc260f0c55608dd1a949ade4

merged gsoc into master

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-27 08:49:45 +0100
Author date: 2014-09-27 08:49:45 +0100

Commit id: bb01e0fe0b4f04335925472a7c2b91bd22b57755

included KK's segfault patch and fixed unit test accordingly

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-27 08:44:50 +0100
Author date: 2014-09-27 08:44:50 +0100

Commit id: 708bd0b8ac4b2b5bae9a9b91588a260f2eeefb46

add message about pwiz backend in Bioc 3.1

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-25 01:20:52 +0100
Author date: 2014-09-25 01:20:52 +0100

Commit id: 4c1410ec3c8f153ad0a4b04722cad5a7d77cfd4c

restoring ramp as default backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-25 01:06:21 +0100
Author date: 2014-09-25 01:06:21 +0100

Commit id: c5d60529934813456555934bbeed29502100b41b

show pwiz method

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 21:09:38 +0100
Author date: 2014-09-21 21:09:38 +0100

Commit id: 20bfbfa1db25ec247f2313804d9b73c086a2d920

add close,mzRpwiz-method alias

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 21:04:48 +0100
Author date: 2014-09-21 21:04:48 +0100

Commit id: f80ecdc2a7f14c311b42ad279c62307a6e0aad30

test that close(pwiz) works

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 20:45:50 +0100
Author date: 2014-09-21 20:45:50 +0100

Commit id: d18dc8b0c7197c72b1bb2a70e7becfe983ced9a1

fixed signature for pwiz close method

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 20:44:41 +0100
Author date: 2014-09-21 20:44:41 +0100

Commit id: c0d7451e6b31068cde89f08ac5037a1509857cc5

fix codoc mismatch

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 19:02:00 +0100
Author date: 2014-09-21 19:02:00 +0100

Commit id: 14974a3d0890a7e2a1a7179aaa483e20a5700ef9

add close for pwiz backend to news

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:58:06 +0100
Author date: 2014-09-21 18:58:06 +0100

Commit id: c9d2bbb339c0ecdc9870dbd7a59bfbb94ef67f73

dummy close for pwiz backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:56:48 +0100
Author date: 2014-09-21 18:56:48 +0100

Commit id: 6d608b453328d6c751dc828d2586b016eb17b095

more close calls to remove for pwiz backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:52:55 +0100
Author date: 2014-09-21 18:52:55 +0100

Commit id: 5650801e07df64e2d74302ec98a31938bb62f11f

no isInitialised with pwiz

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:41:57 +0100
Author date: 2014-09-21 18:41:57 +0100

Commit id: 2a3d0eeb24673eb74c3ffa38fefb1883f9bee15d

no close with pwiz

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:46:38 +0100
Author date: 2014-09-21 17:46:38 +0100

Commit id: b3ae014569b6e46ccb6b396dfb9320dd7ba8fb16

bump version to avoid confusions

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:30:28 +0100
Author date: 2014-09-21 17:30:28 +0100

Commit id: a1bd596ffbeef73b4b505342f45742f9997e33d1

using pwiz as default raw data backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:29:02 +0100
Author date: 2014-09-21 17:29:02 +0100

Commit id: 51b4ea21d9cf034d54b0911bf281af3a937375de

Steffen's changes in v 1.11.11

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 16:21:14 +0100
Author date: 2014-09-20 16:21:14 +0100

Commit id: 81cde1ca48974585c9d6f51927087a922b13dd89

add new length to doc header

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 16:06:46 +0100
Author date: 2014-09-20 16:06:46 +0100

Commit id: 3fe883cb7ecad4867908fb907374a4df63b50a1f

show and length mzRident methods

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 15:56:26 +0100
Author date: 2014-09-20 15:56:26 +0100

Commit id: 3efb44e00fb94cdf0eb8207634218cbb47ab1b54

VignetteBuilder: knitr

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-27 01:03:36 +0100
Author date: 2014-08-27 01:03:36 +0100

Commit id: 73b0f902dfaa53f359318708f0606dc1f4677057

BiocStyle vig

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-26 23:59:29 +0100
Author date: 2014-08-26 23:59:29 +0100

Commit id: 185f281d07ed7b4a7f093eaf7b61271a88c85e20

update readme

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-26 23:20:02 +0100
Author date: 2014-08-26 23:20:02 +0100

Commit id: d5cc992e128594d331592b2bd57871fabf6737c9

update to build

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:41:17 +0100
Author date: 2014-08-17 22:41:17 +0100

Commit id: 27318416c94859102a061838a1a3f83d378414e3

bump to 1.99

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:12:44 +0100
Author date: 2014-08-17 22:12:44 +0100

Commit id: 13caefb4d4b469f0406ed96509ea4cebce8235b0

pulled from https://github.com/thirdwing/mzR

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:00:57 +0100
Author date: 2014-08-17 22:00:57 +0100

Commit id: 14822efb6c2238eda371718043bec9cc8fb27558

doc

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-16 22:06:51 -0400
Author date: 2014-08-16 22:06:51 -0400

Commit id: 323424443efac769c436fb87128fad64a0358187

R_init_mzR.c

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-10 00:46:14 -0400
Author date: 2014-08-10 00:46:14 -0400

Commit id: a91c0601e674efbb6949331a53ea9c6af53a4ba5

vignettes

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-06 21:03:23 -0400
Author date: 2014-08-06 21:03:23 -0400

Commit id: 4607e0a595f60a083d1eb90b804348ac5a8c1fb4

update with msdata

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-05 12:33:40 -0400
Author date: 2014-08-05 12:33:40 -0400

Commit id: cc09a790eda22b7d64226116ada89bad9089e0b2

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-04 22:29:15 -0400
Author date: 2014-08-04 22:29:15 -0400

Commit id: fac511ee0f7841791bbf5380f2c948fd045b3adb

unit test against mzID

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-04 22:16:03 -0400
Author date: 2014-08-04 22:16:03 -0400

Commit id: 449952e31fe354b2589d8a723a4f8a842812ede6

enzymes() returns data.frame

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:29:59 -0400
Author date: 2014-08-03 16:29:59 -0400

Commit id: 874fba33e8029023d5e3bbd168dc998d51544c9d

writing support dropped

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:14:26 -0400
Author date: 2014-08-03 16:14:26 -0400

Commit id: 338f3e80dd8f98419555ab1a4aa443e14d089f24

modifications()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:02:20 -0400
Author date: 2014-08-03 16:02:20 -0400

Commit id: 34ee62ee27e7b012b9ce2bd696d63e5f80185200

psms() update

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 15:41:36 -0400
Author date: 2014-08-03 15:41:36 -0400

Commit id: b8bdea9a1e2a7ab3410eea5c26566ef74e488d95

score()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 14:14:53 -0400
Author date: 2014-08-03 14:14:53 -0400

Commit id: a42f1195b3f0b40c28aa2acfb782e517633206c9

psms()

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-03 13:54:34 -0400
Author date: 2014-08-03 13:54:34 -0400

Commit id: 6c2a87019e3b328dbecc1a965d3e41e6539e0d90

para() update, numeric correction

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-02 23:57:41 -0400
Author date: 2014-08-02 23:57:41 -0400

Commit id: 119edf40600beb8e3b8e8006a0d955a887d06b1d

update para()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-30 10:54:40 -0400
Author date: 2014-07-30 10:54:40 -0400

Commit id: 69ac718d0418f2ab3ba824a735975ae6c04aec00

update database()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-30 10:38:42 -0400
Author date: 2014-07-30 10:38:42 -0400

Commit id: f7818556b2e1e3296a727eca6d2853a8b7a16b12

clean

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 21:35:59 -0400
Author date: 2014-07-29 21:35:59 -0400

Commit id: f67403a92b6beca4128c36b42367414463234253

database()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 21:33:07 -0400
Author date: 2014-07-29 21:33:07 -0400

Commit id: 8b0255a9c7da6ccc6c7796f49f608b792bac0dfe

para()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 20:33:14 -0400
Author date: 2014-07-29 20:33:14 -0400

Commit id: 183afed91ad6beb07fffb5cbe4673773619d938b

Rd

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-29 00:36:40 -0400
Author date: 2014-07-29 00:36:40 -0400

Commit id: 73d380115e205eedc211869d6eace3564b3fc1cf

modified: vignettes/mzR.Rnw

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-27 00:49:10 -0400
Author date: 2014-07-27 00:49:10 -0400

Commit id: 93214634ff41a9da84019320dfe6314cb7f94422

score

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-26 19:42:34 -0400
Author date: 2014-07-26 19:42:34 -0400

Commit id: cbdee47033cf10927b0dc33a02208c9ff9d89771

same header info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-22 12:45:46 -0400
Author date: 2014-07-22 12:45:46 -0400

Commit id: 1e6ebe39851ecddedf01daa2c69fcd1f2dba906c

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: inst/unitTests/runit.backends.R modified: man/metadata.Rd modified: man/mzR-class.Rd

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-18 00:40:10 -0400
Author date: 2014-07-18 00:40:10 -0400

Commit id: 0ed92085be5af56a78cdf0f1732a356c48d7a0f9

1.11.10

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-17 21:31:27 -0400
Author date: 2014-07-17 21:31:27 -0400

Commit id: b6e254b2cca93778bfcdc549b75052d0b19bb2bb

fixed

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-16 01:40:10 -0400
Author date: 2014-07-16 01:40:10 -0400

Commit id: 096aa2a6f5aebb5b99bc2e22a0fb023b1353b141

Merge pull request #3 from lgatto/master

fix backend checking
Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-07-15 21:20:15 -0400
Author date: 2014-07-15 21:20:15 -0400

Commit id: 6d8623c47c0b53e6805b9757c178c4639319a29d

fix backend checking

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-07-15 23:32:46 +0100
Author date: 2014-07-15 23:32:46 +0100

Commit id: 9060e3435a76ace952d915c3bb993e04ac93f12a

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-14 10:52:41 -0400
Author date: 2014-07-14 10:52:41 -0400

Commit id: 068ec46671400a2db3bfb10f001f30599b8495e8

modified: ChangeLog

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 17:29:16 -0400
Author date: 2014-07-12 17:29:16 -0400

Commit id: a8f42c9de00ed64470733eb5c63567e99d40e867

more info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 14:57:33 -0400
Author date: 2014-07-12 14:57:33 -0400

Commit id: 4a88ad7c2c8ec911c44a45d16dedced9530505c2

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 14:13:29 -0400
Author date: 2014-07-12 14:13:29 -0400

Commit id: 935d44c5a52b895fe6ff663c062e006e4f25fab0

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 13:52:33 -0400
Author date: 2014-07-12 13:52:33 -0400

Commit id: f1c05ff287215f385938a116042d09bcea2aae88

modified: R/methods-mzRident.R modified: man/mzR-class.Rd modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 11:20:58 -0400
Author date: 2014-07-12 11:20:58 -0400

Commit id: ca620536203355349c7267ad15a2ab6a2d248319

pass R CMD check

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-12 00:36:08 -0400
Author date: 2014-07-12 00:36:08 -0400

Commit id: add1d1c98fe60955953036641671527337e89363

modified: R/methods-mzRident.R modified: man/metadata.Rd modified: man/mzR-class.Rd modified: src/Makevars modified: src/Makevars.win

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 23:48:02 -0400
Author date: 2014-07-11 23:48:02 -0400

Commit id: 050051489df378a26aa97cccfefbf7ebe4102ef5

pepInfo()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 18:10:10 -0400
Author date: 2014-07-11 18:10:10 -0400

Commit id: f093e39599ea2357c91816b7ff9de102f33e8e68

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 15:12:28 -0400
Author date: 2014-07-11 15:12:28 -0400

Commit id: 3dc85db859c4d36040d3edb9ceb57074b0476f2d

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 14:49:47 -0400
Author date: 2014-07-11 14:49:47 -0400

Commit id: ab1261cb3bfe1c02de5f7a053e6de5223686488d

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 13:47:12 -0400
Author date: 2014-07-11 13:47:12 -0400

Commit id: 01a4a2be981724624719580cd8e4f0866091f295

version

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:48:50 -0400
Author date: 2014-07-11 01:48:50 -0400

Commit id: 5f49d13b736cebd65484a5993cdcce253853d4e7

remove mz5

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:41:00 -0400
Author date: 2014-07-11 01:41:00 -0400

Commit id: fb3dbe2f1bf007cd033fd803426d4be2e362b3e2

Update H5public.h

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-07-07 08:46:19 -0400
Author date: 2014-07-07 08:46:19 -0400

Commit id: 2446f08fdadd11c38a1cb54dddfe1e52b1a7bca9

modified: src/pwiz/utility/chemistry/Chemistry.hpp modified: src/pwiz/utility/misc/Std.hpp modified: src/pwiz/utility/misc/sha1calc.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 19:41:41 -0400
Author date: 2014-07-04 19:41:41 -0400

Commit id: b7c28c0db06b2dc9f8f5a7dcd218b7581ffd8121

compiled

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 18:05:54 -0400
Author date: 2014-07-04 18:05:54 -0400

Commit id: 1ffe5c024dafd51c2342f4d1dd930cb8d67d8041

modified: DESCRIPTION modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 10:09:46 -0400
Author date: 2014-07-04 10:09:46 -0400

Commit id: 06e03716f187508072c33d3f0e9e79e135b22c05

modified: src/Makevars modified: src/hdf5/src/H5public.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 22:32:09 -0400
Author date: 2014-07-03 22:32:09 -0400

Commit id: 488ed2bd55151ece46c8cb5ac1df11f73b7c47a3

modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 21:48:39 -0400
Author date: 2014-07-03 21:48:39 -0400

Commit id: 06f4d0a3832e47ad4a69e53d7b9b751dbb9f2770

modified: src/hdf5/src/H5public.h modified: src/pwiz/utility/misc/SHA1.cpp modified: src/pwiz/utility/misc/SHA1.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 21:47:50 -0400
Author date: 2014-07-03 21:47:50 -0400

Commit id: ff58989379a67f20ac8797ba437d430d8b5a2d62

modified: src/RcppIdent.cpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-30 09:42:05 -0400
Author date: 2014-06-30 09:42:05 -0400

Commit id: 58dfa68675768c13950299c43229c1b0f1f1824b

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 21:17:18 -0400
Author date: 2014-06-28 21:17:18 -0400

Commit id: 6c228ae30c477e76add7e3ea805e386f1a0d862d

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 20:16:55 -0400
Author date: 2014-06-28 20:16:55 -0400

Commit id: 464d4e83a9e06732f7c3f1a0172a9cb2bbd53943

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 17:21:01 -0400
Author date: 2014-06-28 17:21:01 -0400

Commit id: ed36541a5fc99192f9df55222f2a2d9a6352ae33

idInfo

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 17:02:20 -0400
Author date: 2014-06-28 17:02:20 -0400

Commit id: 1ed6dceee93d2f57a66a94b15774212403d42200

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 15:19:47 -0400
Author date: 2014-06-28 15:19:47 -0400

Commit id: 47b2a99876650729a329ebeebc174d9873919667

modified: DESCRIPTION

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 13:12:13 -0400
Author date: 2014-06-28 13:12:13 -0400

Commit id: ecad541c1e2d92f7be63433c5bf362d7b7f955b2

mzid supported done

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 13:04:27 -0400
Author date: 2014-06-28 13:04:27 -0400

Commit id: 684340ce7ee5b8fadbd4dfa839e3b0d7ba9b1c91

mzid file support

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-28 01:02:19 -0400
Author date: 2014-06-28 01:02:19 -0400

Commit id: 7382b1321539a2838ae75da6f9c1ff9cbe98bb6b

mzid

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 23:38:36 -0400
Author date: 2014-06-27 23:38:36 -0400

Commit id: 5423b4c653762d90ce6d4bf7dcf1d591a2a9987f

modified: R/methods-mzRpwiz.R modified: R/zzz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 23:27:36 -0400
Author date: 2014-06-27 23:27:36 -0400

Commit id: 9e20328e920207328eb68b9fa59c198d0d634a0f

Update AllGenerics.R

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-27 22:52:37 -0400
Author date: 2014-06-27 22:52:37 -0400

Commit id: 19731b9e51b72027eb02ee6be5aa7343c5b12ace

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRpwiz.R modified: man/metadata.Rd modified: man/mzR-class.Rd modified: man/openMSfile.Rd modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h modified: src/RcppPwizModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 22:03:31 -0400
Author date: 2014-06-27 22:03:31 -0400

Commit id: 94ac2b4ba810d0f820a9266be782667e375ede9a

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 10:15:58 -0400
Author date: 2014-06-27 10:15:58 -0400

Commit id: 1259a8db48d4f7aa9ffe403dd5ee574bbfd238fb

modified: R/zzz.R modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-27 00:44:31 -0400
Author date: 2014-06-27 00:44:31 -0400

Commit id: 9791bc574989cdefe279071dbf3a47232e1d8c86

identadata src

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-27 00:22:35 -0400
Author date: 2014-06-27 00:22:35 -0400

Commit id: ede49e01e23c6586777d72fdd0dfef4bd40729f2

software info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 22:20:57 -0400
Author date: 2014-06-26 22:20:57 -0400

Commit id: 431b2b42a93ff52a05d82801d1830ba81c72f18f

writeMSfile()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 21:53:11 -0400
Author date: 2014-06-26 21:53:11 -0400

Commit id: 53a7a31378bd42adcf779cd1fbe9e2d052a507d7

deleted: src/hdf5/c++/src/H5 deleted: src/hdf5/c++/src/H5DataTy deleted: src/pwiz/data/common/BinaryIndexSt deleted: src/pwiz/data/common/ParamT deleted: src/pwiz/data/m deleted: src/pwiz/data/msdata/BinaryDataEnc deleted: src/pwiz/data/msdata/Chroma deleted: src/pwiz/data/msdata/MSNu deleted: src/pwiz/data/msdata/Seri deleted: src/pwiz/data/msdata/Serializer deleted: src/pwiz/data/msdata/Serializer_mz deleted: src/pwiz/data/msdata/Sp deleted: src/pwiz/data/msdata/Spec deleted: src/pwiz/data/msdata/mz5/Refer deleted: src/pwiz/utility/mis deleted: src/pwiz/utility/misc/IntegerS

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 19:04:22 -0400
Author date: 2014-06-26 19:04:22 -0400

Commit id: 359a40045162a49d94d68f0d60f2c6bb43970a2c

modified: NAMESPACE modified: R/AllGenerics.R modified: R/io.R modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h modified: src/RcppPwizModule.cpp new file: src/boost/filesystem/src/operations new file: src/hdf5/c++/src/H5 new file: src/hdf5/c++/src/H5DataTy new file: src/pwiz/data/common/BinaryIndexSt new file: src/pwiz/data/common/ParamT new file: src/pwiz/data/m new file: src/pwiz/data/msdata/BinaryDataEnc new file: src/pwiz/data/msdata/Chroma new file: src/pwiz/data/msdata/MSNu new file: src/pwiz/data/msdata/Seri new file: src/pwiz/data/msdata/Serializer new file: src/pwiz/data/msdata/Serializer_mz new file: src/pwiz/data/msdata/Sp new file: src/pwiz/data/msdata/Spec new file: src/pwiz/data/msdata/mz5/Refer new file: src/pwiz/utility/mis new file: src/pwiz/utility/misc/IntegerS

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 19:00:48 -0400
Author date: 2014-06-26 19:00:48 -0400

Commit id: 2ce04488e7a8e623a7dfd2b9408da0b9dd5059a4

modified: inst/unitTests/runit.backends.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 15:59:21 -0400
Author date: 2014-06-26 15:59:21 -0400

Commit id: 3103fd4fa92ddd63700c8b5940344db44e97be09

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 13:33:44 -0400
Author date: 2014-06-26 13:33:44 -0400

Commit id: 329f7c1201360f5ebf5703d4837b25ae332e7a85

modified: man/metadata.Rd modified: man/mzR-class.Rd modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 11:35:13 -0400
Author date: 2014-06-26 11:35:13 -0400

Commit id: 0adf852da9ccec69103038ca96b30e8715d3c898

modified: inst/unitTests/runit.backends.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 11:20:03 -0400
Author date: 2014-06-26 11:20:03 -0400

Commit id: 219b5287ca5531577b4a6c80f403957ddef5ab94

modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-26 01:33:43 -0400
Author date: 2014-06-26 01:33:43 -0400

Commit id: 14316dcb1c16ca922d9962ed9ecdaac324e1a151

deleted: src/R_init_mzR.c modified: src/RcppPwiz.cpp deleted: src/ramp_base64.cpp deleted: src/ramp_base64.h

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-26 01:04:14 -0400
Author date: 2014-06-26 01:04:14 -0400

Commit id: efb21501a1b05b680b3d35aa124216f9977b5993

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 23:44:07 -0400
Author date: 2014-06-25 23:44:07 -0400

Commit id: 4e9e1dec2879178547d681603aec46259a6a9978

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:54:26 -0400
Author date: 2014-06-25 22:54:26 -0400

Commit id: 0e7fc23b1ff7508fed6331c0e517a8dc6fa33a0c

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:28:24 -0400
Author date: 2014-06-25 22:28:24 -0400

Commit id: 9ad55a2cdd89791bf75ad23f0ee91b3fc70624ad

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:13:35 -0400
Author date: 2014-06-25 22:13:35 -0400

Commit id: c9fecd83ebf31f142c22030f4593fe5ac675323a

modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 23:31:33 -0400
Author date: 2014-06-24 23:31:33 -0400

Commit id: 4edf517724950d6771fd19c979a460711baa5891

modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 23:01:49 -0400
Author date: 2014-06-24 23:01:49 -0400

Commit id: 22ca998b6b6d3a7496f293f44909436a5b7d8ad0

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 21:31:58 -0400
Author date: 2014-06-24 21:31:58 -0400

Commit id: 6beb4ce5c49cafa644766e23453ed6d10bb89c34

modified: man/metadata.Rd modified: man/mzR-class.Rd

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-22 12:02:07 -0400
Author date: 2014-06-22 12:02:07 -0400

Commit id: dc5e65d93bb67d1b4a1488b90099946e22eed13c

deleted: .travis.yml

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-22 11:26:02 -0400
Author date: 2014-06-22 11:26:02 -0400

Commit id: be53359804d6c7416c715c3eb259fb931c6c117a

modified: .travis.yml modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:33:37 -0400
Author date: 2014-06-21 21:33:37 -0400

Commit id: 1afd9887dac232f3e72fe9d20d44a72b42e28461

deleted: .Rinstignore

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:27:46 -0400
Author date: 2014-06-21 21:27:46 -0400

Commit id: bd4c954bd246787137eb0d961a91bb80b774cb6a

new file: .Rbuildignore new file: .travis.yml

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:25:47 -0400
Author date: 2014-06-21 21:25:47 -0400

Commit id: 3bc8fcca8002a62458a2b2dd1c6b7cf6a8cfab9f

fixed error on windows and snow leopard

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:18:50 -0400
Author date: 2014-06-21 21:18:50 -0400

Commit id: ed9c622443eb992cf3322d687312e3f56bf8be72

Update Makevars.win

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-15 00:55:16 +0800
Author date: 2014-06-15 00:55:16 +0800

Commit id: bf8c7bd931cd93b5db6d84c9c1bf323ea7702e74

new file: src/boost/signals/connection.hpp new file: src/boost/signals/detail/config.hpp new file: src/boost/signals/detail/gen_signal_N.pl new file: src/boost/signals/detail/named_slot_map.hpp new file: src/boost/signals/detail/signal_base.hpp new file: src/boost/signals/detail/signals_common.hpp new file: src/boost/signals/detail/slot_call_iterator.hpp new file: src/boost/signals/signal0.hpp new file: src/boost/signals/signal1.hpp new file: src/boost/signals/signal10.hpp new file: src/boost/signals/signal2.hpp new file: src/boost/signals/signal3.hpp new file: src/boost/signals/signal4.hpp new file: src/boost/signals/signal5.hpp new file: src/boost/signals/signal6.hpp new file: src/boost/signals/signal7.hpp new file: src/boost/signals/signal8.hpp new file: src/boost/signals/signal9.hpp new file: src/boost/signals/signal_template.hpp new file: src/boost/signals/slot.hpp new file: src/boost/signals/trackable.hpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-14 12:52:52 -0400
Author date: 2014-06-14 12:52:52 -0400

Commit id: 5ac3655c7e81f429859eb6b509208f8ec785e1f9

modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-07 11:42:14 -0400
Author date: 2014-06-07 11:42:14 -0400

Commit id: f9f42e3d83adbaf98a201e50866821bc0e43598a

modified: ChangeLog modified: src/RcppPwiz.cpp modified: src/hdf5/src/H5FDmulti.c

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-07 11:24:01 -0400
Author date: 2014-06-07 11:24:01 -0400

Commit id: d8d6f92e46efa93f8234e542b1c4f8f98cee59e5

modified: R/zzz.R.in

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 17:28:36 -0400
Author date: 2014-06-06 17:28:36 -0400

Commit id: e64a8bb7bb7988047466848e5b449038ae9460b3

modified: R/zzz.R modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 16:40:29 -0400
Author date: 2014-06-06 16:40:29 -0400

Commit id: 0a44cc02ea9b5417ac51f60632fc1b6100c6d160

modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 16:01:08 -0400
Author date: 2014-06-06 16:01:08 -0400

Commit id: 4d19d457031e0ae9af343a44774f5deebae01cc8

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 14:16:37 -0400
Author date: 2014-06-06 14:16:37 -0400

Commit id: effcb581a573e13b7b7cc9b459ef2dec4885b4be

modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-06 04:33:43 -0400
Author date: 2014-06-06 04:33:43 -0400

Commit id: 028f6748d4cf81d47569edcd67fe25064b084e60

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-04 23:21:43 -0400
Author date: 2014-06-04 23:21:43 -0400

Commit id: d95b557d2c637630ca784889cd0ef1f56b8423d5

Update methods-mzRpwiz.R

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:51:47 -0400
Author date: 2014-06-04 21:51:47 -0400

Commit id: aad52653c2ceb33655364d5a39c0559225746cfb

Update RcppPwizModule.cpp

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:50:32 -0400
Author date: 2014-06-04 21:50:32 -0400

Commit id: 4fda90cc08feb731aeb65c6015a033fbe46c372e

Update RcppPwiz.cpp

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:48:06 -0400
Author date: 2014-06-04 21:48:06 -0400

Commit id: 660d2e984fabdd20997ff8b648d361c7d9aae711

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-02 13:07:57 -0400
Author date: 2014-06-02 13:07:57 -0400

Commit id: ec6bbdf496a57f2f39b2e4c3bbada75a060e5bbe

modified: src/boost_aux/boost/utility/singleton.hpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-02 09:21:07 -0400
Author date: 2014-06-02 09:21:07 -0400

Commit id: a093954cb779467026288c7f51cca083e0a20661

modified: src/pwiz/data/msdata/ramp/ramp.cpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-05-29 07:36:21 -0400
Author date: 2014-05-29 07:36:21 -0400

Commit id: 4510a1cda50ee8f1f43b667297918dcffed45af2

modified: src/Makevars modified: src/cramp.h modified: src/pwiz/data/msdata/ramp/ramp.cpp deleted: src/ramp.cpp deleted: src/ramp.h modified: src/rampR.cpp deleted: src/ramp_base64.cpp deleted: src/ramp_base64.h

Committed by: qkou
Author Name: qkou
Commit date: 2014-05-28 20:17:42 -0400
Author date: 2014-05-28 20:17:42 -0400


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@94635 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 28/09/2014 18:06:01
Showing1 changed files
src/pwiz/data/identdata/IdentDataFile.cpp
History View file @84a4b1664f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,212 @@
1 
+//
2 
+// $Id: IdentDataFile.cpp 2820 2011-06-27 22:51:16Z chambm $
3 
+//
4 
+//
5 
+// Original author: Robert Burke <robert.burke@proteowizard.org>
6 
+//
7 
+// Copyright 2009 Spielberg Family Center for Applied Proteomics
8 
+//   University of Southern California, Los Angeles, California  90033
9 
+//
10 
+// Licensed under the Apache License, Version 2.0 (the "License");
11 
+// you may not use this file except in compliance with the License.
12 
+// You may obtain a copy of the License at
13 
+//
14 
+// http://www.apache.org/licenses/LICENSE-2.0
15 
+//
16 
+// Unless required by applicable law or agreed to in writing, software
17 
+// distributed under the License is distributed on an "AS IS" BASIS,
18 
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19 
+// See the License for the specific language governing permissions and
20 
+// limitations under the License.
21 
+//
22 
+
23 
+#define PWIZ_SOURCE
24 
+
25 
+#include "IdentDataFile.hpp"
26 
+#include "TextWriter.hpp"
27 
+#include "Serializer_mzid.hpp"
28 
+#include "Serializer_pepXML.hpp"
29 
+#include "DefaultReaderList.hpp"
30 
+#include "pwiz/utility/misc/Filesystem.hpp"
31 
+#include "pwiz/utility/misc/Std.hpp"
32 
+#include "pwiz/utility/minimxml/XMLWriter.hpp" // for charcounter defn
33 
+#include "boost/iostreams/device/file.hpp"
34 
+#include "boost/iostreams/filtering_stream.hpp"
35 
+#include "boost/iostreams/filter/gzip.hpp"
36 
+
37 
+
38 
+namespace pwiz {
39 
+namespace identdata {
40 
+
41 
+
42 
+using namespace pwiz::util;
43 
+
44 
+
45 
+namespace {
46 
+
47 
+
48 
+void readFile(const string& filename,
49 
+              IdentData& mzid,
50 
+              const Reader& reader,
51 
+              const string& head,
52 
+              const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
53 
+              bool ignoreSequenceCollectionAndAnalysisData)
54 
+{
55 
+    if (!reader.accept(filename, head))
56 
+        throw runtime_error("[IdentDataFile::readFile()] Unsupported file format.");
57 
+
58 
+    Reader::Config config;
59 
+    config.ignoreSequenceCollectionAndAnalysisData = ignoreSequenceCollectionAndAnalysisData;
60 
+    config.iterationListenerRegistry = iterationListenerRegistry;
61 
+    reader.read(filename, head, mzid, config);
62 
+}
63 
+
64 
+
65 
+shared_ptr<DefaultReaderList> defaultReaderList_;
66 
+
67 
+
68 
+} // namespace
69 
+
70 
+
71 
+PWIZ_API_DECL IdentDataFile::IdentDataFile(const string& filename,
72 
+                                           const Reader* reader,
73 
+                                           const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
74 
+                                           bool ignoreSequenceCollectionAndAnalysisData)
75 
+{
76 
+    // peek at head of file
77 
+    string head = read_file_header(filename, 512);
78 
+
79 
+    if (reader)
80 
+    {
81 
+        readFile(filename, *this, *reader, head, iterationListenerRegistry, ignoreSequenceCollectionAndAnalysisData);
82 
+    }
83 
+    else
84 
+    {
85 
+        if (!defaultReaderList_.get())
86 
+            defaultReaderList_ = shared_ptr<DefaultReaderList>(new DefaultReaderList);
87 
+        readFile(filename, *this, *defaultReaderList_, head, iterationListenerRegistry, ignoreSequenceCollectionAndAnalysisData);
88 
+    }
89 
+}
90 
+
91 
+
92 
+PWIZ_API_DECL
93 
+void IdentDataFile::write(const string& filename,
94 
+                          const WriteConfig& config,
95 
+                          const IterationListenerRegistry* iterationListenerRegistry)
96 
+{
97 
+    write(*this, filename, config, iterationListenerRegistry);
98 
+}
99 
+
100 
+
101 
+PWIZ_API_DECL
102 
+void IdentDataFile::write(ostream& os,
103 
+                          const std::string& filename,
104 
+                          const WriteConfig& config,
105 
+                          const IterationListenerRegistry* iterationListenerRegistry)
106 
+{
107 
+    write(*this, filename, os, config, iterationListenerRegistry);
108 
+}
109 
+
110 
+
111 
+namespace {
112 
+
113 
+
114 
+shared_ptr<ostream> openFile(const string& filename)
115 
+{
116 
+    shared_ptr<ostream> result(new ofstream(filename.c_str(), ios::binary));
117 
+
118 
+    if (!result.get() || !*result)
119 
+        throw runtime_error(("[IdentDataFile::openFile()] Unable to open file " + filename).c_str());
120 
+
121 
+    return result;
122 
+}
123 
+
124 
+
125 
+void writeStream(ostream& os, const IdentData& idd, const string& filename,
126 
+                 const IdentDataFile::WriteConfig& config,
127 
+                 const IterationListenerRegistry* iterationListenerRegistry)
128 
+{
129 
+    switch (config.format)
130 
+    {
131 
+        case IdentDataFile::Format_Text:
132 
+        {
133 
+            TextWriter(os,0)(idd);
134 
+            break;
135 
+        }
136 
+
137 
+        case IdentDataFile::Format_MzIdentML:
138 
+        {
139 
+            Serializer_mzIdentML serializer;
140 
+            serializer.write(os, idd, iterationListenerRegistry);
141 
+            break;
142 
+        }
143 
+
144 
+        case IdentDataFile::Format_pepXML:
145 
+        {
146 
+            Serializer_pepXML serializer;
147 
+            serializer.write(os, idd, filename, iterationListenerRegistry);
148 
+            break;
149 
+        }
150 
+
151 
+        default:
152 
+            throw runtime_error("[IdentDataFile::write()] Format not implemented.");
153 
+    }
154 
+}
155 
+
156 
+
157 
+} // namespace
158 
+
159 
+
160 
+PWIZ_API_DECL
161 
+void IdentDataFile::write(const IdentData& idd,
162 
+                          const string& filename,
163 
+                          const WriteConfig& config,
164 
+                          const IterationListenerRegistry* iterationListenerRegistry)
165 
+{
166 
+    shared_ptr<ostream> os = openFile(filename);
167 
+    writeStream(*os, idd, filename, config, iterationListenerRegistry);
168 
+}
169 
+
170 
+
171 
+PWIZ_API_DECL
172 
+void IdentDataFile::write(const IdentData& idd,
173 
+                          const string& filename,
174 
+                          ostream& os,
175 
+                          const WriteConfig& config,
176 
+                          const IterationListenerRegistry* iterationListenerRegistry)
177 
+{
178 
+    WriteConfig config2(config);
179 
+    //config2.gzipped = false;
180 
+    writeStream(os, idd, filename, config2, iterationListenerRegistry);
181 
+}
182 
+
183 
+
184 
+PWIZ_API_DECL ostream& operator<<(ostream& os, IdentDataFile::Format format)
185 
+{
186 
+    switch (format)
187 
+    {
188 
+        case IdentDataFile::Format_Text:
189 
+            os << "Text";
190 
+            return os;
191 
+        case IdentDataFile::Format_MzIdentML:
192 
+            os << "mzIdentML";
193 
+            return os;
194 
+        case IdentDataFile::Format_pepXML:
195 
+            os << "pepXML";
196 
+            return os;
197 
+        default:
198 
+            os << "Unknown";
199 
+            return os;
200 
+    }
201 
+}
202 
+
203 
+
204 
+PWIZ_API_DECL ostream& operator<<(ostream& os, const IdentDataFile::WriteConfig& config)
205 
+{
206 
+    os << config.format;
207 
+    return os;
208 
+}
209 
+
210 
+
211 
+} // namespace identdata
212 
+} // namespace pwiz