1. affxparser
  2. Commit 4bc22e97cc87c564f3f306ba080c73adcea6b7cf
Browse code

Updated to Fusion release 1.0.7. This might break stuff...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@19161 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 11/08/2006 22:57:54
Showing 108 changed files
src/Makevars
History View file @ 4bc22e9
... ... 
@@ -21,11 +21,9 @@ PKG_CPPFLAGS=\
21 21 
  -Ifusion_sdk/calvin_files/writers/src\
22 22 
  -Ifusion_sdk/file\
23 23 
  -Ifusion_sdk/portability\
24 
- -Ifusion_sdk/gcast/src\
25 24 
  -D_USE_MEM_MAPPING_
26 25
27 26 
 SOURCES.fusion = \
28 
-	fusion_sdk/calvin_files/data/src/BitFlag.cpp\
29 27 
 	fusion_sdk/calvin_files/data/src/CDFData.cpp\
30 28 
 	fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp\
31 29 
 	fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp\
src/Makevars.win
History View file @ 4bc22e9
... ... 
@@ -16,11 +16,9 @@ PKG_CPPFLAGS+=\
16 16 
  -Ifusion_sdk/calvin_files/writers/src\
17 17 
  -Ifusion_sdk/file\
18 18 
  -Ifusion_sdk/portability\
19 
- -Ifusion_sdk/gcast/src\
20 19 
  -D_USE_MEM_MAPPING_
21 20
22 21 
 SOURCES.fusion = \
23 
-	fusion_sdk/calvin_files/data/src/BitFlag.cpp\
24 22 
 	fusion_sdk/calvin_files/data/src/CDFData.cpp\
25 23 
 	fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp\
26 24 
 	fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp\
src/R_affx_cel_parser.cpp
History View file @ 4bc22e9
... ... 
@@ -145,10 +145,12 @@ extern "C" {
145 145
146 146 
     char* celFileName = CHAR(STRING_ELT(fname,0));
147 147 
     cel.SetFileName(celFileName);
148 
-    if (cel.ReadHeader() == false) {
148 
+    // if (cel.ReadHeader() == false) {
149 
+    if (cel.Exists() == false) {
149 150 
       Rprintf("Unable to read file: %s\n", celFileName);
150 151 
       return R_NilValue;
151 152 
     }
153 
+    cel.Read();
152 154
153 155 
     return R_affx_extract_cel_file_meta(cel);
154 156 
   }
src/fusion_sdk/calvin_files/data/src/BitFlag.cpp
History View file @ 4bc22e9
155 157 
deleted file mode 100644
... ... 
@@ -1,60 +0,0 @@
1 
-#include "BitFlag.h"
2 
-
3 
-using namespace affymetrix_calvin_io;
4 
-
5 
-BitFlag::BitFlag()
6 
-{
7 
-	Clear();
8 
-}
9 
-
10 
-BitFlag::BitFlag(u_int16_t p)
11 
-{
12 
-	SetFlags(p);
13 
-}
14 
-
15 
-BitFlag::~BitFlag() {}
16 
-
17 
-void BitFlag::Clear()
18 
-{
19 
-	flags.reset();
20 
-}
21 
-
22 
-u_int16_t BitFlag::GetFlags() const
23 
-{
24 
-	return (u_int16_t)flags.to_ulong();
25 
-}
26 
-
27 
-void BitFlag::SetFlags(u_int16_t p)
28 
-{
29 
-	for(int i = 0; i < 8; i++)
30 
-	{
31 
-		if(p & (1 << i))
32 
-		{
33 
-			SetFlag(i, true);
34 
-		}
35 
-		else
36 
-		{
37 
-			SetFlag(i, false);
38 
-		}
39 
-	}
40 
-}
41 
-
42 
-bool BitFlag::GetFlag(u_int32_t index) const
43 
-{
44 
-	return flags.test(index);
45 
-}
46 
-
47 
-void BitFlag::SetFlag(u_int32_t index, bool p)
48 
-{
49 
-	flags.set(index, p);
50 
-}
51 
-
52 
-bool BitFlag::HasDefaultDataSetHdr() const
53 
-{
54 
-	return GetFlag(DEFAULT_DATA_SET_HDR_FLAG);
55 
-}
56 
-
57 
-void BitFlag::SetDefaultDataSetHdr(bool p)
58 
-{
59 
-	SetFlag(DEFAULT_DATA_SET_HDR_FLAG, p);
60 
-}
src/fusion_sdk/calvin_files/data/src/BitFlag.h
History View file @ 4bc22e9
61 0 
deleted file mode 100644
... ... 
@@ -1,84 +0,0 @@
1 
-/////////////////////////////////////////////////////////////////
2 
-//
3 
-// Copyright (C) 2005 Affymetrix, Inc.
4 
-//
5 
-// This library is free software; you can redistribute it and/or modify
6 
-// it under the terms of the GNU Lesser General Public License as published
7 
-// by the Free Software Foundation; either version 2.1 of the License,
8 
-// or (at your option) any later version.
9 
-//
10 
-// This library is distributed in the hope that it will be useful, but
11 
-// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
12 
-// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
13 
-// for more details.
14 
-//
15 
-// You should have received a copy of the GNU Lesser General Public License
16 
-// along with this library; if not, write to the Free Software Foundation, Inc.,
17 
-// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 
-//
19 
-/////////////////////////////////////////////////////////////////
20 
-
21 
-#ifndef _BitFlag_HEADER_
22 
-#define _BitFlag_HEADER_
23 
-
24 
-#include "AffymetrixBaseTypes.h"
25 
-#include <bitset>
26 
-
27 
-
28 
-#ifdef _MSC_VER
29 
-#pragma warning(disable: 4290) // don't show warnings about throw keyword on function declarations.
30 
-#endif
31 
-
32 
-namespace affymetrix_calvin_io
33 
-{
34 
-
35 
-static u_int8_t DEFAULT_DATA_SET_HDR_FLAG = 0;
36 
-
37 
-class BitFlag
38 
-{
39 
-private:
40 
-
41 
-	std::bitset<16> flags;
42 
-
43 
-public:
44 
-
45 
-	BitFlag();
46 
-
47 
-	BitFlag(u_int16_t p);
48 
-
49 
-	~BitFlag();
50 
-
51 
-	/*! Clear all flags. */
52 
-	void Clear();
53 
-
54 
-	/*! Get all flags.
55 
-	 * @return number with flags set.
56 
-	 */
57 
-	u_int16_t GetFlags() const;
58 
-
59 
-	/*! Set all flags.
60 
-	 * @param p number with flags set.
61 
-	 */
62 
-	void SetFlags(u_int16_t p);
63 
-
64 
-	/*! True if the default data set header flag has been set.
65 
-	 * @return true if the default data set header flag has been set.
66 
-	 */
67 
-	bool HasDefaultDataSetHdr() const;
68 
-
69 
-	/*! Set the default data set header flag.
70 
-	 * @param p true or false.
71 
-	 */
72 
-	void SetDefaultDataSetHdr(bool p);
73 
-
74 
-private:
75 
-
76 
-	bool GetFlag(u_int32_t index) const;
77 
-
78 
-	void SetFlag(u_int32_t index, bool p);
79 
-
80 
-};
81 
-
82 
-}
83 
-
84 
-#endif // _BitFlag_HEADER_
src/fusion_sdk/calvin_files/data/src/CHPSignalData.cpp
History View file @ 4bc22e9
85 0 
similarity index 69%
86 1 
rename from src/fusion_sdk/calvin_files/data/src/CHPSignalData.cpp
87 2 
rename to src/fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp
... ... 
@@ -18,7 +18,7 @@
18 18 
 //
19 19 
 /////////////////////////////////////////////////////////////////
20 20
21 
-#include "CHPSignalData.h"
21 
+#include "CHPQuantificationData.h"
22 22 
 #include "DataSetHeader.h"
23 23 
 #include "StringUtils.h"
24 24
... ... 
@@ -29,7 +29,7 @@ using namespace affymetrix_calvin_utilities;
29 29 
 /*! A prefix for chip summary parameter ids. */
30 30 
 static const std::wstring CHIP_SUMMARY_PARAMETER_NAME_PREFIX = L"affymetrix-chipsummary-";
31 31
32 
-CHPSignalData::CHPSignalData()
32 
+CHPQuantificationData::CHPQuantificationData()
33 33 
 {
34 34 
     maxProbeSetName = -1;
35 35 
 	firstColumnType = UnicodeCharColType;
... ... 
@@ -37,47 +37,47 @@ CHPSignalData::CHPSignalData()
37 37 
 	Clear();
38 38 
 }
39 39
40 
-CHPSignalData::CHPSignalData(const std::string& filename)
40 
+CHPQuantificationData::CHPQuantificationData(const std::string& filename)
41 41 
 {
42 42 
     maxProbeSetName = -1;
43 43 
 	firstColumnType = UnicodeCharColType;
44 44 
 	entries = NULL;
45 45 
 	Clear();
46 46 
 	SetFilename(filename);
47 
-	DataGroupHeader dcHdr(SIGNAL_SIGNAL_NAME);
47 
+	DataGroupHeader dcHdr(QUANTIFICATION_QUANTIFICATION_NAME);
48 48 
 	genericData.Header().AddDataGroupHdr(dcHdr);
49 
-	genericData.Header().GetGenericDataHdr()->SetFileTypeId(CHP_SIGNAL_TYPE);
49 
+	genericData.Header().GetGenericDataHdr()->SetFileTypeId(CHP_QUANTIFICATION_TYPE);
50 50 
 }
51 51
52 
-CHPSignalData::~CHPSignalData()
52 
+CHPQuantificationData::~CHPQuantificationData()
53 53 
 {
54 54 
 	Clear();
55 55 
 }
56 56
57 
-void CHPSignalData::Clear()
57 
+void CHPQuantificationData::Clear()
58 58 
 {
59 59 
 	if (entries){ entries->Delete();  entries = 0; }
60 60 
 	genericData.Header().Clear();
61 61 
 }
62 62
63 
-void CHPSignalData::SetFilename(const std::string &p)
63 
+void CHPQuantificationData::SetFilename(const std::string &p)
64 64 
 {
65 65 
 	genericData.Header().SetFilename(p);
66 66 
 }
67 67
68 
-std::string CHPSignalData::GetFilename() const
68 
+std::string CHPQuantificationData::GetFilename() const
69 69 
 {
70 70 
 	return ((GenericData&)genericData).Header().GetFilename();
71 71 
 }
72 72
73 
-int32_t CHPSignalData::GetEntryCount()
73 
+int32_t CHPQuantificationData::GetEntryCount()
74 74 
 {
75 75 
 	DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0);
76 76 
 	DataSetHeader dpHdr = dcHdr->GetDataSet(0);
77 77 
 	return dpHdr.GetRowCnt();
78 78 
 }
79 79
80 
-void CHPSignalData::SetEntryCount(int32_t ln, int32_t maxln)
80 
+void CHPQuantificationData::SetEntryCount(int32_t ln, int32_t maxln)
81 81 
 {
82 82 
     firstColumnType = ASCIICharColType;
83 83 
 	maxProbeSetName = maxln;
... ... 
@@ -85,12 +85,12 @@ void CHPSignalData::SetEntryCount(int32_t ln, int32_t maxln)
85 85 
 	DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0);
86 86 
 	DataSetHeader dpHdr;
87 87 
 	dpHdr.SetRowCnt(ln);
88 
-	dpHdr.SetName(SIGNAL_SIGNAL_NAME);
88 
+	dpHdr.SetName(QUANTIFICATION_QUANTIFICATION_NAME);
89 89 
 	AddColumns(dpHdr, false);
90 90 
 	dcHdr->AddDataSetHdr(dpHdr);
91 91 
 }
92 92
93 
-void CHPSignalData::SetEntryCount(int32_t ln)
93 
+void CHPQuantificationData::SetEntryCount(int32_t ln)
94 94 
 {
95 95 
     firstColumnType = IntColType;
96 96 
 	maxProbeSetName = -1;
... ... 
@@ -98,14 +98,14 @@ void CHPSignalData::SetEntryCount(int32_t ln)
98 98 
 	DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0);
99 99 
 	DataSetHeader dpHdr;
100 100 
 	dpHdr.SetRowCnt(ln);
101 
-	dpHdr.SetName(SIGNAL_SIGNAL_NAME);
101 
+	dpHdr.SetName(QUANTIFICATION_QUANTIFICATION_NAME);
102 102 
 	AddColumns(dpHdr, true);
103 103 
 	dcHdr->AddDataSetHdr(dpHdr);
104 104 
 }
105 105
106 
-void CHPSignalData::GetSignalEntry(int index, affymetrix_calvin_data::ProbeSetSignalData &entry)
106 
+void CHPQuantificationData::GetQuantificationEntry(int index, affymetrix_calvin_data::ProbeSetQuantificationData &entry)
107 107 
 {
108 
-	OpenSignalDataSet();
108 
+	OpenQuantificationDataSet();
109 109 
 	if (entries && entries->IsOpen())
110 110 
 	{
111 111 
         entry.id = -1;
... ... 
@@ -120,20 +120,20 @@ void CHPSignalData::GetSignalEntry(int index, affymetrix_calvin_data::ProbeSetSi
120 120 
 		}
121 121 
         else if (firstColumnType == IntColType)
122 122 
             entries->GetData(index, 0, entry.id);
123 
-		entries->GetData(index, 1, entry.signal);
123 
+        entries->GetData(index, 1, entry.quantification);
124 124 
 	}
125 125 
 }
126 126
127 
-void CHPSignalData::AddColumns(DataSetHeader& hdr, bool keyIsID)
127 
+void CHPQuantificationData::AddColumns(DataSetHeader& hdr, bool keyIsID)
128 128 
 {
129 129 
     if (keyIsID == false)
130 
-        hdr.AddAsciiColumn(SIGNAL_PROBE_SET_NAME, maxProbeSetName);
130 
+        hdr.AddAsciiColumn(QUANTIFICATION_PROBE_SET_NAME, maxProbeSetName);
131 131 
     else
132 
-        hdr.AddIntColumn(SIGNAL_PROBE_SET_ID);
133 
-	hdr.AddFloatColumn(SIGNAL_SIGNAL_NAME);
132 
+        hdr.AddIntColumn(QUANTIFICATION_PROBE_SET_ID);
133 
+	hdr.AddFloatColumn(QUANTIFICATION_QUANTIFICATION_NAME);
134 134 
 }
135 135
136 
-void CHPSignalData::OpenSignalDataSet()
136 
+void CHPQuantificationData::OpenQuantificationDataSet()
137 137 
 {
138 138 
 	if (entries == NULL)
139 139 
 	{
... ... 
@@ -146,37 +146,37 @@ void CHPSignalData::OpenSignalDataSet()
146 146 
 	}
147 147 
 }
148 148
149 
-std::wstring CHPSignalData::GetArrayType()
149 
+std::wstring CHPQuantificationData::GetArrayType()
150 150 
 {
151 151 
 	return GetWStringFromGenericHdr(ARRAY_TYPE_PARAM_NAME);
152 152 
 }
153 153
154 
-void CHPSignalData::SetArrayType(const std::wstring& value)
154 
+void CHPQuantificationData::SetArrayType(const std::wstring& value)
155 155 
 {
156 156 
 	SetWStringToGenericHdr(ARRAY_TYPE_PARAM_NAME, value, ARRAY_TYPE_MAX_LEN);
157 157 
 }
158 158
159 
-std::wstring CHPSignalData::GetAlgName()
159 
+std::wstring CHPQuantificationData::GetAlgName()
160 160 
 {
161 161 
 	return GetWStringFromGenericHdr(ALGORITHM_NAME_PARAM_NAME);
162 162 
 }
163 163
164 
-void CHPSignalData::SetAlgName(const std::wstring& value)
164 
+void CHPQuantificationData::SetAlgName(const std::wstring& value)
165 165 
 {
166 166 
 	SetWStringToGenericHdr(ALGORITHM_NAME_PARAM_NAME, value);
167 167 
 }
168 168
169 
-std::wstring CHPSignalData::GetAlgVersion()
169 
+std::wstring CHPQuantificationData::GetAlgVersion()
170 170 
 {
171 171 
 	return GetWStringFromGenericHdr(ALG_VERSION_PARAM_NAME);
172 172 
 }
173 173
174 
-void CHPSignalData::SetAlgVersion(const std::wstring& value)
174 
+void CHPQuantificationData::SetAlgVersion(const std::wstring& value)
175 175 
 {
176 176 
 	SetWStringToGenericHdr(ALG_VERSION_PARAM_NAME, value);
177 177 
 }
178 178
179 
-ParameterNameValueTypeList CHPSignalData::GetAlgParams()
179 
+ParameterNameValueTypeList CHPQuantificationData::GetAlgParams()
180 180 
 {
181 181 
 	ParameterNameValueTypeList nvt;
182 182 
 	ParameterNameValueTypeIt begin, end;
... ... 
@@ -198,7 +198,7 @@ ParameterNameValueTypeList CHPSignalData::GetAlgParams()
198 198 
 	return nvt;
199 199 
 }
200 200
201 
-void CHPSignalData::AddAlgParams(const ParameterNameValueTypeList& params)
201 
+void CHPQuantificationData::AddAlgParams(const ParameterNameValueTypeList& params)
202 202 
 {
203 203 
 	ParameterNameValueType param;
204 204 
 	GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
... ... 
@@ -210,7 +210,7 @@ void CHPSignalData::AddAlgParams(const ParameterNameValueTypeList& params)
210 210 
 	}
211 211 
 }
212 212
213 
-ParameterNameValueTypeList CHPSignalData::GetSummaryParams()
213 
+ParameterNameValueTypeList CHPQuantificationData::GetSummaryParams()
214 214 
 {
215 215 
 	ParameterNameValueTypeList nvt;
216 216 
 	ParameterNameValueTypeIt begin, end;
... ... 
@@ -232,7 +232,7 @@ ParameterNameValueTypeList CHPSignalData::GetSummaryParams()
232 232 
 	return nvt;
233 233 
 }
234 234
235 
-void CHPSignalData::AddSummaryParams(const ParameterNameValueTypeList& params)
235 
+void CHPQuantificationData::AddSummaryParams(const ParameterNameValueTypeList& params)
236 236 
 {
237 237 
 	ParameterNameValueType param;
238 238 
 	GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
... ... 
@@ -244,7 +244,7 @@ void CHPSignalData::AddSummaryParams(const ParameterNameValueTypeList& params)
244 244 
 	}
245 245 
 }
246 246
247 
-std::wstring CHPSignalData::GetWStringFromGenericHdr(const std::wstring& name)
247 
+std::wstring CHPQuantificationData::GetWStringFromGenericHdr(const std::wstring& name)
248 248 
 {
249 249 
 	std::wstring result;
250 250 
 	ParameterNameValueType paramType;
... ... 
@@ -256,7 +256,7 @@ std::wstring CHPSignalData::GetWStringFromGenericHdr(const std::wstring& name)
256 256 
 	return result;
257 257 
 }
258 258
259 
-void CHPSignalData::SetWStringToGenericHdr(const std::wstring& name, const std::wstring value, int32_t reserve)
259 
+void CHPQuantificationData::SetWStringToGenericHdr(const std::wstring& name, const std::wstring value, int32_t reserve)
260 260 
 {
261 261 
 	ParameterNameValueType paramType;
262 262 
 	paramType.SetName(name);
src/fusion_sdk/calvin_files/data/src/CHPSignalData.h
History View file @ 4bc22e9
263 263 
similarity index 80%
264 264 
rename from src/fusion_sdk/calvin_files/data/src/CHPSignalData.h
265 265 
rename to src/fusion_sdk/calvin_files/data/src/CHPQuantificationData.h
... ... 
@@ -18,44 +18,44 @@
18 18 
 //
19 19 
 /////////////////////////////////////////////////////////////////
20 20
21 
-#ifndef _CHPSignalData_HEADER_
22 
-#define _CHPSignalData_HEADER_
21 
+#ifndef _CHPQuantificationData_HEADER_
22 
+#define _CHPQuantificationData_HEADER_
23 23
24 24 
 #include <string>
25 25 
 #include "FileHeader.h"
26 26 
 #include "GenericData.h"
27 27 
 #include "AffymetrixBaseTypes.h"
28 
-#include "ProbeSetSignalData.h"
28 
+#include "ProbeSetQuantificationData.h"
29 29
30 30 
 namespace affymetrix_calvin_io
31 31 
 {
32 32
33 
-/*! The identifier to identify a signal CHP file. */
34 
-#define CHP_SIGNAL_TYPE std::string("affymetrix-signal-analysis")
33 
+/*! The identifier to identify a quantification CHP file. */
34 
+#define CHP_QUANTIFICATION_TYPE std::string("affymetrix-quantification-analysis")
35 35
36 
-/*! The group and data set and column name to store the signal data. */
37 
-#define SIGNAL_SIGNAL_NAME std::wstring(L"Signal")
36 
+/*! The group and data set and column name to store the quantification data. */
37 
+#define QUANTIFICATION_QUANTIFICATION_NAME std::wstring(L"Quantification")
38 38
39 39 
 /*! The column name for the probe set name. */
40 
-#define SIGNAL_PROBE_SET_NAME std::wstring(L"ProbeSetName")
40 
+#define QUANTIFICATION_PROBE_SET_NAME std::wstring(L"ProbeSetName")
41 41
42 42 
 /*! The column name for the probe set id. */
43 
-#define SIGNAL_PROBE_SET_ID std::wstring(L"ProbeSetId")
43 
+#define QUANTIFICATION_PROBE_SET_ID std::wstring(L"ProbeSetId")
44 44
45 
-/*! Holds data associated with signal array CHP files. */
46 
-class CHPSignalData
45 
+/*! Holds data associated with quantification CHP files. */
46 
+class CHPQuantificationData
47 47 
 {
48 48 
 public:
49 49 
 	/*! Constructor */
50 
-	CHPSignalData();
50 
+	CHPQuantificationData();
51 51
52 52 
 	/*! Constructor with file name.
53 53 
 	 * @param filename The name of the CHP file.
54 54 
 	 */
55 
-	CHPSignalData(const std::string& filename);
55 
+	CHPQuantificationData(const std::string& filename);
56 56
57 57 
 	/*! Destructor */
58 
-	~CHPSignalData();
58 
+	~CHPQuantificationData();
59 59
60 60 
 private:
61 61 
 	/*! Flag indicating if the probe set names were stored in wide character format. */
... ... 
@@ -160,12 +160,12 @@ public:
160 160
161 161 
 	/*! Gets the sequence data.
162 162 
 	 * @param index The row index.
163 
-	 * @param entry The signal value.
163 
+	 * @param entry The quantification value.
164 164 
 	 */
165 
-	void GetSignalEntry(int index, affymetrix_calvin_data::ProbeSetSignalData &entry);
165 
+	void GetQuantificationEntry(int index, affymetrix_calvin_data::ProbeSetQuantificationData &entry);
166 166
167 167 
 	/*! Opens a group for reading. */
168 
-	void OpenSignalDataSet();
168 
+	void OpenQuantificationDataSet();
169 169
170 170 
 private:
171 171
src/fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp
History View file @ 4bc22e9
172 172 
new file mode 100644
... ... 
@@ -0,0 +1,269 @@
1 
+/////////////////////////////////////////////////////////////////
2 
+//
3 
+// Copyright (C) 2006 Affymetrix, Inc.
4 
+//
5 
+// This library is free software; you can redistribute it and/or modify
6 
+// it under the terms of the GNU Lesser General Public License as published
7 
+// by the Free Software Foundation; either version 2.1 of the License,
8 
+// or (at your option) any later version.
9 
+//
10 
+// This library is distributed in the hope that it will be useful, but
11 
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
12 
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
13 
+// for more details.
14 
+//
15 
+// You should have received a copy of the GNU Lesser General Public License
16 
+// along with this library; if not, write to the Free Software Foundation, Inc.,
17 
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 
+//
19 
+/////////////////////////////////////////////////////////////////
20 
+
21 
+#include "CHPQuantificationDetectionData.h"
22 
+#include "DataSetHeader.h"
23 
+#include "StringUtils.h"
24 
+
25 
+using namespace affymetrix_calvin_io;
26 
+using namespace affymetrix_calvin_parameter;
27 
+using namespace affymetrix_calvin_utilities;
28 
+
29 
+/*! A prefix for chip summary parameter ids. */
30 
+static const std::wstring CHIP_SUMMARY_PARAMETER_NAME_PREFIX = L"affymetrix-chipsummary-";
31 
+
32 
+CHPQuantificationDetectionData::CHPQuantificationDetectionData()
33 
+{
34 
+    maxProbeSetName = -1;
35 
+	firstColumnType = UnicodeCharColType;
36 
+	entries = NULL;
37 
+	Clear();
38 
+}
39 
+
40 
+CHPQuantificationDetectionData::CHPQuantificationDetectionData(const std::string& filename)
41 
+{
42 
+    maxProbeSetName = -1;
43 
+	firstColumnType = UnicodeCharColType;
44 
+	entries = NULL;
45 
+	Clear();
46 
+	SetFilename(filename);
47 
+	DataGroupHeader dcHdr(QUANTIFICATION_DETECTION_NAME);
48 
+	genericData.Header().AddDataGroupHdr(dcHdr);
49 
+	genericData.Header().GetGenericDataHdr()->SetFileTypeId(CHP_QUANTIFICATION_DETECTION_TYPE);
50 
+}
51 
+
52 
+CHPQuantificationDetectionData::~CHPQuantificationDetectionData()
53 
+{
54 
+	Clear();
55 
+}
56 
+
57 
+void CHPQuantificationDetectionData::Clear()
58 
+{
59 
+	if (entries){ entries->Delete();  entries = 0; }
60 
+	genericData.Header().Clear();
61 
+}
62 
+
63 
+void CHPQuantificationDetectionData::SetFilename(const std::string &p)
64 
+{
65 
+	genericData.Header().SetFilename(p);
66 
+}
67 
+
68 
+std::string CHPQuantificationDetectionData::GetFilename() const
69 
+{
70 
+	return ((GenericData&)genericData).Header().GetFilename();
71 
+}
72 
+
73 
+int32_t CHPQuantificationDetectionData::GetEntryCount()
74 
+{
75 
+	DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0);
76 
+	DataSetHeader dpHdr = dcHdr->GetDataSet(0);
77 
+	return dpHdr.GetRowCnt();
78 
+}
79 
+
80 
+void CHPQuantificationDetectionData::SetEntryCount(int32_t ln, int32_t maxln)
81 
+{
82 
+    firstColumnType = ASCIICharColType;
83 
+	maxProbeSetName = maxln;
84 
+	ParameterNameValueType param;
85 
+	DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0);
86 
+	DataSetHeader dpHdr;
87 
+	dpHdr.SetRowCnt(ln);
88 
+	dpHdr.SetName(QUANTIFICATION_DETECTION_NAME);
89 
+	AddColumns(dpHdr, false);
90 
+	dcHdr->AddDataSetHdr(dpHdr);
91 
+}
92 
+
93 
+void CHPQuantificationDetectionData::SetEntryCount(int32_t ln)
94 
+{
95 
+    firstColumnType = IntColType;
96 
+	maxProbeSetName = -1;
97 
+	ParameterNameValueType param;
98 
+	DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0);
99 
+	DataSetHeader dpHdr;
100 
+	dpHdr.SetRowCnt(ln);
101 
+	dpHdr.SetName(QUANTIFICATION_DETECTION_NAME);
102 
+	AddColumns(dpHdr, true);
103 
+	dcHdr->AddDataSetHdr(dpHdr);
104 
+}
105 
+
106 
+void CHPQuantificationDetectionData::GetQuantificationDetectionEntry(int index, affymetrix_calvin_data::ProbeSetQuantificationDetectionData &entry)
107 
+{
108 
+	OpenQuantificationDetectionDataSet();
109 
+	if (entries && entries->IsOpen())
110 
+	{
111 
+        entry.id = -1;
112 
+        entry.name.clear();
113 
+		if (firstColumnType == ASCIICharColType)
114 
+			entries->GetData(index, 0, entry.name);
115 
+		else if (firstColumnType == UnicodeCharColType)
116 
+		{
117 
+            std::wstring wprobeSetName;
118 
+            entries->GetData(index, 0, wprobeSetName);
119 
+            entry.name = StringUtils::ConvertWCSToMBS(wprobeSetName);
120 
+		}
121 
+        else if (firstColumnType == IntColType)
122 
+            entries->GetData(index, 0, entry.id);
123 
+        entries->GetData(index, 1, entry.quantification);
124 
+        entries->GetData(index, 2, entry.pvalue);
125 
+	}
126 
+}
127 
+
128 
+void CHPQuantificationDetectionData::AddColumns(DataSetHeader& hdr, bool keyIsID)
129 
+{
130 
+    if (keyIsID == false)
131 
+        hdr.AddAsciiColumn(QUANTIFICATION_DETECTION_PROBE_SET_NAME, maxProbeSetName);
132 
+    else
133 
+        hdr.AddIntColumn(QUANTIFICATION_DETECTION_PROBE_SET_ID);
134 
+	hdr.AddFloatColumn(QUANTIFICATION_DETECTION_QUANTIFICATION_NAME);
135 
+    hdr.AddFloatColumn(QUANTIFICATION_DETECTION_DETECTION_NAME);
136 
+}
137 
+
138 
+void CHPQuantificationDetectionData::OpenQuantificationDetectionDataSet()
139 
+{
140 
+	if (entries == NULL)
141 
+	{
142 
+		entries = genericData.DataSet(0, 0);
143 
+		if (entries)
144 
+		{
145 
+			entries->Open();
146 
+			firstColumnType = entries->Header().GetColumnInfo(0).GetColumnType();
147 
+		}
148 
+	}
149 
+}
150 
+
151 
+std::wstring CHPQuantificationDetectionData::GetArrayType()
152 
+{
153 
+	return GetWStringFromGenericHdr(ARRAY_TYPE_PARAM_NAME);
154 
+}
155 
+
156 
+void CHPQuantificationDetectionData::SetArrayType(const std::wstring& value)
157 
+{
158 
+	SetWStringToGenericHdr(ARRAY_TYPE_PARAM_NAME, value, ARRAY_TYPE_MAX_LEN);
159 
+}
160 
+
161 
+std::wstring CHPQuantificationDetectionData::GetAlgName()
162 
+{
163 
+	return GetWStringFromGenericHdr(ALGORITHM_NAME_PARAM_NAME);
164 
+}
165 
+
166 
+void CHPQuantificationDetectionData::SetAlgName(const std::wstring& value)
167 
+{
168 
+	SetWStringToGenericHdr(ALGORITHM_NAME_PARAM_NAME, value);
169 
+}
170 
+
171 
+std::wstring CHPQuantificationDetectionData::GetAlgVersion()
172 
+{
173 
+	return GetWStringFromGenericHdr(ALG_VERSION_PARAM_NAME);
174 
+}
175 
+
176 
+void CHPQuantificationDetectionData::SetAlgVersion(const std::wstring& value)
177 
+{
178 
+	SetWStringToGenericHdr(ALG_VERSION_PARAM_NAME, value);
179 
+}
180 
+
181 
+ParameterNameValueTypeList CHPQuantificationDetectionData::GetAlgParams()
182 
+{
183 
+	ParameterNameValueTypeList nvt;
184 
+	ParameterNameValueTypeIt begin, end;
185 
+	ParameterNameValueType param;
186 
+
187 
+	genericData.Header().GetGenericDataHdr()->GetNameValIterators(begin, end);
188 
+	while(begin != end)
189 
+	{
190 
+		std::wstring key = begin->GetName();
191 
+		if(key.compare(0, ALGORITHM_PARAM_NAME_PREFIX_S.size(),ALGORITHM_PARAM_NAME_PREFIX_S) == 0)
192 
+		{
193 
+			param = *begin;
194 
+			key.erase(0, ALGORITHM_PARAM_NAME_PREFIX_S.size());
195 
+			param.SetName(key);
196 
+			nvt.push_back(param);
197 
+		}
198 
+		begin++;
199 
+	}
200 
+	return nvt;
201 
+}
202 
+
203 
+void CHPQuantificationDetectionData::AddAlgParams(const ParameterNameValueTypeList& params)
204 
+{
205 
+	ParameterNameValueType param;
206 
+	GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
207 
+	for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); it++)
208 
+	{
209 
+		param = *it;
210 
+		param.SetName(ALGORITHM_PARAM_NAME_PREFIX_S + param.GetName());
211 
+		hdr->AddNameValParam(param);
212 
+	}
213 
+}
214 
+
215 
+ParameterNameValueTypeList CHPQuantificationDetectionData::GetSummaryParams()
216 
+{
217 
+	ParameterNameValueTypeList nvt;
218 
+	ParameterNameValueTypeIt begin, end;
219 
+	ParameterNameValueType param;
220 
+
221 
+	genericData.Header().GetGenericDataHdr()->GetNameValIterators(begin, end);
222 
+	while(begin != end)
223 
+	{
224 
+		std::wstring key = begin->GetName();
225 
+		if(key.compare(0, CHIP_SUMMARY_PARAMETER_NAME_PREFIX.size(),CHIP_SUMMARY_PARAMETER_NAME_PREFIX) == 0)
226 
+		{
227 
+			param = *begin;
228 
+			key.erase(0, CHIP_SUMMARY_PARAMETER_NAME_PREFIX.size());
229 
+			param.SetName(key);
230 
+			nvt.push_back(param);
231 
+		}
232 
+		begin++;
233 
+	}
234 
+	return nvt;
235 
+}
236 
+
237 
+void CHPQuantificationDetectionData::AddSummaryParams(const ParameterNameValueTypeList& params)
238 
+{
239 
+	ParameterNameValueType param;
240 
+	GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
241 
+	for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); it++)
242 
+	{
243 
+		param = *it;
244 
+		param.SetName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX + param.GetName());
245 
+		hdr->AddNameValParam(param);
246 
+	}
247 
+}
248 
+
249 
+std::wstring CHPQuantificationDetectionData::GetWStringFromGenericHdr(const std::wstring& name)
250 
+{
251 
+	std::wstring result;
252 
+	ParameterNameValueType paramType;
253 
+	GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
254 
+	if (hdr->FindNameValParam(name, paramType))
255 
+	{
256 
+		result = paramType.GetValueText();
257 
+	}
258 
+	return result;
259 
+}
260 
+
261 
+void CHPQuantificationDetectionData::SetWStringToGenericHdr(const std::wstring& name, const std::wstring value, int32_t reserve)
262 
+{
263 
+	ParameterNameValueType paramType;
264 
+	paramType.SetName(name);
265 
+	paramType.SetValueText(value, reserve);
266 
+	GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
267 
+	hdr->AddNameValParam(paramType);
268 
+}
269 
+
src/fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h
History View file @ 4bc22e9
0 270 
new file mode 100644
... ... 
@@ -0,0 +1,201 @@
1 
+/////////////////////////////////////////////////////////////////
2 
+//
3 
+// Copyright (C) 2006 Affymetrix, Inc.
4 
+//
5 
+// This library is free software; you can redistribute it and/or modify
6 
+// it under the terms of the GNU Lesser General Public License as published
7 
+// by the Free Software Foundation; either version 2.1 of the License,
8 
+// or (at your option) any later version.
9 
+//
10 
+// This library is distributed in the hope that it will be useful, but
11 
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
12 
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
13 
+// for more details.
14 
+//
15 
+// You should have received a copy of the GNU Lesser General Public License
16 
+// along with this library; if not, write to the Free Software Foundation, Inc.,
17 
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 
+//
19 
+/////////////////////////////////////////////////////////////////
20 
+
21 
+#ifndef _CHPQuantificationDetectionData_HEADER_
22 
+#define _CHPQuantificationDetectionData_HEADER_
23 
+
24 
+#include <string>
25 
+#include "FileHeader.h"
26 
+#include "GenericData.h"
27 
+#include "AffymetrixBaseTypes.h"
28 
+#include "ProbeSetQuantificationDetectionData.h"
29 
+
30 
+namespace affymetrix_calvin_io
31 
+{
32 
+
33 
+/*! The identifier to identify a quantification/detection CHP file. */
34 
+#define CHP_QUANTIFICATION_DETECTION_TYPE std::string("affymetrix-quantification-detection-analysis")
35 
+
36 
+/*! The group and data set to store the quantification/detection data. */
37 
+#define QUANTIFICATION_DETECTION_NAME std::wstring(L"QuantificationDetection")
38 
+
39 
+/*! The column name for the probe set name. */
40 
+#define QUANTIFICATION_DETECTION_PROBE_SET_NAME std::wstring(L"ProbeSetName")
41 
+
42 
+/*! The column name for the probe set id. */
43 
+#define QUANTIFICATION_DETECTION_PROBE_SET_ID std::wstring(L"ProbeSetId")
44 
+
45 
+/*! The column name for the quantification value. */
46 
+#define QUANTIFICATION_DETECTION_QUANTIFICATION_NAME std::wstring(L"Quantification")
47 
+
48 
+/*! The column name for the detection value. */
49 
+#define QUANTIFICATION_DETECTION_DETECTION_NAME std::wstring(L"Detection")
50 
+
51 
+/*! Holds data associated with quantification/detection CHP files. */
52 
+class CHPQuantificationDetectionData
53 
+{
54 
+public:
55 
+	/*! Constructor */
56 
+	CHPQuantificationDetectionData();
57 
+
58 
+	/*! Constructor with file name.
59 
+	 * @param filename The name of the CHP file.
60 
+	 */
61 
+	CHPQuantificationDetectionData(const std::string& filename);
62 
+
63 
+	/*! Destructor */
64 
+	~CHPQuantificationDetectionData();
65 
+
66 
+private:
67 
+	/*! Flag indicating if the probe set names were stored in wide character format. */
68 
+    DataSetColumnTypes firstColumnType;
69 
+
70 
+	/*! The generic data item. */
71 
+	GenericData genericData;
72 
+
73 
+	/*! chp data sets */
74 
+	DataSet* entries;
75 
+
76 
+	/*! The maximum length of a probe set name. */
77 
+	int maxProbeSetName;
78 
+
79 
+public:
80 
+
81 
+	/*! The maximum length of a probe set name. */
82 
+	int GetMaxProbeSetName() const { return maxProbeSetName; }
83 
+
84 
+	/*! Clears the members. */
85 
+	void Clear();
86 
+
87 
+	/*! Sets the file name.
88 
+	 * @param p The name of the CHP file
89 
+	 */
90 
+	void SetFilename(const std::string &p);
91 
+
92 
+	/*! Gets the file name.
93 
+	 * @return The file name.
94 
+	 */
95 
+	std::string GetFilename() const;
96 
+
97 
+	/*! Sets the array type */
98 
+	std::wstring GetArrayType();
99 
+
100 
+	/*! Sets the array type.  */
101 
+	void SetArrayType(const std::wstring& value);
102 
+
103 
+	/*! Sets the number of entries (probe sets). Use this function if names are to be stored.
104 
+	 * @param ln The number of probe sets.
105 
+	 * @param maxln The maximum length of a probe set name.
106 
+	 */
107 
+	void SetEntryCount(int32_t ln, int32_t maxln);
108 
+
109 
+	/*! Sets the number of entries (probe sets). Use this function if ids are to be stored.
110 
+	 * @param ln The number of probe sets.
111 
+	 */
112 
+	void SetEntryCount(int32_t ln);
113 
+
114 
+	/*! Gets the number of entries (probe sets) */
115 
+	int32_t GetEntryCount();
116 
+
117 
+	/*! Gets the name of the algorithm.
118 
+	 * @return The algorithm name.
119 
+	 */
120 
+	std::wstring GetAlgName();
121 
+
122 
+	/*! Sets the name of the algorithm.
123 
+	 * @param value The algorithm name.
124 
+	 */
125 
+	void SetAlgName(const std::wstring& value);
126 
+
127 
+	/*! Gets the algorithm version.
128 
+	 * @return The version.
129 
+	 */
130 
+	std::wstring GetAlgVersion();
131 
+
132 
+	/*! Sets the algorithm version.
133 
+	 * @param value The version.
134 
+	 */
135 
+	void SetAlgVersion(const std::wstring& value);
136 
+
137 
+	/*! Gets the algorithm parameters
138 
+	 * @return The algoirhtm parameters.
139 
+	 */
140 
+	ParameterNameValueTypeList GetAlgParams();
141 
+
142 
+	/*! Adds the algorithm parameters.
143 
+	 * @param params The algorithm parameters.
144 
+	 */
145 
+	void AddAlgParams(const ParameterNameValueTypeList& params);
146 
+
147 
+	/*! Gets the summary parameters
148 
+	 * @return The summary parameters.
149 
+	 */
150 
+	ParameterNameValueTypeList GetSummaryParams();
151 
+
152 
+	/*! Adds the summary parameters.
153 
+	 * @param params The summary parameters.
154 
+	 */
155 
+	void AddSummaryParams(const ParameterNameValueTypeList& params);
156 
+
157 
+	/*! Gets the file header.
158 
+	 * @return The file header.
159 
+	 */
160 
+	FileHeader* GetFileHeader() { return &genericData.Header(); }
161 
+
162 
+	/*! Gets the generic data object.
163 
+	 * @return The data object.
164 
+	 */
165 
+	GenericData& GetGenericData() { return genericData; }
166 
+
167 
+	/*! Gets the sequence data.
168 
+	 * @param index The row index.
169 
+	 * @param entry The quantification/detection value.
170 
+	 */
171 
+	void GetQuantificationDetectionEntry(int index, affymetrix_calvin_data::ProbeSetQuantificationDetectionData &entry);
172 
+
173 
+	/*! Opens a group for reading. */
174 
+	void OpenQuantificationDetectionDataSet();
175 
+
176 
+private:
177 
+
178 
+	/*! Gets a parameter value as a string.
179 
+	 * @param name The name of the parameter.
180 
+	 * @return The string representation.
181 
+	 */
182 
+	std::wstring GetWStringFromGenericHdr(const std::wstring& name);
183 
+
184 
+	/*! Adds a parameter name/value pair to the parameters section.
185 
+	 * @param name The name of the parameter.
186 
+	 * @param value The value of the parameter.
187 
+	 * @param reserve The length of the string to reserve.
188 
+	 */
189 
+	void SetWStringToGenericHdr(const std::wstring& name, const std::wstring value, int32_t reserve=-1);
190 
+
191 
+	/*! Adds the columns to the data set.
192 
+	 * @param hdr The data set header.
193 
+	 * @param keyIsID True if the probe set ids are to be stored, false for probe set names.
194 
+	 */
195 
+	void AddColumns(DataSetHeader& hdr, bool keyIsID);
196 
+
197 
+};
198 
+
199 
+}
200 
+
201 
+#endif
src/fusion_sdk/calvin_files/data/src/DataException.h
History View file @ 4bc22e9
... ... 
@@ -1,67 +1,70 @@
1 
-/////////////////////////////////////////////////////////////////
2 
-//
3 
-// Copyright (C) 2005 Affymetrix, Inc.
4 
-//
5 
-// This library is free software; you can redistribute it and/or modify
6 
-// it under the terms of the GNU Lesser General Public License as published
7 
-// by the Free Software Foundation; either version 2.1 of the License,
8 
-// or (at your option) any later version.
9 
-//
10 
-// This library is distributed in the hope that it will be useful, but
11 
-// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
12 
-// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
13 
-// for more details.
14 
-//
15 
-// You should have received a copy of the GNU Lesser General Public License
16 
-// along with this library; if not, write to the Free Software Foundation, Inc.,
17 
-// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 
-//
19 
-/////////////////////////////////////////////////////////////////
20 
-
21 
-#ifndef _DataException_HEADER_
22 
-#define _DataException_HEADER_
23 
-
24 
-/*! \file DataException.h This file provides class definition for the data exceptions.
25 
- */
26 
-
27 
-#include "ExceptionBase.h"
28 
-
29 
-namespace affymetrix_calvin_exceptions
30 
-{
31 
-
32 
-class DataSetNotOpenException : public CalvinException
33 
-{
34 
-};
35 
-
36 
-class ColumnIndexOutOfBoundsException : public CalvinException
37 
-{
38 
-};
39 
-
40 
-class RowIndexOutOfBoundsException : public CalvinException
41 
-{
42 
-};
43 
-
44 
-class UnexpectedColumnTypeException : public CalvinException
45 
-{
46 
-};
47 
-
48 
-class DataGroupNotFoundException : public CalvinException
49 
-{
50 
-};
51 
-
52 
-class DataSetNotFoundException : public CalvinException
53 
-{
54 
-};
55 
-
56 
-class ProbeSetNotFoundException : public CalvinException
57 
-{
58 
-};
59 
-
60 
-class CDFAccessNotSupportedByModeException : public CalvinException
61 
-{
62 
-};
63 
-
64 
-
65 
-}
66 
-
67 
-#endif // _DataException_HEADER_
1 
+/////////////////////////////////////////////////////////////////
2 
+//
3 
+// Copyright (C) 2005 Affymetrix, Inc.
4 
+//
5 
+// This library is free software; you can redistribute it and/or modify
6 
+// it under the terms of the GNU Lesser General Public License as published
7 
+// by the Free Software Foundation; either version 2.1 of the License,
8 
+// or (at your option) any later version.
9 
+//
10 
+// This library is distributed in the hope that it will be useful, but
11 
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
12 
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
13 
+// for more details.
14 
+//
15 
+// You should have received a copy of the GNU Lesser General Public License
16 
+// along with this library; if not, write to the Free Software Foundation, Inc.,
17 
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 
+//
19 
+/////////////////////////////////////////////////////////////////
20 
+
21 
+#ifndef _DataException_HEADER_
22 
+#define _DataException_HEADER_
23 
+
24 
+/*! \file DataException.h This file provides class definition for the data exceptions.
25 
+ */
26 
+
27 
+#include "ExceptionBase.h"
28 
+
29 
+namespace affymetrix_calvin_exceptions
30 
+{
31 
+
32 
+class DataSetNotOpenException : public CalvinException
33 
+{
34 
+};
35 
+
36 
+class ColumnIndexOutOfBoundsException : public CalvinException
37 
+{
38 
+};
39 
+
40 
+class RowIndexOutOfBoundsException : public CalvinException
41 
+{
42 
+};
43 
+
44 
+class UnexpectedColumnTypeException : public CalvinException
45 
+{
46 
+};
47 
+
48 
+class DataGroupNotFoundException : public CalvinException
49 
+{
50 
+};
51 
+
52 
+class DataSetNotFoundException : public CalvinException
53 
+{
54 
+};
55 
+
56 
+class ProbeSetNotFoundException : public CalvinException
57 
+{
58 
+};
59 
+
60 
+class CDFAccessNotSupportedByModeException : public CalvinException
61 
+{
62 
+};
63 
+
64 
+class DataSetRemapException : public CalvinException
65 
+{
66 
+};
67 
+
68 
+}
69 
+
70 
+#endif // _DataException_HEADER_
src/fusion_sdk/calvin_files/data/src/DataGroup.cpp
History View file @ 4bc22e9
... ... 
@@ -23,7 +23,7 @@
23 23
24 24 
 using namespace affymetrix_calvin_io;
25 25
26 
-#if !defined(_MSC_VER) && !defined(WIN32)
26 
+#ifndef _MSC_VER
27 27 
 #include <sys/mman.h>
28 28 
 #endif
29 29
src/fusion_sdk/calvin_files/data/src/DataSet.cpp
History View file @ 4bc22e9
... ... 
@@ -28,7 +28,6 @@ using namespace affymetrix_calvin_io;
28 28
29 29 
 #ifndef _MSC_VER
30 30 
 #include <unistd.h>
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-#ifndef WIN32
32 31 
 #include <sys/mman.h>
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34 33 
 #ifndef PAGE_SIZE
... ... 
@@ -44,7 +43,6 @@ using namespace affymetrix_calvin_io;
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 #define PAGE_TRUNC(ptr) (ptr&(PAGE_MASK))
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 #endif
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 #endif
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-#endif
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49 47 
 /*
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  * Initialize the object to use memory-mapping to access the file.
... ... 
@@ -58,7 +56,7 @@ DataSet::DataSet(const std::string& fileName_, const DataSetHeader& header_, voi
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 	data = 0;
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 	isOpen = false;
60 58
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	fileMapHandle = handle;
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 #else
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 	fp = 0;
... ... 
@@ -82,7 +80,7 @@ DataSet::DataSet(const std::string& fileName_, const affymetrix_calvin_io::DataS
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 	data = 0;
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 	isOpen = false;
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	fileMapHandle = 0;
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 #else
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 	fp = 0;
... ... 
@@ -134,7 +132,7 @@ bool DataSet::Open()
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  */
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 bool DataSet::OpenMM()
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 {
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	if (MapDataWin32(header.GetDataStartFilePos(), header.GetDataSize()) == false)
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 		return false;
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 #else
... ... 
@@ -179,7 +177,7 @@ void DataSet::Close()
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 		ClearStreamData();
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 }
181 179
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 std::string GetErrorMsg()
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 {
... ... 
@@ -291,7 +289,7 @@ bool DataSet::MapDataPosix(u_int32_t start, u_int32_t bytes)
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  */
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 void DataSet::UnmapFile()
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 {
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	// Unmap the view
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 	if (mappedData != 0 )
... ... 
@@ -385,7 +383,7 @@ char* DataSet::FilePosition(int32_t rowStart, int32_t col, int32_t rowCount)
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 	// Byte offset in data set + byte offset of data set in file
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 	u_int32_t startByte = BytesPerRow()*rowStart + columnByteOffsets[col] + header.GetDataStartFilePos();
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	if (useMemoryMapping)
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 	{
... ... 
@@ -405,11 +403,20 @@ char* DataSet::FilePosition(int32_t rowStart, int32_t col, int32_t rowCount)
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 				if (reverseStartByte < header.GetDataStartFilePos())
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 					reverseStartByte = header.GetDataStartFilePos();
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-				MapDataWin32(reverseStartByte, header.GetDataSize() - reverseStartByte);
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-
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+				if (MapDataWin32(reverseStartByte, header.GetDataStartFilePos() + header.GetDataSize() - reverseStartByte) == false)
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+				{
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+					affymetrix_calvin_exceptions::DataSetRemapException e;
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+					throw e;
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+				}
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 			}
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 			else	// forward
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-				MapDataWin32(startByte, header.GetDataSize() - startByte);
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+			{
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+				if (MapDataWin32(startByte, header.GetDataStartFilePos() + header.GetDataSize() - startByte) == false)
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+				{
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+					affymetrix_calvin_exceptions::DataSetRemapException e;
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+					throw e;
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+				}
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+			}
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 		}
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 	}
415 422 
 #endif
src/fusion_sdk/calvin_files/data/src/DataSet.h
History View file @ 4bc22e9
... ... 
@@ -28,7 +28,7 @@
28 28 
 #include <string>
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 #include <fstream>
30 30
31 
-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 #include <windows.h>
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 #endif
34 34
... ... 
@@ -215,6 +215,7 @@ protected:
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 	 *	@param rowCount The number of rows to ensure are mapped starting at rowStart
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 	 *	@return Pointer to the data element at rowStart
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 	 *	@exception affymetrix_calvin_exceptions::DataSetNotOpenException The file is not open.
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+	 *	@exception affymetrix_calvin_exceptions::DataSetRemapException There was an error during a remap.
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 	 */
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 	char* FilePosition(int32_t rowStart, int32_t col, int32_t rowCount=1);
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... ... 
@@ -247,7 +248,7 @@ protected:
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 	template<typename T> void ClearAndSizeVector(std::vector<T>& values, u_int32_t size);
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 	/*! Platform specific memory-mapping method */
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	bool MapDataWin32(u_int32_t start, u_int32_t bytes);
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... ... 
@@ -275,7 +276,7 @@ protected:
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 	 */
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 	Int32Vector columnByteOffsets;
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	/*! Handle returned by CreateFileMapping */
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 	HANDLE fileMapHandle;
src/fusion_sdk/calvin_files/data/src/DataSetHeader.h
History View file @ 4bc22e9
... ... 
@@ -30,7 +30,6 @@
30 30 
 #include "GenericDataHeader.h"
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 #include "AffyStlCollectionTypes.h"
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 #include "ColumnInfo.h"
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-#include "BitFlag.h"
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35 34 
 #ifdef _MSC_VER
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 #pragma warning(disable: 4290) // don't show warnings about throw keyword on function declarations.
... ... 
@@ -131,7 +130,7 @@ public:
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 	void SetHeaderStartFilePos(u_int32_t pos) { headerStartFilePos = pos; }
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 	/*! Get the file position of the start of the DataSet header. */
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 	u_int32_t GetHeaderStartFilePos() const { return headerStartFilePos; }
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-	/*!
133 
+
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 	/*! Set the file position of the start of the DataSet data.
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 	*  The value set here is not written to the file.
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 	*/
src/fusion_sdk/calvin_files/data/src/GenericData.cpp
History View file @ 4bc22e9
... ... 
@@ -33,7 +33,7 @@ using namespace affymetrix_calvin_io;
33 33 
  */
34 34 
 GenericData::GenericData()
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 {
36 
-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	fileMapHandle = NULL;
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 	fileHandle = INVALID_HANDLE_VALUE;
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 #endif
... ... 
@@ -262,7 +262,7 @@ DataSet* GenericData::DataSet(const std::wstring& dataGroupName, const std::wstr
262 262 
 DataSet* GenericData::CreateDataSet(DataSetHeader* dsh)
263 263 
 {
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 	void* handle = 0;
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-#if defined(_MSC_VER) || defined(WIN32)
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+#ifdef _MSC_VER
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 	handle = fileMapHandle;
267 267 
 #endif
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 	ReadFullDataSetHeader(dsh);
... ... 
@@ -310,7 +310,7 @@ affymetrix_calvin_io::DataGroup GenericData::DataGroup(u_int32_t dataGroupFilePo
310 310 
 		fs.close();
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 	void* handle = 0;
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-#if defined(_MSC_VER) || defined(WIN32)
313 
+#ifdef _MSC_VER
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 	handle = fileMapHandle;
315 315 
 #endif
316 316
... ... 
@@ -423,7 +423,7 @@ bool GenericData::IsDSHPartiallyRead(const DataSetHeader* dph)
423 423 
 {
424 424 
 	if (dph == 0)
425 425 
 		return false;
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-	if (dph->GetRowCnt() == 0 && dph->GetColumnCnt() == 0)
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+	if (dph->GetRowCnt() == 0 && dph->GetColumnCnt() == 0 && dph->GetNameValParamCnt() == 0)
427 427 
 		return true;
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 	return false;
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 }
... ... 
@@ -465,7 +465,7 @@ void GenericData::Close()
465 465 
  */
466 466 
 bool GenericData::MapFile()
467 467 
 {
468 
-#if defined(_MSC_VER) || defined(WIN32)	// On Windows the map is open in the GenericData object, otherwise it is opened in the DataSet
468 
+#ifdef _MSC_VER	// On Windows the map is open in the GenericData object, otherwise it is opened in the DataSet
469 469 
 	if (fileHandle == INVALID_HANDLE_VALUE)
470 470 
 	{
471 471 
 		// Create the file.
... ... 
@@ -494,7 +494,7 @@ bool GenericData::MapFile()
494 494 
  */
495 495 
 void GenericData::UnmapFile()
496 496 
 {
497 
-#if defined(_MSC_VER) || defined(WIN32)
497 
+#ifdef _MSC_VER
498 498
499 499 
 	if (fileHandle != INVALID_HANDLE_VALUE)
500 500 
 	{
src/fusion_sdk/calvin_files/data/src/GenericData.h
History View file @ 4bc22e9
... ... 
@@ -231,7 +231,7 @@ protected:
231 231 
 	/*! The header and generic header objects */
232 232 
 	affymetrix_calvin_io::FileHeader header;
233 233
234 
-#if defined(_MSC_VER) || defined(WIN32)
234 
+#ifdef _MSC_VER
235 235 
 	/*! Handle returned by CreateFileMapping */
236 236 
 	HANDLE fileMapHandle;
237 237
src/fusion_sdk/calvin_files/data/src/ProbeSetSignalData.h
History View file @ 4bc22e9
238 238 
similarity index 72%
239 239 
rename from src/fusion_sdk/calvin_files/data/src/ProbeSetSignalData.h
240 240 
rename to src/fusion_sdk/calvin_files/data/src/ProbeSetQuantificationData.h
... ... 
@@ -18,10 +18,10 @@
18 18 
 //
19 19 
 /////////////////////////////////////////////////////////////////
20 20
21 
-#ifndef _ProbeSetSignalData_HEADER_
22 
-#define _ProbeSetSignalData_HEADER_
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+#ifndef _ProbeSetQuantificationData_HEADER_
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+#define _ProbeSetQuantificationData_HEADER_
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24 
-/*! \file ProbeSetSignalData.h This file provides types to hold signal results.
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+/*! \file ProbeSetQuantificationData.h This file provides types to hold quantification results.
25 25 
  */
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27 27 
 #include <string>
... ... 
@@ -30,8 +30,8 @@
30 30 
 namespace affymetrix_calvin_data
31 31 
 {
32 32
33 
-/*! Stores data for a signal of a probe set. */
34 
-typedef struct _ProbeSetSignalData
33 
+/*! Stores data for a quantification of a probe set. */
34 
+typedef struct _ProbeSetQuantificationData
35 35 
 {
36 36 
 	/*! The name of the probe set. */
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 	std::string name;
... ... 
@@ -39,10 +39,10 @@ typedef struct _ProbeSetSignalData
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     /*! The probe set id. */
40 40 
     int32_t id;
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42 
-	/*! The signal associated to the name. */
43 
-	float signal;
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+	/*! The quantification associated to the name. */
43 
+	float quantification;
44 44
45 
-} ProbeSetSignalData;
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+} ProbeSetQuantificationData;
46 46
47 47 
 }
48 48
src/fusion_sdk/calvin_files/data/src/ProbeSetQuantificationDetectionData.h
History View file @ 4bc22e9
49 49 
new file mode 100644
... ... 
@@ -0,0 +1,53 @@
1 
+/////////////////////////////////////////////////////////////////
2 
+//
3 
+// Copyright (C) 2006 Affymetrix, Inc.
4 
+//
5 
+// This library is free software; you can redistribute it and/or modify
6 
+// it under the terms of the GNU Lesser General Public License as published
7 
+// by the Free Software Foundation; either version 2.1 of the License,
8 
+// or (at your option) any later version.
9 
+//
10 
+// This library is distributed in the hope that it will be useful, but
11 
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
12 
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
13 
+// for more details.
14 
+//
15 
+// You should have received a copy of the GNU Lesser General Public License
16 
+// along with this library; if not, write to the Free Software Foundation, Inc.,
17 
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 
+//
19 
+/////////////////////////////////////////////////////////////////
20 
+
21 
+#ifndef _ProbeSetQuantificationDetectionData_HEADER_
22 
+#define _ProbeSetQuantificationDetectionData_HEADER_
23 
+
24 
+/*! \file ProbeSetQuantificationDetectionData.h This file provides types to hold quantification and detection results.
25 
+ */