1. affxparser
  2. Commit a5a28055b34cf1fec2470bbf77d5413ce2e27f4d
Browse code

Updated to Fusions 1.1.0

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@44422 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 29/01/2010 19:45:03
Showing 479 changed files
DESCRIPTION
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@@ -1,11 +1,10 @@
1 1 
 Package: affxparser
2 
-Version: 1.19.0
3 
-Date: 2009-09-22
2 
+Version: 1.19.1
4 3 
 Title: Affymetrix File Parsing SDK
5 4 
 Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper Daniel Hansen, Martin Morgan
6 5 
 Maintainer: Kasper Daniel Hansen <khansen@stat.berkeley.edu>
7 6 
 Description: Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR).  It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK.  Both ASCII- and binary-based files are supported.  Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL).  These files can be read either in full or in part.  For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.
8 
-FusionDetails: Fusion SDK v1.0.12 (November 2008)
7 
+FusionDetails: Fusion SDK v1.1.0
9 8 
 License: LGPL (>= 2)
10 9 
 Depends: R (>= 2.6.0)
11 10 
 Suggests: R.utils, AffymetrixDataTestFiles
inst/NEWS
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@@ -1,6 +1,9 @@
1 1 
 Package: affxparser
2 2 
 ===================
3 3
4 
+Version: 1.19.1 [2010-01-29]
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+o Updated Fusion SDK to 1.1.0
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+
4 7 
 Version: 1.19.0 [2009-10-27]
5 8 
 o Devel version bumped because of the new Bioconductor release.
6 9
inst/info/CDFFileData.cpp.patch
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new file mode 100644
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@@ -0,0 +1,15 @@
1 
+Index: CDFFileData.cpp
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+===================================================================
3 
+--- CDFFileData.cpp	(revision 44417)
4 
+@@ -747,8 +747,8 @@
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+ 		ReadNextLine(instr, str, MAXLINELENGTH); // #qc ProbeSets
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+ 		subStr=strchr(str,'=')+1;
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+ 		m_Header.m_NumQCProbeSets = atoi(subStr);
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+-		char strref[65000];
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+-		ReadNextLine(instr, strref, 65000);	// The reference string.
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++		char strref[400000];
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++		ReadNextLine(instr, strref, 400000);	// The reference string.
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+ 		subStr=strchr(strref,'=')+1;
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+ 		m_Header.m_Reference = subStr;
14 
+ 	}
inst/info/Makefile.fusion
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similarity index 68%
1 16 
rename from inst/info/Makefile.fusion
2 17 
rename to inst/info/Makefile
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@@ -1,8 +1,16 @@
1 
-fusion=affy/sdk
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-affxparser=~/Work/packages/affxparser/src/fusion_sdk
1 
+## Usual workflow
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+##   first make cleanfusion
3 
+##   then make compare
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+##     check for files and directories that ought to be deleted
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+##   then copy
6 
+
7 
+fusion=~/Work/packages/affy/sdk
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+affxparser_base=~/Work/packages/affxparser
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+affxparser_fusion=${affxparser_base}/src/fusion_sdk
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+affxparser_patchdir=${affxparser_base}/inst/info
3 11
4 12 
 compare :
5 
-	diff -rq ${fusion} ${affxparser} | grep Only | grep -v svn | cat
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+	diff -rq ${fusion} ${affxparser_fusion} | grep Only | grep -v svn | cat
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7 15 
 cleanfusion :
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 	rm -Rf	 \
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@@ -38,7 +46,13 @@ cleanfusion :
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 	${fusion}/calvin_files/parsers/data \
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 	${fusion}/calvin_files/utils/data \
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 	${fusion}/calvin_files/writers/data \
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+	${fusion}/calvin_files/lib-calvin-devnet.vcproj \
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+	${fusion}/calvin_files/lib-fusion-apt.vcproj \
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 	${fusion}/file/file.vcproj \
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 	${fusion}/file/file.sln \
43 53 
 	${fusion}/file/lib-file-apt.vcproj \
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-	${fusion}/style.css
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+	${fusion}/style.css \
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+
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+patch:
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+	patch ${affxparser_fusion}/file/CDFFileData.cpp ${affxparser_patchdir}/CDFFileData.cpp.patch
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+
inst/info/changes2fusion.txt
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@@ -1,27 +1,18 @@
1 
-Issue: long CDF reference string
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-line 723 and 724 of *** has the number 65000 changed to 400000
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+In general, see the patchfile(s) in this directory
2 
+
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+CDFFIleData.cpp.pacth
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+  Issue: long CDF reference string
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+  Fix: change the number 65000 to 400000 in lines 723, 724
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+
7 
+There may be issues in that GCC 4.3.1+ has stricter include
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+statements: our old notes tells us to #include <stdlib.h> but
9 
+Affy seems to use <cstdlib>, we'll see if it works.
3 10
4 
-Issue: GCC 4.3.1+ has stricter include statements
5 
-- use of wstring
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- in fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h
7 
- requires #include <string>
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9 12 
 - use of atoi()
10 13 
  in fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp
11 14 
  requires #include <stdlib.h>
12 15
13 
-- use of memset() and memcpy()
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- in fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp
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- requires #include <string.h>
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-
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-- use of memcpy()
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- in fusion_sdk/calvin_files/parsers/src/FileInput.cpp
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- requires #include <string.h>
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-
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-- use of strlen()
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- in fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp
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- requires #include <string.h>
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-
25 16 
 - use of wcstombs and mbstowcs
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  in fusion_sdk/calvin_files/utils/src/StringUtils.cpp
27 18 
  requires #include <stdlib.h>
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@@ -29,16 +20,3 @@ Issue: GCC 4.3.1+ has stricter include statements
29 20 
 - use of EXIT_FAILURE and EXIT_SUCCESS
30 21 
  in fusion_sdk/file/BPMAPFileData.cpp
31 22 
  requires #include <stdlib.h>
32 
-
33 
-- use of strncmp(), strchr(), strlen() and atoi()
34 
- in fusion_sdk/file/CDFFileData.cpp
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- requires #include <string.h> and #include <stdlib.h>
36 
-
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-- use of strlen() and strcmp()
38 
- in fusion_sdk/file/CHPFileData.cpp
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- requires #include <string.h>
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-
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-- use of strcmp()
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- in fusion_sdk/util/Convert.cpp
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- requires #include <string.h>
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-
man/readBpmap.Rd
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@@ -21,7 +21,7 @@ readBpmapSeqinfo(filename, seqIndices = NULL, verbose = 0)
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   \item{filename}{The filename as a character.}
22 22 
   \item{seqIndices}{A vector of integers, detailing the indices of the
23 23 
     sequences being read. If \code{NULL}, the entire file is being read.}
24 
-  \item{readProbeSeq}{}
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+  \item{readProbeSeq}{Do we read the probe sequences.}
25 25 
   \item{readSeqInfo}{Do we read the sequence information (a list
26 26 
     containing information such as sequence name, number of hits etc.)}
27 27 
   \item{readPMXY}{Do we read the (x,y) coordinates of the PM-probes.}
src/Makevars
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@@ -95,8 +95,13 @@ PKG_SOURCES = \
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 	fusion_sdk/file/FileIO.cpp\
96 96 
 	fusion_sdk/file/FileWriter.cpp\
97 97 
 	fusion_sdk/file/TsvFile/TsvFile.cpp\
98 
+	fusion_sdk/util/AffxByteArray.cpp\
99 
+	fusion_sdk/util/AffxConv.cpp\
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+	fusion_sdk/util/AffxFile.cpp\
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 	fusion_sdk/util/MsgStream.cpp\
99 102 
 	fusion_sdk/util/Util.cpp\
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+	fusion_sdk/util/Err.cpp\
104 
+	fusion_sdk/util/Verbose.cpp\
100 105 
 	fusion_sdk/util/RowFile.cpp\
101 106 
 	fusion_sdk/util/TableFile.cpp\
102 107 
 	fusion_sdk/util/Convert.cpp\
src/fusion_sdk/apt/apt.h
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@@ -0,0 +1,38 @@
1 
+////////////////////////////////////////////////////////////////
2 
+//
3 
+// Copyright (C) 2005 Affymetrix, Inc.
4 
+//
5 
+// This program is free software; you can redistribute it and/or modify
6 
+// it under the terms of the GNU General Public License (version 2) as
7 
+// published by the Free Software Foundation.
8 
+//
9 
+// This program is distributed in the hope that it will be useful,
10 
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
11 
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
12 
+// General Public License for more details.
13 
+//
14 
+// You should have received a copy of the GNU General Public License
15 
+// along with this program;if not, write to the
16 
+//
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+// Free Software Foundation, Inc.,
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+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
19 
+//
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+////////////////////////////////////////////////////////////////
21 
+
22 
+#ifndef _APT_H_
23 
+#define _APT_H_
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+
25 
+#ifdef WIN32
26 
+#ifdef APT_LIB_EXPORTS // when building DLL, target project defines this macro
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+#define APTLIB_API __declspec(dllexport)
28 
+#elif defined(APT_LIB_IMPORTS) // when using DLL, client project defines this macro
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+#define APTLIB_API __declspec(dllimport)
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+#else // when building or using target static library, or whatever: define it as nothing
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+#define APTLIB_API
32 
+#endif // APT_EXPORT
33 
+#else
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+#define APTLIB_API
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+#endif // WIN32
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+
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+#endif /* _APT_H_ */
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+
src/fusion_sdk/calvin_files/array/src/ArrayAttributes.cpp
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@@ -18,7 +18,8 @@
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 ////////////////////////////////////////////////////////////////
19 19
20 20
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-#include "ArrayAttributes.h"
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+#include "calvin_files/array/src/ArrayAttributes.h"
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+//
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23 24 
 using namespace affymetrix_calvin_array;
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src/fusion_sdk/calvin_files/array/src/ArrayAttributes.h
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 /*! \file ArrayAttributes.h This file provides interfaces to store attributes about a physical array.
25 25 
  */
26 26
27 
-#include "AffymetrixGuid.h"
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-#include "Parameter.h"
29 
-#include "PATAssignment.h"
30 
-#include "ArrayMedia.h"
31 
-#include "CreateStep.h"
27 
+#include "calvin_files/array/src/ArrayMedia.h"
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+#include "calvin_files/array/src/CreateStep.h"
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+#include "calvin_files/array/src/PATAssignment.h"
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+#include "calvin_files/parameter/src/Parameter.h"
31 
+#include "calvin_files/utils/src/AffymetrixGuid.h"
32 
+//
33 
+#include <cstring>
32 34 
 #include <string>
33 35 
 #include <vector>
36 
+//
34 37
35 38 
 namespace affymetrix_calvin_array
36 39 
 {
src/fusion_sdk/calvin_files/array/src/ArrayAudit.cpp
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 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "ArrayAudit.h"
21 
+#include "calvin_files/array/src/ArrayAudit.h"
22 
+//
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23 24 
 using namespace affymetrix_calvin_array;
24 25
src/fusion_sdk/calvin_files/array/src/ArrayAudit.h
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24 24 
 /*! \file ArrayAudit.h This file provides interfaces for an audit item in an array file.
25 25 
  */
26 26
27 
-#include "AffymetrixBaseTypes.h"
28 
-#include "AffymetrixGuid.h"
29 
-#include "Parameter.h"
30 
-#include "DateTime.h"
31 
-#include <string>
27 
+#include "calvin_files/parameter/src/Parameter.h"
28 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
29 
+#include "calvin_files/utils/src/AffymetrixGuid.h"
30 
+#include "calvin_files/utils/src/DateTime.h"
31 
+//
32 
+#include <cstring>
32 33 
 #include <list>
34 
+#include <string>
35 
+//
33 36
34 37 
 namespace affymetrix_calvin_array
35 38 
 {
src/fusion_sdk/calvin_files/array/src/ArrayAuditActionTypes.h
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24 24 
 /*! \file ArrayAuditActionTypes.h Defines constants for various array file audit actions.
25 25 
  */
26 26
27 
-#include "AffymetrixBaseTypes.h"
27 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
28 
+//
28 29
29 30 
 namespace affymetrix_calvin_array
30 31 
 {
src/fusion_sdk/calvin_files/array/src/ArrayData.cpp
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18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "ArrayData.h"
21 
+#include "calvin_files/array/src/ArrayData.h"
22 
+//
22 23
23 24 
 using namespace affymetrix_calvin_array;
24 25
src/fusion_sdk/calvin_files/array/src/ArrayData.h
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@@ -24,13 +24,16 @@
24 24 
 /*! \file ArrayData.h This file provides interfaces to store information in an array file.
25 25 
  */
26 26
27 
-#include "ArrayId.h"
28 
-#include "AffymetrixBaseTypes.h"
29 
-#include "AffymetrixGuid.h"
30 
-#include "Parameter.h"
31 
-#include "ParameterNameValueType.h"
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-#include "ArrayAttributes.h"
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+#include "calvin_files/array/src/ArrayAttributes.h"
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+#include "calvin_files/array/src/ArrayId.h"
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+#include "calvin_files/parameter/src/Parameter.h"
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+#include "calvin_files/parameter/src/ParameterNameValueType.h"
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+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
32 
+#include "calvin_files/utils/src/AffymetrixGuid.h"
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+//
34 
+#include <cstring>
33 35 
 #include <string>
36 
+//
34 37
35 38 
 namespace affymetrix_calvin_array
36 39 
 {
src/fusion_sdk/calvin_files/array/src/ArrayMedia.cpp
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18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "ArrayMedia.h"
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+#include "calvin_files/array/src/ArrayMedia.h"
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+//
22 23
23 24 
 using namespace affymetrix_calvin_array;
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src/fusion_sdk/calvin_files/array/src/ArrayMedia.h
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@@ -23,7 +23,9 @@
23 23
24 24 
 /*! \file ArrayMedia.h This file a type for defining the media type of an array. */
25 25
26 
+#include <cstring>
26 27 
 #include <string>
28 
+//
27 29
28 30 
 namespace affymetrix_calvin_array
29 31 
 {
src/fusion_sdk/calvin_files/array/src/CreateStep.cpp
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 ////////////////////////////////////////////////////////////////
19 19
20 20
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-#include "CreateStep.h"
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+#include "calvin_files/array/src/CreateStep.h"
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+//
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23 24 
 using namespace affymetrix_calvin_array;
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src/fusion_sdk/calvin_files/array/src/CreateStep.h
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@@ -24,7 +24,9 @@
24 24 
 /*! \file CreateStep.h This file provides a type for definining a step that created an array object.
25 25 
  */
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27 
+#include <cstring>
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 #include <string>
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+//
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29 31 
 namespace affymetrix_calvin_array
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 {
src/fusion_sdk/calvin_files/array/src/PATAssignment.cpp
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 ////////////////////////////////////////////////////////////////
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20 20
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-#include "PATAssignment.h"
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+#include "calvin_files/array/src/PATAssignment.h"
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+//
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23 24 
 using namespace affymetrix_calvin_array;
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src/fusion_sdk/calvin_files/array/src/PATAssignment.h
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@@ -24,7 +24,9 @@
24 24 
 /*! \file PATAssignment.h This file provides a type to define the method the probe array type was assigned.
25 25 
  */
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27 
+#include <cstring>
27 28 
 #include <string>
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+//
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29 31 
 namespace affymetrix_calvin_array
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 {
src/fusion_sdk/calvin_files/data/src/AllelePeaks.h
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new file mode 100644
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1 
+////////////////////////////////////////////////////////////////
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+//
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+// Copyright (C) 2008 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
7 
+// (version 2.1) as published by the Free Software Foundation.
8 
+//
9 
+// This library is distributed in the hope that it will be useful, but
10 
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
11 
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
12 
+// for more details.
13 
+//
14 
+// You should have received a copy of the GNU Lesser General Public License
15 
+// along with this library; if not, write to the Free Software Foundation, Inc.,
16 
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
17 
+//
18 
+////////////////////////////////////////////////////////////////
19 
+
20 
+
21 
+#ifndef _AllelePeaks_HEADER_
22 
+#define _AllelePeaks_HEADER_
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+
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+/*! \file AllelePeaks.h This file provides types to hold allele peak results.
25 
+ */
26 
+
27 
+#include "calvin_files/parameter/src/ParameterNameValueType.h"
28 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
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+//
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+#include <cstring>
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+#include <string>
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+#include <vector>
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+//
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+namespace affymetrix_calvin_data
35 
+{
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+
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+/*! Holds the allele peak results */
38 
+typedef struct _AllelePeaks
39 
+{
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+	/*! The name of the marker. */
41 
+	std::string name;
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+
43 
+	/*! The chromosome value. */
44 
+	u_int8_t chr;
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+
46 
+	/*! The physical position. */
47 
+	u_int32_t position;
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+
49 
+	/*! The allele peaks. */
50 
+	std::vector<affymetrix_calvin_parameter::ParameterNameValueType> peaks;
51 
+
52 
+} AllelePeaks;
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+
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+}
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+
56 
+#endif
src/fusion_sdk/calvin_files/data/src/CDFData.cpp
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18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "CDFData.h"
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-#include "DataSetHeader.h"
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-#include "DataException.h"
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+#include "calvin_files/data/src/CDFData.h"
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+//
23 
+#include "calvin_files/data/src/DataException.h"
24 
+#include "calvin_files/data/src/DataSetHeader.h"
25 
+//
24 26
25 27 
 using namespace affymetrix_calvin_io;
26 28 
 using namespace affymetrix_calvin_exceptions;
src/fusion_sdk/calvin_files/data/src/CDFData.h
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@@ -23,14 +23,17 @@
23 23 
 #ifndef _CDFData_HEADER_
24 24 
 #define _CDFData_HEADER_
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26 
-#include <string>
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-#include "FileHeader.h"
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-#include "GenericData.h"
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-#include "CDFProbeSetInformation.h"
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-#include "CDFQCProbeSetInformation.h"
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-#include "AffymetrixBaseTypes.h"
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-#include "AffymetrixParameterConsts.h"
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+#include "calvin_files/data/src/CDFProbeSetInformation.h"
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+#include "calvin_files/data/src/CDFQCProbeSetInformation.h"
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+#include "calvin_files/data/src/FileHeader.h"
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+#include "calvin_files/data/src/GenericData.h"
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+#include "calvin_files/parameter/src/AffymetrixParameterConsts.h"
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+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
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+//
33 
+#include <cstring>
33 34 
 #include <map>
35 
+#include <string>
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+//
34 37
35 38 
 #ifdef _MSC_VER
36 39 
 #pragma warning(disable: 4290) // don't show warnings about throw keyword on function declarations.
src/fusion_sdk/calvin_files/data/src/CDFDataTypes.h
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@@ -37,6 +37,8 @@ enum CDFDataTypeIds {
37 37 
     CopyNumber,     /*! A copy number probe set. */
38 38 
     GenotypeControl,   /*! A genotype control probe set. */
39 39 
     ExpressionControl, /*! An expression control probe set. */
40 
+    Marker,			/*! A polymorphic marker probe set. */
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+	MultichannelMarker	/*! A multichannel marker probe set. */
40 42
41 43 
 };
42 44
... ... 
@@ -56,6 +58,28 @@ enum DirectionType
56 58 
     ProbeEitherDirection
57 59 
 };
58 60
61 
+/*! Defines the type of probe replication of a group   */
62 
+enum ReplicationType
63 
+{
64 
+	/*! Unspecified replication type */
65 
+	UnknownProbeRepType,
66 
+
67 
+	/*! Different
68 
+	 * All probes in the probe group have different sequences
69 
+	 */
70 
+	DifferentProbeRepType,
71 
+
72 
+	/*! Mixed
73 
+	 * Some probes in the probe group have identical sequences
74 
+	 */
75 
+	MixedProbeRepType,
76 
+
77 
+	/* Identical
78 
+	 * All probes in the probe group have identical sequences
79 
+	 */
80 
+	IdenticalProbeRepType
81 
+};
82 
+
59 83 
 }
60 84
61 85 
 #endif
src/fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp
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@@ -18,10 +18,12 @@
18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "CDFData.h"
22 
-#include "DataSet.h"
23 
-#include "CDFProbeGroupInformation.h"
24 
-#include "CDFProbeInformation.h"
21 
+#include "calvin_files/data/src/CDFProbeGroupInformation.h"
22 
+//
23 
+#include "calvin_files/data/src/CDFData.h"
24 
+#include "calvin_files/data/src/CDFProbeInformation.h"
25 
+#include "calvin_files/data/src/DataSet.h"
26 
+//
25 27
26 28 
 using namespace affymetrix_calvin_io;
27 29
... ... 
@@ -58,6 +60,8 @@ void CDFProbeGroupInformation::SetDataSet(DataSet* ds)
58 60 
 	cellCnt = 0;
59 61 
 	wobbleSituation = 0;
60 62 
 	alleleCode = 0;
63 
+	channel = 0;
64 
+	repType = 0;
61 65 
 	probeSetNumber = 0;
62 66 
 	cellsPerList = 0;
63 67
... ... 
@@ -81,11 +85,19 @@ void CDFProbeGroupInformation::SetDataSet(DataSet* ds)
81 85
82 86 
 	// Wobble situation
83 87 
 //	if (dsh.FindNameValParam(CDF_WOBBLE_SITUATION, nvt))
84 
-//		wobbleSituation = nvt.GetValueUInt8();
88 
+//		wobbleSituation = nvt.GetValueUInt16();
85 89
86 90 
 	// Allele code
87 91 
 //	if (dsh.FindNameValParam(CDF_ALLELE, nvt))
88 
-//		allele = nvt.GetValueUInt8();
92 
+//		alleleCode = nvt.GetValueUInt16();
93 
+
94 
+	// Channel
95 
+//	if (dsh.FindNameValParam(CDF_CHANNEL, nvt))
96 
+//		channel = nvt.GetValueUInt8();
97 
+
98 
+	// Probe replication type
99 
+//	if (dsh.FindNameValParam(CDF_REP_TYPE, nvt))
100 
+//		repType = nvt.GetValueUInt8();
89 101
90 102 
 	// List (atom)
91 103 
 	if (dsh.FindNameValParam(CDF_ATOMS, nvt))
src/fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h
History View file @ a5a2805
... ... 
@@ -28,6 +28,10 @@
28 28 
 #include <windows.h>
29 29 
 #endif
30 30
31 
+#include "calvin_files/data/src/CDFProbeSetInformation.h"
32 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
33 
+//
34 
+
31 35 
 namespace affymetrix_calvin_io
32 36 
 {
33 37
... ... 
@@ -56,6 +60,10 @@ public:
56 60 
 	u_int16_t GetWobbleSituation() const { return wobbleSituation; }
57 61 
 	/*! Get the allele */
58 62 
 	u_int16_t GetAlleleCode() const { return alleleCode; }
63 
+	/*! Get the channel */
64 
+	u_int8_t GetChannel() const { return channel; }
65 
+	/*! Get the probe replication type */
66 
+	ReplicationType GetRepType() const { return (ReplicationType)repType; }
59 67 
 	/*! Get information for the probe by index */
60 68 
 	void GetCell(int32_t cell_index, CDFProbeInformation& info);
61 69
... ... 
@@ -78,6 +86,10 @@ protected:
78 86 
 	u_int16_t wobbleSituation;
79 87 
 	/*! Allele */
80 88 
 	u_int16_t alleleCode;
89 
+	/*! Channel */
90 
+	u_int8_t channel;
91 
+	/*! Probe replication type */
92 
+	u_int8_t repType;
81 93 
 	/*! Probe set number - same as ProbeSetNumber in C++ */
82 94 
 	u_int32_t probeSetNumber;
83 95 
 	/*! Cells per list (atom) - same as NumCellsPerList in C++ */
src/fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp
History View file @ a5a2805
... ... 
@@ -18,7 +18,8 @@
18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "CDFProbeInformation.h"
21 
+#include "calvin_files/data/src/CDFProbeInformation.h"
22 
+//
22 23
23 24 
 using namespace affymetrix_calvin_io;
24 25
src/fusion_sdk/calvin_files/data/src/CDFProbeInformation.h
History View file @ a5a2805
... ... 
@@ -23,14 +23,15 @@
23 23
24 24 
 /*! \file CDFProbeInformation.h This file defines the CDFProbeInformation class.
25 25 
  */
26 
-
27 
-#include "DataSet.h"
28 
-#include "AffymetrixBaseTypes.h"
29 
-
30 26 
 #ifdef _MSC_VER
31 27 
 #include <windows.h>
32 28 
 #endif
33 29
30 
+#include "calvin_files/data/src/DataSet.h"
31 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
32 
+//
33 
+
34 
+
34 35 
 namespace affymetrix_calvin_io
35 36 
 {
36 37 
 /*! Class that exposes the CDF probe information */
src/fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp
History View file @ a5a2805
... ... 
@@ -18,10 +18,12 @@
18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "CDFData.h"
22 
-#include "DataSet.h"
23 
-#include "CDFProbeSetInformation.h"
24 
-#include "CDFProbeGroupInformation.h"
21 
+#include "calvin_files/data/src/CDFProbeSetInformation.h"
22 
+//
23 
+#include "calvin_files/data/src/CDFData.h"
24 
+#include "calvin_files/data/src/CDFProbeGroupInformation.h"
25 
+#include "calvin_files/data/src/DataSet.h"
26 
+//
25 27
26 28 
 using namespace affymetrix_calvin_io;
27 29
src/fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h
History View file @ a5a2805
... ... 
@@ -24,14 +24,16 @@
24 24 
 /*! \file CDFProbeSetInformation.h This file defines the CDFProbeSetInformation class.
25 25 
  */
26 26
27 
-#include "DataGroup.h"
28 
-#include "CDFDataTypes.h"
29 
-#include "AffymetrixBaseTypes.h"
30 
-
31 27 
 #ifdef _MSC_VER
32 28 
 #include <windows.h>
33 29 
 #endif
34 30
31 
+#include "calvin_files/data/src/CDFDataTypes.h"
32 
+#include "calvin_files/data/src/DataGroup.h"
33 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
34 
+//
35 
+
36 
+
35 37 
 namespace affymetrix_calvin_io
36 38 
 {
37 39
src/fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp
History View file @ a5a2805
... ... 
@@ -18,7 +18,8 @@
18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "CDFQCProbeInformation.h"
21 
+#include "calvin_files/data/src/CDFQCProbeInformation.h"
22 
+//
22 23
23 24 
 using namespace affymetrix_calvin_io;
24 25
src/fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h
History View file @ a5a2805
... ... 
@@ -24,8 +24,9 @@
24 24 
 /*! \file CDFQCProbeInformation.h This file defines the CDFQCProbeInformation class.
25 25 
  */
26 26
27 
-#include "DataSet.h"
28 
-#include "AffymetrixBaseTypes.h"
27 
+#include "calvin_files/data/src/DataSet.h"
28 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
29 
+//
29 30
30 31 
 namespace affymetrix_calvin_io
31 32 
 {
src/fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp
History View file @ a5a2805
... ... 
@@ -18,10 +18,12 @@
18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "CDFData.h"
22 
-#include "DataSet.h"
23 
-#include "CDFQCProbeSetInformation.h"
24 
-#include "CDFQCProbeInformation.h"
21 
+#include "calvin_files/data/src/CDFQCProbeSetInformation.h"
22 
+//
23 
+#include "calvin_files/data/src/CDFData.h"
24 
+#include "calvin_files/data/src/CDFQCProbeInformation.h"
25 
+#include "calvin_files/data/src/DataSet.h"
26 
+//
25 27
26 28 
 using namespace affymetrix_calvin_io;
27 29
src/fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h
History View file @ a5a2805
... ... 
@@ -21,13 +21,20 @@
21 21 
 #ifndef _CDFQCProbeSetInformation_HEADER_
22 22 
 #define _CDFQCProbeSetInformation_HEADER_
23 23
24 
-/*! \file CDFQCProbeSetInformation.h This file defines the CDFQCProbeSetInformation class.
25 
- */
26 
-
27 24 
 #ifdef _MSC_VER
28 25 
 #include <windows.h>
29 26 
 #endif
30 27
28 
+/*! \file CDFQCProbeSetInformation.h This file defines the CDFQCProbeSetInformation class.
29 
+ */
30 
+
31 
+#include "calvin_files/data/src/DataSet.h"
32 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
33 
+//
34 
+#include <cstring>
35 
+#include <string>
36 
+//
37 
+
31 38 
 namespace affymetrix_calvin_io
32 39 
 {
33 40
src/fusion_sdk/calvin_files/data/src/CELData.cpp
History View file @ a5a2805
... ... 
@@ -18,13 +18,19 @@
18 18 
 ////////////////////////////////////////////////////////////////
19 19
20 20
21 
-#include "CELData.h"
22 
-#include "DataSetHeader.h"
23 
-#include "ExceptionBase.h"
24 
-#include "GenericDataTypes.h"
21 
+#include "calvin_files/data/src/CELData.h"
22 
+//
23 
+#include "calvin_files/data/src/DataSetHeader.h"
24 
+#include "calvin_files/data/src/GenericDataTypes.h"
25 
+#include "calvin_files/exception/src/ExceptionBase.h"
26 
+#include "calvin_files/utils/src/StringUtils.h"
27 
+//
28 
+#include <sys/stat.h>
29 
+//
25 30
26 31 
 using namespace affymetrix_calvin_io;
27 32 
 using namespace affymetrix_calvin_exceptions;
33 
+using namespace affymetrix_calvin_parameter;
28 34
29 35 
 /*
30 36 
  * Default constructor
... ... 
@@ -72,17 +78,66 @@ void CelFileData::Clear()
72 78 
 	setPixelMetaData = false;
73 79 
 	setOutlierMetaData = false;
74 80 
 	setMaskMetaData = false;
81 
+	CloseDataSets();
82 
+	ResetMaskAndOutliers();
83 
+	cachedRows = -1;
84 
+	cachedCols = -1;
85 
+	intensityColumnType = -1;
86 
+	activeChannel = CelDataGroupName;
87 
+}
88 
+
89 
+void CelFileData::CloseDataSets()
90 
+{
91 
+	if (dpInten)
92 
+	{
93 
+		dpInten->Delete();
94 
+		dpInten = 0;
95 
+	}
96 
+	if (dpStdev)
97 
+	{
98 
+		dpStdev->Delete();
99 
+		dpStdev = 0;
100 
+	}
101 
+	if (dpPixels)
102 
+	{
103 
+		dpPixels->Delete();
104 
+		dpPixels = 0;
105 
+	}
106 
+}
75 107
76 
-	if (dpInten){ dpInten->Delete(); dpInten = 0; }
77 
-	if (dpStdev) { dpStdev->Delete(); dpStdev = 0; }
78 
-	if (dpPixels) { dpPixels->Delete(); dpPixels = 0; }
108 
+void CelFileData::ResetMaskAndOutliers()
109 
+{
79 110 
 	outlierPlaneRead = false;
80 111 
 	outliers.clear();
81 112 
 	maskPlaneRead = false;
82 113 
 	masked.clear();
83 
-	cachedRows = -1;
84 
-	cachedCols = -1;
85 
-	intensityColumnType = -1;
114 
+}
115 
+
116 
+void CelFileData::SetActiveChannel(const std::wstring &channel)
117 
+{
118 
+	if(activeChannel != channel)
119 
+	{
120 
+		activeChannel = channel;
121 
+		CloseDataSets();
122 
+		ResetMaskAndOutliers();
123 
+	}
124 
+}
125 
+
126 
+/*
127 
+ * Check if the file exists.
128 
+ */
129 
+bool CelFileData::Exists()
130 
+{
131 
+	std::string filename = genericData.Header().GetFilename();
132 
+
133 
+	if (filename != "")
134 
+	{
135 
+		// Find the file stats.
136 
+		struct stat st;
137 
+		return ((stat(filename.c_str(), &st) == 0)? true: false);
138 
+	}
139 
+
140 
+	return false;
86 141 
 }
87 142
88 143 
 /*
... ... 
@@ -103,99 +158,99 @@ std::string CelFileData::GetFilename() const
103 158
104 159 
 void CelFileData::SetIntensityCount(int32_t ln)
105 160 
 {
106 
-	DataSetHeader dpHdr;
107 
-	dpHdr.SetRowCnt(ln);
108 
-	dpHdr.SetName(CelIntensityLabel);
109 
-	dpHdr.AddFloatColumn(CelIntensityLabel);
161 
+	DataSetHeader setHdr;
162 
+	setHdr.SetRowCnt(ln);
163 
+	setHdr.SetName(CelIntensityLabel);
164 
+	setHdr.AddFloatColumn(CelIntensityLabel);
110 165 
 	if(setIntensityMetaData)
111 166 
 	{
112 
-		UpdateDataSetRowCount(dpHdr);
167 
+		UpdateDataSetRowCount(setHdr);
113 168 
 	}
114 169 
 	else
115 170 
 	{
116 
-		InsertDataSetHeader(dpHdr);
171 
+		InsertDataSetHeader(setHdr);
117 172 
 		setIntensityMetaData = true;
118 173 
 	}
119 174 
 }
120 175
121 176 
 void CelFileData::SetStdDevCount(int32_t ln)
122 177 
 {
123 
-	DataSetHeader dpHdr;
124 
-	dpHdr.SetRowCnt(ln);
125 
-	dpHdr.SetName(CelStdDevLabel);
126 
-	dpHdr.AddFloatColumn(CelStdDevLabel);
178 
+	DataSetHeader setHdr;
179 
+	setHdr.SetRowCnt(ln);
180 
+	setHdr.SetName(CelStdDevLabel);
181 
+	setHdr.AddFloatColumn(CelStdDevLabel);
127 182 
 	if(setStdDevMetaData)
128 183 
 	{
129 
-		UpdateDataSetRowCount(dpHdr);
184 
+		UpdateDataSetRowCount(setHdr);
130 185 
 	}
131 186 
 	else
132 187 
 	{
133 
-		InsertDataSetHeader(dpHdr);
188 
+		InsertDataSetHeader(setHdr);
134 189 
 		setStdDevMetaData = true;
135 190 
 	}
136 191 
 }
137 192
138 193 
 void CelFileData::SetPixelCount(int32_t ln)
139 194 
 {
140 
-	DataSetHeader dpHdr;
141 
-	dpHdr.SetRowCnt(ln);
142 
-	dpHdr.SetName(CelPixelLabel);
143 
-	dpHdr.AddShortColumn(CelPixelLabel);
195 
+	DataSetHeader setHdr;
196 
+	setHdr.SetRowCnt(ln);
197 
+	setHdr.SetName(CelPixelLabel);
198 
+	setHdr.AddShortColumn(CelPixelLabel);
144 199 
 	if(setPixelMetaData)
145 200 
 	{
146 
-		UpdateDataSetRowCount(dpHdr);
201 
+		UpdateDataSetRowCount(setHdr);
147 202 
 	}
148 203 
 	else
149 204 
 	{
150 
-		InsertDataSetHeader(dpHdr);
205 
+		InsertDataSetHeader(setHdr);
151 206 
 		setPixelMetaData = true;
152 207 
 	}
153 208 
 }
154 209
155 210 
 void CelFileData::SetOutlierCount(int32_t ln)
156 211 
 {
157 
-	DataSetHeader dpHdr;
158 
-	dpHdr.SetRowCnt(ln);
159 
-	dpHdr.SetName(CelOutlierLabel);
160 
-	dpHdr.AddShortColumn(L"X");
161 
-	dpHdr.AddShortColumn(L"Y");
212 
+	DataSetHeader setHdr;
213 
+	setHdr.SetRowCnt(ln);
214 
+	setHdr.SetName(CelOutlierLabel);
215 
+	setHdr.AddShortColumn(L"X");
216 
+	setHdr.AddShortColumn(L"Y");
162 217 
 	if(setOutlierMetaData)
163 218 
 	{
164 
-		UpdateDataSetRowCount(dpHdr);
219 
+		UpdateDataSetRowCount(setHdr);
165 220 
 	}
166 221 
 	else
167 222 
 	{
168 
-		InsertDataSetHeader(dpHdr);
223 
+		InsertDataSetHeader(setHdr);
169 224 
 		setOutlierMetaData = true;
170 225 
 	}
171 226 
 }
172 227
173 228 
 void CelFileData::SetMaskCount(int32_t ln)
174 229 
 {
175 
-	DataSetHeader dpHdr;
176 
-	dpHdr.SetRowCnt(ln);
177 
-	dpHdr.SetName(CelMaskLabel);
178 
-	dpHdr.AddShortColumn(L"X");
179 
-	dpHdr.AddShortColumn(L"Y");
230 
+	DataSetHeader setHdr;
231 
+	setHdr.SetRowCnt(ln);
232 
+	setHdr.SetName(CelMaskLabel);
233 
+	setHdr.AddShortColumn(L"X");
234 
+	setHdr.AddShortColumn(L"Y");
180 235 
 	if(setMaskMetaData)
181 236 
 	{
182 
-		UpdateDataSetRowCount(dpHdr);
237 
+		UpdateDataSetRowCount(setHdr);
183 238 
 	}
184 239 
 	else
185 240 
 	{
186 
-		InsertDataSetHeader(dpHdr);
241 
+		InsertDataSetHeader(setHdr);
187 242 
 		setMaskMetaData = true;
188 243 
 	}
189 244 
 }
190 245
191 246 
 void CelFileData::UpdateDataSetRowCount(const DataSetHeader &hdr)
192 247 
 {
193 
-	DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0);
248 
+	DataGroupHeader* grpHdr = &genericData.Header().GetDataGroup(0);
194 249 
 	bool found = false;
195 
-	int sz = dcHdr->GetDataSetCnt();
250 
+	int sz = grpHdr->GetDataSetCnt();
196 251 
 	for(int i = 0; i < sz; i++)
197 252 
 	{
198 
-		DataSetHeader* dpHdr = &dcHdr->GetDataSet(i);
253 
+		DataSetHeader* dpHdr = &grpHdr->GetDataSet(i);
199 254 
 		if(dpHdr->GetName() == hdr.GetName())
200 255 
 		{
201 256 
 			dpHdr->SetRowCnt(hdr.GetRowCnt());
... ... 
@@ -242,7 +297,7 @@ void CelFileData::PrepareIntensityPlane()
242 297 
 {
243 298 
 	if (dpInten == 0)
244 299 
 	{
245 
-		dpInten = genericData.DataSet(CelDataGroupName, CelIntensityLabel);
300 
+		dpInten = genericData.DataSet(activeChannel, CelIntensityLabel);
246 301 
 		if (dpInten)
247 302 
 		{
248 303 
 			dpInten->Open();
... ... 
@@ -258,9 +313,11 @@ void CelFileData::PrepareStdevPlane()
258 313 
 {
259 314 
 	if (dpStdev == 0)
260 315 
 	{
261 
-		dpStdev = genericData.DataSet(CelDataGroupName, CelStdDevLabel);
316 
+		dpStdev = genericData.DataSet(activeChannel, CelStdDevLabel);
262 317 
 		if (dpStdev)
318 
+		{
263 319 
 			dpStdev->Open();
320 
+		}
264 321 
 	}
265 322 
 }
266 323
... ... 
@@ -271,9 +328,11 @@ void CelFileData::PrepareNumPixelPlane()
271 328 
 {
272 329 
 	if (dpPixels == 0)
273 330 
 	{
274 
-		dpPixels = genericData.DataSet(CelDataGroupName, CelPixelLabel);
331 
+		dpPixels = genericData.DataSet(activeChannel, CelPixelLabel);
275 332 
 		if (dpPixels)
333 
+		{
276 334 
 			dpPixels->Open();
335 
+		}
277 336 
 	}
278 337 
 }
279 338
... ... 
@@ -283,28 +342,34 @@ void CelFileData::PrepareNumPixelPlane()
283 342 
 void CelFileData::PrepareOutlierPlane()
284 343 
 {
285 344 
 	if (outlierPlaneRead)
345 
+	{
286 346 
 		return;
287 
-
347 
+	}
288 348 
 	outlierPlaneRead = true;	// Read attempted
289 349
290 
-	DataSet* dpOutlier = genericData.DataSet(CelDataGroupName, CelOutlierLabel);
291 
-	if (dpOutlier)
292 
-	{
293 
-		if (dpOutlier->Open())
294 
-		{
295 
-			int32_t rows = dpOutlier->Rows();
296 
-
297 
-			for (int32_t row = 0; row < rows; ++row)
298 
-			{
299 
-				int16_t x = 0, y = 0;
300 
-				dpOutlier->GetData(row, 0, x);
301 
-				dpOutlier->GetData(row, 1, y);
302 
-				XYCoord xy(x,y);
303 
-				outliers.insert(xy);
304 
-			}
305 
-		}
306 
-		dpOutlier->Delete();
307 
-	}
350 
+    try {
351 
+	    DataSet* dpOutlier = genericData.DataSet(activeChannel, CelOutlierLabel);
352 
+	    if (dpOutlier)
353 
+	    {
354 
+		    if (dpOutlier->Open())
355 
+		    {
356 
+			    int32_t rows = dpOutlier->Rows();
357 
+
358 
+			    for (int32_t row = 0; row < rows; ++row)
359 
+			    {
360 
+				    int16_t x = 0, y = 0;
361 
+				    dpOutlier->GetData(row, 0, x);
362 
+				    dpOutlier->GetData(row, 1, y);
363 
+				    XYCoord xy(x,y);
364 
+				    outliers.insert(xy);
365 
+			    }
366 
+		    }
367 
+		    dpOutlier->Delete();
368 
+		    dpOutlier = 0;
369 
+	    }
370 
+    }
371 
+    catch(affymetrix_calvin_exceptions::DataSetNotFoundException) {
372 
+    }
308 373 
 }
309 374
310 375 
 /*
... ... 
@@ -313,28 +378,34 @@ void CelFileData::PrepareOutlierPlane()
313 378 
 void CelFileData::PrepareMaskedPlane()
314 379 
 {
315 380 
 	if (maskPlaneRead)
381 
+	{
316 382 
 		return;
317 
-
383 
+	}
318 384 
 	maskPlaneRead = true;	// Read attempted
319 385
320 
-	DataSet* dpMasked = genericData.DataSet(CelDataGroupName, CelMaskLabel);
321 
-	if (dpMasked)
322 
-	{
323 
-		if (dpMasked->Open())
324 
-		{
325 
-			int32_t rows = dpMasked->Rows();
326 
-
327 
-			for (int32_t row = 0; row < rows; ++row)
328 
-			{
329 
-				int16_t x = 0, y = 0;
330 
-				dpMasked->GetData(row, 0, x);
331 
-				dpMasked->GetData(row, 1, y);
332 
-				XYCoord xy(x,y);
333 
-				masked.insert(xy);
334 
-			}
335 
-		}
336 
-		dpMasked->Delete();
337 
-	}
386 
+    try {
387 
+	    DataSet* dpMasked = genericData.DataSet(activeChannel, CelMaskLabel);
388 
+	    if (dpMasked)
389 
+	    {
390 
+		    if (dpMasked->Open())
391 
+		    {
392 
+			    int32_t rows = dpMasked->Rows();
393 
+
394 
+			    for (int32_t row = 0; row < rows; ++row)
395 
+			    {
396 
+				    int16_t x = 0, y = 0;
397 
+				    dpMasked->GetData(row, 0, x);
398 
+				    dpMasked->GetData(row, 1, y);
399 
+				    XYCoord xy(x,y);
400 
+				    masked.insert(xy);
401 
+			    }
402 
+		    }
403 
+		    dpMasked->Delete();
404 
+		    dpMasked = 0;
405 
+	    }
406 
+    }
407 
+    catch(affymetrix_calvin_exceptions::DataSetNotFoundException) {
408 
+    }
338 409 
 }
339 410
340 411 
 /*
... ... 
@@ -409,6 +480,18 @@ void CelFileData::GetData(int32_t cellIdx, float& intensity, float& stdev, int16
409 480 
 	masked = IsMasked(cellIdx);
410 481 
 }
411 482
483 
+/*
484 
+ * Get the intensity as used in FusionCELData
485 
+ */
486 
+float CelFileData::GetIntensity(int index)
487 
+{
488 
+  // allocate a vector, fill it with one item
489 
+	FloatVector v;
490 
+	this->GetIntensities(index, 1, v);
491 
+  // and return that one item.
492 
+	return v.at(0);
493 
+}
494 
+
412 495 
 /*
413 496 
  * Get the intensities for a range of cell indexes.
414 497 
  */
... ... 
@@ -424,7 +507,7 @@ bool CelFileData::GetIntensities(int32_t cellIdxStart, int32_t count, FloatVecto
424 507 
 			Uint16Vector uint16Vector;
425 508 
 			dpInten->GetData(0, cellIdxStart, count, uint16Vector);
426 509 
 			values.resize(uint16Vector.size());
427 
-			for (int32_t i = 0; i < uint16Vector.size(); ++i)
510 
+			for (u_int32_t i = 0; i < uint16Vector.size(); ++i)
428 511 
 				values[i] = (float)uint16Vector[i];
429 512 
 		}
430 513
... ... 
@@ -503,8 +586,6 @@ bool CelFileData::GetMasked(int32_t cellIdxStart, int32_t count, BoolVector& val
503 586 
 void CelFileData::GetOutlierCoords(XYCoordVector& coords)
504 587 
 {
505 588 
 	PrepareOutlierPlane();
506 
-	//std::set<XYCoord>::iterator begin = outliers.begin();
507 
-	//std::set<XYCoord>::iterator end = outliers.end();
508 589 
 	for (std::set<XYCoord>::iterator ii = outliers.begin(); ii != outliers.end(); ++ii)
509 590 
 	{
510 591 
 		XYCoord xy(ii->xCoord, ii->yCoord);
... ... 
@@ -518,8 +599,6 @@ void CelFileData::GetOutlierCoords(XYCoordVector& coords)
518 599 
 void CelFileData::GetMaskedCoords(XYCoordVector& coords)
519 600 
 {
520 601 
 	PrepareMaskedPlane();
521 
-	//std::set<XYCoord>::iterator begin = masked.begin();
522 
-	//std::set<XYCoord>::iterator end = masked.end();
523 602 
 	for (std::set<XYCoord>::iterator ii = masked.begin(); ii != masked.end(); ++ii)
524 603 
 	{
525 604 
 		XYCoord xy(ii->xCoord, ii->yCoord);
... ... 
@@ -684,6 +763,48 @@ void CelFileData::SetCols(int32_t value)
684 763 
 	cachedCols = value;
685 764 
 }
686 765
766 
+bool CelFileData::IsMultiColor()
767 
+{
768 
+	return (GetChannels().size() > 1);
769 
+}
770 
+
771 
+WStringVector CelFileData::GetChannels()
772 
+{
773 
+	// look for tag - "affymetrix-channel-wavelength"
774 
+	// if not found then set the channel to "Default Group"
775 
+	// else parse and return.
776 
+	WStringVector result;
777 
+	GenericDataHeader* gdh = this->GetFileHeader()->GetGenericDataHdr()->FindParent(MULTI_SCAN_ACQUISITION_DATA_TYPE);
778 
+	if (gdh == NULL)
779 
+	{
780 
+		result.push_back(CelDataGroupName);
781 
+	}
782 
+	else
783 
+	{
784 
+		// found the right header, now look for the parameter
785 
+		ParameterNameValueType nvt;
786 
+		if (gdh->FindNameValParam(L"affymetrix-channel-wavelength", nvt))
787 
+		{
788 
+			std::wstring channels = nvt.ToString();
789 
+			std::wstring::size_type idx = channels.find_first_of(L";", 0);
790 
+			while (idx != std::wstring::npos)
791 
+			{
792 
+				result.push_back(channels.substr(0, idx));
793 
+				channels = channels.substr(idx+1);
794 
+				idx = channels.find_first_of(L";", 0);
795 
+			}
796 
+			result.push_back(channels);
797 
+		}
798 
+		// Only one channel is found, this is the case when MC scanner operates in single channel mode.
799 
+		if (result.size() == 1)
800 
+		{
801 
+			result.clear();
802 
+			result.push_back(CelDataGroupName);
803 
+		}
804 
+	}
805 
+	return result;
806 
+}
807 
+
687 808 
 /*
688 809 
  * Get the number of cols of cells
689 810 
  */
... ... 
@@ -781,17 +902,68 @@ void CelFileData::ComputeXY(int32_t cellIdx, int16_t& x, int16_t& y)
781 902 
 	x = (int16_t)(cellIdx - GetCols()*y);
782 903 
 }
783 904
905 
+/*
906 
+ */
907 
+std::wstring CelFileData::GetDatHeader()
908 
+{
909 
+	std::wstring datHeader;
910 
+
911 
+	//GenDataHdrVectorIt begin, end;
912 
+	GenericDataHeader* gdh = this->GetFileHeader()->GetGenericDataHdr()->FindParent(MULTI_SCAN_ACQUISITION_DATA_TYPE);
913 
+	if (gdh)
914 
+	{
915 
+		// found the right header, now look for the parameter
916 
+		ParameterNameValueType nvt;
917 
+		if (gdh->FindNameValParam(DAT_HEADER_PARAM_NAME, nvt))
918 
+		{
919 
+			if (nvt.GetParameterType() == ParameterNameValueType::TextType)
920 
+				datHeader = nvt.GetValueText();
921 
+		}
922 
+		else if (gdh->FindNameValParam(PARTIAL_DAT_HEADER_PARAM_NAME, nvt))
923 
+		{
924 
+			if (nvt.GetParameterType() == ParameterNameValueType::TextType)
925 
+			{
926 
+				std::wstring partialDatHeader = nvt.GetValueText();
927 
+
928 
+				u_int16_t min = 0;
929 
+				u_int16_t max = 0;
930 
+
931 
+				// Find the max and min parameters and append to the string.
932 
+				if (gdh->FindNameValParam(MAX_PIXEL_INTENSITY_PARAM_NAME, nvt))
933 
+				{
934 
+					if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type)
935 
+						max = nvt.GetValueUInt16();
936 
+				}
937 
+
938 
+				if (gdh->FindNameValParam(MIN_PIXEL_INTENSITY_PARAM_NAME, nvt))
939 
+				{
940 
+					if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type)
941 
+						min = nvt.GetValueUInt16();
942 
+				}
943 
+
944 
+				wchar_t buf[30]=L"";
945 
+				FormatString2(buf, 30, L"[%d..%d]", min, max);
946 
+				datHeader = buf;
947 
+				datHeader += partialDatHeader;
948 
+			}
949 
+		}
950 
+	}
951 
+	return datHeader;
952 
+}
953 
+
784 954 
 /*
785 955 
  * Find a DataSetHeader by name.
786 956 
  */
787 957 
 DataSetHeader* CelFileData::FindDataSetHeader(const std::wstring& name)
788 958 
 {
789 
-	DataGroupHeader* dch = genericData.FindDataGroupHeader(CelDataGroupName);
790 
-	if (dch)
959 
+	DataGroupHeader* grpHdr = genericData.FindDataGroupHeader(activeChannel);
960 
+	if (grpHdr)
791 961 
 	{
792 
-		DataSetHeader* dph = genericData.FindDataSetHeader(dch, name);
793 
-		if (dph)
794 
-			return dph;
962 
+		DataSetHeader* setHdr = genericData.FindDataSetHeader(grpHdr, name);
963 
+		if (setHdr)
964 
+		{
965 
+			return setHdr;
966 
+		}
795 967 
 	}
796 968 
 	return 0;
797 969 
 }
... ... 
@@ -845,3 +1017,28 @@ bool CelFileData::FindAlgorithmParameter(const std::wstring& name, ParameterName
845 1017 
 	}
846 1018 
 	return false;
847 1019 
 }
1020 
+
1021 
+
1022 
+/*
1023 
+ * Returns the list of parameters associated with a data set.
1024 
+ */
1025 
+ParameterNameValueTypeList CelFileData::GetDataSetParameters(const std::wstring &setName)
1026 
+{
1027 
+	ParameterNameValueTypeList params;
1028 
+	DataSet *set = genericData.DataSet(activeChannel, setName);