1. affxparser
  2. Commit 158e02d3a28c6da6ad7306c8be8218294c12fb41
Browse code

updated to Fusion 1.1.2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@68460 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 14/08/2012 21:06:53
Showing 227 changed files
DESCRIPTION
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@@ -1,11 +1,11 @@
1 1 
 Package: affxparser
2 
-Version: 1.29.7
2 
+Version: 1.29.8
3 3 
 Date: 2012-08-14
4 4 
 Title: Affymetrix File Parsing SDK
5 5 
 Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper Daniel Hansen, Martin Morgan
6 6 
 Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
7 7 
 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 v1.1.0
8 
+FusionDetails: Fusion SDK v1.1.2
9 9 
 License: LGPL (>= 2)
10 10 
 Depends: R (>= 2.6.0)
11 11 
 Suggests: R.utils (>= 1.12.1), AffymetrixDataTestFiles
cleanup
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12 12 
new file mode 100755
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@@ -0,0 +1,90 @@
1 
+rm -f src/affxparser.so\
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+   src/R_affx_cdf_parser.o\
3 
+   src/R_affx_bpmap_parser.o\
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+   src/R_affx_clf_pgf_parser.o\
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+   src/R_affx_cel_parser.o\
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+   src/R_affx_cdf_extras.o\
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+   src/R_affx_chp_parser.o\
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+   src/fusion_sdk/file/FileIO.o\
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+   src/fusion_sdk/file/BPMAPFileWriter.o\
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+   src/fusion_sdk/file/CELFileData.o\
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+   src/fusion_sdk/file/CDFFileData.o\
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+   src/fusion_sdk/file/BPMAPFileData.o\
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+   src/fusion_sdk/file/CHPFileData.o\
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+   src/fusion_sdk/file/FileWriter.o\
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+   src/fusion_sdk/file/TsvFile/ClfFile.o\
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+   src/fusion_sdk/file/TsvFile/PgfFile.o\
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+   src/fusion_sdk/file/TsvFile/TsvFile.o\
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+   src/fusion_sdk/util/MsgStream.o\
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+   src/fusion_sdk/util/AffxByteArray.o\
20 
+   src/fusion_sdk/util/Fs.o\
21 
+   src/fusion_sdk/util/TableFile.o\
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+   src/fusion_sdk/util/Verbose.o\
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+   src/fusion_sdk/util/Err.o\
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+   src/fusion_sdk/util/Convert.o\
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+   src/fusion_sdk/util/RowFile.o\
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+   src/fusion_sdk/util/AffxConv.o\
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+   src/fusion_sdk/util/Util.o\
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+   src/fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/CelFileReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/DataSetReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/CDFFileReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/CHPFileReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/GenericFileReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/FileInput.o\
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+   src/fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/DataGroupReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o\
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+   src/fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o\
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+   src/fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o\
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+   src/fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o\
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+   src/fusion_sdk/calvin_files/utils/src/StringUtils.o\
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+   src/fusion_sdk/calvin_files/utils/src/DateTime.o\
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+   src/fusion_sdk/calvin_files/utils/src/FileUtils.o\
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+   src/fusion_sdk/calvin_files/utils/src/checksum.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCDFData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCHPData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/FusionCELData.o\
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+   src/fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o\
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+   src/fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o\
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+   src/fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o\
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+   src/fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o\
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+   src/fusion_sdk/calvin_files/data/src/DataGroupHeader.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o\
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+   src/fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPQuantificationData.o\
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+   src/fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o\
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+   src/fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o\
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+   src/fusion_sdk/calvin_files/data/src/ColumnInfo.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPMultiDataData.o\
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+   src/fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o\
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+   src/fusion_sdk/calvin_files/data/src/GenericDataHeader.o\
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+   src/fusion_sdk/calvin_files/data/src/DataGroup.o\
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+   src/fusion_sdk/calvin_files/data/src/CDFProbeInformation.o\
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+   src/fusion_sdk/calvin_files/data/src/CELData.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPTilingData.o\
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+   src/fusion_sdk/calvin_files/data/src/DataSet.o\
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+   src/fusion_sdk/calvin_files/data/src/CDFData.o\
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+   src/fusion_sdk/calvin_files/data/src/FileHeader.o\
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+   src/fusion_sdk/calvin_files/data/src/DataSetHeader.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPData.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o\
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+   src/fusion_sdk/calvin_files/data/src/GenericData.o\
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+   src/fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o\
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+   src/fusion_sdk/calvin_files/exception/src/ExceptionBase.o
inst/NEWS
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@@ -1,6 +1,9 @@
1 1 
 Package: affxparser
2 2 
 ===================
3 3
4 
+Version: 1.29.8 [2012-08-14]
5 
+o Upgraded to Fusion SDK 1.1.2.
6 
+
4 7 
 Version: 1.29.7 [2012-08-14]
5 8 
 o Rearranged patchdir.
6 9
inst/info/Makefile
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@@ -4,10 +4,11 @@
4 4 
 ##     check for files and directories that ought to be deleted
5 5 
 ##   then copy
6 6
7 
-fusion=~/Work/packages/affy/sdk
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+fusion=~/Work/packages/fusion_sdk
8 8 
 affxparser_base=~/Work/packages/affxparser
9 9 
 affxparser_fusion=${affxparser_base}/src/fusion_sdk
10 10 
 affxparser_patchdir_1.1.0=${affxparser_base}/inst/info/fusion_1.1.0_patches
11 
+affxparser_patchdir_1.1.2=${affxparser_base}/inst/info/fusion_1.1.2_patches
11 12
12 13 
 compare :
13 14 
 	diff -rq ${fusion} ${affxparser_fusion} | grep Only | grep -v svn | cat
... ... 
@@ -21,11 +22,18 @@ cleanfusion :
21 22 
 	${fusion}/libraries_and_tools \
22 23 
 	${fusion}/parser_examples \
23 24 
 	${fusion}/sample_data \
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+	${fusion}/images \
26 
+	${fusion}/css \
24 27 
 	${fusion}/*.html \
25 28 
 	${fusion}/*.gif \
26 29 
 	${fusion}/portability/CPPTest \
27 30 
 	${fusion}/file/CPPTest \
28 31 
 	${fusion}/file/readme.html \
32 
+	${fusion}/file/TsvFile/*.vcproj \
33 
+	${fusion}/file/TsvFile/*.csv \
34 
+	${fusion}/file/TsvFile/*.pgf \
35 
+	${fusion}/file/TsvFile/*.tsv \
36 
+	${fusion}/file/TsvFile/*.txt \
29 37 
 	${fusion}/calvin_files/makefile.g5 \
30 38 
 	${fusion}/calvin_files/template/test \
31 39 
 	${fusion}/calvin_files/array/test \
... ... 
@@ -51,11 +59,23 @@ cleanfusion :
51 59 
 	${fusion}/file/file.vcproj \
52 60 
 	${fusion}/file/file.sln \
53 61 
 	${fusion}/file/lib-file-apt.vcproj \
62 
+	${fusion}/util/lib-util-devnet.vcproj \
54 63 
 	${fusion}/style.css \
55 64
65 
+
56 66 
 patch_1.1.0:
57 67 
 #	patch -N ${affxparser_fusion}/file/CDFFileData.cpp ${affxparser_patchdir_1.1.0}/CDFFileData.cpp-patch
58 68 
 	patch -N ${affxparser_fusion}/portability/affy-base-types.h ${affxparser_patchdir_1.1.0}/affy-base-types.h-patch
59 69 
 	patch -N ${affxparser_fusion}/util/AffxConv.cpp ${affxparser_patchdir_1.1.0}/AffxConv.cpp-patch
60 70 
 	patch -N ${affxparser_fusion}/util/AffxByteArray.cpp ${affxparser_patchdir_1.1.0}/AffxByteArray.cpp-patch
61 71 
 	patch -N ${affxparser_fusion}/calvin_files/portability/src/AffymetrixBaseTypes.h ${affxparser_patchdir_1.1.0}/AffymetrixBaseTypes.h-patch
72 
+
73 
+patch_1.1.2:
74 
+	patch -N ${affxparser_fusion}/file/CDFFileData.cpp ${affxparser_patchdir_1.1.2}/CDFFileData.cpp-patch
75 
+	patch -N ${affxparser_fusion}/portability/affy-base-types.h ${affxparser_patchdir_1.1.2}/affy-base-types.h-patch
76 
+	patch -N ${affxparser_fusion}/util/AffxConv.cpp ${affxparser_patchdir_1.1.2}/AffxConv.cpp-patch
77 
+	patch -N ${affxparser_fusion}/util/AffxByteArray.cpp ${affxparser_patchdir_1.1.2}/AffxByteArray.cpp-patch
78 
+	patch -N ${affxparser_fusion}/calvin_files/portability/src/AffymetrixBaseTypes.h ${affxparser_patchdir_1.1.2}/AffymetrixBaseTypes.h-patch
79 
+	patch -N ${affxparser_fusion}/calvin_files/utils/src/FileUtils.cpp ${affxparser_patchdir_1.1.2}/FileUtils.cpp-patch
80 
+
81 
+
inst/info/fusion_1.1.2_patches/AffxByteArray.cpp-patch
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62 82 
new file mode 100644
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@@ -0,0 +1,11 @@
1 
+--- /Users/khansen/Work/packages/affxparser/src/fusion_sdk/util/AffxByteArray.cpp	2010-02-07 11:22:29.000000000 -0500
2 
+@@ -667,7 +667,7 @@
3 
+ 	if (getSize() > 0)
4 
+ 	{
5 
+ 		char *psz = (char *)malloc(getSize() + 1);
6 
+-#ifdef WIN32
7 
++#if defined WIN32 && !defined WIN64
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+ 		strncpy_s(psz, getSize() + 1, (char *)getData(), getSize());
9 
+ #else
10 
+ 		strncpy(psz, (char *)getData(), getSize());
inst/info/fusion_1.1.2_patches/AffxConv.cpp-patch
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0 11 
new file mode 100644
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@@ -0,0 +1,23 @@
1 
+--- fusion_sdk/util/AffxConv.cpp	2012-08-14 11:50:46.000000000 -0600
2 
+@@ -41,6 +41,11 @@
3 
+ #include <stdio.h>
4 
+ //
5 
+
6 
++#ifdef WIN64
7 
++# undef WIN32
8 
++#endif
9 
++
10 
++
11 
+ using namespace std;
12 
+
13 
+ /**
14 
+@@ -111,7 +116,7 @@
15 
+ std::string getInt(int i, bool bCommas)
16 
+ {
17 
+ 	char szValue[64];
18 
+-#ifdef WIN32
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++#ifdef WIN32 && !defined(__MINGW32__)
20 
+ 	sprintf_s(szValue, 64, "%d", i);
21 
+ #else
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+ 	sprintf(szValue, "%d", i);
inst/info/fusion_1.1.2_patches/AffymetrixBaseTypes.h-patch
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0 23 
new file mode 100644
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@@ -0,0 +1,13 @@
1 
+--- /Users/khansen/Work/packages/affxparser/src/fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h	2010-01-29 13:20:58.000000000 -0500
2 
+@@ -24,6 +24,10 @@
3 
+ /*! \file AffymetrixBaseTypes.h This file provides type definitions for atom types.
4 
+  */
5 
+
6 
++#ifdef WIN64
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++#include <stdint.h>
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++#endif
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++
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+ /* Define the type for the Windows platform. */
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+ #ifdef WIN32
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+
inst/info/fusion_1.1.2_patches/CDFFileData.cpp-patch
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new file mode 100644
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@@ -0,0 +1,13 @@
1 
+--- fusion_sdk/file/CDFFileData.cpp	2012-08-14 11:50:21.000000000 -0600
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+@@ -919,8 +919,8 @@
3 
+         ReadNextLine(instr, str, MAXLINELENGTH); // #qc ProbeSets
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+         subStr=strchr(str,'=')+1;
5 
+         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;
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+     }
inst/info/fusion_1.1.2_patches/FileUtils.cpp-patch
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new file mode 100644
... ... 
@@ -0,0 +1,10 @@
1 
+--- affxparser/src/fusion_sdk/calvin_files/utils/src/FileUtils.cpp	2012-08-14 14:11:38.000000000 -0600
2 
+@@ -35,7 +35,6 @@
3 
+ #include <direct.h>
4 
+ #define 	S_ISDIR(m)   (((m) & S_IFMT) == S_IFDIR)
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+ #else
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+-#include <unistd.h>
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+ #include <dirent.h>
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+ #endif
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+
inst/info/fusion_1.1.2_patches/affy-base-types.h-patch
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0 10 
new file mode 100644
... ... 
@@ -0,0 +1,13 @@
1 
+--- /Users/khansen/Work/packages/affxparser/src/fusion_sdk/portability/affy-base-types.h	2010-02-07 11:31:11.000000000 -0500
2 
+@@ -60,6 +60,10 @@
3 
+ #define Min(a,b) std::min(a,b)
4 
+ #endif           // _MSC_VER
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+
6 
++#ifdef WIN64
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++#include <stdint.h>
8 
++#endif
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++
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+ /* "WIN32" should always be defined by MS C++  */
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+ /* It shouldnt be defined on any other platform */
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+ #ifndef WIN32
src/Makevars
History View file @ 158e02d
... ... 
@@ -41,6 +41,7 @@ PKG_SOURCES = \
41 41 
 	fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp\
42 42 
 	fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp\
43 43 
 	fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp\
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+	fusion_sdk/calvin_files/data/src/ColumnInfo.cpp\
44 45 
 	fusion_sdk/calvin_files/data/src/DataGroup.cpp\
45 46 
 	fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp\
46 47 
 	fusion_sdk/calvin_files/data/src/DataSet.cpp\
... ... 
@@ -94,13 +95,15 @@ PKG_SOURCES = \
94 95 
 	fusion_sdk/file/CHPFileData.cpp\
95 96 
 	fusion_sdk/file/FileIO.cpp\
96 97 
 	fusion_sdk/file/FileWriter.cpp\
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+	fusion_sdk/file/TsvFile/ClfFile.cpp\
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+	fusion_sdk/file/TsvFile/PgfFile.cpp\
97 100 
 	fusion_sdk/file/TsvFile/TsvFile.cpp\
98 101 
 	fusion_sdk/util/AffxByteArray.cpp\
99 102 
 	fusion_sdk/util/AffxConv.cpp\
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-	fusion_sdk/util/AffxFile.cpp\
101 103 
 	fusion_sdk/util/MsgStream.cpp\
102 104 
 	fusion_sdk/util/Util.cpp\
103 105 
 	fusion_sdk/util/Err.cpp\
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+	fusion_sdk/util/Fs.cpp\
104 107 
 	fusion_sdk/util/Verbose.cpp\
105 108 
 	fusion_sdk/util/RowFile.cpp\
106 109 
 	fusion_sdk/util/TableFile.cpp\
src/Makevars.win
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... ... 
@@ -39,6 +39,7 @@ PKG_SOURCES = \
39 39 
 	fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp\
40 40 
 	fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp\
41 41 
 	fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp\
42 
+	fusion_sdk/calvin_files/data/src/ColumnInfo.cpp\
42 43 
 	fusion_sdk/calvin_files/data/src/DataGroup.cpp\
43 44 
 	fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp\
44 45 
 	fusion_sdk/calvin_files/data/src/DataSet.cpp\
... ... 
@@ -92,13 +93,15 @@ PKG_SOURCES = \
92 93 
 	fusion_sdk/file/CHPFileData.cpp\
93 94 
 	fusion_sdk/file/FileIO.cpp\
94 95 
 	fusion_sdk/file/FileWriter.cpp\
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+	fusion_sdk/file/TsvFile/ClfFile.cpp\
97 
+	fusion_sdk/file/TsvFile/PgfFile.cpp\
95 98 
 	fusion_sdk/file/TsvFile/TsvFile.cpp\
96 99 
 	fusion_sdk/util/AffxByteArray.cpp\
97 100 
 	fusion_sdk/util/AffxConv.cpp\
98 
-	fusion_sdk/util/AffxFile.cpp\
99 101 
 	fusion_sdk/util/MsgStream.cpp\
100 102 
 	fusion_sdk/util/Util.cpp\
101 103 
 	fusion_sdk/util/Err.cpp\
104 
+	fusion_sdk/util/Fs.cpp\
102 105 
 	fusion_sdk/util/Verbose.cpp\
103 106 
 	fusion_sdk/util/RowFile.cpp\
104 107 
 	fusion_sdk/util/TableFile.cpp\
src/fusion_sdk/calvin_files/data/src/CDFData.cpp
History View file @ 158e02d
... ... 
@@ -64,6 +64,11 @@ void CDFData::Clear()
64 64 
 	nameToFilePosMap.clear();
65 65 
 }
66 66
67 
+int32_t CDFData::GetFormatVersion()
68 
+{
69 
+	return 0;
70 
+}
71 
+
67 72 
 void CDFData::SetArrayRows(u_int32_t value)
68 73 
 {
69 74 
 	SetUInt32ToGenericHdr(CDF_ROWS_PARAM, value);
... ... 
@@ -283,13 +288,13 @@ void CDFData::GetProbeSetInformation(int32_t index, CDFProbeSetInformation& info
283 288 
 {
284 289 
 	if (GetDataTypeId() == AFFY_CNTRL_PS)
285 290 
 	{
286 
-		ProbeSetNotFoundException e;
291 
+		ProbeSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
287 292 
 		throw e;
288 293 
 	}
289 294
290 295 
 	if (index >= genericData.Header().GetNumDataGroups()-1)
291 296 
 	{
292 
-		ProbeSetNotFoundException e;
297 
+		ProbeSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
293 298 
 		throw e;
294 299 
 	}
295 300
... ... 
@@ -306,7 +311,7 @@ void CDFData::GetProbeSetInformation(int32_t index, CDFProbeSetInformation& info
306 311 
 		}
307 312 
 		else
308 313 
 		{
309 
-			CDFAccessNotSupportedByModeException e;
314 
+			CDFAccessNotSupportedByModeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
310 315 
 			throw e;
311 316 
 		}
312 317 
 	}
... ... 
@@ -318,7 +323,7 @@ void CDFData::GetProbeSetInformation(int32_t index, CDFProbeSetInformation& info
318 323 
 	}
319 324 
 	else
320 325 
 	{
321 
-		CDFAccessNotSupportedByModeException e;
326 
+		CDFAccessNotSupportedByModeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
322 327 
 		throw e;
323 328 
 	}
324 329 
 }
... ... 
@@ -327,13 +332,13 @@ void CDFData::GetProbeSetInformation(const std::wstring& probeSetName, CDFProbeS
327 332 
 {
328 333 
 	if (GetDataTypeId() == AFFY_CNTRL_PS)
329 334 
 	{
330 
-		ProbeSetNotFoundException e;
335 
+		ProbeSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
331 336 
 		throw e;
332 337 
 	}
333 338
334 339 
 	if (mode != ProbeSetNameMode)
335 340 
 	{
336 
-		CDFAccessNotSupportedByModeException e;
341 
+		CDFAccessNotSupportedByModeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
337 342 
 		throw e;
338 343 
 	}
339 344
... ... 
@@ -347,13 +352,13 @@ void CDFData::GetQCProbeSetInformation(int32_t index, CDFQCProbeSetInformation&
347 352 
 {
348 353 
 	if (GetDataTypeId() != AFFY_CNTRL_PS)
349 354 
 	{
350 
-		ProbeSetNotFoundException e;
355 
+		ProbeSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
351 356 
 		throw e;
352 357 
 	}
353 358
354 359 
 	if (index >= genericData.Header().GetNumDataGroups()-1)
355 360 
 	{
356 
-		ProbeSetNotFoundException e;
361 
+		ProbeSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
357 362 
 		throw e;
358 363 
 	}
359 364
... ... 
@@ -371,7 +376,7 @@ void CDFData::GetQCProbeSetInformation(int32_t index, CDFQCProbeSetInformation&
371 376 
 		}
372 377 
 		else
373 378 
 		{
374 
-			CDFAccessNotSupportedByModeException e;
379 
+			CDFAccessNotSupportedByModeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
375 380 
 			throw e;
376 381 
 		}
377 382 
 	}
... ... 
@@ -384,7 +389,7 @@ void CDFData::GetQCProbeSetInformation(int32_t index, CDFQCProbeSetInformation&
384 389 
 	}
385 390 
 	else
386 391 
 	{
387 
-		CDFAccessNotSupportedByModeException e;
392 
+		CDFAccessNotSupportedByModeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
388 393 
 		throw e;
389 394 
 	}
390 395 
 }
... ... 
@@ -393,13 +398,13 @@ void CDFData::GetQCProbeSetInformation(const std::wstring& probeSetName, CDFQCPr
393 398 
 {
394 399 
 	if (GetDataTypeId() != AFFY_CNTRL_PS)
395 400 
 	{
396 
-		ProbeSetNotFoundException e;
401 
+		ProbeSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
397 402 
 		throw e;
398 403 
 	}
399 404
400 405 
 	if (mode != ProbeSetNameMode)
401 406 
 	{
402 
-		CDFAccessNotSupportedByModeException e;
407 
+		CDFAccessNotSupportedByModeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
403 408 
 		throw e;
404 409 
 	}
405 410
... ... 
@@ -413,7 +418,7 @@ u_int32_t CDFData::GetTOCFilePosByIndex(int32_t index)
413 418 
 {
414 419 
 	if (tocDataSet == 0 || tocDataSet->IsOpen() == false)
415 420 
 	{
416 
-		DataSetNotOpenException e;
421 
+		DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
417 422 
 		throw e;
418 423 
 	}
419 424
... ... 
@@ -426,14 +431,14 @@ u_int32_t CDFData::GetTOCFilePosByName(const std::wstring& name)
426 431 
 {
427 432 
 	if (tocDataSet == 0 || tocDataSet->IsOpen() == false)
428 433 
 	{
429 
-		DataSetNotOpenException e;
434 
+		DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
430 435 
 		throw e;
431 436 
 	}
432 437
433 438 
 	std::map<std::wstring, u_int32_t>::iterator ii = nameToFilePosMap.find(name);
434 439 
 	if (ii == nameToFilePosMap.end())
435 440 
 	{
436 
-		ProbeSetNotFoundException e;
441 
+		ProbeSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
437 442 
 		throw e;
438 443 
 	}
439 444 
 	else
... ... 
@@ -450,7 +455,7 @@ std::wstring CDFData::GetProbeSetName(int32_t index)
450 455
451 456 
 		if (tocDataSet == 0)
452 457 
 		{
453 
-			DataSetNotOpenException e;
458 
+			DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
454 459 
 			throw e;
455 460 
 		}
456 461 
 	}
... ... 
@@ -460,14 +465,14 @@ std::wstring CDFData::GetProbeSetName(int32_t index)
460 465 
 		tocDataSet->Open();
461 466 
 		if (tocDataSet->IsOpen() == false)
462 467 
 		{
463 
-			DataSetNotOpenException e;
468 
+			DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
464 469 
 			throw e;
465 470 
 		}
466 471 
 	}
467 472
468 473 
 	if (index < 0 || index >= tocDataSet->Rows())
469 474 
 	{
470 
-		ProbeSetNotFoundException e;
475 
+		ProbeSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
471 476 
 		throw e;
472 477 
 	}
473 478
src/fusion_sdk/calvin_files/data/src/CDFData.h
History View file @ 158e02d
... ... 
@@ -111,6 +111,11 @@ public:
111 111 
 	 */
112 112 
 	std::string GetFilename();
113 113
114 
+	/*! Get format version.
115 
+	 * @return The CDF format version.
116 
+	 */
117 
+	int32_t GetFormatVersion();
118 
+
114 119 
 	/*! Gets the probe set count.
115 120 
 	 * @return The number of probe sets.
116 121 
 	 */
src/fusion_sdk/calvin_files/data/src/CELData.cpp
History View file @ 158e02d
... ... 
@@ -23,6 +23,7 @@
23 23 
 #include "calvin_files/data/src/DataSetHeader.h"
24 24 
 #include "calvin_files/data/src/GenericDataTypes.h"
25 25 
 #include "calvin_files/exception/src/ExceptionBase.h"
26 
+#include "calvin_files/utils/src/FileUtils.h"
26 27 
 #include "calvin_files/utils/src/StringUtils.h"
27 28 
 //
28 29 
 #include <sys/stat.h>
... ... 
@@ -133,8 +134,7 @@ bool CelFileData::Exists()
133 134 
 	if (filename != "")
134 135 
 	{
135 136 
 		// Find the file stats.
136 
-		struct stat st;
137 
-		return ((stat(filename.c_str(), &st) == 0)? true: false);
137 
+          return FileUtils::Exists(filename.c_str());
138 138 
 	}
139 139
140 140 
 	return false;
src/fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp
History View file @ 158e02d
... ... 
@@ -219,6 +219,32 @@ const static std::wstring A_SIGNAL = L"ASignal";
219 219 
 const static std::wstring B_SIGNAL = L"BSignal";
220 220 
 const static std::wstring SCAR = L"SCAR";
221 221
222 
+const static std::wstring CONTRAST = L"Contrast";
223 
+const static std::wstring SIGNAL_STRENGTH = L"SignalStrength";
224 
+
225 
+	/*! constructor */
226 
+DataSetInfo::DataSetInfo()    {
227 
+  entries = NULL;
228 
+  maxName = -1;
229 
+  maxSegmentType = -1;
230 
+  maxReferenceSegmentID = -1;
231 
+  maxFamilialSegmentID = -1;
232 
+  maxFamilialARRID = -1;
233 
+  maxFamilialCHPID = -1;
234 
+  maxFamilialCHPFile = -1;
235 
+  maxFamilialRole = -1;
236 
+  maxFamilialCHPFile = -1;
237 
+  dataSetIndex = -1;
238 
+}
239 
+
240 
+std::wstring CHPMultiDataData::GetGroupName(MultiDataType dataType) {
241 
+  return dataTypeGroupNames[dataType];
242 
+}
243 
+
244 
+/*! The data set information */
245 
+std::map<MultiDataType, DataSetInfo> &CHPMultiDataData::GetDataSetInfo() {
246 
+  return dataSetInfo;
247 
+}
222 248
223 249 
 /*! used for full column index for log2Ratio */
224 250 
 const static int cnlog2RatioIndexOffset = 4;
... ... 
@@ -286,6 +312,20 @@ void CHPMultiDataData::Clear()
286 312 
 	genericData.Header().Clear();
287 313 
 }
288 314
315 
+/*! Gets the file header.
316 
+ * @return The file header.
317 
+ */
318 
+FileHeader* CHPMultiDataData::GetFileHeader() {
319 
+  return &genericData.Header();
320 
+}
321 
+
322 
+/*! Gets the generic data object.
323 
+ * @return The data object.
324 
+ */
325 
+GenericData& CHPMultiDataData::GetGenericData() {
326 
+  return genericData;
327 
+}
328 
+
289 329 
 void CHPMultiDataData::SetFilename(const std::string &p)
290 330 
 {
291 331 
 	genericData.Header().SetFilename(p);
... ... 
@@ -534,16 +574,36 @@ void CHPMultiDataData::GetEntry(MultiDataType dataType, int index, affymetrix_ca
534 574 
 	}
535 575 
 }
536 576
577 
+
578 
+
537 579 
 void CHPMultiDataData::GetEntry(MultiDataType dataType, int index, affymetrix_calvin_data::MarkerABSignals &entry)
580 
+{
581 
+	DataSetInfo *ds = OpenMultiDataDataSet(dataType);
582 
+
583 
+	if (ds && ds->entries && ds->entries->IsOpen())
584 
+	{
585 
+		int colIndex = 0;
586 
+		ds->entries->GetData(index, colIndex++, entry.index);
587 
+		GetExtraMetricEntries(ds, index, colIndex, entry.metrics);
588 
+	}
589 
+}
590 
+
591 
+
592 
+void CHPMultiDataData::GetEntry(MultiDataType dataType, int index, affymetrix_calvin_data::CytoGenotypeCallData &entry)
538 593 
 {
539 594 
 	DataSetInfo *ds = OpenMultiDataDataSet(dataType);
540 595 
 	if (ds && ds->entries && ds->entries->IsOpen())
541 596 
 	{
542 597 
 		int colIndex = 0;
543 598 
 		ds->entries->GetData(index, colIndex++, entry.index);
599 
+		ds->entries->GetData(index, colIndex++, entry.call);
600 
+		ds->entries->GetData(index, colIndex++, entry.confidence);
601 
+		ds->entries->GetData(index, colIndex++, entry.forcedCall);
544 602 
 		ds->entries->GetData(index, colIndex++, entry.aSignal);
545 603 
 		ds->entries->GetData(index, colIndex++, entry.bSignal);
546 
-		ds->entries->GetData(index, colIndex++, entry.scar);
604 
+		ds->entries->GetData(index, colIndex++, entry.signalStrength);
605 
+		ds->entries->GetData(index, colIndex++, entry.contrast);
606 
+		GetExtraMetricEntries(ds, index, colIndex, entry.metrics);
547 607 
 	}
548 608 
 }
549 609
... ... 
@@ -1060,9 +1120,20 @@ void CHPMultiDataData::AddColumns(DataSetInfo &info, DataSetHeader& hdr)
1060 1120
1061 1121 
 	case MarkerABSignalsMultiDataType:
1062 1122 
 		hdr.AddUIntColumn(PROBE_SET_INDEX);
1123 
+		/*hdr.AddFloatColumn(A_SIGNAL);
1124 
+		hdr.AddFloatColumn(B_SIGNAL);
1125 
+		hdr.AddFloatColumn(SCAR);*/
1126 
+		break;
1127 
+
1128 
+	case CytoGenotypeCallMultiDataType:
1129 
+		hdr.AddUIntColumn(PROBE_SET_INDEX);
1130 
+		hdr.AddByteColumn(CALL);
1131 
+		hdr.AddFloatColumn(CONFIDENCE);
1132 
+		hdr.AddByteColumn(FORCE);
1063 1133 
 		hdr.AddFloatColumn(A_SIGNAL);
1064 1134 
 		hdr.AddFloatColumn(B_SIGNAL);
1065 
-		hdr.AddFloatColumn(SCAR);
1135 
+		hdr.AddFloatColumn(SIGNAL_STRENGTH);
1136 
+		hdr.AddFloatColumn(CONTRAST);
1066 1137 
 		break;
1067 1138
1068 1139 
 	default:
... ... 
@@ -1180,7 +1251,11 @@ DataSetInfo *CHPMultiDataData::OpenMultiDataDataSet(MultiDataType dataType)
1180 1251 
 		}
1181 1252 
 		else if (dataType == MarkerABSignalsMultiDataType)
1182 1253 
 		{
1183 
-			startCol = 4;
1254 
+			startCol = 1;
1255 
+		}
1256 
+		else if (dataType = CytoGenotypeCallMultiDataType)
1257 
+		{
1258 
+			startCol = 8;
1184 1259 
 		}
1185 1260 
 		for (int32_t icol=startCol; icol<ncols; icol++)
1186 1261 
 		{
... ... 
@@ -1256,6 +1331,19 @@ void CHPMultiDataData::AddAlgParams(const ParameterNameValueTypeList& params)
1256 1331 
 	}
1257 1332 
 }
1258 1333
1334 
+void CHPMultiDataData::AddAppMetaInfo(const ParameterNameValueTypeList& params)
1335 
+{
1336 
+	ParameterNameValueType param;
1337 
+	GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
1338 
+	for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); ++it)
1339 
+	{
1340 
+		param = *it;
1341 
+		param.SetName(APPLICATION_META_INFO_PREFIX_S + param.GetName());
1342 
+		hdr->AddNameValParam(param);
1343 
+	}
1344 
+}
1345 
+
1346 
+
1259 1347 
 ParameterNameValueTypeList CHPMultiDataData::GetSummaryParams()
1260 1348 
 {
1261 1349 
 	ParameterNameValueTypeList nvt;
src/fusion_sdk/calvin_files/data/src/CHPMultiDataData.h
History View file @ 158e02d
... ... 
@@ -30,6 +30,7 @@
30 30 
 #include "calvin_files/data/src/GenericData.h"
31 31 
 #include "calvin_files/data/src/MarkerABSignals.h"
32 32 
 #include "calvin_files/data/src/ProbeSetMultiDataData.h"
33 
+#include "calvin_files/data/src/CytoGenotypeCallMultiDataData.h"
33 34 
 #include "calvin_files/portability/src/AffymetrixBaseTypes.h"
34 35 
 //
35 36 
 #include <cstring>
... ... 
@@ -73,7 +74,8 @@ typedef enum MultiDataType {
73 74 
     SegmentDenovoCopyNumberMultiDataType,
74 75 
     SegmentHemizygousParentOfOriginMultiDataType,
75 76 
 	AllelePeaksMultiDataType,
76 
-	MarkerABSignalsMultiDataType
77 
+	MarkerABSignalsMultiDataType,
78 
+	CytoGenotypeCallMultiDataType
77 79 
 } MultiDataType_t;
78 80
79 81 
 /*! The data set name. */
... ... 
@@ -107,7 +109,8 @@ const static std::wstring MultiDataDataSetNames[] =
107 109 
     L"DenovoCopyNumber",
108 110 
     L"HemizygousParentOfOrigin",
109 111 
 	L"AllelePeaks",
110 
-	L"MarkerABSignal"
112 
+	L"MarkerABSignal",
113 
+	L"Calls"
111 114 
 };
112 115
113 116 
 /*! The data types. */
... ... 
@@ -141,7 +144,8 @@ const static MultiDataType MultiDataDataTypes[] =
141 144 
     SegmentDenovoCopyNumberMultiDataType,
142 145 
     SegmentHemizygousParentOfOriginMultiDataType,
143 146 
 	AllelePeaksMultiDataType,
144 
-	MarkerABSignalsMultiDataType
147 
+	MarkerABSignalsMultiDataType,
148 
+	CytoGenotypeCallMultiDataType
145 149 
 };
146 150
147 151 
 /*! Holds data set information. */
... ... 
@@ -185,20 +189,7 @@ public:
185 189 
 	std::vector<ColumnInfo> metricColumns;
186 190
187 191 
 	/*! constructor */
188 
-	DataSetInfo()
189 
-    {
190 
-        entries = NULL;
191 
-        maxName = -1;
192 
-        maxSegmentType = -1;
193 
-        maxReferenceSegmentID = -1;
194 
-        maxFamilialSegmentID = -1;
195 
-        maxFamilialARRID = -1;
196 
-        maxFamilialCHPID = -1;
197 
-        maxFamilialCHPFile = -1;
198 
-        maxFamilialRole = -1;
199 
-        maxFamilialCHPFile = -1;
200 
-        dataSetIndex = -1;
201 
-    }
192 
+	DataSetInfo();
202 193 
 };
203 194
204 195 
 /*! Holds data associated with genotype or expression CHP files. */
... ... 
@@ -230,10 +221,10 @@ private:
230 221
231 222 
 public:
232 223
233 
-    std::wstring GetGroupName(MultiDataType dataType) { return dataTypeGroupNames[dataType]; }
224 
+    std::wstring GetGroupName(MultiDataType dataType);
234 225
235 226 
 	/*! The data set information */
236 
-	std::map<MultiDataType, DataSetInfo> &GetDataSetInfo() { return dataSetInfo; }
227 
+    std::map<MultiDataType, DataSetInfo> &GetDataSetInfo();
237 228
238 229 
 	/*! The maximum length of a probe set name.
239 230 
 	* @param dataType The data type
... ... 
@@ -340,6 +331,11 @@ public:
340 331 
 	*/
341 332 
 	void AddAlgParams(const ParameterNameValueTypeList& params);
342 333
334 
+	/*! Adds the application meta data information
335 
+	* @param params The application meta data
336 
+	*/
337 
+        void AddAppMetaInfo(const ParameterNameValueTypeList& params);
338 
+
343 339 
 	/*! Gets the summary parameters
344 340 
 	* @return The summary parameters.
345 341 
 	*/
... ... 
@@ -353,12 +349,12 @@ public:
353 349 
 	/*! Gets the file header.
354 350 
 	* @return The file header.
355 351 
 	*/
356 
-	FileHeader* GetFileHeader() { return &genericData.Header(); }
352 
+	FileHeader* GetFileHeader();
357 353
358 354 
 	/*! Gets the generic data object.
359 355 
 	* @return The data object.
360 356 
 	*/
361 
-	GenericData& GetGenericData() { return genericData; }
357 
+	GenericData& GetGenericData();
362 358
363 359 
 	/*! Gets the probe set data.
364 360 
 	* @param dataType The data type
... ... 
@@ -409,6 +405,13 @@ public:
409 405 
 	*/
410 406 
 	void GetEntry(MultiDataType dataType, int index, affymetrix_calvin_data::MarkerABSignals &entry);
411 407
408 
+	/*! Gets the genotype data for cyto.
409 
+	* @param dataType The data type
410 
+	* @param index The row index.
411 
+	* @param entry The results.
412 
+	*/
413 
+	void GetEntry(MultiDataType dataType, int index, affymetrix_calvin_data::CytoGenotypeCallData &entry);
414 
+
412 415 
 	/*! Gets the probe set data.
413 416 
 	* @param dataType The data type
414 417 
 	* @param index The row index.
src/fusion_sdk/calvin_files/data/src/ColumnInfo.cpp
History View file @ 158e02d
415 418 
new file mode 100644
... ... 
@@ -0,0 +1,60 @@
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
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 
+/*! \file ColumnInfo.cpp This file defines column information class of various types.
22 
+ */
23 
+
24 
+#include "calvin_files/data/src/ColumnInfo.h"
25 
+
26 
+
27 
+namespace affymetrix_calvin_io
28 
+{
29 
+
30 
+/*! Constructor - used only by dervied types
31 
+ *	@param name_ Name of the column.
32 
+ *	@param type_ Type of data in the column.
33 
+ *	@param size_ Size of each element of in the column.
34 
+ *	@param len_ Number of elements of type in the column.
35 
+ *	@param overhead_ Number of extra bytes in the column
36 
+ */
37 
+ColumnInfo::ColumnInfo(const std::wstring& name_, DataSetColumnTypes type_, int32_t size_, int32_t len_, int32_t overhead_) : name(name_), type(type_), size(size_), len(len_), overhead(overhead_){
38 
+}
39 
+
40 
+/*! Constructor - used by the file read operation
41 
+ * @param name_ Name of the column.
42 
+ * @param type_ Type of data in the column.
43 
+ * @param totalSize Total size of the colum in bytes.
44 
+ */
45 
+ColumnInfo::ColumnInfo(const std::wstring& name_, DataSetColumnTypes type_, int32_t totalSize)
46 
+    : name(name_), type(type_), size(totalSize), len(1), overhead(0)
47 
+{
48 
+  if (type == ASCIICharColType || type == UnicodeCharColType) {
49 
+    overhead = 4;
50 
+    if (type == UnicodeCharColType) {
51 
+      size = sizeof(int16_t);
52 
+      len = (totalSize - overhead) / sizeof(int16_t);
53 
+    } else if (type == ASCIICharColType) {
54 
+      size = sizeof(int8_t);
55 
+      len = (totalSize - overhead) / sizeof(int8_t);
56 
+    }
57 
+  }
58 
+}
59 
+
60 
+};
src/fusion_sdk/calvin_files/data/src/ColumnInfo.h
History View file @ 158e02d
... ... 
@@ -75,10 +75,7 @@ protected:
75 75 
 	 *	@param len_ Number of elements of type in the column.
76 76 
 	 *	@param overhead_ Number of extra bytes in the column
77 77 
 	 */
78 
-	ColumnInfo(const std::wstring& name_, DataSetColumnTypes type_, int32_t size_, int32_t len_, int32_t overhead_)
79 
-		: name(name_), type(type_), size(size_), len(len_), overhead(overhead_)
80 
-	{
81 
-	}
78 
+	ColumnInfo(const std::wstring& name_, DataSetColumnTypes type_, int32_t size_, int32_t len_, int32_t overhead_);
82 79
83 80 
 public:
84 81
... ... 
@@ -87,24 +84,7 @@ public:
87 84 
 	 *	@param type_ Type of data in the column.
88 85 
 	 *	@param totalSize Total size of the colum in bytes.
89 86 
 	 */
90 
-	ColumnInfo(const std::wstring& name_, DataSetColumnTypes type_, int32_t totalSize)
91 
-		: name(name_), type(type_), size(totalSize), len(1), overhead(0)
92 
-	{
93 
-		if (type == ASCIICharColType || type == UnicodeCharColType)
94 
-		{
95 
-			overhead = 4;
96 
-			if (type == UnicodeCharColType)
97 
-			{
98 
-				size = sizeof(int16_t);
99 
-				len = (totalSize-overhead)/sizeof(int16_t);
100 
-			}
101 
-			else if (type == ASCIICharColType)
102 
-			{
103 
-				size = sizeof(int8_t);
104 
-				len = (totalSize-overhead)/sizeof(int8_t);
105 
-			}
106 
-		}
107 
-	}
87 
+	ColumnInfo(const std::wstring& name_, DataSetColumnTypes type_, int32_t totalSize);
108 88
109 89 
 	/*! Equiality operator
110 90 
 	 *	@param p object to compare against
src/fusion_sdk/calvin_files/data/src/CytoGenotypeCallMultiDataData.h
History View file @ 158e02d
111 91 
new file mode 100644
... ... 
@@ -0,0 +1,69 @@
1 
+////////////////////////////////////////////////////////////////
2 
+//
3 
+// 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 _Cyto_GenotypeCall_HEADER_
22 
+#define _Cyto_GenotypeCall_HEADER_
23 
+
24 
+/*! \file CytoGenotypeCallMultiDataType.h This file provides types to hold genotyping results for cytgo arrays.
25 
+ */
26 
+
27 
+#include "calvin_files/parameter/src/ParameterNameValueType.h"
28 
+#include "calvin_files/portability/src/AffymetrixBaseTypes.h"
29 
+//
30 
+
31 
+namespace affymetrix_calvin_data
32 
+{
33 
+
34 
+/*! Holds the marker AB signal results */
35 
+typedef struct _CytoGenotypeCallData
36 
+{
37 
+	/*! The index relative to the probeset in the CopyNumber
38 
+	data set of the ProbeSet data group (0 based). */
39 
+	u_int32_t index;
40 
+
41 
+	 /*! The call. */
42 
+    u_int8_t call;
43 
+
44 
+	/*! The cpnfidence */
45 
+    float confidence;
46 
+
47 
+	 /*! The forced call. */
48 
+    u_int8_t forcedCall;
49 
+
50 
+	/*! The A signal */
51 
+    float aSignal;
52 
+
53 
+	/*! The B signal */
54 
+    float bSignal;
55 
+
56 
+	/*! The signal strength */
57 
+    float signalStrength;
58 
+
59 
+	/*! The contrast */
60 
+    float contrast;
61 
+
62 
+	/*! The extra metrics. */
63 
+	std::vector<affymetrix_calvin_parameter::ParameterNameValueType> metrics;
64 
+
65 
+} CytoGenotypeCallData;
66 
+
67 
+}
68 
+
69 
+#endif
src/fusion_sdk/calvin_files/data/src/DataException.cpp
History View file @ 158e02d
0 70 
new file mode 100644
... ... 
@@ -0,0 +1,63 @@
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
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 
+
22 
+#include "calvin_files/data/src/DataException.h"
23 
+//
24 
+
25 
+namespace affymetrix_calvin_exceptions
26 
+{
27 
+
28 
+  const  std::wstring DataSetNotOpenException::ToString() {
29 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::DataSetNotOpenException thrown.";
30 
+  }
31 
+  const std::wstring ColumnIndexOutOfBoundsException::ToString() {
32 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::ColumnIndexOutOfBoundsException thrown.";
33 
+  }
34 
+
35 
+  const std::wstring  RowIndexOutOfBoundsException::ToString() {
36 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::RowIndexOutOfBoundsException thrown.";
37 
+  }
38 
+
39 
+  const std::wstring UnexpectedColumnTypeException::ToString() {
40 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::UnexpectedColumnTypeException thrown.";
41 
+  }
42 
+
43 
+  const std::wstring DataGroupNotFoundException::ToString() {
44 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::DataGroupNotFoundException thrown.";
45 
+  }
46 
+
47 
+  const std::wstring DataSetNotFoundException::ToString() {
48 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::DataSetNotFoundException thrown.";
49 
+  }
50 
+
51 
+  const std::wstring ProbeSetNotFoundException::ToString() {
52 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::ProbeSetNotFoundException thrown.";
53 
+  }
54 
+
55 
+  const std::wstring CDFAccessNotSupportedByModeException::ToString() {
56 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::CDFAccessNotSupportedByModeException thrown.";
57 
+  }
58 
+
59 
+  const std::wstring DataSetRemapException::ToString() {
60 
+    return SystemInfo() + L"affymetrix_calvin_exceptions::DataSetRemapException thrown.";
61 
+  }
62 
+
63 
+}
src/fusion_sdk/calvin_files/data/src/DataException.h
History View file @ 158e02d
... ... 
@@ -32,38 +32,86 @@ namespace affymetrix_calvin_exceptions
32 32
33 33 
 class DataSetNotOpenException : public CalvinException
34 34 
 {
35 
+public:
36 
+  DataSetNotOpenException() : CalvinException() {}
37 
+  DataSetNotOpenException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
38 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
39 
+  const std::wstring ToString();
35 40 
 };
36 41
37 42 
 class ColumnIndexOutOfBoundsException : public CalvinException
38 43 
 {
44 
+public:
45 
+  ColumnIndexOutOfBoundsException() : CalvinException() {}
46 
+  ColumnIndexOutOfBoundsException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
47 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
48 
+  const std::wstring ToString();
39 49 
 };
40 50
41 51 
 class RowIndexOutOfBoundsException : public CalvinException
42 52 
 {
53 
+public:
54 
+  RowIndexOutOfBoundsException() : CalvinException() {}
55 
+  RowIndexOutOfBoundsException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
56 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
57 
+  const std::wstring ToString();
43 58 
 };
44 59
45 60 
 class UnexpectedColumnTypeException : public CalvinException
46 61 
 {
62 
+public:
63 
+  UnexpectedColumnTypeException() : CalvinException() {}
64 
+  UnexpectedColumnTypeException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
65 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
66 
+  const std::wstring ToString();
47 67 
 };
48 68
49 69 
 class DataGroupNotFoundException : public CalvinException
50 70 
 {
71 
+public:
72 
+  DataGroupNotFoundException() : CalvinException() {}
73 
+  DataGroupNotFoundException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
74 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
75 
+  const std::wstring ToString();
51 76 
 };
52 77
53 78 
 class DataSetNotFoundException : public CalvinException
54 79 
 {
80 
+public:
81 
+  DataSetNotFoundException() : CalvinException() {}
82 
+  DataSetNotFoundException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
83 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
84 
+
85 
+  const std::wstring ToString();
55 86 
 };
56 87
57 88 
 class ProbeSetNotFoundException : public CalvinException
58 89 
 {
90 
+public:
91 
+  ProbeSetNotFoundException() : CalvinException() {}
92 
+  ProbeSetNotFoundException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
93 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
94 
+  const std::wstring ToString();
59 95 
 };
60 96
61 97 
 class CDFAccessNotSupportedByModeException : public CalvinException
62 98 
 {
99 
+public:
100 
+  CDFAccessNotSupportedByModeException() : CalvinException() {}
101 
+  CDFAccessNotSupportedByModeException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
102 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
103 
+  const std::wstring ToString();
63 104 
 };
64 105
65 106 
 class DataSetRemapException : public CalvinException
66 107 
 {
108 
+public:
109 
+  DataSetRemapException() : CalvinException() {}
110 
+  DataSetRemapException(std::wstring _Source, std::wstring _Description, std::wstring _TimeStamp, std::string _FileName, u_int16_t _LineNumber, u_int64_t _ErrorCode):
111 
+    CalvinException(_Source, _Description, _TimeStamp, _FileName,  _LineNumber, _ErrorCode) {}
112 
+
113 
+  const std::wstring ToString();
114 
+
67 115 
 };
68 116
69 117 
 }
src/fusion_sdk/calvin_files/data/src/DataGroup.cpp
History View file @ 158e02d
... ... 
@@ -65,7 +65,7 @@ affymetrix_calvin_io::DataSet* DataGroup::DataSet(u_int32_t dataSetIdx)
65 65 
 	}
66 66 
 	else
67 67 
 	{
68 
-		affymetrix_calvin_exceptions::DataSetNotFoundException e;
68 
+		affymetrix_calvin_exceptions::DataSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
69 69 
 		throw e;
70 70 
 	}
71 71 
 }
... ... 
@@ -90,7 +90,7 @@ affymetrix_calvin_io::DataSet* DataGroup::DataSet(const std::wstring& dataSetNam
90 90 
 	}
91 91 
 	else
92 92 
 	{
93 
-		affymetrix_calvin_exceptions::DataSetNotFoundException e;
93 
+		affymetrix_calvin_exceptions::DataSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
94 94 
 		throw e;
95 95 
 	}
96 96 
 }
src/fusion_sdk/calvin_files/data/src/DataSet.cpp
History View file @ 158e02d
... ... 
@@ -23,6 +23,8 @@
23 23 
 #include "calvin_files/data/src/GenericData.h"
24 24 
 #include "calvin_files/parsers/src/FileInput.h"
25 25 
 //
26 
+#include "util/Fs.h"
27 
+//
26 28 
 #include <sys/stat.h>
27 29 
 #include <sys/types.h>
28 30 
 //
... ... 
@@ -264,10 +266,9 @@ bool DataSet::MapDataPosix(u_int32_t start, u_int32_t bytes)
264 266 
 	mapLen = bytes + page_offset;
265 267
266 268 
 	// Get the file size
267 
-	struct stat st;
268 
-	if (stat(fileName.c_str(), &st) == 0)
269 
+	if (Fs::fileExists(fileName))
269 270 
 	{
270 
-		int fileLen = st.st_size;
271 
+          int64_t fileLen = Fs::fileSize(fileName);
271 272 
 		if (fileLen < page_start + mapLen)
272 273 
 			mapLen = fileLen - page_start;
273 274 
 	}
... ... 
@@ -338,19 +339,19 @@ void DataSet::CheckRowColumnAndType(int32_t row, int32_t col, DataSetColumnTypes
338 339 
 {
339 340 
 	if (isOpen == false)
340 341 
 	{
341 
-		affymetrix_calvin_exceptions::DataSetNotOpenException e;
342 
+		affymetrix_calvin_exceptions::DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
342 343 
 		throw e;
343 344 
 	}
344 345
345 346 
 	if (col < 0 || col >= header.GetColumnCnt())
346 347 
 	{
347 
-		affymetrix_calvin_exceptions::ColumnIndexOutOfBoundsException e;
348 
+		affymetrix_calvin_exceptions::ColumnIndexOutOfBoundsException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
348 349 
 		throw e;
349 350 
 	}
350 351
351 352 
 	if (row < 0 || row >= header.GetRowCnt())
352 353 
 	{
353 
-		affymetrix_calvin_exceptions::RowIndexOutOfBoundsException e;
354 
+		affymetrix_calvin_exceptions::RowIndexOutOfBoundsException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
354 355 
 		throw e;
355 356 
 	}
356 357
... ... 
@@ -358,7 +359,7 @@ void DataSet::CheckRowColumnAndType(int32_t row, int32_t col, DataSetColumnTypes
358 359
359 360 
 	if (header.GetColumnInfo(col).GetColumnType() != type)
360 361 
 	{
361 
-		affymetrix_calvin_exceptions::UnexpectedColumnTypeException e;
362 
+		affymetrix_calvin_exceptions::UnexpectedColumnTypeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
362 363 
 		throw e;
363 364 
 	}
364 365 
 }
... ... 
@@ -370,7 +371,7 @@ char* DataSet::FilePosition(int32_t rowStart, int32_t col, int32_t rowCount)
370 371 
 {
371 372 
 	if (isOpen == false)
372 373 
 	{
373 
-		affymetrix_calvin_exceptions::DataSetNotOpenException e;
374 
+		affymetrix_calvin_exceptions::DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
374 375 
 		throw e;
375 376 
 	}
376 377
... ... 
@@ -408,7 +409,7 @@ char* DataSet::FilePosition(int32_t rowStart, int32_t col, int32_t rowCount)
408 409
409 410 
 				if (MapDataWin32(reverseStartByte, header.GetDataStartFilePos() + header.GetDataSize() - reverseStartByte) == false)
410 411 
 				{
411 
-					affymetrix_calvin_exceptions::DataSetRemapException e;
412 
+					affymetrix_calvin_exceptions::DataSetRemapException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
412 413 
 					throw e;
413 414 
 				}
414 415 
 			}
... ... 
@@ -416,7 +417,7 @@ char* DataSet::FilePosition(int32_t rowStart, int32_t col, int32_t rowCount)
416 417 
 			{
417 418 
 				if (MapDataWin32(startByte, header.GetDataStartFilePos() + header.GetDataSize() - startByte) == false)
418 419 
 				{
419 
-					affymetrix_calvin_exceptions::DataSetRemapException e;
420 
+					affymetrix_calvin_exceptions::DataSetRemapException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
420 421 
 					throw e;
421 422 
 				}
422 423 
 			}
src/fusion_sdk/calvin_files/data/src/DataSet.h
History View file @ 158e02d
... ... 
@@ -193,10 +193,11 @@ public:
193 193 
 	 */
194 194 
 	int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
195 195
196 
-protected:
196 
+//protected:
197 197 
 	/*! Destructor. */
198 198 
 	~DataSet();
199 199
200 
+protected:
200 201 
 	/*! Open the DataSet using memory-mapping
201 202 
 	 *	@return True if the DataSet was successully mapped.
202 203 
 	 */
src/fusion_sdk/calvin_files/data/src/GenericData.cpp
History View file @ 158e02d
... ... 
@@ -24,6 +24,8 @@
24 24 
 #include "calvin_files/parsers/src/DataGroupHeaderReader.h"
25 25 
 #include "calvin_files/parsers/src/DataSetHeaderReader.h"
26 26 
 //
27 
+#include "util/Fs.h"
28 
+//
27 29 
 #include <algorithm>
28 30 
 #include <cstring>
29 31 
 #include <iterator>
... ... 
@@ -132,7 +134,7 @@ u_int32_t GenericData::DataSetCnt(u_int32_t dataGroupIdx)
132 134 
 		return dch->GetDataSetCnt();
133 135 
 	else
134 136 
 	{
135 
-		affymetrix_calvin_exceptions::DataGroupNotFoundException e;
137 
+		affymetrix_calvin_exceptions::DataGroupNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
136 138 
 		throw e;
137 139 
 	}
138 140 
 }
... ... 
@@ -147,7 +149,7 @@ u_int32_t GenericData::DataSetCnt(const std::wstring& dataGroupName)
147 149 
 		return dch->GetDataSetCnt();
148 150 
 	else
149 151 
 	{
150 
-		affymetrix_calvin_exceptions::DataGroupNotFoundException e;
152 
+		affymetrix_calvin_exceptions::DataGroupNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
151 153 
 		throw e;
152 154 
 	}
153 155 
 }
... ... 
@@ -160,7 +162,7 @@ void GenericData::DataSetNames(u_int32_t dataGroupIdx, std::vector<std::wstring>
160 162 
 	DataGroupHeader* dch = FindDataGroupHeader(dataGroupIdx);
161 163 
 	if (dch == 0)
162 164 
 	{
163 
-		affymetrix_calvin_exceptions::DataGroupNotFoundException e;
165 
+		affymetrix_calvin_exceptions::DataGroupNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
164 166 
 		throw e;
165 167 
 	}
166 168
... ... 
@@ -182,7 +184,7 @@ void GenericData::DataSetNames(const std::wstring& dataGroupName, std::vector<st
182 184 
 	DataGroupHeader* dch = FindDataGroupHeader(dataGroupName);
183 185 
 	if (dch == 0)
184 186 
 	{
185 
-		affymetrix_calvin_exceptions::DataGroupNotFoundException e;
187 
+		affymetrix_calvin_exceptions::DataGroupNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
186 188 
 		throw e;
187 189 
 	}
188 190
... ... 
@@ -203,7 +205,7 @@ DataSet* GenericData::DataSet(u_int32_t dataGroupIdx, u_int32_t dataSetIdx)
203 205 
 {
204 206 
 	if (Open() == false)
205 207 
 	{
206 
-		affymetrix_calvin_exceptions::FileNotOpenException e;
208 
+		affymetrix_calvin_exceptions::FileNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
207 209 
 		throw e;
208 210 
 	}
209 211
... ... 
@@ -217,13 +219,13 @@ DataSet* GenericData::DataSet(u_int32_t dataGroupIdx, u_int32_t dataSetIdx)
217 219 
 		}
218 220 
 		else
219 221 
 		{
220 
-			affymetrix_calvin_exceptions::DataSetNotFoundException e;
222 
+			affymetrix_calvin_exceptions::DataSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
221 223 
 			throw e;
222 224 
 		}
223 225 
 	}
224 226 
 	else
225 227 
 	{
226 
-		affymetrix_calvin_exceptions::DataGroupNotFoundException e;
228 
+		affymetrix_calvin_exceptions::DataGroupNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
227 229 
 		throw e;
228 230 
 	}
229 231 
 }
... ... 
@@ -235,7 +237,7 @@ DataSet* GenericData::DataSet(const std::wstring& dataGroupName, const std::wstr
235 237 
 {
236 238 
 	if (Open() == false)
237 239 
 	{
238 
-		affymetrix_calvin_exceptions::FileNotOpenException e;
240 
+		affymetrix_calvin_exceptions::FileNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
239 241 
 		throw e;
240 242 
 	}
241 243
... ... 
@@ -249,13 +251,13 @@ DataSet* GenericData::DataSet(const std::wstring& dataGroupName, const std::wstr
249 251 
 		}
250 252 
 		else
251 253 
 		{
252 
-			affymetrix_calvin_exceptions::DataSetNotFoundException e;
254 
+			affymetrix_calvin_exceptions::DataSetNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
253 255 
 			throw e;
254 256 
 		}
255 257 
 	}
256 258 
 	else
257 259 
 	{
258 
-		affymetrix_calvin_exceptions::DataGroupNotFoundException e;
260 
+		affymetrix_calvin_exceptions::DataGroupNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
259 261 
 		throw e;
260 262 
 	}
261 263 
 }
... ... 
@@ -287,7 +289,7 @@ affymetrix_calvin_io::DataGroup GenericData::DataGroup(u_int32_t dataGroupFilePo
287 289 
 {
288 290 
 	if (Open() == false)
289 291 
 	{
290 
-		affymetrix_calvin_exceptions::FileNotOpenException e;
292 
+		affymetrix_calvin_exceptions::FileNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
291 293 
 		throw e;
292 294 
 	}
293 295
... ... 
@@ -437,10 +439,10 @@ bool GenericData::IsDSHPartiallyRead(const DataSetHeader* dph)
437 439 
  */
438 440 
 void GenericData::OpenFStream(std::ifstream& ifs)
439 441 
 {
440 
-	ifs.open(Header().GetFilename().c_str(), std::ios::in | std::ios::binary);
441 
-	if (!ifs)
442 
+  Fs::aptOpen(ifs, Header().GetFilename(), std::ios::in | std::ios::binary);
443 
+  if (!ifs.is_open() && !ifs.good())
442 444 
 	{
443 
-		affymetrix_calvin_exceptions::FileNotFoundException e;
445 
+		affymetrix_calvin_exceptions::FileNotFoundException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
444 446 
 		throw e;
445 447 
 	}
446 448 
 }
... ... 
@@ -472,13 +474,16 @@ bool GenericData::MapFile()
472 474 
 #ifdef _MSC_VER	// On Windows the map is open in the GenericData object, otherwise it is opened in the DataSet
473 475 
 	if (fileHandle == INVALID_HANDLE_VALUE)
474 476 
 	{
475 
-		// Create the file.
476 
-		fileHandle = CreateFile(Header().GetFilename().c_str(), GENERIC_READ, FILE_SHARE_READ,
477 
-				NULL, OPEN_EXISTING, FILE_ATTRIBUTE_NORMAL, NULL);
478 
-		if (fileHandle == INVALID_HANDLE_VALUE)
479 
-		{
480 
-			return false;
481 
-		}
477 
+          // Create the file.
478 
+          std::wstring filename = Fs::convertToUncPathW(Header().GetFilename(), 10);
479 
+
480 
+          fileHandle = CreateFileW(filename.c_str(), GENERIC_READ, FILE_SHARE_READ,
481 
+                                  NULL, OPEN_EXISTING, FILE_ATTRIBUTE_NORMAL, NULL);
482 
+          if (fileHandle == INVALID_HANDLE_VALUE)
483 
+            {
484 
+				Verbose::out(1, Fs::MSC_VER_GetLastErrorString(std::string("GenericData::MapFile ") + Util::toString(filename) + ": "));
485 
+              return false;
486 
+            }
482 487 
 	}
483 488 
 	if (fileMapHandle == NULL)
484 489 
 	{
... ... 
@@ -489,6 +494,7 @@ bool GenericData::MapFile()
489