git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@18256 bc3139a8-67e5-0310-9ffc-ced21a209358
Kasper D. Hansen authored on 01/06/2006 00:33:01
| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
#!/bin/bash |
| 2 |
-cd cvs_head/affy/sdk |
|
| 2 |
+cd sdk |
|
| 3 | 3 |
rm -R TestDataFiles file_formats interface_docs java \ |
| 4 | 4 |
libraries_and_tools parser_examples sample_data *.html *.gif \ |
| 5 | 5 |
portability/CPPTest file/CPPTest calvin_files/makefile.g5 \ |
| ... | ... |
@@ -8,11 +8,11 @@ rm -R TestDataFiles file_formats interface_docs java \ |
| 8 | 8 |
calvin_files/data/test calvin_files/data/data\ |
| 9 | 9 |
calvin_files/exception/test\ |
| 10 | 10 |
calvin_files/fusion/test calvin_files/fusion/data\ |
| 11 |
- calvin_files/fusion/com calvin_files/fusion/swig-java\ |
|
| 11 |
+ calvin_files/fusion/com\ |
|
| 12 | 12 |
calvin_files/fusion/swig-cs calvin_files/fusion/swig-perl\ |
| 13 | 13 |
calvin_files/parameter/test\ |
| 14 | 14 |
calvin_files/parsers/test calvin_files/parsers/data\ |
| 15 | 15 |
calvin_files/portability/test\ |
| 16 | 16 |
calvin_files/utils/test calvin_files/utils/data\ |
| 17 |
- calvin_files/writers/test |
|
| 17 |
+ calvin_files/writers/test calvin_files/writers/data |
|
| 18 | 18 |
cd - |
| ... | ... |
@@ -40,13 +40,22 @@ extern "C" {
|
| 40 | 40 |
* |
| 41 | 41 |
* We also read the object. |
| 42 | 42 |
* - - - - - - - - - - - - - - - - - - - - - - - - - - - */ |
| 43 |
- SEXP returnList, returnListNames; |
|
| 43 |
+ SEXP returnList, returnListNames, tmp; |
|
| 44 |
+ int kk =0; |
|
| 45 |
+ |
|
| 44 | 46 |
PROTECT(returnList = NEW_LIST(2)); |
| 45 |
- SET_VECTOR_ELT(returnList, 0, ScalarReal(bpmap.GetVersion())); |
|
| 46 |
- SET_VECTOR_ELT(returnList, 1, ScalarInteger(bpmap.GetNumberSequences())); |
|
| 47 | 47 |
PROTECT(returnListNames = NEW_CHARACTER(2)); |
| 48 |
- SET_STRING_ELT(returnListNames, 0, mkChar("version"));
|
|
| 49 |
- SET_STRING_ELT(returnListNames, 1, mkChar("numSequences"));
|
|
| 48 |
+ |
|
| 49 |
+ SET_STRING_ELT(returnListNames, kk, mkChar("version"));
|
|
| 50 |
+ tmp = NEW_NUMERIC(1); |
|
| 51 |
+ SET_VECTOR_ELT(returnList, kk++, tmp); |
|
| 52 |
+ REAL(tmp)[0] = bpmap.GetVersion(); |
|
| 53 |
+ |
|
| 54 |
+ SET_STRING_ELT(returnListNames, kk, mkChar("numSequences"));
|
|
| 55 |
+ tmp = NEW_INTEGER(1); |
|
| 56 |
+ SET_VECTOR_ELT(returnList, kk++, tmp); |
|
| 57 |
+ INTEGER(tmp)[0] = bpmap.GetNumberSequences(); |
|
| 58 |
+ |
|
| 50 | 59 |
setAttrib(returnList, R_NamesSymbol, returnListNames); |
| 51 | 60 |
bpmap.Close(); |
| 52 | 61 |
UNPROTECT(2); |
| ... | ... |
@@ -66,35 +75,55 @@ extern "C" {
|
| 66 | 75 |
if (i_verboseFlag >= R_AFFX_REALLY_VERBOSE) {
|
| 67 | 76 |
Rprintf(" Reading seqInfo\n");
|
| 68 | 77 |
} |
| 69 |
- SEXP seqInfo, seqInfoNames, |
|
| 78 |
+ SEXP seqInfo, seqInfoNames, tmp, |
|
| 70 | 79 |
seqInfoParameters, seqInfoParameterNames; |
| 80 |
+ int kk = 0; |
|
| 81 |
+ |
|
| 71 | 82 |
PROTECT(seqInfo = NEW_LIST(8)); |
| 72 | 83 |
PROTECT(seqInfoNames = NEW_CHARACTER(8)); |
| 73 |
- SET_VECTOR_ELT(seqInfo, 0, |
|
| 74 |
- ScalarString(mkChar(seq.GetName().c_str()))); |
|
| 75 |
- SET_STRING_ELT(seqInfoNames, 0, mkChar("name"));
|
|
| 76 |
- SET_VECTOR_ELT(seqInfo, 1, |
|
| 77 |
- ScalarString(mkChar(seq.GroupName().c_str()))); |
|
| 78 |
- SET_STRING_ELT(seqInfoNames, 1, mkChar("groupname"));
|
|
| 79 |
- SET_VECTOR_ELT(seqInfo, 2, |
|
| 80 |
- ScalarString(mkChar(seq.FullName().c_str()))); |
|
| 81 |
- SET_STRING_ELT(seqInfoNames, 2, mkChar("fullname"));
|
|
| 82 |
- SET_VECTOR_ELT(seqInfo, 3, |
|
| 83 |
- ScalarString(mkChar(seq.GetSeqVersion().c_str()))); |
|
| 84 |
- SET_STRING_ELT(seqInfoNames, 3, mkChar("version"));
|
|
| 84 |
+ |
|
| 85 |
+ SEXP tmp1; |
|
| 86 |
+ PROTECT(tmp1 = 1); |
|
| 87 |
+ UNPROTECT(1); |
|
| 88 |
+ |
|
| 89 |
+ SET_STRING_ELT(seqInfoNames, kk, mkChar("name"));
|
|
| 90 |
+ tmp = NEW_CHARACTER(1); |
|
| 91 |
+ SET_VECTOR_ELT(seqInfo, kk++, tmp); |
|
| 92 |
+ SET_STRING_ELT(tmp, 0, mkChar(seq.GetName().c_str())); |
|
| 93 |
+ |
|
| 94 |
+ SET_STRING_ELT(seqInfoNames, kk, mkChar("groupname"));
|
|
| 95 |
+ tmp = NEW_CHARACTER(1); |
|
| 96 |
+ SET_VECTOR_ELT(seqInfo, kk++, tmp); |
|
| 97 |
+ SET_STRING_ELT(tmp, 0, mkChar(seq.GroupName().c_str())); |
|
| 98 |
+ |
|
| 99 |
+ SET_STRING_ELT(seqInfoNames, kk, mkChar("fullname"));
|
|
| 100 |
+ tmp = NEW_CHARACTER(1); |
|
| 101 |
+ SET_VECTOR_ELT(seqInfo, kk++, tmp); |
|
| 102 |
+ SET_STRING_ELT(tmp, 0, mkChar(seq.FullName().c_str())); |
|
| 103 |
+ |
|
| 104 |
+ SET_STRING_ELT(seqInfoNames, kk, mkChar("version"));
|
|
| 105 |
+ tmp = NEW_CHARACTER(1); |
|
| 106 |
+ SET_VECTOR_ELT(seqInfo, kk++, tmp); |
|
| 107 |
+ SET_STRING_ELT(tmp, 0, mkChar(seq.GetSeqVersion().c_str())); |
|
| 108 |
+ |
|
| 109 |
+ SET_STRING_ELT(seqInfoNames, kk, mkChar("mapping"));
|
|
| 110 |
+ tmp = NEW_CHARACTER(1); |
|
| 111 |
+ SET_VECTOR_ELT(seqInfo, kk++, tmp); |
|
| 85 | 112 |
if(seq.GetProbeMapping() == 0) |
| 86 |
- SET_VECTOR_ELT(seqInfo, 4, |
|
| 87 |
- ScalarString(mkChar("pmmm")));
|
|
| 113 |
+ SET_STRING_ELT(tmp, 0, mkChar("pmmm"));
|
|
| 88 | 114 |
else |
| 89 |
- SET_VECTOR_ELT(seqInfo, 4, |
|
| 90 |
- ScalarString(mkChar("onlypm")));
|
|
| 91 |
- SET_STRING_ELT(seqInfoNames, 4, mkChar("mapping"));
|
|
| 92 |
- SET_VECTOR_ELT(seqInfo, 5, |
|
| 93 |
- ScalarInteger(seq.GetNumber() + 1)); |
|
| 94 |
- SET_STRING_ELT(seqInfoNames, 5, mkChar("number"));
|
|
| 95 |
- SET_VECTOR_ELT(seqInfo, 6, |
|
| 96 |
- ScalarInteger(seq.GetNumberHits())); |
|
| 97 |
- SET_STRING_ELT(seqInfoNames, 6, mkChar("numberOfHits"));
|
|
| 115 |
+ SET_VECTOR_ELT(tmp, 0, mkChar("onlypm"));
|
|
| 116 |
+ |
|
| 117 |
+ SET_STRING_ELT(seqInfoNames, kk, mkChar("number"));
|
|
| 118 |
+ tmp = NEW_INTEGER(1); |
|
| 119 |
+ SET_VECTOR_ELT(seqInfo, kk++, tmp); |
|
| 120 |
+ INTEGER(tmp)[0] = seq.GetNumber() + 1; |
|
| 121 |
+ |
|
| 122 |
+ SET_STRING_ELT(seqInfoNames, kk, mkChar("numberOfHits"));
|
|
| 123 |
+ tmp = NEW_INTEGER(1); |
|
| 124 |
+ SET_VECTOR_ELT(seqInfo, kk++, tmp); |
|
| 125 |
+ INTEGER(tmp)[0] = seq.GetNumberHits(); |
|
| 126 |
+ |
|
| 98 | 127 |
/* Now we read the parameters, which is basically |
| 99 | 128 |
* a long character vector of different parameter |
| 100 | 129 |
* values */ |
| ... | ... |
@@ -592,6 +592,38 @@ std::wstring CelFileData::GetArrayType() |
| 592 | 592 |
return GetWStringFromGenericHdr(ARRAY_TYPE_PARAM_NAME); |
| 593 | 593 |
} |
| 594 | 594 |
|
| 595 |
+/* |
|
| 596 |
+ * Set the master file |
|
| 597 |
+ */ |
|
| 598 |
+void CelFileData::SetMasterFileName(const std::wstring& value) |
|
| 599 |
+{
|
|
| 600 |
+ SetWStringToGenericHdr(MASTER_FILE_PARAM_NAME, value); |
|
| 601 |
+} |
|
| 602 |
+ |
|
| 603 |
+/* |
|
| 604 |
+ * Get the master file |
|
| 605 |
+ */ |
|
| 606 |
+std::wstring CelFileData::GetMasterFileName() |
|
| 607 |
+{
|
|
| 608 |
+ return GetWStringFromGenericHdr(MASTER_FILE_PARAM_NAME); |
|
| 609 |
+} |
|
| 610 |
+ |
|
| 611 |
+/* |
|
| 612 |
+ * Set the library package |
|
| 613 |
+ */ |
|
| 614 |
+void CelFileData::SetLibraryPackageName(const std::wstring& value) |
|
| 615 |
+{
|
|
| 616 |
+ SetWStringToGenericHdr(LIBRARY_PACKAGE_PARAM_NAME, value); |
|
| 617 |
+} |
|
| 618 |
+ |
|
| 619 |
+/* |
|
| 620 |
+ * Get the library package |
|
| 621 |
+ */ |
|
| 622 |
+std::wstring CelFileData::GetLibraryPackageName() |
|
| 623 |
+{
|
|
| 624 |
+ return GetWStringFromGenericHdr(LIBRARY_PACKAGE_PARAM_NAME); |
|
| 625 |
+} |
|
| 626 |
+ |
|
| 595 | 627 |
/* |
| 596 | 628 |
* Set name of the algorithm used to generate the results. |
| 597 | 629 |
*/ |
| ... | ... |
@@ -608,6 +640,22 @@ std::wstring CelFileData::GetAlgorithmName() |
| 608 | 640 |
return GetWStringFromGenericHdr(ALGORITHM_NAME_PARAM_NAME); |
| 609 | 641 |
} |
| 610 | 642 |
|
| 643 |
+/* |
|
| 644 |
+ * Set name of the algorithm used to generate the results. |
|
| 645 |
+ */ |
|
| 646 |
+void CelFileData::SetAlgorithmVersion(const std::wstring& value) |
|
| 647 |
+{
|
|
| 648 |
+ SetWStringToGenericHdr(ALG_VERSION_PARAM_NAME, value); |
|
| 649 |
+} |
|
| 650 |
+ |
|
| 651 |
+/* |
|
| 652 |
+ * Get the name of the algorithm used to generate the results. |
|
| 653 |
+ */ |
|
| 654 |
+std::wstring CelFileData::GetAlgorithmVersion() |
|
| 655 |
+{
|
|
| 656 |
+ return GetWStringFromGenericHdr(ALG_VERSION_PARAM_NAME); |
|
| 657 |
+} |
|
| 658 |
+ |
|
| 611 | 659 |
/* |
| 612 | 660 |
* Set the number of rows of cells |
| 613 | 661 |
*/ |
| ... | ... |
@@ -30,7 +30,7 @@ |
| 30 | 30 |
#include "Coords.h" |
| 31 | 31 |
#include <set> |
| 32 | 32 |
|
| 33 |
-#ifdef WIN32 |
|
| 33 |
+#ifdef _MSC_VER |
|
| 34 | 34 |
#pragma warning(disable: 4290) // don't show warnings about throw keyword on function declarations. |
| 35 | 35 |
#endif |
| 36 | 36 |
|
| ... | ... |
@@ -149,6 +149,26 @@ public: |
| 149 | 149 |
*/ |
| 150 | 150 |
std::wstring GetArrayType(); |
| 151 | 151 |
|
| 152 |
+ /*! Set the master file |
|
| 153 |
+ * @param value master file name |
|
| 154 |
+ */ |
|
| 155 |
+ void SetMasterFileName(const std::wstring& value); |
|
| 156 |
+ |
|
| 157 |
+ /*! Get the master file |
|
| 158 |
+ * @return master file name |
|
| 159 |
+ */ |
|
| 160 |
+ std::wstring GetMasterFileName(); |
|
| 161 |
+ |
|
| 162 |
+ /*! Set the library package |
|
| 163 |
+ * @param value library package name |
|
| 164 |
+ */ |
|
| 165 |
+ void SetLibraryPackageName(const std::wstring& value); |
|
| 166 |
+ |
|
| 167 |
+ /*! Get the library package |
|
| 168 |
+ * @return library package name |
|
| 169 |
+ */ |
|
| 170 |
+ std::wstring GetLibraryPackageName(); |
|
| 171 |
+ |
|
| 152 | 172 |
/*! Set name of the algorithm used to generate the results. |
| 153 | 173 |
* @param value algorithm name |
| 154 | 174 |
*/ |
| ... | ... |
@@ -158,6 +178,14 @@ public: |
| 158 | 178 |
* @return Algorithm name |
| 159 | 179 |
*/ |
| 160 | 180 |
std::wstring GetAlgorithmName(); |
| 181 |
+ /*! Set version of the algorithm used to generate the results. |
|
| 182 |
+ * @param value algorithm name |
|
| 183 |
+ */ |
|
| 184 |
+ void SetAlgorithmVersion(const std::wstring& value); |
|
| 185 |
+ /* |
|
| 186 |
+ * Get the version of the algorithm used to generate the results. |
|
| 187 |
+ */ |
|
| 188 |
+ std::wstring CelFileData::GetAlgorithmVersion(); |
|
| 161 | 189 |
|
| 162 | 190 |
/*! Set the number of rows of cells on the array. |
| 163 | 191 |
* @param value Number of rows of cells. |
| ... | ... |
@@ -31,14 +31,16 @@ static const std::wstring CHIP_SUMMARY_PARAMETER_NAME_PREFIX = L"affymetrix-chip |
| 31 | 31 |
|
| 32 | 32 |
CHPSignalData::CHPSignalData() |
| 33 | 33 |
{
|
| 34 |
- wideProbeSetNames = false; |
|
| 34 |
+ maxProbeSetName = -1; |
|
| 35 |
+ firstColumnType = UnicodeCharColType; |
|
| 35 | 36 |
entries = NULL; |
| 36 | 37 |
Clear(); |
| 37 | 38 |
} |
| 38 | 39 |
|
| 39 | 40 |
CHPSignalData::CHPSignalData(const std::string& filename) |
| 40 | 41 |
{
|
| 41 |
- wideProbeSetNames = false; |
|
| 42 |
+ maxProbeSetName = -1; |
|
| 43 |
+ firstColumnType = UnicodeCharColType; |
|
| 42 | 44 |
entries = NULL; |
| 43 | 45 |
Clear(); |
| 44 | 46 |
SetFilename(filename); |
| ... | ... |
@@ -77,13 +79,27 @@ int32_t CHPSignalData::GetEntryCount() |
| 77 | 79 |
|
| 78 | 80 |
void CHPSignalData::SetEntryCount(int32_t ln, int32_t maxln) |
| 79 | 81 |
{
|
| 82 |
+ firstColumnType = ASCIICharColType; |
|
| 80 | 83 |
maxProbeSetName = maxln; |
| 81 | 84 |
ParameterNameValueType param; |
| 82 | 85 |
DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0); |
| 83 | 86 |
DataSetHeader dpHdr; |
| 84 | 87 |
dpHdr.SetRowCnt(ln); |
| 85 | 88 |
dpHdr.SetName(SIGNAL_SIGNAL_NAME); |
| 86 |
- AddColumns(dpHdr); |
|
| 89 |
+ AddColumns(dpHdr, false); |
|
| 90 |
+ dcHdr->AddDataSetHdr(dpHdr); |
|
| 91 |
+} |
|
| 92 |
+ |
|
| 93 |
+void CHPSignalData::SetEntryCount(int32_t ln) |
|
| 94 |
+{
|
|
| 95 |
+ firstColumnType = IntColType; |
|
| 96 |
+ maxProbeSetName = -1; |
|
| 97 |
+ ParameterNameValueType param; |
|
| 98 |
+ DataGroupHeader* dcHdr = &genericData.Header().GetDataGroup(0); |
|
| 99 |
+ DataSetHeader dpHdr; |
|
| 100 |
+ dpHdr.SetRowCnt(ln); |
|
| 101 |
+ dpHdr.SetName(SIGNAL_SIGNAL_NAME); |
|
| 102 |
+ AddColumns(dpHdr, true); |
|
| 87 | 103 |
dcHdr->AddDataSetHdr(dpHdr); |
| 88 | 104 |
} |
| 89 | 105 |
|
| ... | ... |
@@ -92,21 +108,28 @@ void CHPSignalData::GetSignalEntry(int index, affymetrix_calvin_data::ProbeSetSi |
| 92 | 108 |
OpenSignalDataSet(); |
| 93 | 109 |
if (entries && entries->IsOpen()) |
| 94 | 110 |
{
|
| 95 |
- if (wideProbeSetNames == false) |
|
| 111 |
+ entry.id = -1; |
|
| 112 |
+ entry.name.clear(); |
|
| 113 |
+ if (firstColumnType == ASCIICharColType) |
|
| 96 | 114 |
entries->GetData(index, 0, entry.name); |
| 97 |
- else |
|
| 115 |
+ else if (firstColumnType == UnicodeCharColType) |
|
| 98 | 116 |
{
|
| 99 |
- std::wstring wprobeSetName; |
|
| 100 |
- entries->GetData(index, 0, wprobeSetName); |
|
| 101 |
- entry.name = StringUtils::ConvertWCSToMBS(wprobeSetName); |
|
| 117 |
+ std::wstring wprobeSetName; |
|
| 118 |
+ entries->GetData(index, 0, wprobeSetName); |
|
| 119 |
+ entry.name = StringUtils::ConvertWCSToMBS(wprobeSetName); |
|
| 102 | 120 |
} |
| 121 |
+ else if (firstColumnType == IntColType) |
|
| 122 |
+ entries->GetData(index, 0, entry.id); |
|
| 103 | 123 |
entries->GetData(index, 1, entry.signal); |
| 104 | 124 |
} |
| 105 | 125 |
} |
| 106 | 126 |
|
| 107 |
-void CHPSignalData::AddColumns(DataSetHeader& hdr) |
|
| 127 |
+void CHPSignalData::AddColumns(DataSetHeader& hdr, bool keyIsID) |
|
| 108 | 128 |
{
|
| 109 |
- hdr.AddAsciiColumn(SIGNAL_PROBE_SET_NAME, maxProbeSetName); |
|
| 129 |
+ if (keyIsID == false) |
|
| 130 |
+ hdr.AddAsciiColumn(SIGNAL_PROBE_SET_NAME, maxProbeSetName); |
|
| 131 |
+ else |
|
| 132 |
+ hdr.AddIntColumn(SIGNAL_PROBE_SET_ID); |
|
| 110 | 133 |
hdr.AddFloatColumn(SIGNAL_SIGNAL_NAME); |
| 111 | 134 |
} |
| 112 | 135 |
|
| ... | ... |
@@ -118,7 +141,7 @@ void CHPSignalData::OpenSignalDataSet() |
| 118 | 141 |
if (entries) |
| 119 | 142 |
{
|
| 120 | 143 |
entries->Open(); |
| 121 |
- wideProbeSetNames = (entries->Header().GetColumnInfo(0).GetColumnType() == UnicodeCharColType); |
|
| 144 |
+ firstColumnType = entries->Header().GetColumnInfo(0).GetColumnType(); |
|
| 122 | 145 |
} |
| 123 | 146 |
} |
| 124 | 147 |
} |
| ... | ... |
@@ -39,6 +39,9 @@ namespace affymetrix_calvin_io |
| 39 | 39 |
/*! The column name for the probe set name. */ |
| 40 | 40 |
#define SIGNAL_PROBE_SET_NAME std::wstring(L"ProbeSetName") |
| 41 | 41 |
|
| 42 |
+/*! The column name for the probe set id. */ |
|
| 43 |
+#define SIGNAL_PROBE_SET_ID std::wstring(L"ProbeSetId") |
|
| 44 |
+ |
|
| 42 | 45 |
/*! Holds data associated with signal array CHP files. */ |
| 43 | 46 |
class CHPSignalData |
| 44 | 47 |
{
|
| ... | ... |
@@ -56,7 +59,7 @@ public: |
| 56 | 59 |
|
| 57 | 60 |
private: |
| 58 | 61 |
/*! Flag indicating if the probe set names were stored in wide character format. */ |
| 59 |
- bool wideProbeSetNames; |
|
| 62 |
+ DataSetColumnTypes firstColumnType; |
|
| 60 | 63 |
|
| 61 | 64 |
/*! The generic data item. */ |
| 62 | 65 |
GenericData genericData; |
| ... | ... |
@@ -91,11 +94,16 @@ public: |
| 91 | 94 |
/*! Sets the array type. */ |
| 92 | 95 |
void SetArrayType(const std::wstring& value); |
| 93 | 96 |
|
| 94 |
- /*! Sets the number of entries (probe sets) |
|
| 97 |
+ /*! Sets the number of entries (probe sets). Use this function if names are to be stored. |
|
| 95 | 98 |
* @param ln The number of probe sets. |
| 96 | 99 |
* @param maxln The maximum length of a probe set name. |
| 97 | 100 |
*/ |
| 98 | 101 |
void SetEntryCount(int32_t ln, int32_t maxln); |
| 102 |
+ |
|
| 103 |
+ /*! Sets the number of entries (probe sets). Use this function if ids are to be stored. |
|
| 104 |
+ * @param ln The number of probe sets. |
|
| 105 |
+ */ |
|
| 106 |
+ void SetEntryCount(int32_t ln); |
|
| 99 | 107 |
|
| 100 | 108 |
/*! Gets the number of entries (probe sets) */ |
| 101 | 109 |
int32_t GetEntryCount(); |
| ... | ... |
@@ -176,9 +184,9 @@ private: |
| 176 | 184 |
|
| 177 | 185 |
/*! Adds the columns to the data set. |
| 178 | 186 |
* @param hdr The data set header. |
| 179 |
- * @param maxProbeSetName The max probe set name length. |
|
| 187 |
+ * @param keyIsID True if the probe set ids are to be stored, false for probe set names. |
|
| 180 | 188 |
*/ |
| 181 |
- void AddColumns(DataSetHeader& hdr); |
|
| 189 |
+ void AddColumns(DataSetHeader& hdr, bool keyIsID); |
|
| 182 | 190 |
|
| 183 | 191 |
}; |
| 184 | 192 |
|
| ... | ... |
@@ -26,7 +26,7 @@ |
| 26 | 26 |
|
| 27 | 27 |
using namespace affymetrix_calvin_io; |
| 28 | 28 |
|
| 29 |
-#ifndef WIN32 |
|
| 29 |
+#ifndef _MSC_VER |
|
| 30 | 30 |
#include <unistd.h> |
| 31 | 31 |
#include <sys/mman.h> |
| 32 | 32 |
|
| ... | ... |
@@ -56,7 +56,7 @@ DataSet::DataSet(const std::string& fileName_, const DataSetHeader& header_, voi |
| 56 | 56 |
data = 0; |
| 57 | 57 |
isOpen = false; |
| 58 | 58 |
|
| 59 |
-#ifdef WIN32 |
|
| 59 |
+#ifdef _MSC_VER |
|
| 60 | 60 |
fileMapHandle = handle; |
| 61 | 61 |
#else |
| 62 | 62 |
fp = 0; |
| ... | ... |
@@ -80,7 +80,7 @@ DataSet::DataSet(const std::string& fileName_, const affymetrix_calvin_io::DataS |
| 80 | 80 |
data = 0; |
| 81 | 81 |
isOpen = false; |
| 82 | 82 |
|
| 83 |
-#ifdef WIN32 |
|
| 83 |
+#ifdef _MSC_VER |
|
| 84 | 84 |
fileMapHandle = 0; |
| 85 | 85 |
#else |
| 86 | 86 |
fp = 0; |
| ... | ... |
@@ -132,7 +132,7 @@ bool DataSet::Open() |
| 132 | 132 |
*/ |
| 133 | 133 |
bool DataSet::OpenMM() |
| 134 | 134 |
{
|
| 135 |
-#ifdef WIN32 |
|
| 135 |
+#ifdef _MSC_VER |
|
| 136 | 136 |
if (MapDataWin32(header.GetDataStartFilePos(), header.GetDataSize()) == false) |
| 137 | 137 |
return false; |
| 138 | 138 |
#else |
| ... | ... |
@@ -177,7 +177,7 @@ void DataSet::Close() |
| 177 | 177 |
ClearStreamData(); |
| 178 | 178 |
} |
| 179 | 179 |
|
| 180 |
-#ifdef WIN32 |
|
| 180 |
+#ifdef _MSC_VER |
|
| 181 | 181 |
|
| 182 | 182 |
std::string GetErrorMsg() |
| 183 | 183 |
{
|
| ... | ... |
@@ -289,7 +289,7 @@ bool DataSet::MapDataPosix(u_int32_t start, u_int32_t bytes) |
| 289 | 289 |
*/ |
| 290 | 290 |
void DataSet::UnmapFile() |
| 291 | 291 |
{
|
| 292 |
-#ifdef WIN32 |
|
| 292 |
+#ifdef _MSC_VER |
|
| 293 | 293 |
|
| 294 | 294 |
// Unmap the view |
| 295 | 295 |
if (mappedData != 0 ) |
| ... | ... |
@@ -383,7 +383,7 @@ char* DataSet::FilePosition(int32_t rowStart, int32_t col, int32_t rowCount) |
| 383 | 383 |
// Byte offset in data set + byte offset of data set in file |
| 384 | 384 |
u_int32_t startByte = BytesPerRow()*rowStart + columnByteOffsets[col] + header.GetDataStartFilePos(); |
| 385 | 385 |
|
| 386 |
-#ifdef WIN32 |
|
| 386 |
+#ifdef _MSC_VER |
|
| 387 | 387 |
|
| 388 | 388 |
if (useMemoryMapping) |
| 389 | 389 |
{
|
| ... | ... |
@@ -21,9 +21,6 @@ |
| 21 | 21 |
#ifndef _DataSet_HEADER_ |
| 22 | 22 |
#define _DataSet_HEADER_ |
| 23 | 23 |
|
| 24 |
-/*! \file DataSet.h This file provides access to the DataSet data. |
|
| 25 |
- */ |
|
| 26 |
- |
|
| 27 | 24 |
#include "AffymetrixBaseTypes.h" |
| 28 | 25 |
#include "AffyStlCollectionTypes.h" |
| 29 | 26 |
#include "DataSetHeader.h" |
| ... | ... |
@@ -31,7 +28,7 @@ |
| 31 | 28 |
#include <string> |
| 32 | 29 |
#include <fstream> |
| 33 | 30 |
|
| 34 |
-#ifdef WIN32 |
|
| 31 |
+#ifdef _MSC_VER |
|
| 35 | 32 |
#include <windows.h> |
| 36 | 33 |
#endif |
| 37 | 34 |
|
| ... | ... |
@@ -250,7 +247,7 @@ protected: |
| 250 | 247 |
template<typename T> void ClearAndSizeVector(std::vector<T>& values, u_int32_t size); |
| 251 | 248 |
|
| 252 | 249 |
/*! Platform specific memory-mapping method */ |
| 253 |
-#ifdef WIN32 |
|
| 250 |
+#ifdef _MSC_VER |
|
| 254 | 251 |
|
| 255 | 252 |
bool MapDataWin32(u_int32_t start, u_int32_t bytes); |
| 256 | 253 |
|
| ... | ... |
@@ -261,7 +258,7 @@ protected: |
| 261 | 258 |
#endif |
| 262 | 259 |
|
| 263 | 260 |
protected: |
| 264 |
- /*! name of the file containing the data dataGroup. */ |
|
| 261 |
+ /*! name of the file containing the data data set*. */ |
|
| 265 | 262 |
std::string fileName; |
| 266 | 263 |
|
| 267 | 264 |
/*! copy of the DataSetHeader */ |
| ... | ... |
@@ -278,7 +275,7 @@ protected: |
| 278 | 275 |
*/ |
| 279 | 276 |
Int32Vector columnByteOffsets; |
| 280 | 277 |
|
| 281 |
-#ifdef WIN32 |
|
| 278 |
+#ifdef _MSC_VER |
|
| 282 | 279 |
|
| 283 | 280 |
/*! Handle returned by CreateFileMapping */ |
| 284 | 281 |
HANDLE fileMapHandle; |
| ... | ... |
@@ -32,7 +32,7 @@ |
| 32 | 32 |
#include "ColumnInfo.h" |
| 33 | 33 |
#include "BitFlag.h" |
| 34 | 34 |
|
| 35 |
-#ifdef WIN32 |
|
| 35 |
+#ifdef _MSC_VER |
|
| 36 | 36 |
#pragma warning(disable: 4290) // don't show warnings about throw keyword on function declarations. |
| 37 | 37 |
#endif |
| 38 | 38 |
|
| ... | ... |
@@ -51,9 +51,9 @@ public: |
| 51 | 51 |
|
| 52 | 52 |
private: |
| 53 | 53 |
|
| 54 |
- /*! total rows in the dataGroup */ |
|
| 54 |
+ /*! total rows in the data set */ |
|
| 55 | 55 |
int32_t rowCount; |
| 56 |
- /*! data dataGroup name */ |
|
| 56 |
+ /*! data data set name */ |
|
| 57 | 57 |
std::wstring name; |
| 58 | 58 |
/*! name/value pairs */ |
| 59 | 59 |
ParameterNameValueTypeVector nameValParams; |
| ... | ... |
@@ -33,7 +33,7 @@ using namespace affymetrix_calvin_io; |
| 33 | 33 |
*/ |
| 34 | 34 |
GenericData::GenericData() |
| 35 | 35 |
{
|
| 36 |
-#ifdef WIN32 |
|
| 36 |
+#ifdef _MSC_VER |
|
| 37 | 37 |
fileMapHandle = NULL; |
| 38 | 38 |
fileHandle = INVALID_HANDLE_VALUE; |
| 39 | 39 |
#endif |
| ... | ... |
@@ -262,7 +262,7 @@ DataSet* GenericData::DataSet(const std::wstring& dataGroupName, const std::wstr |
| 262 | 262 |
DataSet* GenericData::CreateDataSet(DataSetHeader* dsh) |
| 263 | 263 |
{
|
| 264 | 264 |
void* handle = 0; |
| 265 |
-#ifdef WIN32 |
|
| 265 |
+#ifdef _MSC_VER |
|
| 266 | 266 |
handle = fileMapHandle; |
| 267 | 267 |
#endif |
| 268 | 268 |
ReadFullDataSetHeader(dsh); |
| ... | ... |
@@ -310,7 +310,7 @@ affymetrix_calvin_io::DataGroup GenericData::DataGroup(u_int32_t dataGroupFilePo |
| 310 | 310 |
fs.close(); |
| 311 | 311 |
|
| 312 | 312 |
void* handle = 0; |
| 313 |
-#ifdef WIN32 |
|
| 313 |
+#ifdef _MSC_VER |
|
| 314 | 314 |
handle = fileMapHandle; |
| 315 | 315 |
#endif |
| 316 | 316 |
|
| ... | ... |
@@ -465,7 +465,7 @@ void GenericData::Close() |
| 465 | 465 |
*/ |
| 466 | 466 |
bool GenericData::MapFile() |
| 467 | 467 |
{
|
| 468 |
-#ifdef WIN32 // On Windows the map is open in the GenericData object, otherwise it is opened in the DataSet |
|
| 468 |
+#ifdef _MSC_VER // On Windows the map is open in the GenericData object, otherwise it is opened in the DataSet |
|
| 469 | 469 |
if (fileHandle == INVALID_HANDLE_VALUE) |
| 470 | 470 |
{
|
| 471 | 471 |
// Create the file. |
| ... | ... |
@@ -494,7 +494,7 @@ bool GenericData::MapFile() |
| 494 | 494 |
*/ |
| 495 | 495 |
void GenericData::UnmapFile() |
| 496 | 496 |
{
|
| 497 |
-#ifdef WIN32 |
|
| 497 |
+#ifdef _MSC_VER |
|
| 498 | 498 |
|
| 499 | 499 |
if (fileHandle != INVALID_HANDLE_VALUE) |
| 500 | 500 |
{
|
| ... | ... |
@@ -35,7 +35,7 @@ |
| 35 | 35 |
#include <string> |
| 36 | 36 |
#include <vector> |
| 37 | 37 |
|
| 38 |
-#ifdef WIN32 |
|
| 38 |
+#ifdef _MSC_VER |
|
| 39 | 39 |
#include <windows.h> |
| 40 | 40 |
#endif |
| 41 | 41 |
|
| ... | ... |
@@ -231,7 +231,7 @@ protected: |
| 231 | 231 |
/*! The header and generic header objects */ |
| 232 | 232 |
affymetrix_calvin_io::FileHeader header; |
| 233 | 233 |
|
| 234 |
-#ifdef WIN32 |
|
| 234 |
+#ifdef _MSC_VER |
|
| 235 | 235 |
/*! Handle returned by CreateFileMapping */ |
| 236 | 236 |
HANDLE fileMapHandle; |
| 237 | 237 |
|
| ... | ... |
@@ -25,6 +25,7 @@ |
| 25 | 25 |
*/ |
| 26 | 26 |
|
| 27 | 27 |
#include <string> |
| 28 |
+#include "AffymetrixBaseTypes.h" |
|
| 28 | 29 |
|
| 29 | 30 |
namespace affymetrix_calvin_data |
| 30 | 31 |
{
|
| ... | ... |
@@ -35,6 +36,9 @@ typedef struct _ProbeSetSignalData |
| 35 | 36 |
/*! The name of the probe set. */ |
| 36 | 37 |
std::string name; |
| 37 | 38 |
|
| 39 |
+ /*! The probe set id. */ |
|
| 40 |
+ int32_t id; |
|
| 41 |
+ |
|
| 38 | 42 |
/*! The signal associated to the name. */ |
| 39 | 43 |
float signal; |
| 40 | 44 |
|
| ... | ... |
@@ -35,7 +35,7 @@ namespace affymetrix_calvin_exceptions |
| 35 | 35 |
class CalvinException |
| 36 | 36 |
{
|
| 37 | 37 |
protected: |
| 38 |
- /*! Source in the WIN32 use case is used for registry lookup to determine the resource file. |
|
| 38 |
+ /*! Source in the _MSC_VER use case is used for registry lookup to determine the resource file. |
|
| 39 | 39 |
The message code is used incojuction with source to lookup the specific message string based on code. |
| 40 | 40 |
*/ |
| 41 | 41 |
std::wstring sourceName; |
| ... | ... |
@@ -130,6 +130,14 @@ public: |
| 130 | 130 |
* \return The chip type of the cell. |
| 131 | 131 |
*/ |
| 132 | 132 |
virtual std::wstring GetChipType() { return calvinCel.GetArrayType(); }
|
| 133 |
+ /*! \brief Get the library package |
|
| 134 |
+ * \return library package name |
|
| 135 |
+ */ |
|
| 136 |
+ std::wstring GetLibraryPackageName() { return calvinCel.GetLibraryPackageName(); }
|
|
| 137 |
+ /*! \brief Get the master file |
|
| 138 |
+ * \return master file name |
|
| 139 |
+ */ |
|
| 140 |
+ std::wstring GetMasterFileName() { return calvinCel.GetMasterFileName(); }
|
|
| 133 | 141 |
/*! \brief Get cell margin. |
| 134 | 142 |
\return The cell margin. |
| 135 | 143 |
*/ |
| ... | ... |
@@ -236,6 +236,24 @@ std::wstring FusionCELData::GetChipType() |
| 236 | 236 |
return adapter->GetChipType(); |
| 237 | 237 |
} |
| 238 | 238 |
|
| 239 |
+/* |
|
| 240 |
+ * Get the library package |
|
| 241 |
+ */ |
|
| 242 |
+std::wstring FusionCELData::GetLibraryPackageName() |
|
| 243 |
+{
|
|
| 244 |
+ CheckAdapter(); |
|
| 245 |
+ return adapter->GetLibraryPackageName(); |
|
| 246 |
+} |
|
| 247 |
+ |
|
| 248 |
+/* |
|
| 249 |
+ * Get the master file |
|
| 250 |
+ */ |
|
| 251 |
+std::wstring FusionCELData::GetMasterFileName() |
|
| 252 |
+{
|
|
| 253 |
+ CheckAdapter(); |
|
| 254 |
+ return adapter->GetMasterFileName(); |
|
| 255 |
+} |
|
| 256 |
+ |
|
| 239 | 257 |
/* |
| 240 | 258 |
* Retrieve cell margin. |
| 241 | 259 |
*/ |
| ... | ... |
@@ -151,6 +151,16 @@ public: |
| 151 | 151 |
*/ |
| 152 | 152 |
std::wstring GetChipType(); |
| 153 | 153 |
|
| 154 |
+ /*! Get the library package |
|
| 155 |
+ * @return library package name (blank for GCOS format CEL files) |
|
| 156 |
+ */ |
|
| 157 |
+ std::wstring GetLibraryPackageName(); |
|
| 158 |
+ |
|
| 159 |
+ /*! Get the master file |
|
| 160 |
+ * @return master file name (blank for GCOS format CEL files) |
|
| 161 |
+ */ |
|
| 162 |
+ std::wstring GetMasterFileName(); |
|
| 163 |
+ |
|
| 154 | 164 |
/*! Retrieve cell margin |
| 155 | 165 |
* @return Cell margin |
| 156 | 166 |
*/ |
| ... | ... |
@@ -142,6 +142,14 @@ public: |
| 142 | 142 |
* \return The chip type of the cell. |
| 143 | 143 |
*/ |
| 144 | 144 |
virtual std::wstring GetChipType() = 0; |
| 145 |
+ /*! \brief Get the master file |
|
| 146 |
+ * \return master file name |
|
| 147 |
+ */ |
|
| 148 |
+ virtual std::wstring GetMasterFileName() = 0; |
|
| 149 |
+ /*! \brief Get the library package |
|
| 150 |
+ * \return library package name |
|
| 151 |
+ */ |
|
| 152 |
+ virtual std::wstring GetLibraryPackageName() = 0; |
|
| 145 | 153 |
/*! \brief Get cell margin. |
| 146 | 154 |
\return The cell margin. |
| 147 | 155 |
*/ |
| ... | ... |
@@ -132,6 +132,14 @@ public: |
| 132 | 132 |
* \return The chip type of the cell. |
| 133 | 133 |
*/ |
| 134 | 134 |
virtual std::wstring GetChipType(); |
| 135 |
+ /*! \brief Get the library package |
|
| 136 |
+ * \return blank value |
|
| 137 |
+ */ |
|
| 138 |
+ virtual std::wstring GetLibraryPackageName() { return L""; }
|
|
| 139 |
+ /*! \brief Get the master file |
|
| 140 |
+ * \return blank value |
|
| 141 |
+ */ |
|
| 142 |
+ virtual std::wstring GetMasterFileName() { return L""; }
|
|
| 135 | 143 |
/*! \brief Get cell margin. |
| 136 | 144 |
\return The cell margin. |
| 137 | 145 |
*/ |
| ... | ... |
@@ -29,6 +29,12 @@ namespace affymetrix_calvin_parameter |
| 29 | 29 |
/*! Defines the static attribute name for the probe array type of the physical array. */ |
| 30 | 30 |
#define ARRAY_TYPE_PARAM_NAME L"affymetrix-array-type" |
| 31 | 31 |
|
| 32 |
+/*! Defines the static attribute name for the master file. */ |
|
| 33 |
+#define MASTER_FILE_PARAM_NAME L"affymetrix-master-file" |
|
| 34 |
+ |
|
| 35 |
+/*! Defines the static attribute name for the library package. */ |
|
| 36 |
+#define LIBRARY_PACKAGE_PARAM_NAME L"affymetrix-library-package" |
|
| 37 |
+ |
|
| 32 | 38 |
/*! Defines the number of characters to reserve in the parameter list for the array type name */ |
| 33 | 39 |
#define ARRAY_TYPE_MAX_LEN 100 |
| 34 | 40 |
|
| 37 | 37 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,48 @@ |
| 1 |
+///////////////////////////////////////////////////////////////// |
|
| 2 |
+// |
|
| 3 |
+// Copyright (C) 2006 Affymetrix, Inc. |
|
| 4 |
+// |
|
| 5 |
+// This library is free software; you can redistribute it and/or modify |
|
| 6 |
+// it under the terms of the GNU Lesser General Public License as published |
|
| 7 |
+// by the Free Software Foundation; either version 2.1 of the License, |
|
| 8 |
+// or (at your option) any later version. |
|
| 9 |
+// |
|
| 10 |
+// This library is distributed in the hope that it will be useful, but |
|
| 11 |
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY |
|
| 12 |
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License |
|
| 13 |
+// for more details. |
|
| 14 |
+// |
|
| 15 |
+// You should have received a copy of the GNU Lesser General Public License |
|
| 16 |
+// along with this library; if not, write to the Free Software Foundation, Inc., |
|
| 17 |
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
|
| 18 |
+// |
|
| 19 |
+///////////////////////////////////////////////////////////////// |
|
| 20 |
+ |
|
| 21 |
+#include "ParameterFileData.h" |
|
| 22 |
+ |
|
| 23 |
+using namespace affymetrix_calvin_parameter; |
|
| 24 |
+ |
|
| 25 |
+/* |
|
| 26 |
+ * Clear the members. |
|
| 27 |
+ */ |
|
| 28 |
+ParameterFileData::ParameterFileData() |
|
| 29 |
+{
|
|
| 30 |
+ Clear(); |
|
| 31 |
+} |
|
| 32 |
+ |
|
| 33 |
+/* |
|
| 34 |
+ * Clear the members. |
|
| 35 |
+ */ |
|
| 36 |
+void ParameterFileData::Clear() |
|
| 37 |
+{
|
|
| 38 |
+ parameters.clear(); |
|
| 39 |
+ |
|
| 40 |
+ parameterFileAttributes.company.clear(); |
|
| 41 |
+ parameterFileAttributes.userName.clear(); |
|
| 42 |
+ parameterFileAttributes.contentVersion.clear(); |
|
| 43 |
+ |
|
| 44 |
+ implementationAttributes.name.clear(); |
|
| 45 |
+ implementationAttributes.version.clear(); |
|
| 46 |
+ implementationAttributes.executableFileName.clear(); |
|
| 47 |
+ implementationAttributes.description.clear(); |
|
| 48 |
+} |
| 0 | 49 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,107 @@ |
| 1 |
+///////////////////////////////////////////////////////////////// |
|
| 2 |
+// |
|
| 3 |
+// Copyright (C) 2006 Affymetrix, Inc. |
|
| 4 |
+// |
|
| 5 |
+// This library is free software; you can redistribute it and/or modify |
|
| 6 |
+// it under the terms of the GNU Lesser General Public License as published |
|
| 7 |
+// by the Free Software Foundation; either version 2.1 of the License, |
|
| 8 |
+// or (at your option) any later version. |
|
| 9 |
+// |
|
| 10 |
+// This library is distributed in the hope that it will be useful, but |
|
| 11 |
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY |
|
| 12 |
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License |
|
| 13 |
+// for more details. |
|
| 14 |
+// |
|
| 15 |
+// You should have received a copy of the GNU Lesser General Public License |
|
| 16 |
+// along with this library; if not, write to the Free Software Foundation, Inc., |
|
| 17 |
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
|
| 18 |
+// |
|
| 19 |
+///////////////////////////////////////////////////////////////// |
|
| 20 |
+ |
|
| 21 |
+#ifndef _ParameterFileData_HEADER_ |
|
| 22 |
+#define _ParameterFileData_HEADER_ |
|
| 23 |
+ |
|
| 24 |
+/*! \file ParameterFileData.h This file provides definitions for data in a parameter file. |
|
| 25 |
+ */ |
|
| 26 |
+ |
|
| 27 |
+#include <string> |
|
| 28 |
+#include <list> |
|
| 29 |
+ |
|
| 30 |
+namespace affymetrix_calvin_parameter |
|
| 31 |
+{
|
|
| 32 |
+ |
|
| 33 |
+/*! The attributes in the ParameterFile element. */ |
|
| 34 |
+typedef struct _ParameterFileAttributesType |
|
| 35 |
+{
|
|
| 36 |
+ std::wstring company; /*! The company name. */ |
|
| 37 |
+ std::wstring userName; /*! The user name. */ |
|
| 38 |
+ std::wstring contentVersion; /*! The content version. */ |
|
| 39 |
+} ParameterFileAttributesType; |
|
| 40 |
+ |
|
| 41 |
+/*! The attributes in the Implementation element. */ |
|
| 42 |
+typedef struct _ImplementationAttributesType |
|
| 43 |
+{
|
|
| 44 |
+ std::wstring name; /*! The name. */ |
|
| 45 |
+ std::wstring version; /*! The version number. */ |
|
| 46 |
+ std::wstring executableFileName; /*! The exe file name. */ |
|
| 47 |
+ std::wstring description; /*! The description */ |
|
| 48 |
+} ImplementationAttributesType; |
|
| 49 |
+ |
|
| 50 |
+/*! The attributes in the Parameter element. */ |
|
| 51 |
+typedef struct _ParameterType |
|
| 52 |
+{
|
|
| 53 |
+ std::wstring name; /*! The name. */ |
|
| 54 |
+ std::wstring index; /*! The index. */ |
|
| 55 |
+ std::wstring displayName; /*! The display name. */ |
|
| 56 |
+ std::wstring category; /*! The category. */ |
|
| 57 |
+ std::wstring isEditable; /*! The idEditable flag */ |
|
| 58 |
+ std::wstring type; /*! The type */ |
|
| 59 |
+ std::wstring currentValue; /*! The current value */ |
|
| 60 |
+ std::wstring minValue; /*! The minimum value */ |
|
| 61 |
+ std::wstring maxValue; /*! The maximum value */ |
|
| 62 |
+ std::wstring defaultValue; /*! The default value */ |
|
| 63 |
+ std::wstring precision; /*! The precision for floating point numbers */ |
|
| 64 |
+ std::wstring maxLength; /*! The maximum length of a string value */ |
|
| 65 |
+ std::wstring description; /*! The description */ |
|
| 66 |
+} ParameterType; |
|
| 67 |
+ |
|
| 68 |
+/*! A list of parameters. */ |
|
| 69 |
+typedef std::list<ParameterType> ParameterTypeList; |
|
| 70 |
+ |
|
| 71 |
+/*! Provides data storage for ParameterFile files. This version |
|
| 72 |
+ does not store all of the contents of a parameter file. |
|
| 73 |
+ Missing items includes the ParameterSet, MetaData and Control |
|
| 74 |
+ elements. |
|
| 75 |
+*/ |
|
| 76 |
+class ParameterFileData |
|
| 77 |
+{
|
|
| 78 |
+public: |
|
| 79 |
+ /*! Clears the members in the class. */ |
|
| 80 |
+ void Clear(); |
|
| 81 |
+ |
|
| 82 |
+ /*! Constructor. */ |
|
| 83 |
+ ParameterFileData(); |
|
| 84 |
+ |
|
| 85 |
+ /*! The parameter file attributes. */ |
|
| 86 |
+ ParameterFileAttributesType &ParameterFileAttributes() { return parameterFileAttributes; }
|
|
| 87 |
+ |
|
| 88 |
+ /*! The implementation attributes. */ |
|
| 89 |
+ ImplementationAttributesType &ImplementationAttributes() { return implementationAttributes; }
|
|
| 90 |
+ |
|
| 91 |
+ /*! The list of parameters. */ |
|
| 92 |
+ ParameterTypeList &Parameters() { return parameters; }
|
|
| 93 |
+ |
|
| 94 |
+private: |
|
| 95 |
+ /*! The parameter file attributes. */ |
|
| 96 |
+ ParameterFileAttributesType parameterFileAttributes; |
|
| 97 |
+ |
|
| 98 |
+ /*! The implementation attributes. */ |
|
| 99 |
+ ImplementationAttributesType implementationAttributes; |
|
| 100 |
+ |
|
| 101 |
+ /*! The list of parameters. */ |
|
| 102 |
+ ParameterTypeList parameters; |
|
| 103 |
+}; |
|
| 104 |
+ |
|
| 105 |
+} |
|
| 106 |
+ |
|
| 107 |
+#endif // _ParameterFileData_HEADER_ |
| 39 | 39 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,89 @@ |
| 1 |
+///////////////////////////////////////////////////////////////// |
|
| 2 |
+// |
|
| 3 |
+// Copyright (C) 2006 Affymetrix, Inc. |
|
| 4 |
+// |
|
| 5 |
+// This library is free software; you can redistribute it and/or modify |
|
| 6 |
+// it under the terms of the GNU Lesser General Public License as published |
|
| 7 |
+// by the Free Software Foundation; either version 2.1 of the License, |
|
| 8 |
+// or (at your option) any later version. |
|
| 9 |
+// |
|
| 10 |
+// This library is distributed in the hope that it will be useful, but |
|
| 11 |
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY |
|
| 12 |
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License |
|
| 13 |
+// for more details. |
|
| 14 |
+// |
|
| 15 |
+// You should have received a copy of the GNU Lesser General Public License |
|
| 16 |
+// along with this library; if not, write to the Free Software Foundation, Inc., |
|
| 17 |
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
|
| 18 |
+// |
|
| 19 |
+///////////////////////////////////////////////////////////////// |
|
| 20 |
+ |
|
| 21 |
+#include "ParameterFileReader.h" |
|
| 22 |
+#include "SAXParameterFileHandlers.h" |
|
| 23 |
+#include <xercesc/util/PlatformUtils.hpp> |
|
| 24 |
+#include <xercesc/parsers/SAXParser.hpp> |
|
| 25 |
+#include <sys/stat.h> |
|
| 26 |
+#include <sys/types.h> |
|
| 27 |
+ |
|
| 28 |
+using namespace affymetrix_calvin_io; |
|
| 29 |
+using namespace affymetrix_calvin_parameter; |
|
| 30 |
+XERCES_CPP_NAMESPACE_USE; |
|
| 31 |
+ |
|
| 32 |
+/* |
|
| 33 |
+ * Initialize the class. |
|
| 34 |
+ */ |
|
| 35 |
+ParameterFileReader::ParameterFileReader() |
|
| 36 |
+{
|
|
| 37 |
+} |
|
| 38 |
+ |
|
| 39 |
+/* |
|
| 40 |
+ * Clear the data. |
|
| 41 |
+ */ |
|
| 42 |
+ParameterFileReader::~ParameterFileReader() |
|
| 43 |
+{
|
|
| 44 |
+} |
|
| 45 |
+ |
|
| 46 |
+/* |
|
| 47 |
+ * Read the entire file using the XML SAX parser. |
|
| 48 |
+ */ |
|
| 49 |
+bool ParameterFileReader::Read(const std::string &fileName, ParameterFileData ¶meterFileData) |
|
| 50 |
+{
|
|
| 51 |
+ parameterFileData.Clear(); |
|
| 52 |
+ |
|
| 53 |
+ // Initialize the XML4C2 system |
|
| 54 |
+ try |
|
| 55 |
+ {
|
|
| 56 |
+ XMLPlatformUtils::Initialize(); |
|
| 57 |
+ } |
|
| 58 |
+ catch (const XMLException&) |
|
| 59 |
+ {
|
|
| 60 |
+ return false; |
|
| 61 |
+ } |
|
| 62 |
+ |
|
| 63 |
+ bool status = false; |
|
| 64 |
+ SAXParser* parser = new SAXParser; |
|
| 65 |
+ parser->setValidationScheme(SAXParser::Val_Never); |
|
| 66 |
+ parser->setLoadExternalDTD(false); |
|
| 67 |
+ parser->setDoNamespaces(false); |
|
| 68 |
+ parser->setDoSchema(false); |
|
| 69 |
+ parser->setValidationSchemaFullChecking(false); |
|
| 70 |
+ SAXParameterFileHandlers handler(¶meterFileData); |
|
| 71 |
+ parser->setDocumentHandler(&handler); |
|
| 72 |
+ parser->setErrorHandler(&handler); |
|
| 73 |
+ try |
|
| 74 |
+ {
|
|
| 75 |
+ parser->parse(fileName.c_str()); |
|
| 76 |
+ int errorCount = parser->getErrorCount(); |
|
| 77 |
+ if (errorCount == 0) |
|
| 78 |
+ {
|
|
| 79 |
+ status = true; |
|
| 80 |
+ } |
|
| 81 |
+ } |
|
| 82 |
+ catch (...) |
|
| 83 |
+ {
|
|
| 84 |
+ status = false; |
|
| 85 |
+ } |
|
| 86 |
+ delete parser; |
|
| 87 |
+ XMLPlatformUtils::Terminate(); |
|
| 88 |
+ return status; |
|
| 89 |
+} |
| 0 | 90 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,59 @@ |
| 1 |
+///////////////////////////////////////////////////////////////// |
|
| 2 |
+// |
|
| 3 |
+// Copyright (C) 2006 Affymetrix, Inc. |
|
| 4 |
+// |
|
| 5 |
+// This library is free software; you can redistribute it and/or modify |
|
| 6 |
+// it under the terms of the GNU Lesser General Public License as published |
|
| 7 |
+// by the Free Software Foundation; either version 2.1 of the License, |
|
| 8 |
+// or (at your option) any later version. |
|
| 9 |
+// |
|
| 10 |
+// This library is distributed in the hope that it will be useful, but |
|
| 11 |
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY |
|
| 12 |
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License |
|
| 13 |
+// for more details. |
|
| 14 |
+// |
|
| 15 |
+// You should have received a copy of the GNU Lesser General Public License |
|
| 16 |
+// along with this library; if not, write to the Free Software Foundation, Inc., |
|
| 17 |
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
|
| 18 |
+// |
|
| 19 |
+///////////////////////////////////////////////////////////////// |
|
| 20 |
+ |
|
| 21 |
+#ifndef _ParameterFileReader_HEADER_ |
|
| 22 |
+#define _ParameterFileReader_HEADER_ |
|
| 23 |
+ |
|
| 24 |
+/*! \file ParameterFileReader.h This file provides interfaces to read a parameter file. |
|
| 25 |
+ */ |
|
| 26 |
+ |
|
| 27 |
+#include "ParameterFileData.h" |
|
| 28 |
+#include <string> |
|
| 29 |
+#include <fstream> |
|
| 30 |
+ |
|
| 31 |
+namespace affymetrix_calvin_io |
|
| 32 |
+{
|
|
| 33 |
+ |
|
| 34 |
+/*! This class provides interfaces to read a parameter file. This version |
|
| 35 |
+ does not store all of the contents of a parameter file. |
|
| 36 |
+ Missing items includes the ParameterSet, MetaData and Control |
|
| 37 |
+ elements. |
|
| 38 |
+*/ |
|
| 39 |
+class ParameterFileReader |
|
| 40 |
+{
|
|
| 41 |
+public: |
|
| 42 |
+ /*! Constructor */ |
|
| 43 |
+ ParameterFileReader(); |
|
| 44 |
+ |
|
| 45 |
+ /*! Destructor */ |
|
| 46 |
+ ~ParameterFileReader(); |
|
| 47 |
+ |
|
| 48 |
+public: |
|
| 49 |
+ /*! Reads the entire contents of the file. |
|
| 50 |
+ * |
|
| 51 |
+ * @param fileName The name of the parameter file to read. |
|
| 52 |
+ * @param parameterData The parameter data from the input file. |
|
| 53 |
+ */ |
|
| 54 |
+ bool Read(const std::string &fileName, affymetrix_calvin_parameter::ParameterFileData ¶meterFileData); |
|
| 55 |
+}; |
|
| 56 |
+ |
|
| 57 |
+}; |
|
| 58 |
+ |
|
| 59 |
+#endif // _ParameterFileReader_HEADER_ |
| 37 | 37 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,231 @@ |
| 1 |
+///////////////////////////////////////////////////////////////// |
|
| 2 |
+// |
|
| 3 |
+// Copyright (C) 2006 Affymetrix, Inc. |
|
| 4 |
+// |
|
| 5 |
+// This library is free software; you can redistribute it and/or modify |
|
| 6 |
+// it under the terms of the GNU Lesser General Public License as published |
|
| 7 |
+// by the Free Software Foundation; either version 2.1 of the License, |
|
| 8 |
+// or (at your option) any later version. |
|
| 9 |
+// |
|
| 10 |
+// This library is distributed in the hope that it will be useful, but |
|
| 11 |
+// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY |
|
| 12 |
+// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License |
|
| 13 |
+// for more details. |
|
| 14 |
+// |
|
| 15 |
+// You should have received a copy of the GNU Lesser General Public License |
|
| 16 |
+// along with this library; if not, write to the Free Software Foundation, Inc., |
|
| 17 |
+// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
|
| 18 |
+// |
|
| 19 |
+///////////////////////////////////////////////////////////////// |
|
| 20 |
+ |
|
| 21 |
+#include "SAXParameterFileHandlers.h" |
|
| 22 |
+#include "StringUtils.h" |
|
| 23 |
+#include <string> |
|
| 24 |
+#include <map> |
|
| 25 |
+ |
|
| 26 |
+using namespace affymetrix_calvin_io; |
|
| 27 |
+using namespace affymetrix_calvin_parameter; |
|
| 28 |
+using namespace affymetrix_calvin_utilities; |
|
| 29 |
+using namespace std; |
|
| 30 |
+XERCES_CPP_NAMESPACE_USE; |
|
| 31 |
+ |
|
| 32 |
+#ifdef _MSC_VER |
|
| 33 |
+#pragma warning(disable: 4996) // don't show deprecated warnings. |
|
| 34 |