Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
Showing1 changed files
1 1
deleted file mode 100644
... ...
@@ -1,440 +0,0 @@
1
-#include "RcppRamp.h"
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-
3
-RcppRamp::RcppRamp()
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-{
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-    ramp = NULL;
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-    runInfo = Rcpp::List::create( );
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-    isInCacheRunInfo = FALSE;
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-    instrumentInfo = Rcpp::List::create( );
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-    isInCacheInstrumentInfo = FALSE;
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-    allScanHeaderInfo = Rcpp::DataFrame::create( );
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-    isInCacheAllScanHeaderInfo = FALSE;
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-    filename = Rcpp::StringVector::create( );
13
-}
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-
15
-RcppRamp::~RcppRamp()
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-{
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-    RcppRamp::close();
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-}
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-
20
-void RcppRamp::open( const char* fileName, bool declaredScansOnly )
21
-{
22
-    RcppRamp::close();
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-    ramp = new cRamp(fileName, declaredScansOnly);
24
-    if (ramp->OK())
25
-    {
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-        filename = Rcpp::StringVector::create( fileName );
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-    }
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-    else
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-    {
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-        RcppRamp::close();
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-        Rprintf("Failed to open file.\n ");
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-    }
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-}
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-
35
-void RcppRamp::close()
36
-{
37
-    if (ramp != NULL)
38
-    {
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-        delete ramp;
40
-        ramp = NULL;
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-        runInfo = Rcpp::List::create( );
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-        isInCacheRunInfo = FALSE;
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-        instrumentInfo = Rcpp::List::create( );
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-        isInCacheInstrumentInfo = FALSE;
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-        allScanHeaderInfo = Rcpp::List::create( );
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-        isInCacheAllScanHeaderInfo = FALSE;
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-        filename = Rcpp::StringVector::create( );
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-    }
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-}
50
-
51
-
52
-Rcpp::StringVector RcppRamp::getFilename (  )
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-{
54
-    if (ramp != NULL)
55
-    {
56
-        return filename;
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-    }
58
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
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-    return filename;
60
-}
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-
62
-Rcpp::List RcppRamp::getRunInfo (  )
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-{
64
-    if (ramp != NULL)
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-    {
66
-        if (!isInCacheRunInfo)
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-        {
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-            // Rprintf("Read from disk.\n ");
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-            rampRunInfo *info = ramp->getRunInfo();
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-            RunHeaderStruct data = info->m_data;
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-            delete info;
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-            runInfo = Rcpp::List::create(
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-                          Rcpp::_["scanCount"]  = data.scanCount,
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-                          Rcpp::_["lowMZ"]      = data.lowMZ,
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-                          Rcpp::_["highMZ"]     = data.highMZ,
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-                          Rcpp::_["startMZ"]    = data.startMZ,
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-                          Rcpp::_["endMZ"]      = data.endMZ,
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-                          Rcpp::_["dStartTime"] = data.dStartTime,
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-                          Rcpp::_["dEndTime"]   = data.dEndTime
80
-                      );
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-            isInCacheRunInfo = TRUE;
82
-        }
83
-        else
84
-        {
85
-            // Rprintf("Read from cache.\n ");
86
-        }
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-        return runInfo;
88
-    }
89
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
90
-    return runInfo;
91
-}
92
-
93
-Rcpp::List RcppRamp::getInstrumentInfo ( )
94
-{
95
-    if (ramp != NULL)
96
-    {
97
-        if (!isInCacheInstrumentInfo)
98
-        {
99
-            // Rprintf("Read from disk.\n ");
100
-            rampInstrumentInfo *info = ramp->getInstrumentInfo(); // NULL for mzData
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-
102
-            if (info != NULL)
103
-            {
104
-                InstrumentStruct * data = info->m_instrumentStructPtr;
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-
106
-                instrumentInfo = Rcpp::List::create(
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-                                     Rcpp::_["manufacturer"]  = std::string(data->manufacturer),
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-                                     Rcpp::_["model"]         = std::string(data->model),
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-                                     Rcpp::_["ionisation"]    = std::string(data->ionisation),
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-                                     Rcpp::_["analyzer"]      = std::string(data->analyzer),
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-                                     Rcpp::_["detector"]      = std::string(data->detector)
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-                                 ) ;
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-                delete info;
114
-            }
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-            else
116
-            {
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-                instrumentInfo = Rcpp::List::create(
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-                                     Rcpp::_["manufacturer"]  = "",
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-                                     Rcpp::_["model"]         = "",
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-                                     Rcpp::_["ionisation"]    = "",
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-                                     Rcpp::_["analyzer"]      = "",
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-                                     Rcpp::_["detector"]      = ""
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-                                 ) ;
124
-            }
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-            isInCacheInstrumentInfo = TRUE;
126
-        }
127
-        else
128
-        {
129
-            // Rprintf("Read from cache.\n ");
130
-        }
131
-        return(instrumentInfo);
132
-    }
133
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
134
-    return instrumentInfo;
135
-}
136
-
137
-Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )
138
-{
139
-    if (ramp != NULL)
140
-    {
141
-        if ((whichScan <= 0) || (whichScan > ramp->getLastScan()))
142
-        {
143
-            Rprintf("Index whichScan out of bounds [1 ... %d].\n", ramp->getLastScan());
144
-            return Rcpp::List::create( );
145
-        }
146
-        rampScanInfo *info = ramp->getScanHeaderInfo( whichScan );
147
-        ScanHeaderStruct data = info->m_data;
148
-        delete info;
149
-
150
-        std::vector<std::string> names;
151
-        Rcpp::List header(22);
152
-        int i = 0;
153
-
154
-        names.push_back("seqNum");
155
-        header[i++] = Rcpp::wrap(data.seqNum);
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-        names.push_back("acquisitionNum");
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-        header[i++] = Rcpp::wrap(data.acquisitionNum);
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-        names.push_back("msLevel");
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-        header[i++] = Rcpp::wrap(data.msLevel);
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-        names.push_back("polarity");
161
-        header[i++] = Rcpp::wrap(data.polarity);
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-        names.push_back("peaksCount");
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-        header[i++] = Rcpp::wrap(data.peaksCount);
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-        names.push_back("totIonCurrent");
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-        header[i++] = Rcpp::wrap(data.totIonCurrent);
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-        names.push_back("retentionTime");
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-        header[i++] = Rcpp::wrap(data.retentionTime);
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-        names.push_back("basePeakMZ");
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-        header[i++] = Rcpp::wrap(data.basePeakMZ);
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-        names.push_back("basePeakIntensity");
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-        header[i++] = Rcpp::wrap(data.basePeakIntensity);
172
-        names.push_back("collisionEnergy");
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-        header[i++] = Rcpp::wrap(data.collisionEnergy);
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-        names.push_back("ionisationEnergy");
175
-        header[i++] = Rcpp::wrap(data.ionisationEnergy);
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-        names.push_back("lowMZ");
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-        header[i++] = Rcpp::wrap(data.lowMZ);
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-        names.push_back("highMZ");
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-        header[i++] = Rcpp::wrap(data.highMZ);
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-        names.push_back("precursorScanNum");
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-        header[i++] = Rcpp::wrap(data.precursorScanNum);
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-        names.push_back("precursorMZ");
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-        header[i++] = Rcpp::wrap(data.precursorMZ);
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-        names.push_back("precursorCharge");
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-        header[i++] = Rcpp::wrap(data.precursorCharge);
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-        names.push_back("precursorIntensity");
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-        header[i++] = Rcpp::wrap(data.precursorIntensity);
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-        names.push_back("mergedScan");
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-        header[i++] = Rcpp::wrap(data.mergedScan);
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-        names.push_back("mergedResultScanNum");
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-        header[i++] = Rcpp::wrap(data.mergedResultScanNum);
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-        names.push_back("mergedResultStartScanNum");
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-        header[i++] = Rcpp::wrap(data.mergedResultStartScanNum);
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-        names.push_back("mergedResultEndScanNum");
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-        header[i++] = Rcpp::wrap(data.mergedResultEndScanNum);
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-        names.push_back("injectionTime");
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-        header[i++] = 0;
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-
199
-        header.attr("names") = names;
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-
201
-        return  header;
202
-    }
203
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
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-    return Rcpp::List::create( );
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-}
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-
207
-Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
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-{
209
-    if (ramp != NULL)
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-    {
211
-        if (!isInCacheAllScanHeaderInfo)
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-        {
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-            // Rprintf("Read from disk.\n ");
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-            int N = ramp->getLastScan();
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-            rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
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-            ScanHeaderStruct scanHeader;
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-            Rcpp::IntegerVector seqNum(N); // number in sequence observed file (1-based)
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-            Rcpp::IntegerVector acquisitionNum(N); // scan number as declared in File (may be gaps)
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-            Rcpp::IntegerVector  msLevel(N);
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-            Rcpp::IntegerVector  polarity(N);
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-            Rcpp::IntegerVector  peaksCount(N);
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-            Rcpp::NumericVector totIonCurrent(N);
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-            Rcpp::NumericVector retentionTime(N);        /* in seconds */
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-            Rcpp::NumericVector basePeakMZ(N);
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-            Rcpp::NumericVector basePeakIntensity(N);
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-            Rcpp::NumericVector collisionEnergy(N);
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-            Rcpp::NumericVector ionisationEnergy(N);
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-            Rcpp::NumericVector lowMZ(N);
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-            Rcpp::NumericVector highMZ(N);
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-            Rcpp::IntegerVector precursorScanNum(N); /* only if MS level > 1 */
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-            Rcpp::NumericVector precursorMZ(N);  /* only if MS level > 1 */
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-            Rcpp::IntegerVector precursorCharge(N);  /* only if MS level > 1 */
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-            Rcpp::NumericVector precursorIntensity(N);  /* only if MS level > 1 */
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-            Rcpp::IntegerVector mergedScan(N);  /* only if MS level > 1 */
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-            Rcpp::IntegerVector mergedResultScanNum(N); /* scan number of the resultant merged scan */
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-            Rcpp::IntegerVector mergedResultStartScanNum(N); /* smallest scan number of the scanOrigin for merged scan */
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-            Rcpp::IntegerVector mergedResultEndScanNum(N); /* largest scan number of the scanOrigin for merged scan */
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-
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-            for (int whichScan=1; whichScan <= N; whichScan++)
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-            {
241
-                readHeader(ramp->m_handle, ramp->m_scanOffsets[whichScan], &scanHeader);
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-                seqNum[whichScan-1] = scanHeader.seqNum;
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-                acquisitionNum[whichScan-1] = scanHeader.acquisitionNum;
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-                msLevel[whichScan-1] = scanHeader.msLevel;
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-                polarity[whichScan-1] = scanHeader.polarity;
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-                peaksCount[whichScan-1] = scanHeader.peaksCount;
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-                totIonCurrent[whichScan-1] = scanHeader.totIonCurrent;
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-                retentionTime[whichScan-1] = scanHeader.retentionTime;
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-                basePeakMZ[whichScan-1] = scanHeader.basePeakMZ;
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-                basePeakIntensity[whichScan-1] = scanHeader.basePeakIntensity;
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-                collisionEnergy[whichScan-1] = scanHeader.collisionEnergy;
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-                ionisationEnergy[whichScan-1] = scanHeader.ionisationEnergy;
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-                lowMZ[whichScan-1] = scanHeader.lowMZ;
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-                highMZ[whichScan-1] = scanHeader.highMZ;
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-                precursorScanNum[whichScan-1] = scanHeader.precursorScanNum;
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-                precursorMZ[whichScan-1] = scanHeader.precursorMZ;
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-                precursorCharge[whichScan-1] = scanHeader.precursorCharge;
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-                precursorIntensity[whichScan-1] = scanHeader.precursorIntensity;
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-                mergedScan[whichScan-1] = scanHeader.mergedScan;
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-                mergedResultScanNum[whichScan-1] = scanHeader.mergedResultScanNum;
261
-                mergedResultStartScanNum[whichScan-1] = scanHeader.mergedResultStartScanNum;
262
-                mergedResultEndScanNum[whichScan-1] = scanHeader.mergedResultEndScanNum;
263
-            }
264
-
265
-            Rcpp::List header(22);
266
-            std::vector<std::string> names;
267
-            int i = 0;
268
-
269
-            names.push_back("seqNum");
270
-            header[i++] =Rcpp::wrap(seqNum);
271
-            names.push_back("acquisitionNum");
272
-            header[i++] =Rcpp::wrap( acquisitionNum);
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-            names.push_back("msLevel");
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-            header[i++] =Rcpp::wrap(msLevel);
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-            names.push_back("polarity");
276
-            header[i++] =Rcpp::wrap(polarity);
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-            names.push_back("peaksCount");
278
-            header[i++] =Rcpp::wrap(peaksCount);
279
-            names.push_back("totIonCurrent");
280
-            header[i++] =Rcpp::wrap(totIonCurrent);
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-            names.push_back("retentionTime");
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-            header[i++] =Rcpp::wrap(retentionTime);
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-            names.push_back("basePeakMZ");
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-            header[i++] =Rcpp::wrap(basePeakMZ);
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-            names.push_back("basePeakIntensity");
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-            header[i++] =Rcpp::wrap(basePeakIntensity);
287
-            names.push_back("collisionEnergy");
288
-            header[i++] =Rcpp::wrap(collisionEnergy);
289
-            names.push_back("ionisationEnergy");
290
-            header[i++] =Rcpp::wrap(ionisationEnergy);
291
-            names.push_back("lowMZ");
292
-            header[i++] =Rcpp::wrap(lowMZ);
293
-            names.push_back("highMZ");
294
-            header[i++] =Rcpp::wrap(highMZ);
295
-            names.push_back("precursorScanNum");
296
-            header[i++] =Rcpp::wrap(precursorScanNum);
297
-            names.push_back("precursorMZ");
298
-            header[i++] =Rcpp::wrap(precursorMZ);
299
-            names.push_back("precursorCharge");
300
-            header[i++] =Rcpp::wrap(precursorCharge);
301
-            names.push_back("precursorIntensity");
302
-            header[i++] =Rcpp::wrap(precursorIntensity);
303
-            names.push_back("mergedScan");
304
-            header[i++] =Rcpp::wrap(mergedScan);
305
-            names.push_back("mergedResultScanNum");
306
-            header[i++] =Rcpp::wrap(mergedResultScanNum);
307
-            names.push_back("mergedResultStartScanNum");
308
-            header[i++] =Rcpp::wrap(mergedResultStartScanNum);
309
-            names.push_back("mergedResultEndScanNum");
310
-            header[i++] =Rcpp::wrap(mergedResultEndScanNum);
311
-            names.push_back("injectionTime");
312
-            header[i++] = 0;
313
-            
314
-			header.attr("names") = names;
315
-			
316
-            allScanHeaderInfo = header;
317
-            isInCacheAllScanHeaderInfo = TRUE;
318
-        }
319
-        else
320
-        {
321
-            // Rprintf("Read from cache.\n ");
322
-        }
323
-        return(allScanHeaderInfo);
324
-    }
325
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
326
-    return Rcpp::DataFrame::create( );
327
-}
328
-
329
-Rcpp::List RcppRamp::getPeakList ( int whichScan )
330
-{
331
-    if (ramp != NULL)
332
-    {
333
-        if ((whichScan <= 0) || (whichScan > ramp->getLastScan()))
334
-        {
335
-            Rprintf("Index whichScan out of bounds [1 ... %d].\n", ramp->getLastScan());
336
-            return Rcpp::List::create( );
337
-        }
338
-        rampPeakList *pl = ramp->getPeakList( whichScan );
339
-        int peaksCount = 0;
340
-        if (pl != NULL)
341
-        {
342
-            peaksCount = pl->getPeakCount();
343
-        }
344
-        Rcpp::NumericMatrix peaks(peaksCount, 2);
345
-        if (pl != NULL)
346
-        {
347
-            rampPeakInfoStruct *peak;
348
-            peak = pl->getPeak(0);
349
-            peaks(0,0) = peak->mz;
350
-            peaks(0,1) = peak->intensity;
351
-            for (int i=1; i < peaksCount; i++)
352
-            {
353
-                peak++;
354
-                peaks(i,0) = peak->mz;
355
-                peaks(i,1) = peak->intensity;
356
-            }
357
-            delete pl;
358
-        }
359
-        return Rcpp::List::create(
360
-                   Rcpp::_["peaksCount"]  = peaksCount,
361
-                   Rcpp::_["peaks"]  = peaks
362
-               ) ;
363
-    }
364
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
365
-    return Rcpp::List::create( );
366
-}
367
-
368
-Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double whichMzLow, double whichMzHigh, double resMz )
369
-{
370
-    if (ramp != NULL)
371
-    {
372
-        double f = 1 / resMz;
373
-        int low = round(whichMzLow * f);
374
-        int high = round(whichMzHigh * f);
375
-        int dmz = high - low + 1;
376
-        int drt = scanNumbers.size();
377
-        Rcpp::NumericMatrix map3d(drt, dmz);
378
-        for (int i = 0; i < drt; i++)
379
-        {
380
-            for (int j = 0; j < dmz; j++)
381
-            {
382
-                map3d(i,j) = 0.0;
383
-            }
384
-        }
385
-        // map3d = 0.0;
386
-        int j=0;
387
-        //Rprintf("%d\n",1);
388
-        for (int i = 0; i < scanNumbers.size(); i++)
389
-        {
390
-            rampPeakList *pl = ramp->getPeakList( scanNumbers[i] );
391
-            int peaksCount = pl->getPeakCount();
392
-            rampPeakInfoStruct *peak;
393
-            peak = pl->getPeak(0);
394
-            j = round(peak->mz * f) - low;
395
-            if ((j >= 0) & (j < dmz))
396
-            {
397
-                if (peak->intensity > map3d(i,j))
398
-                {
399
-                    map3d(i,j) = peak->intensity;
400
-                }
401
-            }
402
-            for (int k=1; k < peaksCount; k++)
403
-            {
404
-                peak++;
405
-                j = round(peak->mz * f) - low;
406
-                if ((j >= 0) & (j < dmz))
407
-                {
408
-                    if (peak->intensity > map3d(i,j))
409
-                    {
410
-                        map3d(i,j) = peak->intensity;
411
-                    }
412
-                }
413
-            }
414
-            delete pl;
415
-        }
416
-        return(map3d);
417
-    }
418
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
419
-    return Rcpp::NumericMatrix(0,0);
420
-}
421
-
422
-int RcppRamp::getLastScan() const
423
-{
424
-    if (ramp != NULL)
425
-    {
426
-        return ramp->getLastScan();
427
-    }
428
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
429
-    return -1;
430
-}
431
-
432
-bool RcppRamp::OK (  )
433
-{
434
-    if (ramp != NULL)
435
-    {
436
-        return ramp->OK();
437
-    }
438
-    // Rprintf("Warning: Ramp not yet initialized.\n ");
439
-    return false;
440
-}
Browse code

Replace Rcpp::Rcerr with Rf_warningcall (issue #164)

- Replace Rcpp::Rcerr with Rf_warningcall for most functions.
- Also replace Rprintf with Rf_warningcall if backend not initialized.

jotsetung authored on 17/05/2018 11:52:44
Showing1 changed files
... ...
@@ -55,7 +55,7 @@ Rcpp::StringVector RcppRamp::getFilename (  )
55 55
     {
56 56
         return filename;
57 57
     }
58
-    Rprintf("Warning: Ramp not yet initialized.\n ");
58
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
59 59
     return filename;
60 60
 }
61 61
 
... ...
@@ -86,7 +86,7 @@ Rcpp::List RcppRamp::getRunInfo (  )
86 86
         }
87 87
         return runInfo;
88 88
     }
89
-    Rprintf("Warning: Ramp not yet initialized.\n");
89
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
90 90
     return runInfo;
91 91
 }
92 92
 
... ...
@@ -130,7 +130,7 @@ Rcpp::List RcppRamp::getInstrumentInfo ( )
130 130
         }
131 131
         return(instrumentInfo);
132 132
     }
133
-    Rprintf("Warning: Ramp not yet initialized.\n ");
133
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
134 134
     return instrumentInfo;
135 135
 }
136 136
 
... ...
@@ -200,7 +200,7 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )
200 200
 
201 201
         return  header;
202 202
     }
203
-    Rprintf("Warning: Ramp not yet initialized.\n ");
203
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
204 204
     return Rcpp::List::create( );
205 205
 }
206 206
 
... ...
@@ -322,7 +322,7 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
322 322
         }
323 323
         return(allScanHeaderInfo);
324 324
     }
325
-    Rprintf("Warning: Ramp not yet initialized.\n ");
325
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
326 326
     return Rcpp::DataFrame::create( );
327 327
 }
328 328
 
... ...
@@ -361,7 +361,7 @@ Rcpp::List RcppRamp::getPeakList ( int whichScan )
361 361
                    Rcpp::_["peaks"]  = peaks
362 362
                ) ;
363 363
     }
364
-    Rprintf("Warning: Ramp not yet initialized.\n ");
364
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
365 365
     return Rcpp::List::create( );
366 366
 }
367 367
 
... ...
@@ -384,7 +384,7 @@ Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double wh
384 384
         }
385 385
         // map3d = 0.0;
386 386
         int j=0;
387
-        Rprintf("%d\n",1);
387
+        //Rprintf("%d\n",1);
388 388
         for (int i = 0; i < scanNumbers.size(); i++)
389 389
         {
390 390
             rampPeakList *pl = ramp->getPeakList( scanNumbers[i] );
... ...
@@ -415,7 +415,7 @@ Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double wh
415 415
         }
416 416
         return(map3d);
417 417
     }
418
-    Rprintf("Warning: Ramp not yet initialized.\n ");
418
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
419 419
     return Rcpp::NumericMatrix(0,0);
420 420
 }
421 421
 
... ...
@@ -425,7 +425,7 @@ int RcppRamp::getLastScan() const
425 425
     {
426 426
         return ramp->getLastScan();
427 427
     }
428
-    Rprintf("Warning: Ramp not yet initialized.\n ");
428
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
429 429
     return -1;
430 430
 }
431 431
 
Browse code

Report ion injection time in header of pwiz backend

- Add a column injectionTime to the data.frame returned by the header
function (all backends).
- Pwiz backend extracts the ion injection time.
- Update relevant documentation and add unit test(s).

jotsetung authored on 13/06/2017 09:53:14
Showing1 changed files
... ...
@@ -148,7 +148,7 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )
148 148
         delete info;
149 149
 
150 150
         std::vector<std::string> names;
151
-        Rcpp::List header(21);
151
+        Rcpp::List header(22);
152 152
         int i = 0;
153 153
 
154 154
         names.push_back("seqNum");
... ...
@@ -193,6 +193,8 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )
193 193
         header[i++] = Rcpp::wrap(data.mergedResultStartScanNum);
194 194
         names.push_back("mergedResultEndScanNum");
195 195
         header[i++] = Rcpp::wrap(data.mergedResultEndScanNum);
196
+        names.push_back("injectionTime");
197
+        header[i++] = 0;
196 198
 
197 199
         header.attr("names") = names;
198 200
 
... ...
@@ -260,7 +262,7 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
260 262
                 mergedResultEndScanNum[whichScan-1] = scanHeader.mergedResultEndScanNum;
261 263
             }
262 264
 
263
-            Rcpp::List header(21);
265
+            Rcpp::List header(22);
264 266
             std::vector<std::string> names;
265 267
             int i = 0;
266 268
 
... ...
@@ -306,6 +308,8 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
306 308
             header[i++] =Rcpp::wrap(mergedResultStartScanNum);
307 309
             names.push_back("mergedResultEndScanNum");
308 310
             header[i++] =Rcpp::wrap(mergedResultEndScanNum);
311
+            names.push_back("injectionTime");
312
+            header[i++] = 0;
309 313
             
310 314
 			header.attr("names") = names;
311 315
 			
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 3 commits.

Commit information:

Commit id: 2b2d46de53ab6db1651df3979bec62c4be1b4d02

Merge pull request #20 from thirdwing/master

Fix #18
Committed by: Laurent Gatto
Author Name: Laurent Gatto
Commit date: 2015-02-08 10:02:30 +0000
Author date: 2015-02-08 10:02:30 +0000

Commit id: bf3803db2da39fa34a5622568576e44934e27233

remove ListBuilder

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2015-02-07 16:29:54 -0500
Author date: 2015-02-07 16:29:54 -0500

Commit id: a6d4cc7a972c43947a3f7c9f1aed1b5418b4aabf

fix #18

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2015-02-07 15:44:30 -0500
Author date: 2015-02-07 15:44:30 -0500


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@99206 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 08/02/2015 10:03:17
Showing1 changed files
... ...
@@ -1,8 +1,5 @@
1 1
 #include "RcppRamp.h"
2 2
 
3
-#include "ListBuilder.h"
4
-
5
-
6 3
 RcppRamp::RcppRamp()
7 4
 {
8 5
     ramp = NULL;
... ...
@@ -150,37 +147,54 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )
150 147
         ScanHeaderStruct data = info->m_data;
151 148
         delete info;
152 149
 
153
-        //    Rcpp::List header = Rcpp::List::create();
154
-        ListBuilder header;
150
+        std::vector<std::string> names;
151
+        Rcpp::List header(21);
152
+        int i = 0;
155 153
 
156
-        header.add("seqNum",  Rcpp::wrap(data.seqNum));
157
-        header.add("acquisitionNum", Rcpp::wrap(data.acquisitionNum));
158
-        header.add("msLevel",       Rcpp::wrap(data.msLevel));
159
-        header.add("polarity",       Rcpp::wrap(data.polarity));
160
-        header.add("peaksCount",       Rcpp::wrap(data.peaksCount));
161
-        header.add("totIonCurrent",       Rcpp::wrap(data.totIonCurrent));
162
-        header.add("retentionTime",       Rcpp::wrap(data.retentionTime));
163
-        header.add("basePeakMZ",       Rcpp::wrap(data.basePeakMZ));
164
-        header.add("basePeakIntensity",       Rcpp::wrap(data.basePeakIntensity));
165
-        header.add("collisionEnergy",       Rcpp::wrap(data.collisionEnergy));
166
-        header.add("ionisationEnergy",       Rcpp::wrap(data.ionisationEnergy));
167
-        header.add("lowMZ",       Rcpp::wrap(data.lowMZ));
168
-        header.add("highMZ",       Rcpp::wrap(data.highMZ));
169
-        header.add("precursorScanNum",       Rcpp::wrap(data.precursorScanNum));
170
-        header.add("precursorMZ",       Rcpp::wrap(data.precursorMZ));
171
-        header.add("precursorCharge",       Rcpp::wrap(data.precursorCharge));
172
-        header.add("precursorIntensity",       Rcpp::wrap(data.precursorIntensity));
173
-        //  header.add("scanType",       Rcpp::wrap(data.scanType));
174
-        //  header.add("activationMethod",       Rcpp::wrap(data.activationMethod));
175
-        //  header.add("possibleCharges",       Rcpp::wrap(data.possibleCharges));
176
-        // header.add("numPossibleCharges",       Rcpp::wrap(data.numPossibleCharges));
177
-        //  header.add("possibleChargesArray",       Rcpp::wrap(data.possibleChargesArray));
178
-        header.add("mergedScan",       Rcpp::wrap(data.mergedScan));
179
-        header.add("mergedResultScanNum",       Rcpp::wrap(data.mergedResultScanNum));
180
-        header.add("mergedResultStartScanNum",       Rcpp::wrap(data.mergedResultStartScanNum));
181
-        header.add("mergedResultEndScanNum",       Rcpp::wrap(data.mergedResultEndScanNum));
182
-        //			     header.add("filePosition",       data.filePosition
154
+        names.push_back("seqNum");
155
+        header[i++] = Rcpp::wrap(data.seqNum);
156
+        names.push_back("acquisitionNum");
157
+        header[i++] = Rcpp::wrap(data.acquisitionNum);
158
+        names.push_back("msLevel");
159
+        header[i++] = Rcpp::wrap(data.msLevel);
160
+        names.push_back("polarity");
161
+        header[i++] = Rcpp::wrap(data.polarity);
162
+        names.push_back("peaksCount");
163
+        header[i++] = Rcpp::wrap(data.peaksCount);
164
+        names.push_back("totIonCurrent");
165
+        header[i++] = Rcpp::wrap(data.totIonCurrent);
166
+        names.push_back("retentionTime");
167
+        header[i++] = Rcpp::wrap(data.retentionTime);
168
+        names.push_back("basePeakMZ");
169
+        header[i++] = Rcpp::wrap(data.basePeakMZ);
170
+        names.push_back("basePeakIntensity");
171
+        header[i++] = Rcpp::wrap(data.basePeakIntensity);
172
+        names.push_back("collisionEnergy");
173
+        header[i++] = Rcpp::wrap(data.collisionEnergy);
174
+        names.push_back("ionisationEnergy");
175
+        header[i++] = Rcpp::wrap(data.ionisationEnergy);
176
+        names.push_back("lowMZ");
177
+        header[i++] = Rcpp::wrap(data.lowMZ);
178
+        names.push_back("highMZ");
179
+        header[i++] = Rcpp::wrap(data.highMZ);
180
+        names.push_back("precursorScanNum");
181
+        header[i++] = Rcpp::wrap(data.precursorScanNum);
182
+        names.push_back("precursorMZ");
183
+        header[i++] = Rcpp::wrap(data.precursorMZ);
184
+        names.push_back("precursorCharge");
185
+        header[i++] = Rcpp::wrap(data.precursorCharge);
186
+        names.push_back("precursorIntensity");
187
+        header[i++] = Rcpp::wrap(data.precursorIntensity);
188
+        names.push_back("mergedScan");
189
+        header[i++] = Rcpp::wrap(data.mergedScan);
190
+        names.push_back("mergedResultScanNum");
191
+        header[i++] = Rcpp::wrap(data.mergedResultScanNum);
192
+        names.push_back("mergedResultStartScanNum");
193
+        header[i++] = Rcpp::wrap(data.mergedResultStartScanNum);
194
+        names.push_back("mergedResultEndScanNum");
195
+        header[i++] = Rcpp::wrap(data.mergedResultEndScanNum);
183 196
 
197
+        header.attr("names") = names;
184 198
 
185 199
         return  header;
186 200
     }
... ...
@@ -215,11 +229,6 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
215 229
             Rcpp::NumericVector precursorMZ(N);  /* only if MS level > 1 */
216 230
             Rcpp::IntegerVector precursorCharge(N);  /* only if MS level > 1 */
217 231
             Rcpp::NumericVector precursorIntensity(N);  /* only if MS level > 1 */
218
-            // char scanType[SCANTYPE_LENGTH];
219
-            // char activationMethod[SCANTYPE_LENGTH];
220
-            // char possibleCharges[SCANTYPE_LENGTH];
221
-            // int numPossibleCharges;
222
-            // bool possibleChargesArray[CHARGEARRAY_LENGTH]; /* NOTE: does NOT include "precursorCharge" information; only from "possibleCharges" */
223 232
             Rcpp::IntegerVector mergedScan(N);  /* only if MS level > 1 */
224 233
             Rcpp::IntegerVector mergedResultScanNum(N); /* scan number of the resultant merged scan */
225 234
             Rcpp::IntegerVector mergedResultStartScanNum(N); /* smallest scan number of the scanOrigin for merged scan */
... ...
@@ -251,35 +260,56 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
251 260
                 mergedResultEndScanNum[whichScan-1] = scanHeader.mergedResultEndScanNum;
252 261
             }
253 262
 
254
-            ListBuilder header;
255
-            header.add("seqNum", seqNum);
256
-            header.add("acquisitionNum",           acquisitionNum);
257
-            header.add("msLevel",                  msLevel);
258
-            header.add("polarity",               polarity);
259
-            header.add("peaksCount",               peaksCount);
260
-            header.add("totIonCurrent",            totIonCurrent);
261
-            header.add("retentionTime",            retentionTime);
262
-            header.add("basePeakMZ",               basePeakMZ);
263
-            header.add("basePeakIntensity",        basePeakIntensity);
264
-            header.add("collisionEnergy",          collisionEnergy);
265
-            header.add("ionisationEnergy",         ionisationEnergy);
266
-            header.add("lowMZ",                    lowMZ);
267
-            header.add("highMZ",                   highMZ);
268
-            header.add("precursorScanNum",         precursorScanNum);
269
-            header.add("precursorMZ",              precursorMZ);
270
-            header.add("precursorCharge",          precursorCharge);
271
-            header.add("precursorIntensity",       precursorIntensity);
272
-            //  header.add("scanType",                 scanType);
273
-            //  header.add("activationMethod",         activationMethod);
274
-            //  header.add("possibleCharges",          possibleCharges);
275
-            //  header.add("numPossibleCharges",       numPossibleCharges);
276
-            //  header.add("possibleChargesArray",     possibleChargesArray);
277
-            header.add("mergedScan",               mergedScan);
278
-            header.add("mergedResultScanNum",      mergedResultScanNum);
279
-            header.add("mergedResultStartScanNum", mergedResultStartScanNum);
280
-            header.add("mergedResultEndScanNum",   mergedResultEndScanNum);
263
+            Rcpp::List header(21);
264
+            std::vector<std::string> names;
265
+            int i = 0;
281 266
 
282
-            allScanHeaderInfo = header.get();
267
+            names.push_back("seqNum");
268
+            header[i++] =Rcpp::wrap(seqNum);
269
+            names.push_back("acquisitionNum");
270
+            header[i++] =Rcpp::wrap( acquisitionNum);
271
+            names.push_back("msLevel");
272
+            header[i++] =Rcpp::wrap(msLevel);
273
+            names.push_back("polarity");
274
+            header[i++] =Rcpp::wrap(polarity);
275
+            names.push_back("peaksCount");
276
+            header[i++] =Rcpp::wrap(peaksCount);
277
+            names.push_back("totIonCurrent");
278
+            header[i++] =Rcpp::wrap(totIonCurrent);
279
+            names.push_back("retentionTime");
280
+            header[i++] =Rcpp::wrap(retentionTime);
281
+            names.push_back("basePeakMZ");
282
+            header[i++] =Rcpp::wrap(basePeakMZ);
283
+            names.push_back("basePeakIntensity");
284
+            header[i++] =Rcpp::wrap(basePeakIntensity);
285
+            names.push_back("collisionEnergy");
286
+            header[i++] =Rcpp::wrap(collisionEnergy);
287
+            names.push_back("ionisationEnergy");
288
+            header[i++] =Rcpp::wrap(ionisationEnergy);
289
+            names.push_back("lowMZ");
290
+            header[i++] =Rcpp::wrap(lowMZ);
291
+            names.push_back("highMZ");
292
+            header[i++] =Rcpp::wrap(highMZ);
293
+            names.push_back("precursorScanNum");
294
+            header[i++] =Rcpp::wrap(precursorScanNum);
295
+            names.push_back("precursorMZ");
296
+            header[i++] =Rcpp::wrap(precursorMZ);
297
+            names.push_back("precursorCharge");
298
+            header[i++] =Rcpp::wrap(precursorCharge);
299
+            names.push_back("precursorIntensity");
300
+            header[i++] =Rcpp::wrap(precursorIntensity);
301
+            names.push_back("mergedScan");
302
+            header[i++] =Rcpp::wrap(mergedScan);
303
+            names.push_back("mergedResultScanNum");
304
+            header[i++] =Rcpp::wrap(mergedResultScanNum);
305
+            names.push_back("mergedResultStartScanNum");
306
+            header[i++] =Rcpp::wrap(mergedResultStartScanNum);
307
+            names.push_back("mergedResultEndScanNum");
308
+            header[i++] =Rcpp::wrap(mergedResultEndScanNum);
309
+            
310
+			header.attr("names") = names;
311
+			
312
+            allScanHeaderInfo = header;
283 313
             isInCacheAllScanHeaderInfo = TRUE;
284 314
         }
285 315
         else
Browse code

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

Commit information:

Commit id: 289dc240065888efcaa22ae75951e81f94fc800f

Fix package description after merge

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

Commit id: 88248e8d6d86bb54dc260f0c55608dd1a949ade4

merged gsoc into master

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

Commit id: bb01e0fe0b4f04335925472a7c2b91bd22b57755

included KK's segfault patch and fixed unit test accordingly

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

Commit id: 708bd0b8ac4b2b5bae9a9b91588a260f2eeefb46

add message about pwiz backend in Bioc 3.1

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

Commit id: 4c1410ec3c8f153ad0a4b04722cad5a7d77cfd4c

restoring ramp as default backend

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

Commit id: c5d60529934813456555934bbeed29502100b41b

show pwiz method

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

Commit id: 20bfbfa1db25ec247f2313804d9b73c086a2d920

add close,mzRpwiz-method alias

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

Commit id: f80ecdc2a7f14c311b42ad279c62307a6e0aad30

test that close(pwiz) works

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

Commit id: d18dc8b0c7197c72b1bb2a70e7becfe983ced9a1

fixed signature for pwiz close method

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

Commit id: c0d7451e6b31068cde89f08ac5037a1509857cc5

fix codoc mismatch

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

Commit id: 14974a3d0890a7e2a1a7179aaa483e20a5700ef9

add close for pwiz backend to news

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

Commit id: c9d2bbb339c0ecdc9870dbd7a59bfbb94ef67f73

dummy close for pwiz backend

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

Commit id: 6d608b453328d6c751dc828d2586b016eb17b095

more close calls to remove for pwiz backend

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

Commit id: 5650801e07df64e2d74302ec98a31938bb62f11f

no isInitialised with pwiz

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

Commit id: 2a3d0eeb24673eb74c3ffa38fefb1883f9bee15d

no close with pwiz

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

Commit id: b3ae014569b6e46ccb6b396dfb9320dd7ba8fb16

bump version to avoid confusions

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

Commit id: a1bd596ffbeef73b4b505342f45742f9997e33d1

using pwiz as default raw data backend

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

Commit id: 51b4ea21d9cf034d54b0911bf281af3a937375de

Steffen's changes in v 1.11.11

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

Commit id: 81cde1ca48974585c9d6f51927087a922b13dd89

add new length to doc header

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

Commit id: 3fe883cb7ecad4867908fb907374a4df63b50a1f

show and length mzRident methods

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

Commit id: 3efb44e00fb94cdf0eb8207634218cbb47ab1b54

VignetteBuilder: knitr

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

Commit id: 73b0f902dfaa53f359318708f0606dc1f4677057

BiocStyle vig

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

Commit id: 185f281d07ed7b4a7f093eaf7b61271a88c85e20

update readme

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

Commit id: d5cc992e128594d331592b2bd57871fabf6737c9

update to build

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

Commit id: 27318416c94859102a061838a1a3f83d378414e3

bump to 1.99

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

Commit id: 13caefb4d4b469f0406ed96509ea4cebce8235b0

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

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

Commit id: 14822efb6c2238eda371718043bec9cc8fb27558

doc

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

Commit id: 323424443efac769c436fb87128fad64a0358187

R_init_mzR.c

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

Commit id: a91c0601e674efbb6949331a53ea9c6af53a4ba5

vignettes

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

Commit id: 4607e0a595f60a083d1eb90b804348ac5a8c1fb4

update with msdata

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

Commit id: cc09a790eda22b7d64226116ada89bad9089e0b2

modified: src/RcppPwiz.cpp

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

Commit id: fac511ee0f7841791bbf5380f2c948fd045b3adb

unit test against mzID

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

Commit id: 449952e31fe354b2589d8a723a4f8a842812ede6

enzymes() returns data.frame

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

Commit id: 874fba33e8029023d5e3bbd168dc998d51544c9d

writing support dropped

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

Commit id: 338f3e80dd8f98419555ab1a4aa443e14d089f24

modifications()

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

Commit id: 34ee62ee27e7b012b9ce2bd696d63e5f80185200

psms() update

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

Commit id: b8bdea9a1e2a7ab3410eea5c26566ef74e488d95

score()

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

Commit id: a42f1195b3f0b40c28aa2acfb782e517633206c9

psms()

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

Commit id: 6c2a87019e3b328dbecc1a965d3e41e6539e0d90

para() update, numeric correction

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

Commit id: 119edf40600beb8e3b8e8006a0d955a887d06b1d

update para()

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

Commit id: 69ac718d0418f2ab3ba824a735975ae6c04aec00

update database()

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

Commit id: f7818556b2e1e3296a727eca6d2853a8b7a16b12

clean

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

Commit id: f67403a92b6beca4128c36b42367414463234253

database()

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

Commit id: 8b0255a9c7da6ccc6c7796f49f608b792bac0dfe

para()

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

Commit id: 183afed91ad6beb07fffb5cbe4673773619d938b

Rd

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

Commit id: 73d380115e205eedc211869d6eace3564b3fc1cf

modified: vignettes/mzR.Rnw

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

Commit id: 93214634ff41a9da84019320dfe6314cb7f94422

score

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

Commit id: cbdee47033cf10927b0dc33a02208c9ff9d89771

same header info

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

Commit id: 1e6ebe39851ecddedf01daa2c69fcd1f2dba906c

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

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

Commit id: 0ed92085be5af56a78cdf0f1732a356c48d7a0f9

1.11.10

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

Commit id: b6e254b2cca93778bfcdc549b75052d0b19bb2bb

fixed

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

Commit id: 096aa2a6f5aebb5b99bc2e22a0fb023b1353b141

Merge pull request #3 from lgatto/master

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

Commit id: 6d8623c47c0b53e6805b9757c178c4639319a29d

fix backend checking

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

Commit id: 9060e3435a76ace952d915c3bb993e04ac93f12a

modified: src/RcppIdent.cpp

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

Commit id: 068ec46671400a2db3bfb10f001f30599b8495e8

modified: ChangeLog

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

Commit id: a8f42c9de00ed64470733eb5c63567e99d40e867

more info

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

Commit id: 4a88ad7c2c8ec911c44a45d16dedced9530505c2

modified: src/RcppIdent.cpp

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

Commit id: 935d44c5a52b895fe6ff663c062e006e4f25fab0

modified: src/RcppIdent.cpp

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

Commit id: f1c05ff287215f385938a116042d09bcea2aae88

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

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

Commit id: ca620536203355349c7267ad15a2ab6a2d248319

pass R CMD check

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

Commit id: add1d1c98fe60955953036641671527337e89363

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

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

Commit id: 050051489df378a26aa97cccfefbf7ebe4102ef5

pepInfo()

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

Commit id: f093e39599ea2357c91816b7ff9de102f33e8e68

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

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

Commit id: 3dc85db859c4d36040d3edb9ceb57074b0476f2d

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

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

Commit id: ab1261cb3bfe1c02de5f7a053e6de5223686488d

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

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

Commit id: 01a4a2be981724624719580cd8e4f0866091f295

version

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

Commit id: 5f49d13b736cebd65484a5993cdcce253853d4e7

remove mz5

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

Commit id: fb3dbe2f1bf007cd033fd803426d4be2e362b3e2

Update H5public.h

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

Commit id: 2446f08fdadd11c38a1cb54dddfe1e52b1a7bca9

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

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

Commit id: b7c28c0db06b2dc9f8f5a7dcd218b7581ffd8121

compiled

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

Commit id: 1ffe5c024dafd51c2342f4d1dd930cb8d67d8041

modified: DESCRIPTION modified: src/Makevars.win

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

Commit id: 06e03716f187508072c33d3f0e9e79e135b22c05

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

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

Commit id: 488ed2bd55151ece46c8cb5ac1df11f73b7c47a3

modified: src/Makevars

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

Commit id: 06f4d0a3832e47ad4a69e53d7b9b751dbb9f2770

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

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

Commit id: ff58989379a67f20ac8797ba437d430d8b5a2d62

modified: src/RcppIdent.cpp

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

Commit id: 58dfa68675768c13950299c43229c1b0f1f1824b

modified: src/RcppIdent.cpp

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

Commit id: 6c228ae30c477e76add7e3ea805e386f1a0d862d

modified: src/RcppIdent.cpp

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

Commit id: 464d4e83a9e06732f7c3f1a0172a9cb2bbd53943

modified: src/RcppIdent.cpp

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

Commit id: ed36541a5fc99192f9df55222f2a2d9a6352ae33

idInfo

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

Commit id: 1ed6dceee93d2f57a66a94b15774212403d42200

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

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

Commit id: 47b2a99876650729a329ebeebc174d9873919667

modified: DESCRIPTION

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

Commit id: ecad541c1e2d92f7be63433c5bf362d7b7f955b2

mzid supported done

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

Commit id: 684340ce7ee5b8fadbd4dfa839e3b0d7ba9b1c91

mzid file support

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

Commit id: 7382b1321539a2838ae75da6f9c1ff9cbe98bb6b

mzid

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

Commit id: 5423b4c653762d90ce6d4bf7dcf1d591a2a9987f

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

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

Commit id: 9e20328e920207328eb68b9fa59c198d0d634a0f

Update AllGenerics.R

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

Commit id: 19731b9e51b72027eb02ee6be5aa7343c5b12ace

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

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

Commit id: 94ac2b4ba810d0f820a9266be782667e375ede9a

modified: src/RcppPwiz.cpp

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

Commit id: 1259a8db48d4f7aa9ffe403dd5ee574bbfd238fb

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

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

Commit id: 9791bc574989cdefe279071dbf3a47232e1d8c86

identadata src

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

Commit id: ede49e01e23c6586777d72fdd0dfef4bd40729f2

software info

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

Commit id: 431b2b42a93ff52a05d82801d1830ba81c72f18f

writeMSfile()

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

Commit id: 53a7a31378bd42adcf779cd1fbe9e2d052a507d7

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

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

Commit id: 359a40045162a49d94d68f0d60f2c6bb43970a2c

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

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

Commit id: 2ce04488e7a8e623a7dfd2b9408da0b9dd5059a4

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

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

Commit id: 3103fd4fa92ddd63700c8b5940344db44e97be09

modified: src/RcppPwiz.cpp

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

Commit id: 329f7c1201360f5ebf5703d4837b25ae332e7a85

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

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

Commit id: 0adf852da9ccec69103038ca96b30e8715d3c898

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

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

Commit id: 219b5287ca5531577b4a6c80f403957ddef5ab94

modified: src/RcppPwiz.cpp

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

Commit id: 14316dcb1c16ca922d9962ed9ecdaac324e1a151

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

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

Commit id: efb21501a1b05b680b3d35aa124216f9977b5993

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

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

Commit id: 4e9e1dec2879178547d681603aec46259a6a9978

mz5

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

Commit id: 0e7fc23b1ff7508fed6331c0e517a8dc6fa33a0c

mz5

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

Commit id: 9ad55a2cdd89791bf75ad23f0ee91b3fc70624ad

mz5

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

Commit id: c9fecd83ebf31f142c22030f4593fe5ac675323a

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

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

Commit id: 4edf517724950d6771fd19c979a460711baa5891

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

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

Commit id: 22ca998b6b6d3a7496f293f44909436a5b7d8ad0

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

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

Commit id: 6beb4ce5c49cafa644766e23453ed6d10bb89c34

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

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

Commit id: dc5e65d93bb67d1b4a1488b90099946e22eed13c

deleted: .travis.yml

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

Commit id: be53359804d6c7416c715c3eb259fb931c6c117a

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

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

Commit id: 1afd9887dac232f3e72fe9d20d44a72b42e28461

deleted: .Rinstignore

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

Commit id: bd4c954bd246787137eb0d961a91bb80b774cb6a

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

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

Commit id: 3bc8fcca8002a62458a2b2dd1c6b7cf6a8cfab9f

fixed error on windows and snow leopard

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

Commit id: ed9c622443eb992cf3322d687312e3f56bf8be72

Update Makevars.win

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

Commit id: bf8c7bd931cd93b5db6d84c9c1bf323ea7702e74

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

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

Commit id: 5ac3655c7e81f429859eb6b509208f8ec785e1f9

modified: src/Makevars.win

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

Commit id: f9f42e3d83adbaf98a201e50866821bc0e43598a

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

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

Commit id: d8d6f92e46efa93f8234e542b1c4f8f98cee59e5

modified: R/zzz.R.in

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

Commit id: e64a8bb7bb7988047466848e5b449038ae9460b3

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

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

Commit id: 0a44cc02ea9b5417ac51f60632fc1b6100c6d160

modified: src/Makevars

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

Commit id: 4d19d457031e0ae9af343a44774f5deebae01cc8

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

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

Commit id: effcb581a573e13b7b7cc9b459ef2dec4885b4be

modified: src/RcppPwiz.cpp

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

Commit id: 028f6748d4cf81d47569edcd67fe25064b084e60

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

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

Commit id: d95b557d2c637630ca784889cd0ef1f56b8423d5

Update methods-mzRpwiz.R

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

Commit id: aad52653c2ceb33655364d5a39c0559225746cfb

Update RcppPwizModule.cpp

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

Commit id: 4fda90cc08feb731aeb65c6015a033fbe46c372e

Update RcppPwiz.cpp

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

Commit id: 660d2e984fabdd20997ff8b648d361c7d9aae711

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

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

Commit id: ec6bbdf496a57f2f39b2e4c3bbada75a060e5bbe

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

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

Commit id: a093954cb779467026288c7f51cca083e0a20661

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

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

Commit id: 4510a1cda50ee8f1f43b667297918dcffed45af2

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

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


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

s.neumann authored on 28/09/2014 18:06:01
Showing1 changed files
... ...
@@ -3,364 +3,404 @@
3 3
 #include "ListBuilder.h"
4 4
 
5 5
 
6
-RcppRamp::RcppRamp() {
7
-  ramp = NULL;
8
-  runInfo = Rcpp::List::create( );
9
-  isInCacheRunInfo = FALSE;
10
-  instrumentInfo = Rcpp::List::create( );
11
-  isInCacheInstrumentInfo = FALSE;
12
-  allScanHeaderInfo = Rcpp::DataFrame::create( );
13
-  isInCacheAllScanHeaderInfo = FALSE;
14
-  filename = Rcpp::StringVector::create( );
15
-}
16
-
17
-RcppRamp::~RcppRamp() {
18
-  RcppRamp::close();
19
-}
20
-
21
-void
22
-RcppRamp::open( const char* fileName, bool declaredScansOnly ) {
23
-  RcppRamp::close();
24
-  ramp = new cRamp(fileName, declaredScansOnly);
25
-  if (ramp->OK()) {
26
-    filename = Rcpp::StringVector::create( fileName );
27
-  } else {
28
-    RcppRamp::close();
29
-    Rprintf("Failed to open file.\n ");
30
-  }
31
-}
32
-
33
-void
34
-RcppRamp::close() {
35
-  if (ramp != NULL) {
36
-    delete ramp;
6
+RcppRamp::RcppRamp()
7
+{
37 8
     ramp = NULL;
38 9
     runInfo = Rcpp::List::create( );
39 10
     isInCacheRunInfo = FALSE;
40 11
     instrumentInfo = Rcpp::List::create( );
41 12
     isInCacheInstrumentInfo = FALSE;
42
-    allScanHeaderInfo = Rcpp::List::create( );
13
+    allScanHeaderInfo = Rcpp::DataFrame::create( );
43 14
     isInCacheAllScanHeaderInfo = FALSE;
44 15
     filename = Rcpp::StringVector::create( );
45
-  }
16
+}
17
+
18
+RcppRamp::~RcppRamp()
19
+{
20
+    RcppRamp::close();
21
+}
22
+
23
+void RcppRamp::open( const char* fileName, bool declaredScansOnly )
24
+{
25
+    RcppRamp::close();
26
+    ramp = new cRamp(fileName, declaredScansOnly);
27
+    if (ramp->OK())
28
+    {
29
+        filename = Rcpp::StringVector::create( fileName );
30
+    }
31
+    else
32
+    {
33
+        RcppRamp::close();
34
+        Rprintf("Failed to open file.\n ");
35
+    }
36
+}
37
+
38
+void RcppRamp::close()
39
+{
40
+    if (ramp != NULL)
41
+    {
42
+        delete ramp;
43
+        ramp = NULL;
44
+        runInfo = Rcpp::List::create( );
45
+        isInCacheRunInfo = FALSE;
46
+        instrumentInfo = Rcpp::List::create( );
47
+        isInCacheInstrumentInfo = FALSE;
48
+        allScanHeaderInfo = Rcpp::List::create( );
49
+        isInCacheAllScanHeaderInfo = FALSE;
50
+        filename = Rcpp::StringVector::create( );
51
+    }
46 52
 }
47 53
 
48 54
 
49
-Rcpp::StringVector
50
-RcppRamp::getFilename (  ) {
51
-  if (ramp != NULL) {
55
+Rcpp::StringVector RcppRamp::getFilename (  )
56
+{
57
+    if (ramp != NULL)
58
+    {
59
+        return filename;
60
+    }
61
+    Rprintf("Warning: Ramp not yet initialized.\n ");
52 62
     return filename;
53
-  }
54
-  Rprintf("Warning: Ramp not yet initialized.\n ");
55
-  return filename;
56 63
 }
57 64
 
58
-Rcpp::List
59
-RcppRamp::getRunInfo (  ) {
60
-  if (ramp != NULL) {
61
-    if (!isInCacheRunInfo) {
62
-      // Rprintf("Read from disk.\n ");
63
-      rampRunInfo *info = ramp->getRunInfo();
64
-      RunHeaderStruct data = info->m_data;
65
-      delete info;
66
-      runInfo = Rcpp::List::create(
67
-				   Rcpp::_["scanCount"]  = data.scanCount,
68
-				   Rcpp::_["lowMZ"]      = data.lowMZ,
69
-				   Rcpp::_["highMZ"]     = data.highMZ,
70
-				   Rcpp::_["startMZ"]    = data.startMZ,
71
-				   Rcpp::_["endMZ"]      = data.endMZ,
72
-				   Rcpp::_["dStartTime"] = data.dStartTime,
73
-				   Rcpp::_["dEndTime"]   = data.dEndTime
74
-				   );
75
-      isInCacheRunInfo = TRUE;
76
-    } else {
77
-      // Rprintf("Read from cache.\n ");
65
+Rcpp::List RcppRamp::getRunInfo (  )
66
+{
67
+    if (ramp != NULL)
68
+    {
69
+        if (!isInCacheRunInfo)
70
+        {
71
+            // Rprintf("Read from disk.\n ");
72
+            rampRunInfo *info = ramp->getRunInfo();
73
+            RunHeaderStruct data = info->m_data;
74
+            delete info;
75
+            runInfo = Rcpp::List::create(
76
+                          Rcpp::_["scanCount"]  = data.scanCount,
77
+                          Rcpp::_["lowMZ"]      = data.lowMZ,
78
+                          Rcpp::_["highMZ"]     = data.highMZ,
79
+                          Rcpp::_["startMZ"]    = data.startMZ,
80
+                          Rcpp::_["endMZ"]      = data.endMZ,
81
+                          Rcpp::_["dStartTime"] = data.dStartTime,
82
+                          Rcpp::_["dEndTime"]   = data.dEndTime
83
+                      );
84
+            isInCacheRunInfo = TRUE;
85
+        }
86
+        else
87
+        {
88
+            // Rprintf("Read from cache.\n ");
89
+        }
90
+        return runInfo;
78 91
     }
92
+    Rprintf("Warning: Ramp not yet initialized.\n");
79 93
     return runInfo;
80
-  }
81
-  Rprintf("Warning: Ramp not yet initialized.\n");
82
-  return runInfo;
83 94
 }
84 95
 
85
-Rcpp::List
86
-RcppRamp::getInstrumentInfo ( ) {
87
-  if (ramp != NULL) {
88
-    if (!isInCacheInstrumentInfo) {
89
-      // Rprintf("Read from disk.\n ");
90
-      rampInstrumentInfo *info = ramp->getInstrumentInfo(); // NULL for mzData
96
+Rcpp::List RcppRamp::getInstrumentInfo ( )
97
+{
98
+    if (ramp != NULL)
99
+    {
100
+        if (!isInCacheInstrumentInfo)
101
+        {
102
+            // Rprintf("Read from disk.\n ");
103
+            rampInstrumentInfo *info = ramp->getInstrumentInfo(); // NULL for mzData
104
+
105
+            if (info != NULL)
106
+            {
107
+                InstrumentStruct * data = info->m_instrumentStructPtr;
91 108
 
92
-      if (info != NULL) { 
93
-      InstrumentStruct * data = info->m_instrumentStructPtr;
94
-      
95
-      instrumentInfo = Rcpp::List::create(
96
-					  Rcpp::_["manufacturer"]  = std::string(data->manufacturer),
97
-					  Rcpp::_["model"]         = std::string(data->model),
98
-					  Rcpp::_["ionisation"]    = std::string(data->ionisation),
99
-					  Rcpp::_["analyzer"]      = std::string(data->analyzer),
100
-					  Rcpp::_["detector"]      = std::string(data->detector)
101
-					  ) ;
102
-      delete info; 
103
-      } else {
104
-      instrumentInfo = Rcpp::List::create(
105
-					  Rcpp::_["manufacturer"]  = "",
106
-					  Rcpp::_["model"]         = "",
107
-					  Rcpp::_["ionisation"]    = "",
108
-					  Rcpp::_["analyzer"]      = "",
109
-					  Rcpp::_["detector"]      = ""
110
-					  ) ;
111
-      }
112
-      isInCacheInstrumentInfo = TRUE;
113
-    } else {
114
-      // Rprintf("Read from cache.\n ");
109
+                instrumentInfo = Rcpp::List::create(
110
+                                     Rcpp::_["manufacturer"]  = std::string(data->manufacturer),
111
+                                     Rcpp::_["model"]         = std::string(data->model),
112
+                                     Rcpp::_["ionisation"]    = std::string(data->ionisation),
113
+                                     Rcpp::_["analyzer"]      = std::string(data->analyzer),
114
+                                     Rcpp::_["detector"]      = std::string(data->detector)
115
+                                 ) ;
116
+                delete info;
117
+            }
118
+            else
119
+            {
120
+                instrumentInfo = Rcpp::List::create(
121
+                                     Rcpp::_["manufacturer"]  = "",
122
+                                     Rcpp::_["model"]         = "",
123
+                                     Rcpp::_["ionisation"]    = "",
124
+                                     Rcpp::_["analyzer"]      = "",
125
+                                     Rcpp::_["detector"]      = ""
126
+                                 ) ;
127
+            }
128
+            isInCacheInstrumentInfo = TRUE;
129
+        }
130
+        else
131
+        {
132
+            // Rprintf("Read from cache.\n ");
133
+        }
134
+        return(instrumentInfo);
115 135
     }
116
-    return(instrumentInfo);
117
-  }
118
-  Rprintf("Warning: Ramp not yet initialized.\n ");
119
-  return instrumentInfo;
136
+    Rprintf("Warning: Ramp not yet initialized.\n ");
137
+    return instrumentInfo;
120 138
 }
121 139
 
122
-Rcpp::List
123
-RcppRamp::getScanHeaderInfo ( int whichScan  ) {
124
-  if (ramp != NULL) {
125
-    if ((whichScan <= 0) || (whichScan > ramp->getLastScan())) {
126
-      Rprintf("Index whichScan out of bounds [1 ... %d].\n", ramp->getLastScan());
127
-      return Rcpp::List::create( );
128
-    }
129
-    rampScanInfo *info = ramp->getScanHeaderInfo( whichScan );
130
-    ScanHeaderStruct data = info->m_data;
131
-    delete info;
140
+Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )
141
+{
142
+    if (ramp != NULL)
143
+    {
144
+        if ((whichScan <= 0) || (whichScan > ramp->getLastScan()))
145
+        {
146
+            Rprintf("Index whichScan out of bounds [1 ... %d].\n", ramp->getLastScan());
147
+            return Rcpp::List::create( );
148
+        }
149
+        rampScanInfo *info = ramp->getScanHeaderInfo( whichScan );
150
+        ScanHeaderStruct data = info->m_data;
151
+        delete info;
132 152
 
133
-    //    Rcpp::List header = Rcpp::List::create();
134
-    ListBuilder header;
153
+        //    Rcpp::List header = Rcpp::List::create();
154
+        ListBuilder header;
135 155
 
136
-    header.add("seqNum",  Rcpp::wrap(data.seqNum));
137
-    header.add("acquisitionNum", Rcpp::wrap(data.acquisitionNum));
138
-    header.add("msLevel",       Rcpp::wrap(data.msLevel));
139
-    header.add("polarity",       Rcpp::wrap(data.polarity));
140
-    header.add("peaksCount",       Rcpp::wrap(data.peaksCount));
141
-    header.add("totIonCurrent",       Rcpp::wrap(data.totIonCurrent));
142
-    header.add("retentionTime",       Rcpp::wrap(data.retentionTime));
143
-    header.add("basePeakMZ",       Rcpp::wrap(data.basePeakMZ));
144
-    header.add("basePeakIntensity",       Rcpp::wrap(data.basePeakIntensity));
145
-    header.add("collisionEnergy",       Rcpp::wrap(data.collisionEnergy));
146
-    header.add("ionisationEnergy",       Rcpp::wrap(data.ionisationEnergy));
147
-    header.add("lowMZ",       Rcpp::wrap(data.lowMZ));
148
-    header.add("highMZ",       Rcpp::wrap(data.highMZ));
149
-    header.add("precursorScanNum",       Rcpp::wrap(data.precursorScanNum));
150
-    header.add("precursorMZ",       Rcpp::wrap(data.precursorMZ));
151
-    header.add("precursorCharge",       Rcpp::wrap(data.precursorCharge));
152
-    header.add("precursorIntensity",       Rcpp::wrap(data.precursorIntensity));
153
-    //  header.add("scanType",       Rcpp::wrap(data.scanType));
154
-    //  header.add("activationMethod",       Rcpp::wrap(data.activationMethod));
155
-    //  header.add("possibleCharges",       Rcpp::wrap(data.possibleCharges));
156
-    // header.add("numPossibleCharges",       Rcpp::wrap(data.numPossibleCharges));
157
-    //  header.add("possibleChargesArray",       Rcpp::wrap(data.possibleChargesArray));
158
-    header.add("mergedScan",       Rcpp::wrap(data.mergedScan));
159
-    header.add("mergedResultScanNum",       Rcpp::wrap(data.mergedResultScanNum));
160
-    header.add("mergedResultStartScanNum",       Rcpp::wrap(data.mergedResultStartScanNum));
161
-    header.add("mergedResultEndScanNum",       Rcpp::wrap(data.mergedResultEndScanNum));
162
-    //			     header.add("filePosition",       data.filePosition
156
+        header.add("seqNum",  Rcpp::wrap(data.seqNum));
157
+        header.add("acquisitionNum", Rcpp::wrap(data.acquisitionNum));
158
+        header.add("msLevel",       Rcpp::wrap(data.msLevel));
159
+        header.add("polarity",       Rcpp::wrap(data.polarity));
160
+        header.add("peaksCount",       Rcpp::wrap(data.peaksCount));
161
+        header.add("totIonCurrent",       Rcpp::wrap(data.totIonCurrent));
162
+        header.add("retentionTime",       Rcpp::wrap(data.retentionTime));
163
+        header.add("basePeakMZ",       Rcpp::wrap(data.basePeakMZ));
164
+        header.add("basePeakIntensity",       Rcpp::wrap(data.basePeakIntensity));
165
+        header.add("collisionEnergy",       Rcpp::wrap(data.collisionEnergy));
166
+        header.add("ionisationEnergy",       Rcpp::wrap(data.ionisationEnergy));
167
+        header.add("lowMZ",       Rcpp::wrap(data.lowMZ));
168
+        header.add("highMZ",       Rcpp::wrap(data.highMZ));
169
+        header.add("precursorScanNum",       Rcpp::wrap(data.precursorScanNum));
170
+        header.add("precursorMZ",       Rcpp::wrap(data.precursorMZ));
171
+        header.add("precursorCharge",       Rcpp::wrap(data.precursorCharge));
172
+        header.add("precursorIntensity",       Rcpp::wrap(data.precursorIntensity));
173
+        //  header.add("scanType",       Rcpp::wrap(data.scanType));
174
+        //  header.add("activationMethod",       Rcpp::wrap(data.activationMethod));
175
+        //  header.add("possibleCharges",       Rcpp::wrap(data.possibleCharges));
176
+        // header.add("numPossibleCharges",       Rcpp::wrap(data.numPossibleCharges));
177
+        //  header.add("possibleChargesArray",       Rcpp::wrap(data.possibleChargesArray));
178
+        header.add("mergedScan",       Rcpp::wrap(data.mergedScan));
179
+        header.add("mergedResultScanNum",       Rcpp::wrap(data.mergedResultScanNum));
180
+        header.add("mergedResultStartScanNum",       Rcpp::wrap(data.mergedResultStartScanNum));
181
+        header.add("mergedResultEndScanNum",       Rcpp::wrap(data.mergedResultEndScanNum));
182
+        //			     header.add("filePosition",       data.filePosition
163 183
 
164 184
 
165
-  return  header;
166
-  }
167
-  Rprintf("Warning: Ramp not yet initialized.\n ");
168
-  return Rcpp::List::create( );
185
+        return  header;
186
+    }
187
+    Rprintf("Warning: Ramp not yet initialized.\n ");
188
+    return Rcpp::List::create( );
169 189
 }
170 190
 
171
-Rcpp::DataFrame
172
-RcppRamp::getAllScanHeaderInfo ( ) {
173
-  if (ramp != NULL) {
174
-    if (!isInCacheAllScanHeaderInfo) {
175
-      // Rprintf("Read from disk.\n ");
176
-      int N = ramp->getLastScan();
177
-      rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
178
-      ScanHeaderStruct scanHeader;
179
-      Rcpp::IntegerVector seqNum(N); // number in sequence observed file (1-based)
180
-      Rcpp::IntegerVector acquisitionNum(N); // scan number as declared in File (may be gaps)
181
-      Rcpp::IntegerVector  msLevel(N);
182
-      Rcpp::IntegerVector  polarity(N);
183
-      Rcpp::IntegerVector  peaksCount(N);
184
-      Rcpp::NumericVector totIonCurrent(N);
185
-      Rcpp::NumericVector retentionTime(N);        /* in seconds */
186
-      Rcpp::NumericVector basePeakMZ(N);
187
-      Rcpp::NumericVector basePeakIntensity(N);
188
-      Rcpp::NumericVector collisionEnergy(N);
189
-      Rcpp::NumericVector ionisationEnergy(N);
190
-      Rcpp::NumericVector lowMZ(N);
191
-      Rcpp::NumericVector highMZ(N);
192
-      Rcpp::IntegerVector precursorScanNum(N); /* only if MS level > 1 */
193
-      Rcpp::NumericVector precursorMZ(N);  /* only if MS level > 1 */
194
-      Rcpp::IntegerVector precursorCharge(N);  /* only if MS level > 1 */
195
-      Rcpp::NumericVector precursorIntensity(N);  /* only if MS level > 1 */
196
-      // char scanType[SCANTYPE_LENGTH];
197
-      // char activationMethod[SCANTYPE_LENGTH];
198
-      // char possibleCharges[SCANTYPE_LENGTH];
199
-      // int numPossibleCharges;
200
-      // bool possibleChargesArray[CHARGEARRAY_LENGTH]; /* NOTE: does NOT include "precursorCharge" information; only from "possibleCharges" */
201
-      Rcpp::IntegerVector mergedScan(N);  /* only if MS level > 1 */
202
-      Rcpp::IntegerVector mergedResultScanNum(N); /* scan number of the resultant merged scan */
203
-      Rcpp::IntegerVector mergedResultStartScanNum(N); /* smallest scan number of the scanOrigin for merged scan */
204
-      Rcpp::IntegerVector mergedResultEndScanNum(N); /* largest scan number of the scanOrigin for merged scan */
205
-      
206
-      for (int whichScan=1; whichScan <= N; whichScan++) {
207
-	readHeader(ramp->m_handle, ramp->m_scanOffsets[whichScan], &scanHeader);
208
-	seqNum[whichScan-1] = scanHeader.seqNum;
209
-	acquisitionNum[whichScan-1] = scanHeader.acquisitionNum;
210
-	msLevel[whichScan-1] = scanHeader.msLevel;
211
-	polarity[whichScan-1] = scanHeader.polarity;
212
-	peaksCount[whichScan-1] = scanHeader.peaksCount;
213
-	totIonCurrent[whichScan-1] = scanHeader.totIonCurrent;
214
-	retentionTime[whichScan-1] = scanHeader.retentionTime;
215
-	basePeakMZ[whichScan-1] = scanHeader.basePeakMZ;
216
-	basePeakIntensity[whichScan-1] = scanHeader.basePeakIntensity;
217
-	collisionEnergy[whichScan-1] = scanHeader.collisionEnergy;
218
-	ionisationEnergy[whichScan-1] = scanHeader.ionisationEnergy;
219
-	lowMZ[whichScan-1] = scanHeader.lowMZ;
220
-	highMZ[whichScan-1] = scanHeader.highMZ;
221
-	precursorScanNum[whichScan-1] = scanHeader.precursorScanNum;
222
-	precursorMZ[whichScan-1] = scanHeader.precursorMZ;
223
-	precursorCharge[whichScan-1] = scanHeader.precursorCharge;
224
-	precursorIntensity[whichScan-1] = scanHeader.precursorIntensity;
225
-	mergedScan[whichScan-1] = scanHeader.mergedScan;
226
-	mergedResultScanNum[whichScan-1] = scanHeader.mergedResultScanNum;
227
-	mergedResultStartScanNum[whichScan-1] = scanHeader.mergedResultStartScanNum;
228
-	mergedResultEndScanNum[whichScan-1] = scanHeader.mergedResultEndScanNum;
229
-      }
191
+Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
192
+{
193
+    if (ramp != NULL)
194
+    {
195
+        if (!isInCacheAllScanHeaderInfo)
196
+        {
197
+            // Rprintf("Read from disk.\n ");
198
+            int N = ramp->getLastScan();
199
+            rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
200
+            ScanHeaderStruct scanHeader;
201
+            Rcpp::IntegerVector seqNum(N); // number in sequence observed file (1-based)
202
+            Rcpp::IntegerVector acquisitionNum(N); // scan number as declared in File (may be gaps)
203
+            Rcpp::IntegerVector  msLevel(N);
204
+            Rcpp::IntegerVector  polarity(N);
205
+            Rcpp::IntegerVector  peaksCount(N);
206
+            Rcpp::NumericVector totIonCurrent(N);
207
+            Rcpp::NumericVector retentionTime(N);        /* in seconds */
208
+            Rcpp::NumericVector basePeakMZ(N);
209
+            Rcpp::NumericVector basePeakIntensity(N);
210
+            Rcpp::NumericVector collisionEnergy(N);
211
+            Rcpp::NumericVector ionisationEnergy(N);
212
+            Rcpp::NumericVector lowMZ(N);
213
+            Rcpp::NumericVector highMZ(N);
214
+            Rcpp::IntegerVector precursorScanNum(N); /* only if MS level > 1 */
215
+            Rcpp::NumericVector precursorMZ(N);  /* only if MS level > 1 */
216
+            Rcpp::IntegerVector precursorCharge(N);  /* only if MS level > 1 */
217
+            Rcpp::NumericVector precursorIntensity(N);  /* only if MS level > 1 */
218
+            // char scanType[SCANTYPE_LENGTH];
219
+            // char activationMethod[SCANTYPE_LENGTH];
220
+            // char possibleCharges[SCANTYPE_LENGTH];
221
+            // int numPossibleCharges;
222
+            // bool possibleChargesArray[CHARGEARRAY_LENGTH]; /* NOTE: does NOT include "precursorCharge" information; only from "possibleCharges" */
223
+            Rcpp::IntegerVector mergedScan(N);  /* only if MS level > 1 */
224
+            Rcpp::IntegerVector mergedResultScanNum(N); /* scan number of the resultant merged scan */
225
+            Rcpp::IntegerVector mergedResultStartScanNum(N); /* smallest scan number of the scanOrigin for merged scan */
226
+            Rcpp::IntegerVector mergedResultEndScanNum(N); /* largest scan number of the scanOrigin for merged scan */
227
+
228
+            for (int whichScan=1; whichScan <= N; whichScan++)
229
+            {
230
+                readHeader(ramp->m_handle, ramp->m_scanOffsets[whichScan], &scanHeader);
231
+                seqNum[whichScan-1] = scanHeader.seqNum;
232
+                acquisitionNum[whichScan-1] = scanHeader.acquisitionNum;
233
+                msLevel[whichScan-1] = scanHeader.msLevel;
234
+                polarity[whichScan-1] = scanHeader.polarity;
235
+                peaksCount[whichScan-1] = scanHeader.peaksCount;
236
+                totIonCurrent[whichScan-1] = scanHeader.totIonCurrent;
237
+                retentionTime[whichScan-1] = scanHeader.retentionTime;
238
+                basePeakMZ[whichScan-1] = scanHeader.basePeakMZ;
239
+                basePeakIntensity[whichScan-1] = scanHeader.basePeakIntensity;
240
+                collisionEnergy[whichScan-1] = scanHeader.collisionEnergy;
241
+                ionisationEnergy[whichScan-1] = scanHeader.ionisationEnergy;
242
+                lowMZ[whichScan-1] = scanHeader.lowMZ;
243
+                highMZ[whichScan-1] = scanHeader.highMZ;
244
+                precursorScanNum[whichScan-1] = scanHeader.precursorScanNum;
245
+                precursorMZ[whichScan-1] = scanHeader.precursorMZ;
246
+                precursorCharge[whichScan-1] = scanHeader.precursorCharge;
247
+                precursorIntensity[whichScan-1] = scanHeader.precursorIntensity;
248
+                mergedScan[whichScan-1] = scanHeader.mergedScan;
249
+                mergedResultScanNum[whichScan-1] = scanHeader.mergedResultScanNum;
250
+                mergedResultStartScanNum[whichScan-1] = scanHeader.mergedResultStartScanNum;
251
+                mergedResultEndScanNum[whichScan-1] = scanHeader.mergedResultEndScanNum;
252
+            }
230 253
 
231
-      ListBuilder header;
232
-      header.add("seqNum", seqNum);
233
-      header.add("acquisitionNum",           acquisitionNum);
234
-      header.add("msLevel",                  msLevel);
235
-      header.add("polarity",               polarity);
236
-      header.add("peaksCount",               peaksCount);
237
-      header.add("totIonCurrent",            totIonCurrent);
238
-      header.add("retentionTime",            retentionTime);
239
-      header.add("basePeakMZ",               basePeakMZ);
240
-      header.add("basePeakIntensity",        basePeakIntensity);
241
-      header.add("collisionEnergy",          collisionEnergy);
242
-      header.add("ionisationEnergy",         ionisationEnergy);
243
-      header.add("lowMZ",                    lowMZ);
244
-      header.add("highMZ",                   highMZ);
245
-      header.add("precursorScanNum",         precursorScanNum);
246
-      header.add("precursorMZ",              precursorMZ);
247
-      header.add("precursorCharge",          precursorCharge);
248
-      header.add("precursorIntensity",       precursorIntensity);
249
-      //  header.add("scanType",                 scanType);
250
-      //  header.add("activationMethod",         activationMethod);
251
-      //  header.add("possibleCharges",          possibleCharges);
252
-      //  header.add("numPossibleCharges",       numPossibleCharges);
253
-						  //  header.add("possibleChargesArray",     possibleChargesArray);
254
-      header.add("mergedScan",               mergedScan);
255
-      header.add("mergedResultScanNum",      mergedResultScanNum);
256
-      header.add("mergedResultStartScanNum", mergedResultStartScanNum);
257
-      header.add("mergedResultEndScanNum",   mergedResultEndScanNum);
254
+            ListBuilder header;
255
+            header.add("seqNum", seqNum);
256
+            header.add("acquisitionNum",           acquisitionNum);
257
+            header.add("msLevel",                  msLevel);
258
+            header.add("polarity",               polarity);
259
+            header.add("peaksCount",               peaksCount);
260
+            header.add("totIonCurrent",            totIonCurrent);
261
+            header.add("retentionTime",            retentionTime);
262
+            header.add("basePeakMZ",               basePeakMZ);
263
+            header.add("basePeakIntensity",        basePeakIntensity);
264
+            header.add("collisionEnergy",          collisionEnergy);
265
+            header.add("ionisationEnergy",         ionisationEnergy);
266
+            header.add("lowMZ",                    lowMZ);
267
+            header.add("highMZ",                   highMZ);
268
+            header.add("precursorScanNum",         precursorScanNum);
269
+            header.add("precursorMZ",              precursorMZ);
270
+            header.add("precursorCharge",          precursorCharge);
271
+            header.add("precursorIntensity",       precursorIntensity);
272
+            //  header.add("scanType",                 scanType);
273
+            //  header.add("activationMethod",         activationMethod);
274
+            //  header.add("possibleCharges",          possibleCharges);
275
+            //  header.add("numPossibleCharges",       numPossibleCharges);
276
+            //  header.add("possibleChargesArray",     possibleChargesArray);
277
+            header.add("mergedScan",               mergedScan);
278
+            header.add("mergedResultScanNum",      mergedResultScanNum);
279
+            header.add("mergedResultStartScanNum", mergedResultStartScanNum);
280
+            header.add("mergedResultEndScanNum",   mergedResultEndScanNum);
258 281
 
259
-      allScanHeaderInfo = header.get();
260
-      isInCacheAllScanHeaderInfo = TRUE;
261
-    } else {
262
-      // Rprintf("Read from cache.\n ");
282
+            allScanHeaderInfo = header.get();
283
+            isInCacheAllScanHeaderInfo = TRUE;
284
+        }
285
+        else
286
+        {
287
+            // Rprintf("Read from cache.\n ");
288
+        }
289
+        return(allScanHeaderInfo);
263 290
     }
264
-    return(allScanHeaderInfo);
265
-  }
266
-  Rprintf("Warning: Ramp not yet initialized.\n ");
267
-  return Rcpp::DataFrame::create( );
291
+    Rprintf("Warning: Ramp not yet initialized.\n ");
292
+    return Rcpp::DataFrame::create( );
268 293
 }
269 294
 
270
-Rcpp::List
271
-RcppRamp::getPeakList ( int whichScan ) {
272
-  if (ramp != NULL) {
273
-    if ((whichScan <= 0) || (whichScan > ramp->getLastScan())) {
274
-      Rprintf("Index whichScan out of bounds [1 ... %d].\n", ramp->getLastScan());
275
-      return Rcpp::List::create( );
295
+Rcpp::List RcppRamp::getPeakList ( int whichScan )
296
+{
297
+    if (ramp != NULL)
298
+    {
299
+        if ((whichScan <= 0) || (whichScan > ramp->getLastScan()))
300
+        {
301
+            Rprintf("Index whichScan out of bounds [1 ... %d].\n", ramp->getLastScan());
302
+            return Rcpp::List::create( );
303
+        }
304
+        rampPeakList *pl = ramp->getPeakList( whichScan );
305
+        int peaksCount = 0;
306
+        if (pl != NULL)
307
+        {
308
+            peaksCount = pl->getPeakCount();
309
+        }
310
+        Rcpp::NumericMatrix peaks(peaksCount, 2);
311
+        if (pl != NULL)
312
+        {
313
+            rampPeakInfoStruct *peak;
314
+            peak = pl->getPeak(0);
315
+            peaks(0,0) = peak->mz;
316
+            peaks(0,1) = peak->intensity;
317
+            for (int i=1; i < peaksCount; i++)
318
+            {
319
+                peak++;
320
+                peaks(i,0) = peak->mz;
321
+                peaks(i,1) = peak->intensity;
322
+            }
323
+            delete pl;
324
+        }
325
+        return Rcpp::List::create(
326
+                   Rcpp::_["peaksCount"]  = peaksCount,
327
+                   Rcpp::_["peaks"]  = peaks
328
+               ) ;
276 329
     }
277
-    rampPeakList *pl = ramp->getPeakList( whichScan );
278
-    int peaksCount = 0;
279
-    if (pl != NULL) {
280
-      peaksCount = pl->getPeakCount();
281
-    } 
282
-    Rcpp::NumericMatrix peaks(peaksCount, 2);
283
-    if (pl != NULL) {
284
-      rampPeakInfoStruct *peak;
285
-      peak = pl->getPeak(0);
286
-      peaks(0,0) = peak->mz;
287
-      peaks(0,1) = peak->intensity;
288
-      for (int i=1; i < peaksCount; i++) {
289
-	peak++;
290
-	peaks(i,0) = peak->mz;
291
-	peaks(i,1) = peak->intensity;
292
-      }
293
-      delete pl;
294
-    }
295
-    return Rcpp::List::create(