1. mzR
  2. src
  3. RcppRamp.cpp
Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
Showing1 changed files
src/RcppRamp.cpp
History View file @e3f79ff5f7
1 1 
deleted file mode 100644
... ... 
@@ -1,440 +0,0 @@
1 
-#include "RcppRamp.h"
2 
-
3 
-RcppRamp::RcppRamp()
4 
-{
5 
-    ramp = NULL;
6 
-    runInfo = Rcpp::List::create( );
7 
-    isInCacheRunInfo = FALSE;
8 
-    instrumentInfo = Rcpp::List::create( );
9 
-    isInCacheInstrumentInfo = FALSE;
10 
-    allScanHeaderInfo = Rcpp::DataFrame::create( );
11 
-    isInCacheAllScanHeaderInfo = FALSE;
12 
-    filename = Rcpp::StringVector::create( );
13 
-}
14 
-
15 
-RcppRamp::~RcppRamp()
16 
-{
17 
-    RcppRamp::close();
18 
-}
19 
-
20 
-void RcppRamp::open( const char* fileName, bool declaredScansOnly )
21 
-{
22 
-    RcppRamp::close();
23 
-    ramp = new cRamp(fileName, declaredScansOnly);
24 
-    if (ramp->OK())
25 
-    {
26 
-        filename = Rcpp::StringVector::create( fileName );
27 
-    }
28 
-    else
29 
-    {
30 
-        RcppRamp::close();
31 
-        Rprintf("Failed to open file.\n ");
32 
-    }
33 
-}
34 
-
35 
-void RcppRamp::close()
36 
-{
37 
-    if (ramp != NULL)
38 
-    {
39 
-        delete ramp;
40 
-        ramp = NULL;
41 
-        runInfo = Rcpp::List::create( );
42 
-        isInCacheRunInfo = FALSE;
43 
-        instrumentInfo = Rcpp::List::create( );
44 
-        isInCacheInstrumentInfo = FALSE;
45 
-        allScanHeaderInfo = Rcpp::List::create( );
46 
-        isInCacheAllScanHeaderInfo = FALSE;
47 
-        filename = Rcpp::StringVector::create( );
48 
-    }
49 
-}
50 
-
51 
-
52 
-Rcpp::StringVector RcppRamp::getFilename (  )
53 
-{
54 
-    if (ramp != NULL)
55 
-    {
56 
-        return filename;
57 
-    }
58 
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
59 
-    return filename;
60 
-}
61 
-
62 
-Rcpp::List RcppRamp::getRunInfo (  )
63 
-{
64 
-    if (ramp != NULL)
65 
-    {
66 
-        if (!isInCacheRunInfo)
67 
-        {
68 
-            // Rprintf("Read from disk.\n ");
69 
-            rampRunInfo *info = ramp->getRunInfo();
70 
-            RunHeaderStruct data = info->m_data;
71 
-            delete info;
72 
-            runInfo = Rcpp::List::create(
73 
-                          Rcpp::_["scanCount"]  = data.scanCount,
74 
-                          Rcpp::_["lowMZ"]      = data.lowMZ,
75 
-                          Rcpp::_["highMZ"]     = data.highMZ,
76 
-                          Rcpp::_["startMZ"]    = data.startMZ,
77 
-                          Rcpp::_["endMZ"]      = data.endMZ,
78 
-                          Rcpp::_["dStartTime"] = data.dStartTime,
79 
-                          Rcpp::_["dEndTime"]   = data.dEndTime
80 
-                      );
81 
-            isInCacheRunInfo = TRUE;
82 
-        }
83 
-        else
84 
-        {
85 
-            // Rprintf("Read from cache.\n ");
86 
-        }
87 
-        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
101 
-
102 
-            if (info != NULL)
103 
-            {
104 
-                InstrumentStruct * data = info->m_instrumentStructPtr;
105 
-
106 
-                instrumentInfo = Rcpp::List::create(
107 
-                                     Rcpp::_["manufacturer"]  = std::string(data->manufacturer),
108 
-                                     Rcpp::_["model"]         = std::string(data->model),
109 
-                                     Rcpp::_["ionisation"]    = std::string(data->ionisation),
110 
-                                     Rcpp::_["analyzer"]      = std::string(data->analyzer),
111 
-                                     Rcpp::_["detector"]      = std::string(data->detector)
112 
-                                 ) ;
113 
-                delete info;
114 
-            }
115 
-            else
116 
-            {
117 
-                instrumentInfo = Rcpp::List::create(
118 
-                                     Rcpp::_["manufacturer"]  = "",
119 
-                                     Rcpp::_["model"]         = "",
120 
-                                     Rcpp::_["ionisation"]    = "",
121 
-                                     Rcpp::_["analyzer"]      = "",
122 
-                                     Rcpp::_["detector"]      = ""
123 
-                                 ) ;
124 
-            }
125 
-            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);
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);
196 
-        names.push_back("injectionTime");
197 
-        header[i++] = 0;
198 
-
199 
-        header.attr("names") = names;
200 
-
201 
-        return  header;
202 
-    }
203 
-    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
204 
-    return Rcpp::List::create( );
205 
-}
206 
-
207 
-Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
208 
-{
209 
-    if (ramp != NULL)
210 
-    {
211 
-        if (!isInCacheAllScanHeaderInfo)
212 
-        {
213 
-            // Rprintf("Read from disk.\n ");
214 
-            int N = ramp->getLastScan();
215 
-            rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
216 
-            ScanHeaderStruct scanHeader;
217 
-            Rcpp::IntegerVector seqNum(N); // number in sequence observed file (1-based)
218 
-            Rcpp::IntegerVector acquisitionNum(N); // scan number as declared in File (may be gaps)
219 
-            Rcpp::IntegerVector  msLevel(N);
220 
-            Rcpp::IntegerVector  polarity(N);
221 
-            Rcpp::IntegerVector  peaksCount(N);
222 
-            Rcpp::NumericVector totIonCurrent(N);
223 
-            Rcpp::NumericVector retentionTime(N);        /* in seconds */
224 
-            Rcpp::NumericVector basePeakMZ(N);
225 
-            Rcpp::NumericVector basePeakIntensity(N);
226 
-            Rcpp::NumericVector collisionEnergy(N);
227 
-            Rcpp::NumericVector ionisationEnergy(N);
228 
-            Rcpp::NumericVector lowMZ(N);
229 
-            Rcpp::NumericVector highMZ(N);
230 
-            Rcpp::IntegerVector precursorScanNum(N); /* only if MS level > 1 */
231 
-            Rcpp::NumericVector precursorMZ(N);  /* only if MS level > 1 */
232 
-            Rcpp::IntegerVector precursorCharge(N);  /* only if MS level > 1 */
233 
-            Rcpp::NumericVector precursorIntensity(N);  /* only if MS level > 1 */
234 
-            Rcpp::IntegerVector mergedScan(N);  /* only if MS level > 1 */
235 
-            Rcpp::IntegerVector mergedResultScanNum(N); /* scan number of the resultant merged scan */
236 
-            Rcpp::IntegerVector mergedResultStartScanNum(N); /* smallest scan number of the scanOrigin for merged scan */
237 
-            Rcpp::IntegerVector mergedResultEndScanNum(N); /* largest scan number of the scanOrigin for merged scan */
238 
-
239 
-            for (int whichScan=1; whichScan <= N; whichScan++)
240 
-            {
241 
-                readHeader(ramp->m_handle, ramp->m_scanOffsets[whichScan], &scanHeader);
242 
-                seqNum[whichScan-1] = scanHeader.seqNum;
243 
-                acquisitionNum[whichScan-1] = scanHeader.acquisitionNum;
244 
-                msLevel[whichScan-1] = scanHeader.msLevel;
245 
-                polarity[whichScan-1] = scanHeader.polarity;
246 
-                peaksCount[whichScan-1] = scanHeader.peaksCount;
247 
-                totIonCurrent[whichScan-1] = scanHeader.totIonCurrent;
248 
-                retentionTime[whichScan-1] = scanHeader.retentionTime;
249 
-                basePeakMZ[whichScan-1] = scanHeader.basePeakMZ;
250 
-                basePeakIntensity[whichScan-1] = scanHeader.basePeakIntensity;
251 
-                collisionEnergy[whichScan-1] = scanHeader.collisionEnergy;
252 
-                ionisationEnergy[whichScan-1] = scanHeader.ionisationEnergy;
253 
-                lowMZ[whichScan-1] = scanHeader.lowMZ;
254 
-                highMZ[whichScan-1] = scanHeader.highMZ;
255 
-                precursorScanNum[whichScan-1] = scanHeader.precursorScanNum;
256 
-                precursorMZ[whichScan-1] = scanHeader.precursorMZ;
257 
-                precursorCharge[whichScan-1] = scanHeader.precursorCharge;
258 
-                precursorIntensity[whichScan-1] = scanHeader.precursorIntensity;
259 
-                mergedScan[whichScan-1] = scanHeader.mergedScan;
260 
-                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);
273 
-            names.push_back("msLevel");
274 
-            header[i++] =Rcpp::wrap(msLevel);
275 
-            names.push_back("polarity");
276 
-            header[i++] =Rcpp::wrap(polarity);
277 
-            names.push_back("peaksCount");
278 
-            header[i++] =Rcpp::wrap(peaksCount);
279 
-            names.push_back("totIonCurrent");
280 
-            header[i++] =Rcpp::wrap(totIonCurrent);
281 
-            names.push_back("retentionTime");
282 
-            header[i++] =Rcpp::wrap(retentionTime);
283 
-            names.push_back("basePeakMZ");
284 
-            header[i++] =Rcpp::wrap(basePeakMZ);
285 
-            names.push_back("basePeakIntensity");
286 
-            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
src/RcppRamp.cpp
History View file @f8520e7ab9
... ... 
@@ -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
src/RcppRamp.cpp
History View file @6523a40958
... ... 
@@ -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
src/RcppRamp.cpp
History View file @da59551778
... ... 
@@ -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
src/RcppRamp.cpp
History View file @84a4b1664f
... ... 
@@ -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(