Fixing issue #63 related to MS3 data: some values were set only for M…

…S1 and MS2 levels

Also some refactoring and added a warning on run slice insertion failure (that should not happen anymore !)

README.md

@@ -19,11 +19,17 @@ For details about mzDB concepts (scanSlice, runSlice...) and specifications, hav
 ### Roadmap v0.9.10
 
 Bug fixes:
-- [x] The field mzdb.param_tree can be corrupted for some Thermo raw files (#39)
-- [x] Find and fix memory leak for AB Sciex data (#38)
-- [ ] Issue #26 is for AB Sciex DIA acquisition (and accession 1001954)
 - [x] Issue #24 sample name is empty for AB Sciex analyses (also check for Bruker)
-- [ ] Improve cycle filtering by checking cycle number before centroiding data (#40)
+- [x] Issue #26 is for AB Sciex DIA acquisition (and accession 1001954)
+- [x] Issue #38: Find and fix memory leak for AB Sciex data
+- [x] Issue #39: The field mzdb.param_tree can be corrupted for some Thermo raw files
+- [x] Issue #57: Check MS3 analyses
+- [x] Issue #60: Missing spectra in some mzDB files
+- [x] Issue #61: Problem with DIA analyses
+
+Improvements
+- [x] Issue #40: Improve cycle filtering by checking cycle number before centroiding data
+- [x] Issue #62: Improving DIA storing in bounding boxes
 
 ### Roadmap v1.0
 

pwiz_mzdb/mzdb/writer/bb_inserter.hpp

@@ -110,9 +110,6 @@ class mzBBInserter {
         auto lastRunSliceIdx = bbs.back()->runSliceIdx();
 
         if (m_lastMinRunSliceIdx && firstRunSliceIdx < m_lastMinRunSliceIdx) {
-            //printf("The first spectrum does not contain a low mass contained in the first runSlice.\n");
-            //printf("This is a bug and it will be fixed in a next release of raw2mzdb.\n");
-            //exit(0);
             LOG(ERROR) << "The first spectrum does not contain a low mass contained in the first runSlice.";
             LOG(ERROR) << "This is a bug and it will be fixed in a next release of raw2mzdb.";
             exit(EXIT_FAILURE);
@@ -134,7 +131,12 @@ class mzBBInserter {
                     sqlite3_bind_double(m_mzdbFile.stmt, 5, moz + invBBheight);
                     sqlite3_bind_null(m_mzdbFile.stmt, 6);
                     sqlite3_bind_int(m_mzdbFile.stmt, 7, 1);
-                    sqlite3_step(m_mzdbFile.stmt);
+                    int rc = sqlite3_step(m_mzdbFile.stmt);
+                    if (rc != SQLITE_DONE) {
+                        LOG(ERROR) << "Error inserting run slice, request was:";
+                        LOG(INFO) << "INSERT INTO run_slice VALUES (" << m_runSliceCount << ", " << msLevel << ", " << m_runSliceCount << ", " << moz << ", " << (moz+invBBheight) << ", null, 1);";
+                        LOG(ERROR) << "SQLITE ERROR CODE: " << rc <<":" << sqlite3_errmsg(m_mzdbFile.db);
+                    }
                     sqlite3_reset(m_mzdbFile.stmt);
                     m_runSliceCount++;
                 }
@@ -158,7 +160,12 @@ class mzBBInserter {
                 sqlite3_bind_double(m_mzdbFile.stmt, 5, moz + invBBheight);
                 sqlite3_bind_null(m_mzdbFile.stmt, 6);
                 sqlite3_bind_int(m_mzdbFile.stmt, 7, 1);
-                sqlite3_step(m_mzdbFile.stmt);
+                int rc = sqlite3_step(m_mzdbFile.stmt);
+                if (rc != SQLITE_DONE) {
+                    LOG(ERROR) << "Error inserting run slice, request was:";
+                    LOG(INFO) << "INSERT INTO run_slice VALUES (" << m_runSliceCount << ", " << msLevel << ", " << m_runSliceCount << ", " << moz << ", " << (moz+invBBheight) << ", null, 1);";
+                    LOG(ERROR) << "SQLITE ERROR CODE: " << rc <<":" << sqlite3_errmsg(m_mzdbFile.db);
+                }
                 sqlite3_reset(m_mzdbFile.stmt);
                 m_runSliceCount++;
             }

pwiz_mzdb/mzdb/writer/dda_consumer.h

@@ -63,7 +63,7 @@ class mzDDAConsumer:  QueueingPolicy, mzSpectrumInserter, mzBBInserter {
 
 private:
     // list of all possible data encodings, those who are really used will be inserted on the fly in spectrum_inserter.h
-    vector<DataEncoding> m_dataEncodings;
+
 public:
 
     /**
@@ -106,9 +106,9 @@ class mzDDAConsumer:  QueueingPolicy, mzSpectrumInserter, mzBBInserter {
             const int& msLevel = cycleCollection->msLevel;
 
             // TODO check if spectra are correctly inserted (spectrum values are distinguished for PROFILE and CENTROID/FITTED)
-            this->buildAndInsertData<h_mz_t, h_int_t, l_mz_t, l_int_t>(msLevel, bbMzWidthByMsLevel[msLevel],
-                                                                       highResSpectra, lowResSpectra, runSlices[msLevel]);
-
+            double bbMzWidth = (msLevel == 1 ? bbMzWidthByMsLevel[1] : bbMzWidthByMsLevel[2]);
+            this->buildAndInsertData<h_mz_t, h_int_t, l_mz_t, l_int_t>(msLevel, bbMzWidth, highResSpectra, lowResSpectra, runSlices[msLevel]);
+            
             int newPercent = (int) (((float) progressionCount / nscans * 100.0));
             if (newPercent == lastPercent + 2.0) {
                 mzdb::printProgBar(newPercent);
@@ -128,7 +128,6 @@ class mzDDAConsumer:  QueueingPolicy, mzSpectrumInserter, mzBBInserter {
                   mzParamsCollecter& paramsCollecter,
                   pwiz::msdata::CVID rawFileFormat,
                   vector<DataEncoding> dataEncodings):
-        m_dataEncodings(dataEncodings),
         QueueingPolicy(queue),
         mzSpectrumInserter(mzdbFile, paramsCollecter, rawFileFormat, dataEncodings),
         mzBBInserter(mzdbFile) {}

pwiz_mzdb/mzdb/writer/mzdb_writer.hpp

@@ -399,12 +399,9 @@ class mzDBWriter: private boost::noncopyable {
         bbHeightManager[1] = invms1;
         bbWidthManager[1] = m_mzdbFile.bbWidth;
 
-        // TODO check if it works: MAX_MS used to be fixed at 2 so this loop was never used before !!
-        //for (int msnb = 2; msnb <= MAX_MS; ++msnb) {
-        for (int msnb = 2; msnb <= max_ms_level; ++msnb) {
-            bbHeightManager[msnb] = invmsn;
-            bbWidthManager[msnb] = m_mzdbFile.bbWidthMsn;
-        }
+        // use a single value for every MS level > 1
+        bbHeightManager[2] = invmsn;
+        bbWidthManager[2] = m_mzdbFile.bbWidthMsn;
 
         //---begin a new transaction
         sqlite3_exec(m_mzdbFile.db, "BEGIN;", 0, 0, 0);