- chromatogramHeader returns NA instead of 0 if precursor or product isoaltion
window offset is not defined.
... | ... |
@@ -854,7 +854,7 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom ) |
854 | 854 |
Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichChrom) |
855 | 855 |
{ |
856 | 856 |
if (msd != NULL) { |
857 |
- CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); // Ask CHRIS if I'm correctly dereferencing this... |
|
857 |
+ CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); |
|
858 | 858 |
ChromatogramListPtr clp = msd->run.chromatogramListPtr; |
859 | 859 |
if (clp.get() == 0) { |
860 | 860 |
Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format."); |
... | ... |
@@ -894,8 +894,8 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh |
894 | 894 |
polarity[i] = (param.cvid==MS_negative_scan ? 0 : (param.cvid==MS_positive_scan ? +1 : -1 ) ); |
895 | 895 |
if (!ch->precursor.empty()) { |
896 | 896 |
precursorIsolationWindowTargetMZ[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_target_m_z).value.empty() ? NA_REAL : ch->precursor.isolationWindow.cvParam(MS_isolation_window_target_m_z).valueAs<double>(); |
897 |
- precursorIsolationWindowLowerOffset[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_lower_offset).value.empty() ? 0 : ch->precursor.isolationWindow.cvParam(MS_isolation_window_lower_offset).valueAs<double>(); |
|
898 |
- precursorIsolationWindowUpperOffset[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_upper_offset).value.empty() ? 0 : ch->precursor.isolationWindow.cvParam(MS_isolation_window_upper_offset).valueAs<double>(); |
|
897 |
+ precursorIsolationWindowLowerOffset[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_lower_offset).value.empty() ? NA_REAL : ch->precursor.isolationWindow.cvParam(MS_isolation_window_lower_offset).valueAs<double>(); |
|
898 |
+ precursorIsolationWindowUpperOffset[i] = ch->precursor.isolationWindow.cvParam(MS_isolation_window_upper_offset).value.empty() ? NA_REAL : ch->precursor.isolationWindow.cvParam(MS_isolation_window_upper_offset).valueAs<double>(); |
|
899 | 899 |
precursorCollisionEnergy[i] = ch->precursor.activation.cvParam(MS_collision_energy).value.empty() ? NA_REAL : ch->precursor.activation.cvParam(MS_collision_energy).valueAs<double>(); |
900 | 900 |
} else { |
901 | 901 |
precursorIsolationWindowTargetMZ[i] = NA_REAL; |
... | ... |
@@ -905,8 +905,8 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh |
905 | 905 |
} |
906 | 906 |
if (!ch->product.empty()) { |
907 | 907 |
productIsolationWindowTargetMZ[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_target_m_z).value.empty() ? NA_REAL : ch->product.isolationWindow.cvParam(MS_isolation_window_target_m_z).valueAs<double>(); |
908 |
- productIsolationWindowLowerOffset[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_lower_offset).value.empty() ? 0 : ch->product.isolationWindow.cvParam(MS_isolation_window_lower_offset).valueAs<double>(); |
|
909 |
- productIsolationWindowUpperOffset[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_upper_offset).value.empty() ? 0 : ch->product.isolationWindow.cvParam(MS_isolation_window_upper_offset).valueAs<double>(); |
|
908 |
+ productIsolationWindowLowerOffset[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_lower_offset).value.empty() ? NA_REAL : ch->product.isolationWindow.cvParam(MS_isolation_window_lower_offset).valueAs<double>(); |
|
909 |
+ productIsolationWindowUpperOffset[i] = ch->product.isolationWindow.cvParam(MS_isolation_window_upper_offset).value.empty() ? NA_REAL : ch->product.isolationWindow.cvParam(MS_isolation_window_upper_offset).valueAs<double>(); |
|
910 | 910 |
} else { |
911 | 911 |
productIsolationWindowTargetMZ[i] = NA_REAL; |
912 | 912 |
productIsolationWindowLowerOffset[i] = NA_REAL; |