@@ -3,6 +3,8 @@ CHANGES IN VERSION 2.15.1

  o Fix typo (see https://github.com/sneumann/mzR/pull/162)

  o New .hasSpectra and .hasChromatograms private function (see

    https://github.com/lgatto/MSnbase/issues/343)

+ o Fix bug in score when more cvParams than expected are read - see

+   https://github.com/sneumann/mzR/issues/136 <2018-05-26 Sat>

 CHANGES IN VERSION 2.15.0

 -------------------------

@@ -35,7 +37,7 @@ CHANGES IN VERSION 2.13.3

  o Link against Rhdf5lib, allows to read mz5 also on Windows

  o Use Rhdf5lib 1.1.4 with c++ headers in /include

  o fix BiocStyle related issue in Vignette on Windows

- 

+

 CHANGES IN VERSION 2.13.2

 --------------------------

  o Add chromatogramHeader method to read header information for chromatograms

@@ -47,12 +49,12 @@ CHANGES IN VERSION 2.13.1

    the header function (see MSnbase issue #278).

  o openMsFile automatically determine the backend to use based on file extension

    and content.

- 

+

 CHANGES IN VERSION 2.11.11

 --------------------------

  o Fix problem in writeMSData: ensure precursor data is saved even if precursor

    scan is not available (see MSnbase issue #245).

- 

+

 CHANGES IN VERSION 2.11.10

 --------------------------

  o Fix problem that can cause a SEGFAULT in writeMSData/copyWriteMSData when MS

@@ -70,33 +72,33 @@ CHANGES IN VERSION 2.11.8

  o Report the spectrum ID in the header data.frame (column spectrumId).

  o Fix in copyWriteMSData and writeMSData ensuring that MSn data is correctly

  o Import pwiz r11174 fix for mzML without <componentList> (see #113).

- 

+

 CHANGES IN VERSION 2.11.7

 -------------------------

  o Nothing yet.

  o Import fix by Brian Pratt (pwiz r11174) for mzML without <componentList>

-   Another way to fix #113 

+   Another way to fix #113

  o Removing mz5 support from manual page, as currently unsupported.

- 

+

 CHANGES IN VERSION 2.11.6

 -------------------------

  o runInfo returns the run start time stamp from files providing this

    information (mzML files).

- 

+

 CHANGES IN VERSION 2.11.5

 -------------------------

  o writeMSData and copyWriteMSData functions enabling to export MS data to

    mzML or mzXML files.

- 

+

 CHANGES IN VERSION 2.11.4

 -------------------------

  o Use full TMT file pattern to select a single file

- 

+

 CHANGES IN VERSION 2.11.3

 -------------------------

  o Read ion injection time from mzML files and add it to the data.frame returned

    by the header function.

- 

+

 CHANGES IN VERSION 2.11.2

 -------------------------

  o New getScanHeaderInfo and getAllScanHeaderInfo implementations for the pwiz

@@ -109,7 +111,7 @@ CHANGES IN VERSION 2.11.1

 CHANGES IN VERSION 2.11.0

 -------------------------

  o Bioc devel 3.6

- 

+

 CHANGES IN VERSION 2.10.0

 -------------------------

  o Bioc release 3.5

@@ -120,7 +122,7 @@ CHANGES IN VERSION 2.9.11

 CHANGES IN VERSION 2.9.10

 -------------------------

- o Remove register keyword causing WARNING. 

+ o Remove register keyword causing WARNING.

 CHANGES IN VERSION 2.9.9

 ------------------------

@@ -137,25 +139,25 @@ CHANGES IN VERSION 2.9.7

 CHANGES IN VERSION 2.9.6

 ------------------------

  o Compile on macOS, but hdf5 path hard-coded

- 

+

 CHANGES IN VERSION 2.9.5

 ------------------------

  o Add missing boost/config/platform/macos.hpp <2017-01-25 Wed>

- 

+

 CHANGES IN VERSION 2.9.4

 ------------------------

  o New chromatogram accessors (for pwiz backend only) - see issue #73

    <2017-01-23 Mon>

- 

+

 CHANGES IN VERSION 2.9.3

 ------------------------

  o bump to new Rcpp 0.12.8 version <2017-01-05 Thu>

- 

+

 CHANGES IN VERSION 2.9.2

 ------------------------

  o cleanup CFLAGS and LIBS for libnetcdf

  o add file missing for oaxaca (Apple clang 3.5svn / 600.0.57)

- 

+

 CHANGES IN VERSION 2.9.1

 ------------------------

  o Delete RAMPAdapter pointer in pwiz backend (by jotsetung)

@@ -167,7 +169,7 @@ CHANGES IN VERSION 2.9.1

 CHANGES IN VERSION 2.9.0

 ------------------------

  o Bioc devel 3.5

- 

+

 CHANGES IN VERSION 2.8.0

 ------------------------

  o Bioc release 3.4

@@ -175,40 +177,40 @@ CHANGES IN VERSION 2.8.0

 CHANGES IN VERSION 2.7.13

 -------------------------

  o Fix waring on OSX (see issue #60)

- 

+

 CHANGES IN VERSION 2.7.12

 -------------------------

  o Fixing last warning on MacOS

- 

+

 CHANGES IN VERSION 2.7.11

 -------------------------

  o Fix failing example and test due to updated msdata::protemics data

- 

+

 CHANGES IN VERSION 2.7.10

 -------------------------

  o compiling and loading on Windows (hopefully)

- 

+

 CHANGES IN VERSION 2.7.9

 ------------------------

- o Updating Makevars.win 

- 

+ o Updating Makevars.win

+

 CHANGES IN VERSION 2.7.8

 ------------------------

  o compile pwiz when installing on Windows <2016-09-26 Mon>

- 

+

 CHANGES IN VERSION 2.7.7

 ------------------------

  o add netcdf static lib; potential incompatibility <2016-09-22 Thu>

- 

+

 CHANGES IN VERSION 2.7.6

 ------------------------

  o new isolationWindow accessor <2016-09-23 Fri>

- 

+

 CHANGES IN VERSION 2.7.5

 ------------------------

  o Apply Martin's free/delete patch - see

    https://github.com/sneumann/mzR/issues/52 <2016-09-22 Thu>

- 

+

 CHANGES IN VERSION 2.7.4

 ------------------------

  o upgrade pwiz

@@ -22,7 +22,7 @@ Rcpp::List RcppIdent::getIDInfo(  )

     for (size_t i = 0; i < as.size(); i++)

     {

-        software[i] = as[i]->name + " " + as[i]->version + " " + (as[i]->contactRolePtr.get()!=0?as[i]->contactRolePtr->contactPtr->name:"") ;

+	software[i] = as[i]->name + " " + as[i]->version + " " + (as[i]->contactRolePtr.get()!=0?as[i]->contactRolePtr->contactPtr->name:"") ;

     }

     vector<SpectrumIdentificationProtocolPtr> sip = mzid->analysisProtocolCollection.spectrumIdentificationProtocol;

@@ -30,12 +30,12 @@ Rcpp::List RcppIdent::getIDInfo(  )

     string parentTolerance = "";

     if(!sip[0]->fragmentTolerance.empty())

     {

-        fragmentTolerance = sip[0]->fragmentTolerance.cvParams[0].value + " " + sip[0]->fragmentTolerance.cvParam(MS_search_tolerance_plus_value).unitsName();

+	fragmentTolerance = sip[0]->fragmentTolerance.cvParams[0].value + " " + sip[0]->fragmentTolerance.cvParam(MS_search_tolerance_plus_value).unitsName();

     }

     if(!sip[0]->parentTolerance.empty())

     {

-        parentTolerance = sip[0]->parentTolerance.cvParams[0].value + " " + sip[0]->parentTolerance.cvParam(MS_search_tolerance_plus_value).unitsName();

+	parentTolerance = sip[0]->parentTolerance.cvParams[0].value + " " + sip[0]->parentTolerance.cvParam(MS_search_tolerance_plus_value).unitsName();

     }

     vector<SearchModificationPtr> sm = sip[0]->modificationParams;

@@ -43,7 +43,7 @@ Rcpp::List RcppIdent::getIDInfo(  )

     Rcpp::StringVector mod(sm.size());

     for(size_t i = 0; i < sm.size(); i++)

     {

-        mod[i] = cvTermInfo(sm[i]->cvParams[0].cvid).name;

+	mod[i] = cvTermInfo(sm[i]->cvParams[0].cvid).name;

     }

     vector<EnzymePtr> enz = sip[0]->enzymes.enzymes;

@@ -56,38 +56,38 @@ Rcpp::List RcppIdent::getIDInfo(  )

     for (size_t i = 0; i < enz.size(); i++)

     {

-        name[i] = cvTermInfo(cleavageAgent(*enz[i].get())).name;

-        nTermGain[i] = enz[i]->nTermGain;

-        cTermGain[i] = enz[i]->cTermGain;

-        minDistance[i] = enz[i]->minDistance;

-        missedCleavages[i] = enz[i]->missedCleavages;

+	name[i] = cvTermInfo(cleavageAgent(*enz[i].get())).name;

+	nTermGain[i] = enz[i]->nTermGain;

+	cTermGain[i] = enz[i]->cTermGain;

+	minDistance[i] = enz[i]->minDistance;

+	missedCleavages[i] = enz[i]->missedCleavages;

     }

     enzymes = Rcpp::List::create(

-                  Rcpp::_["name"]  = name,

-                  Rcpp::_["nTermGain"]  = nTermGain,

-                  Rcpp::_["cTermGain"]  = cTermGain,

-                  Rcpp::_["minDistance"]  = minDistance,

-                  Rcpp::_["missedCleavages"]  = missedCleavages

-              );

+		  Rcpp::_["name"]  = name,

+		  Rcpp::_["nTermGain"]  = nTermGain,

+		  Rcpp::_["cTermGain"]  = cTermGain,

+		  Rcpp::_["minDistance"]  = minDistance,

+		  Rcpp::_["missedCleavages"]  = missedCleavages

+	      );

     vector<SpectraDataPtr> sd = mzid->dataCollection.inputs.spectraData;

     Rcpp::StringVector spectra(sd.size());

     for (size_t i = 0; i < sd.size(); i++)

     {

-        spectra[i] = sd[i]->location;

+	spectra[i] = sd[i]->location;

     }

     return Rcpp::List::create(

-               Rcpp::_["FileProvider"]	= provider,

-               Rcpp::_["CreationDate"]	= date,

-               Rcpp::_["software"]	= software,

-               Rcpp::_["ModificationSearched"]	= mod,

-               Rcpp::_["FragmentTolerance"]	= fragmentTolerance,

-               Rcpp::_["ParentTolerance"]	= parentTolerance,

-               Rcpp::_["enzymes"]	= enzymes,

-               Rcpp::_["SpectraSource"]	= spectra

-           );

+	       Rcpp::_["FileProvider"]	= provider,

+	       Rcpp::_["CreationDate"]	= date,

+	       Rcpp::_["software"]	= software,

+	       Rcpp::_["ModificationSearched"]	= mod,

+	       Rcpp::_["FragmentTolerance"]	= fragmentTolerance,

+	       Rcpp::_["ParentTolerance"]	= parentTolerance,

+	       Rcpp::_["enzymes"]	= enzymes,

+	       Rcpp::_["SpectraSource"]	= spectra

+	   );

 }

@@ -115,70 +115,70 @@ Rcpp::DataFrame RcppIdent::getPsmInfo(  )

     for (size_t i = 0; i < spectrumIdResult.size(); i++)

     {

-        for(size_t j = 0; j < spectrumIdResult[i]->spectrumIdentificationItem.size(); j++)

-        {

-            for(size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr.size(); k++)

-            {

-

-                spectrumID.push_back(spectrumIdResult[i]->spectrumID);

-                chargeState.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->chargeState);

-                rank.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->rank);

-                passThreshold.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->passThreshold);

-                experimentalMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->experimentalMassToCharge);

-                calculatedMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->calculatedMassToCharge);

-                seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->peptideSequence);

-                modification.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->modification.size());

-                isDecoy.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->isDecoy);

-                pre.push_back(string(1, spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->pre));

-                post.push_back(string(1, spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->post));

-                start.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->start);

-                end.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->end);

-                if(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr.get()!=0)

-                {

-                    DBSequenceID.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->accession);

-                    DBSequenceLen.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->length);

-                    DBseq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->seq);

-                    if(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->cvParams.size() > 0)

-                    {

-                        DBdesc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->cvParams[0].value);

-                    }

-                    else

-                    {

-                        DBdesc.push_back("");

-                    }

-                }

-                else

-                {

-                    DBSequenceID.push_back("");

-                    DBseq.push_back("");

-                    DBdesc.push_back("");

-                }

-

-            }

-        }

+	for(size_t j = 0; j < spectrumIdResult[i]->spectrumIdentificationItem.size(); j++)

+	{

+	    for(size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr.size(); k++)

+	    {

+

+		spectrumID.push_back(spectrumIdResult[i]->spectrumID);

+		chargeState.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->chargeState);

+		rank.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->rank);

+		passThreshold.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->passThreshold);

+		experimentalMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->experimentalMassToCharge);

+		calculatedMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->calculatedMassToCharge);

+		seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->peptideSequence);

+		modification.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->modification.size());

+		isDecoy.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->isDecoy);

+		pre.push_back(string(1, spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->pre));

+		post.push_back(string(1, spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->post));

+		start.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->start);

+		end.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->end);

+		if(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr.get()!=0)

+		{

+		    DBSequenceID.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->accession);

+		    DBSequenceLen.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->length);

+		    DBseq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->seq);

+		    if(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->cvParams.size() > 0)

+		    {

+			DBdesc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->cvParams[0].value);

+		    }

+		    else

+		    {

+			DBdesc.push_back("");

+		    }

+		}

+		else

+		{

+		    DBSequenceID.push_back("");

+		    DBseq.push_back("");

+		    DBdesc.push_back("");

+		}

+

+	    }

+	}

     }

     return Rcpp::DataFrame::create(

-               Rcpp::_["spectrumID"]	= spectrumID,

-               Rcpp::_["chargeState"]	= chargeState,

-               Rcpp::_["rank"]	= rank,

-               Rcpp::_["passThreshold"]	= passThreshold,

-               Rcpp::_["experimentalMassToCharge"]	= experimentalMassToCharge,

-               Rcpp::_["calculatedMassToCharge"]	= calculatedMassToCharge,

-               Rcpp::_["sequence"]	= seq,

-               Rcpp::_["modNum"]	= modification,

-               Rcpp::_["isDecoy"]	= isDecoy,

-               Rcpp::_["post"]	= post,

-               Rcpp::_["pre"]	= pre,

-               Rcpp::_["start"]	= start,

-               Rcpp::_["end"]	= end,

-               Rcpp::_["DatabaseAccess"]	= DBSequenceID,

-               Rcpp::_["DBseqLength"]	= DBSequenceLen,

-               Rcpp::_["DatabaseSeq"]	= DBseq,

-               Rcpp::_["DatabaseDescription"]	= DBdesc

-           );

+	       Rcpp::_["spectrumID"]	= spectrumID,

+	       Rcpp::_["chargeState"]	= chargeState,

+	       Rcpp::_["rank"]	= rank,

+	       Rcpp::_["passThreshold"]	= passThreshold,

+	       Rcpp::_["experimentalMassToCharge"]	= experimentalMassToCharge,

+	       Rcpp::_["calculatedMassToCharge"]	= calculatedMassToCharge,

+	       Rcpp::_["sequence"]	= seq,

+	       Rcpp::_["modNum"]	= modification,

+	       Rcpp::_["isDecoy"]	= isDecoy,

+	       Rcpp::_["post"]	= post,

+	       Rcpp::_["pre"]	= pre,

+	       Rcpp::_["start"]	= start,

+	       Rcpp::_["end"]	= end,

+	       Rcpp::_["DatabaseAccess"]	= DBSequenceID,

+	       Rcpp::_["DBseqLength"]	= DBSequenceLen,

+	       Rcpp::_["DatabaseSeq"]	= DBseq,

+	       Rcpp::_["DatabaseDescription"]	= DBdesc

+	   );

 }

 Rcpp::DataFrame RcppIdent::getModInfo(  )

@@ -193,28 +193,28 @@ Rcpp::DataFrame RcppIdent::getModInfo(  )

     for (size_t i = 0; i < spectrumIdResult.size(); i++)

     {

-        for(size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem.size() ; k++)

-        {

-            if(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification.size()>0)

-            {

-                for(size_t j = 0 ; j < spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification.size(); j++)

-                {

-                    spectrumID.push_back(spectrumIdResult[i]->spectrumID);

-                    seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->peptideSequence);

-                    name.push_back(cvTermInfo(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->cvParams[0].cvid).name);

-                    mass.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->monoisotopicMassDelta);

-                    loc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->location);

-                }

-            }

-        }

+	for(size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem.size() ; k++)

+	{

+	    if(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification.size()>0)

+	    {

+		for(size_t j = 0 ; j < spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification.size(); j++)

+		{

+		    spectrumID.push_back(spectrumIdResult[i]->spectrumID);

+		    seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->peptideSequence);

+		    name.push_back(cvTermInfo(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->cvParams[0].cvid).name);

+		    mass.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->monoisotopicMassDelta);

+		    loc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->location);

+		}

+	    }

+	}

     }

     return Rcpp::DataFrame::create(

-               Rcpp::_["spectrumID"]	= spectrumID,

-               Rcpp::_["sequence"]	= seq,

-               Rcpp::_["name"]	= name,

-               Rcpp::_["mass"]	= mass,

-               Rcpp::_["location"]	= loc);

+	       Rcpp::_["spectrumID"]	= spectrumID,

+	       Rcpp::_["sequence"]	= seq,

+	       Rcpp::_["name"]	= name,

+	       Rcpp::_["mass"]	= mass,

+	       Rcpp::_["location"]	= loc);

 }

@@ -231,92 +231,81 @@ Rcpp::DataFrame RcppIdent::getSubInfo(  )

     for (size_t i = 0; i < spectrumIdResult.size(); i++)

     {

-        if(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification.size() > 0)

-        {

-            for(size_t j = 0 ; j < spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification.size(); j++)

-            {

-                spectrumID.push_back(spectrumIdResult[i]->spectrumID);

-                seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->peptideSequence);

-                originalResidue.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->originalResidue);

-                replacementResidue.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->replacementResidue);

-                loc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->location);

-            }

-        }

+	if(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification.size() > 0)

+	{

+	    for(size_t j = 0 ; j < spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification.size(); j++)

+	    {

+		spectrumID.push_back(spectrumIdResult[i]->spectrumID);

+		seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->peptideSequence);

+		originalResidue.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->originalResidue);

+		replacementResidue.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->replacementResidue);

+		loc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->location);

+	    }

+	}

     }

     return Rcpp::DataFrame::create(

-               Rcpp::_["spectrumID"]	= spectrumID,

-               Rcpp::_["sequence"]	= seq,

-               Rcpp::_["originalResidue"]	= originalResidue,

-               Rcpp::_["replacementResidue"]	= replacementResidue,

-               Rcpp::_["location"]	= loc

-           );

+	       Rcpp::_["spectrumID"]	= spectrumID,

+	       Rcpp::_["sequence"]	= seq,

+	       Rcpp::_["originalResidue"]	= originalResidue,

+	       Rcpp::_["replacementResidue"]	= replacementResidue,

+	       Rcpp::_["location"]	= loc

+	   );

 }

-Rcpp::DataFrame RcppIdent::getScore(  )

-{

-    vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;

-    vector<string> spectrumID;

-    vector<string> names;

-    int count = 0;

-

-    for(size_t i = 0; i < spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams.size(); i++)

-    {

-        if(!spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams[i].value.empty())

-        {

-            count++;

-            names.push_back(cvTermInfo(spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams[i].cvid).name);

-        }

+Rcpp::DataFrame RcppIdent::getScore(  ) {

+  vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;

+  vector<string> spectrumID;

+  vector<string> names;

+  int count = 0;

+  int nCvParams = 0;

+

+  for (size_t i = 0; i < spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams.size(); i++) {

+    if (!spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams[i].value.empty()) {

+      count++;

+      nCvParams++;

+      names.push_back(cvTermInfo(spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams[i].cvid).name);

     }

-    if(count == 0)

-    {

-        Rcpp::Rcout << "No scoring information available" << std::endl;

-        return Rcpp::DataFrame::create();

+  }

+  if(count == 0) {

+    Rcpp::Rcout << "No scoring information available" << std::endl;

+    return Rcpp::DataFrame::create();

+  } else {

+    vector<vector<double> > score(count);

+    for (size_t i = 0; i < spectrumIdResult.size(); i++) {

+      for (size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem.size(); k++) {

+	for (size_t n = 0; n < spectrumIdResult[i]->spectrumIdentificationItem[k]->peptideEvidencePtr.size(); n++) {

+	  spectrumID.push_back(spectrumIdResult[i]->spectrumID);

+	  count = 0;

+

+	  // The original loop iterated to j <

+	  // spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams.size()

+	  // which failed when some SpectrumIdentificationItem

+	  // suddently have additional cvParams, such as in Mascot

+	  // results - see https://github.com/sneumann/mzR/issues/136

+	  for (size_t j = 0; j < nCvParams; j++) {

+	    if (!spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams[j].value.empty()) {

+	      score[count].push_back(lexical_cast<double>(spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams[j].value));

+	      count++;

+	    }

+	  }

+	}

+      }

     }

-    else

-    {

-        vector<vector<double> > score(count);

-

-        for (size_t i = 0; i < spectrumIdResult.size(); i++)

-        {

-

-            for(size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem.size(); k++)

-            {

-                for(size_t n = 0; n < spectrumIdResult[i]->spectrumIdentificationItem[k]->peptideEvidencePtr.size(); n++)

-                {

-                    spectrumID.push_back(spectrumIdResult[i]->spectrumID);

-                    count = 0;

-                    for(size_t j = 0; j < spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams.size(); j++)

-                    {

-                        if(!spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams[j].value.empty())

-                        {

-                            score[count].push_back(lexical_cast<double>(spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams[j].value));

-                            count++;

-                        }

-

-                    }

-                }

-

-            }

-        }

-

-        Rcpp::List res(score.size() + 1);

-        

-        names.insert(names.begin(), "spectrumID");

-        

-        res[0] = Rcpp::wrap(spectrumID);

-        

-        for(size_t i = 0; i < score.size(); i++)

-        {

-			res[i + 1] = Rcpp::wrap(score[i]);

-        }

-        

-        res.attr("names") = names;

-        Rcpp::DataFrame out(res);

-

-        return out;

+

+    Rcpp::List res(score.size() + 1);

+    names.insert(names.begin(), "spectrumID");

+    res[0] = Rcpp::wrap(spectrumID);

+    for(size_t i = 0; i < score.size(); i++) {

+      res[i + 1] = Rcpp::wrap(score[i]);

     }

+

+    res.attr("names") = names;

+    Rcpp::DataFrame out(res);

+

+    return out;

+  }

 }

 Rcpp::List RcppIdent::getPara(  )

@@ -327,7 +316,7 @@ Rcpp::List RcppIdent::getPara(  )

 	names.push_back("searchType");

 	values.push_back(underscore(cvTermInfo(sip[0]->searchType.cvid).name));

-	

+

     for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)

     {

 		names.push_back(underscore(cvTermInfo(sip[0]->additionalSearchParams.cvParams[i].cvid).name));

@@ -337,18 +326,18 @@ Rcpp::List RcppIdent::getPara(  )

     for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)

     {

 		names.push_back(underscore(sip[0]->additionalSearchParams.userParams[i].name));

-        if(sip[0]->additionalSearchParams.userParams[i].value.empty())

-        {

+	if(sip[0]->additionalSearchParams.userParams[i].value.empty())

+	{

 			values.push_back("true");

-        }

-        else

-        {

+	}

+	else

+	{

 			values.push_back(sip[0]->additionalSearchParams.userParams[i].value);

-        }

+	}

     }

-    

+

     Rcpp::List res(names.size());

-    

+

     for (size_t i = 0; i < names.size(); i++)

     {

 		if (isNumber(values[i]))

@@ -364,7 +353,7 @@ Rcpp::List RcppIdent::getPara(  )

 			res[i] = Rcpp::wrap(values[i]);

 		}

 	}

-    

+

     res.attr("names") = names;

     return res;

 }

@@ -381,21 +370,21 @@ Rcpp::DataFrame RcppIdent::getDB(  )

     std::vector<long> numResidues;

     for (size_t i = 0; i < sdb.size(); i++)

     {

-        dbLocation.push_back(sdb[i]->location);

-        dbID.push_back(sdb[i]->id);

-        dbName.push_back(sdb[i]->name);

-        dbVersion.push_back(sdb[i]->version);

-        numDatabaseSequences.push_back(sdb[i]->numDatabaseSequences);

-        numResidues.push_back(sdb[i]->numResidues);

+	dbLocation.push_back(sdb[i]->location);

+	dbID.push_back(sdb[i]->id);

+	dbName.push_back(sdb[i]->name);

+	dbVersion.push_back(sdb[i]->version);

+	numDatabaseSequences.push_back(sdb[i]->numDatabaseSequences);

+	numResidues.push_back(sdb[i]->numResidues);

     }

     Rcpp::DataFrame database = Rcpp::List::create(

-                                   Rcpp::_["location"]  = dbLocation,

-                                   Rcpp::_["id"]  = dbID,

-                                   Rcpp::_["name"]  = dbName,

-                                   Rcpp::_["numDatabaseSequences"]  = numDatabaseSequences,

-                                   Rcpp::_["numResidues"]  = numResidues,

-                                   Rcpp::_["version"]  = dbVersion

-                               );

+				   Rcpp::_["location"]  = dbLocation,

+				   Rcpp::_["id"]  = dbID,

+				   Rcpp::_["name"]  = dbName,

+				   Rcpp::_["numDatabaseSequences"]  = numDatabaseSequences,

+				   Rcpp::_["numResidues"]  = numResidues,

+				   Rcpp::_["version"]  = dbVersion

+			       );

     return database;

 }