* more C++17 fixes

pwiz_tools/BiblioSpec/src/original-RefFile.h

@@ -33,7 +33,6 @@
 #include <fstream>
 #include <string>
 #include <vector>
-using std::binary_function;
 
 struct refData{ 
   string file;
@@ -75,7 +74,7 @@ class RefFile
 };
 
 //sort by both ms2 file name and scan number
-struct compRefData : public binary_function<refData, refData, bool>
+struct compRefData
 {
   bool operator()(refData r1, refData r2) {
     if( r1.file == r2.file ) {

pwiz_tools/BiblioSpec/src/original-RefSpectrum.h

@@ -39,8 +39,6 @@
 #include "pwiz/utility/misc/Stream.hpp"
 #include "pwiz/utility/misc/Container.hpp"
 
-using std::binary_function;
-
 enum MODS { Meth, Cl };
 
 class RefSpectrum : public Spectrum
@@ -95,7 +93,7 @@ class RefSpectrum : public Spectrum
 };
 
 //sort by both charge and sequence
-struct compRefSpecIon : public binary_function<RefSpectrum, RefSpectrum, bool>
+struct compRefSpecIon
 {
   bool operator()(RefSpectrum s1, RefSpectrum s2) {
     if( s1.getCharge() == s2.getCharge() ) {
@@ -107,7 +105,8 @@ struct compRefSpecIon : public binary_function<RefSpectrum, RefSpectrum, bool>
 };
 
 //sort by both charge and sequence
-struct compRefSpecPtrIon : public binary_function<RefSpectrum*, RefSpectrum*, bool>{
+struct compRefSpecPtrIon
+{
   bool operator()(RefSpectrum* s1, RefSpectrum* s2) {
     if( s1->getCharge() == s2->getCharge() ) {
       if (s1->getSeq() == s2->getSeq()) {
@@ -121,7 +120,7 @@ struct compRefSpecPtrIon : public binary_function<RefSpectrum*, RefSpectrum*, bo
   }
 };
 
-struct compRefSpecPtrId : public binary_function<RefSpectrum*, RefSpectrum*, bool>
+struct compRefSpecPtrId
 {
   bool operator()(RefSpectrum* s1, RefSpectrum* s2) {return s1->getID() <  s2->getID();}
 };

pwiz_tools/BiblioSpec/src/original-Spectrum.h

@@ -38,21 +38,19 @@
 #include <ctime>
 #include <vector>
 
-using std::binary_function;
-
 
 struct PEAK_T 
 { 
   float mass; 
   float intensity; 
 };
 
-struct compPeakInt : public binary_function<PEAK_T, PEAK_T, bool>
+struct compPeakInt
 {
   bool operator()(PEAK_T p1, PEAK_T p2) {return p1.intensity > p2.intensity;}
 };
 
-struct compPeakMz : public binary_function<PEAK_T, PEAK_T, bool>
+struct compPeakMz
 {
   bool operator()(PEAK_T p1, PEAK_T p2) {return p1.mass <  p2.mass;}
 };
@@ -126,21 +124,22 @@ class Spectrum
   void tryMe(const Spectrum& otherSpec);
 };
 
-struct compSpecMz : public binary_function<Spectrum, Spectrum, bool>
+struct compSpecMz
 {
   bool operator()(Spectrum s1, Spectrum s2) {return s1.getMz() <  s2.getMz();}
 };
 
-struct compSpecPtrMz : public binary_function<Spectrum*, Spectrum*, bool>{
+struct compSpecPtrMz
+{
   bool operator()(Spectrum* s1, Spectrum* s2) { return s1->getMz() <  s2->getMz();}
 };
 
-struct compSpecScanNum : public binary_function<Spectrum, Spectrum, bool>
+struct compSpecScanNum
 {
   bool operator()(Spectrum s1, Spectrum s2) {return s1.getScanNum() <  s2.getScanNum();}
 };
 
-struct compSpecPtrScanNum : public binary_function<Spectrum*, Spectrum*, bool>
+struct compSpecPtrScanNum
 {
   bool operator()(Spectrum* s1, Spectrum* s2) {return s1->getScanNum() <  s2->getScanNum();}
 };

pwiz_tools/Bumbershoot/freicore/BaseSpectrum.h

@@ -228,7 +228,8 @@ namespace freicore
         {
             vector<SpectrumType*> v( this->begin(), this->end() );
             this->clear(false);
-            std::random_shuffle( v.begin(), v.end() );
+            std::mt19937 rng(0);
+            std::shuffle(v.begin(), v.end(), rng);
             for( typename vector<SpectrumType*>::const_iterator itr = v.begin(); itr != v.end(); ++itr )
                 this->push_back( *itr );
         }

pwiz_tools/Bumbershoot/freicore/proteinStore.cpp

@@ -232,7 +232,8 @@ namespace freicore
 
     void proteinStore::random_shuffle()
     {
-        std::random_shuffle( storeIndex.begin(), storeIndex.end() );
+        std::mt19937 rng(0);
+        std::shuffle(storeIndex.begin(), storeIndex.end(), rng);
     }
 
     size_t proteinStore::size() const {return storeIndex.size();}

pwiz_tools/Bumbershoot/freicore/stdafx.h

@@ -115,6 +115,7 @@
 #include <cmath>
 #include <ctime>
 #include <bitset>
+#include <random>
 
 //#include <boost/lexical_cast.hpp>
 #include "pwiz/utility/misc/optimized_lexical_cast.hpp"

pwiz_tools/Bumbershoot/idpicker/Qonverter/Merger.cpp

@@ -39,6 +39,7 @@
 #include "boost/make_shared.hpp"
 #include <deque>
 #include <algorithm>
+#include <random>
 
 
 using namespace pwiz::util;
@@ -1007,7 +1008,8 @@ void Merger::merge(const string& mergeTargetFilepath, const std::vector<string>&
     vector<size_t> randomSources;
     for (size_t i = 0; i < mergeSourceFilepaths.size(); ++i)
         randomSources.push_back(i);
-    std::random_shuffle(randomSources.begin(), randomSources.end());
+    std::mt19937 rng(0);
+    std::shuffle(randomSources.begin(), randomSources.end(), rng);
 
     std::deque<shared_ptr<MergeTask> > sourceQueue;
     for(int randomSource : randomSources)

pwiz_tools/Bumbershoot/idpicker/Qonverter/Parser.cpp

@@ -1,16 +1,16 @@
 //
 // $Id$
 //
-// Licensed under the Apache License, Version 2.0 (the "License"); 
-// you may not use this file except in compliance with the License. 
-// You may obtain a copy of the License at 
-//
-// http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software 
-// distributed under the License is distributed on an "AS IS" BASIS, 
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
-// See the License for the specific language governing permissions and 
+// Licensed under the Apache License, Version 2.0 (the "License"); 
+// you may not use this file except in compliance with the License. 
+// You may obtain a copy of the License at 
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software 
+// distributed under the License is distributed on an "AS IS" BASIS, 
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
+// See the License for the specific language governing permissions and 
 // limitations under the License.
 //
 // The Original Code is the IDPicker project.
@@ -44,7 +44,8 @@
 #include "boost/atomic.hpp"
 #include "boost/exception/all.hpp"
 #include "boost/range/algorithm/set_algorithm.hpp"
-#include "Logger.hpp"
+#include "Logger.hpp"
+#include <random>
 
 
 using namespace pwiz::identdata;
@@ -959,7 +960,8 @@ vector<ProteinDatabaseTaskGroup> createTasksPerProteinDatabase(const vector<stri
         taskGroups.back().proteomeDataPtr = proteinDatabaseByFilepath[proteinDatabaseFilepath];
 
         // shuffled so that large and small input files get mixed
-        random_shuffle(inputFilepaths.begin(), inputFilepaths.end());
+        std::mt19937 rng(0);
+        std::shuffle(inputFilepaths.begin(), inputFilepaths.end(), rng);
 
         int processorsUsed = 0;
         for(const string& inputFilepath : inputFilepaths)
@@ -1281,7 +1283,8 @@ void executePeptideFinderTask(PeptideFinderTaskPtr peptideFinderTask, ThreadStat
             peptides.push_back(peptide);
 
         // distinctPeptideIdBySequence is sorted on peptide length, which is bad for the trie
-        random_shuffle(peptides.begin(), peptides.end());
+        std::mt19937 rng(0);
+        std::shuffle(peptides.begin(), peptides.end(), rng);
 
         // maps proteins indexes to protein ids (in the database)
         map<size_t, sqlite3_int64> proteinIdByIndex;

pwiz_tools/Bumbershoot/idpicker/Qonverter/crawdad/msmat/crawutils.cpp

@@ -24,6 +24,7 @@
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <random>
 #include "crawutils.h"
 
 //note that I do not yet have the cephes library for MSVC++
@@ -1201,8 +1202,9 @@ return drand48();
           std::vector< TwoGroupsType > v = permute_two_groups ( g1, g2 );
           if ( N < (int)v.size() ) {
               throw("invalid");
-          }
-          std::random_shuffle( v.begin(), v.end() );
+          }
+          std::mt19937 rng(0);
+          std::shuffle(v.begin(), v.end(), rng);
           v.resize(N);
           return v;
   }

pwiz_tools/Bumbershoot/pepitome/LibraryBabelFish.cpp

@@ -331,7 +331,8 @@ namespace freicore
             while(numAttempts < 100 && !foundDecoy)
             {
                 stringstream shuffledPeptide;
-                std::random_shuffle(movableAAs.begin(),movableAAs.end());
+                std::mt19937 rng(0);
+                std::shuffle(movableAAs.begin(), movableAAs.end(), rng);
                 size_t repeat = 0;
                 size_t nonRepeat = 0;
                 size_t randomAAIndex = 0;
@@ -376,7 +377,8 @@ namespace freicore
             {
                 vector<string> aminoAcids = boost::assign::list_of("A")("R")("N")("D")("C")("E")("Q")("G")("H")("I")("L")("K")("M")("F")("P")("S")("T")("U")("W")("Y")("V");
                 //{"A","R","N","D","E","Q","G","H","I","L","M","F","P","S","T","U","W","Y","V"};
-                std::random_shuffle(aminoAcids.begin(),aminoAcids.end());
+                std::mt19937 rng(0);
+                std::shuffle(aminoAcids.begin(), aminoAcids.end(), rng);
                 vector<string> saltedPeptide;
                 saltedPeptide.push_back(peptide[0]);
                 saltedPeptide.push_back(aminoAcids[0]);

pwiz_tools/Bumbershoot/pepitome/spectraStore.h

@@ -69,6 +69,7 @@
 
 #include <ctype.h>
 #include <sstream>
+#include <random>
 
 using namespace boost::assign;
 using namespace boost::algorithm;
@@ -929,7 +930,8 @@ namespace pepitome
 
         void random_shuffle()
         {
-            std::random_shuffle( begin(), end() );
+            std::mt19937 rng(0);
+            std::shuffle(begin(), end(), rng);
         }
 
         void loadLibrary(const string& libName)
@@ -1046,7 +1048,7 @@ namespace pepitome
                 {
                     bal::split(tokens, buf, bal::is_any_of(":"));
                     string peakInput = tokens[1];
-                    peakInput.erase(peakInput.begin(), std::find_if(peakInput.begin(), peakInput.end(), std::not1(std::ptr_fun<int, int>(std::isspace))));
+                    bal::trim(peakInput);
                     numPeaks = lexical_cast<size_t>(peakInput);
                 }
                 else if(bal::starts_with(buf, "PrecursorMZ"))

pwiz_tools/Bumbershoot/quameter/crawdad/msmat/crawutils.cpp

@@ -1,26 +1,27 @@
-/*
- * Original author: Greg Finney <gfinney .at. u.washington.edu>,
- *                  MacCoss Lab, Department of Genome Sciences, UW
- *
- * Copyright 2009 University of Washington - Seattle, WA
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
+/*
+ * Original author: Greg Finney <gfinney .at. u.washington.edu>,
+ *                  MacCoss Lab, Department of Genome Sciences, UW
+ *
+ * Copyright 2009 University of Washington - Seattle, WA
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 #include <algorithm>
 #include <vector>
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <random>
 #include "crawutils.h"
 
 //note that I do not yet have the cephes library for MSVC++
@@ -1092,22 +1093,22 @@ uint rand_in_range( uint low, uint high) {
  return idx;
 }
 
-void init_rand() {
-#ifdef _MSC_VER
-srand((uint)time(NULL));
-#else
-srand48(time(NULL));
-#endif
-
-}
-
-double get_rand() {
-#ifdef _MSC_VER
-return rand() / (double)RAND_MAX;
-#else
-return drand48();
-#endif
-}
+void init_rand() {
+#ifdef _MSC_VER
+srand((uint)time(NULL));
+#else
+srand48(time(NULL));
+#endif
+
+}
+
+double get_rand() {
+#ifdef _MSC_VER
+return rand() / (double)RAND_MAX;
+#else
+return drand48();
+#endif
+}
 
 
 
@@ -1184,7 +1185,8 @@ return drand48();
           if ( N < (int)v.size() ) {
               throw("invalid");
           }
-          std::random_shuffle( v.begin(), v.end() );
+          std::mt19937 rng(0);
+          std::shuffle(v.begin(), v.end(), rng);
           v.resize(N);
           return v;
   }