Merging changes from iqtree.

1. Corrected a couple of problems (with visibility of
   prepareToConstructTree() implementations).
2. utils/stringfunctions.cpp and utils/stringfunctions.h
   now included in decenttree (and various examples).

Author: James Barbetti

CMakeLists.txt

@@ -601,6 +601,7 @@ add_executable(decenttree
     utils/gzstream.cpp         utils/gzstream.h
     utils/progress.cpp         utils/progress.h 
     utils/operatingsystem.cpp  utils/operatingsystem.h
+    utils/stringfunctions.cpp  utils/stringfunctions.h
     utils/vectortypes.cpp      utils/vectortypes.h)
 
 if(ZLIB_FOUND)

decenttree.cpp

@@ -23,10 +23,11 @@
 #include <string>            //for std::string
 #include <iostream>          //for std::cout
 #include <math.h>            //for log
+#include <utils/argument.h>        //for Argument, ArgumentMap, et al.
 #include <utils/progress.h>        //for progress_display::setProgressDisplay()
 #include <utils/operatingsystem.h> //for getOSName
 #include <utils/hammingdistance.h> //for hammingDistance
-#include <utils/argument.h>        //for Argument, ArgumentMap, et al.
+#include <utils/stringfunctions.h> //for contains
 #include "starttree.h"       //for StartTree::Factory
 #include "flatmatrix.h"      //for FlatMatrix
 #include "distancematrix.h"  //for loadDistanceMatrixInto
@@ -38,20 +39,6 @@
 #define PROBLEM(x) if (1) problems << x << ".\n"; else 0
 
 namespace {
-    bool endsWith(const std::string& s, const char* suffix) {
-        auto suffixLen = strlen(suffix);
-        if (s.length() < suffixLen) {
-            return false;
-        }
-        return s.substr(s.length()-suffixLen, suffixLen) == suffix;
-    }
-
-    std::string string_to_lower(const std::string& input_string) {
-        std::string answer = input_string;
-        std::transform(answer.begin(), answer.end(), answer.begin(),
-                    []( char c){ return std::tolower(c); });
-        return answer;
-    }
 
     bool   correcting_distances     = true;
     bool   is_DNA                   = true;
@@ -399,8 +386,7 @@ class DecentTreeOptions {
         range_restrict(0, 9,  compression_level );
         range_restrict(1, 15, precision );
         format = string_to_lower(format);
-        if (isOutputZipped && 
-            format.find(".gz") == std::string::npos) {
+        if (isOutputZipped && !contains(format, ".gz")) {
             //Ensure that distance file will be compressed
             format += ".gz"; 
         }

decenttree_update.sh

@@ -24,6 +24,7 @@ cp timeutil.h my_assert.h safe_io.h      ../../decenttree/utils
 cp parallel_mergesort.h parallel_sort.h  ../../decenttree/utils
 cp vectortypes.cpp vectortypes.h         ../../decenttree/utils
 cp hammingdistance.h                     ../../decenttree/utils
+cp stringfunctions.h stringfunctions.cpp ../../decenttree/utils
 cd ..
 cp -R zlib-1.2.7      ../decenttree
 cp -R lib             ../decenttree

fancyrapidnj.h

@@ -251,7 +251,10 @@ template <class T=NJFloat> class FancyNJMatrix {
 
         return true;
     }
+    virtual bool prepareToConstructTree() {
+    }
     virtual bool constructTree() {
+        prepareToConstructTree();
         if (original_rank<3) {
             return false;
         }

flatmatrix.cpp

@@ -29,7 +29,8 @@
 //
 
 #include "flatmatrix.h"
-#include "utils/progress.h"
+#include <utils/progress.h>
+#include <utils/stringfunctions.h> //for contains
 #include <math.h>       //for log10
 #include <iostream>     //for std::fstream
 #include <sstream>      //for std::stringstream
@@ -113,8 +114,8 @@ bool FlatMatrix::writeToDistanceFile(const std::string& format,
                                      const std::string& file_name) const {
     #if USE_PROGRESS_DISPLAY
     double rows           = static_cast<double>(getSize());
-    bool   isTriangle     = format.find("lower") != std::string::npos ||
-                            format.find("upper") != std::string::npos;
+    bool   isTriangle     = contains(format,"lower") ||
+                            contains(format,"upper");
     double halfIfTriangle = isTriangle ? 0.5 : 1.0;
 
     double calculations   = rows * rows * halfIfTriangle;
@@ -125,7 +126,7 @@ bool FlatMatrix::writeToDistanceFile(const std::string& format,
     #endif
 
     try {
-        if (format.find(".gz") == std::string::npos) {
+        if (!contains(format,".gz")) {
             std::ofstream out;
             out.exceptions(std::ios::failbit | std::ios::badbit);
             out.open(file_name.c_str());

sequence.cpp

@@ -31,6 +31,7 @@
 #include <utils/hammingdistance.h> //for vectorHamingDistance()
 #include <utils/gzstream.h>        //for pigzstream class
 #include <utils/safe_io.h>         //for safeGetLine()
+#include <utils/stringfunctions.h> //for contains()
 
 bool isNucleotideOrMissing(const char c) {
     return isalnum(c) ||  c == '-' || c == '?'|| 
@@ -633,8 +634,8 @@ bool SequenceLoader::writeDistanceMatrixToFile(bool numbered_names,
     getNumberOfStates();
 
     #if USE_PROGRESS_DISPLAY
-    bool   isTriangle = output_format.find("lower") != std::string::npos ||
-                        output_format.find("upper") != std::string::npos;
+    bool   isTriangle = contains(output_format,"lower") ||
+                        contains(output_format,"upper");
     double halfIfTriangle = isTriangle ? 0.5 : 1.0;
     double calculations   = static_cast<double>(rank) 
                           * static_cast<double>(rank) * halfIfTriangle;

stitchup.cpp

@@ -486,6 +486,8 @@ template < class T=double> class StitchupMatrix: public SquareMatrix<T> {
     virtual void beSilent() {
         silent = true;
     }
+    virtual void prepareToConstructTree() {
+    }
     virtual bool constructTree() {
         prepareToConstructTree();
         if (row_count<3) {
@@ -575,6 +577,7 @@ class NearestTaxonClusterJoiningMatrix: public S {
     using super::clusters;
     using super::rowTotals;
     //member functions from super-class
+    using super::prepareToConstructTree;
     using super::cluster;
     using super::finishClustering;
 
@@ -633,7 +636,6 @@ class NearestTaxonClusterJoiningMatrix: public S {
             progress += (taxon_count-row_count);
         }
         finishClustering();
-
     }
 
     virtual bool constructTree() override {