FileItemGenerator(,skipHeader)

common.cpp

@@ -2831,14 +2831,17 @@ size_t Offset::size = 0;
 FileItemGenerator::FileItemGenerator (size_t progress_displayPeriod,
                                       bool isDir_arg,
                                       bool large_arg,
-                                      const string& fName_arg)
+                                      const string& fName_arg,
+                                      bool skipHeader_arg)
 : ItemGenerator (0, progress_displayPeriod)
 , isDir (isDir_arg)
 , large (large_arg)
 , dirName (fName_arg)
 , fName (fName_arg)
+, skipHeader (skipHeader_arg)
 { 
-  IMPLY (large, isDir);
+  QC_IMPLY (large, isDir);
+  QC_IMPLY (skipHeader, ! isDir);
 
   trimSuffix (dirName,  "/");
 
@@ -2879,7 +2882,14 @@ FileItemGenerator::FileItemGenerator (size_t progress_displayPeriod,
 bool FileItemGenerator::next (string &item)
 { 
   if (! large)
+  {
+    if (skipHeader)
+    {
+      next_ (item);
+      skipHeader = false;
+    }
     return next_ (item);
+  }
 
   for (;;)
   {
@@ -2888,7 +2898,7 @@ bool FileItemGenerator::next (string &item)
       string subDir;
       if (! next_ (subDir))
         return false;
-      fig. reset (new FileItemGenerator (0, true, false, dirName + "/" + subDir));
+      fig. reset (new FileItemGenerator (0, true, false, dirName + "/" + subDir, false));
     }
     ASSERT (fig. get ());
     if (fig->next (item))
@@ -2918,7 +2928,8 @@ bool FileItemGenerator::next_ (string &item)
   if (item. empty () && f. eof ())
     return false;
 
-  prog (item);
+  if (! skipHeader)
+    prog (item);
 	return true;
 }    
 

common.hpp

@@ -779,8 +779,8 @@ template <typename Key, typename Value>
     }
 
 template <typename T, typename UnaryPredicate>
-  inline long count_if (T &t, UnaryPredicate pred)
-    { return std::count_if (t. begin (), t. end (), pred); }
+  inline size_t count_if (T &t, UnaryPredicate pred)
+    { return (size_t) std::count_if (t. begin (), t. end (), pred); }
 
 template <typename To, typename From>
   inline void insertAll (To &to,
@@ -3758,13 +3758,15 @@ struct FileItemGenerator : ItemGenerator, Nocopy
   string fName;
   ifstream f;
   unique_ptr<FileItemGenerator> fig;
+  bool skipHeader {false};
 public:
 
 
   FileItemGenerator (size_t progress_displayPeriod,
                      bool isDir_arg,
                      bool large_arg,
-                     const string& fName_arg);
+                     const string& fName_arg,
+                     bool skipHeader_arg);
  ~FileItemGenerator ()
     { if (isDir)
 	      remove (fName. c_str ());

phylogeny/distTree_new.cpp

@@ -130,7 +130,7 @@ Update: <incremental distance tree directory>/search/")
     if (name. empty ())
     {
       const string newDir (dataDir + "search/");
-      FileItemGenerator fig (1, true, false, newDir);  // PAR
+      FileItemGenerator fig (1, true, false, newDir, false);  // PAR
   	  string item;
   	  while (fig. next (item))
       {

phylogeny/mutation2feature.cpp

@@ -119,7 +119,7 @@ struct ThisApplication : Application
       map<string/*Mutation::geneName*/,unordered_set<Mutation,Mutation::Hash>> gene2muts;  
         // !Mutation::ambig
       {
-        FileItemGenerator fig (1000, true, large, inDirName);  // PAR
+        FileItemGenerator fig (1000, true, large, inDirName, false);  // PAR
         string fName;
     	  while (fig. next (fName))
         {

version.inc

@@ -1,6 +1,7 @@
-#define VERSION "1.9.5"
+#define VERSION "1.9.6"
 
 
+// 1.9.6  10/18/2021  distTree_inc_refresh_dissim.sh
 // 1.9.5  07/23/2021  -prefer_gain is restored in tree2names.sh
 // 1.9.4  06/09/2021  combine_dissims.cpp: -barrier
 // 1.9.3  05/30/2021  align.cpp: ambiguous aa J,U,O are replaced by X, selfScore is using X