From 52c38f16c1e933e765d7d8b1b953ea3cd3606fba Mon Sep 17 00:00:00 2001
From: Vyacheslav Brover <vyacheslav.brover@nih.gov>
Date: Sat, 14 Dec 2024 20:36:44 -0500
Subject: [PATCH] PD-5191 StxTyper ver. 1.0.30, stxtyper --threads

---
 amrfinder.cpp |  6 +++++-
 common.cpp    |  4 +++-
 common.hpp    | 17 ++++++++++++++---
 stx           |  2 +-
 version.txt   |  2 +-
 5 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/amrfinder.cpp b/amrfinder.cpp
index 128346c..1aabbdd 100644
--- a/amrfinder.cpp
+++ b/amrfinder.cpp
@@ -33,6 +33,8 @@
 * Dependencies: NCBI BLAST, HMMer, libcurl, gunzip (optional)
 *
 * Release changes:
+*                               stxtyper --threads
+*   4.0.7   12/12/2024 PD-5192  StxTyper ver. 1.0.30
 *   4.0.6   12/09/2024 PD-5181  StxTyper ver. 1.0.28
 *   4.0.5   11/13/2024 PD-5175  prohibit --database_version and -p or -n
 *   4.0.4   10/29/2024          colorizeDir()
@@ -339,7 +341,7 @@ using namespace GFF_sp;
 const string dataVer_min ("2024-08-14.2");
   // 3.12: "2023-12-15.2"
   // 3.11: "2021-02-18.1"  
-const string stxTyperVersion ("1.0.28");  
+const string stxTyperVersion ("1.0.30");  
 
 
 
@@ -1182,6 +1184,7 @@ struct ThisApplication final : ShellApplication
 	  {
   		stderr. section ("Running stxtyper");
  			const Chronometer_OnePass_cerr cop ("stxtyper");
+ 			ASSERT (threads_max >= 1);
 			exec (  fullProg ("stxtyper") 
 			      + "  -n " + dna_flat 
 			      + prependS (blast_bin, "  --blast_bin ") 
@@ -1191,6 +1194,7 @@ struct ThisApplication final : ShellApplication
 			      + ifS (print_node, "  --print_node")
 			      + "  -q "  // ifS (getVerbosity () == -1, "  -q")
 			      + ifS (qc_on, "  --debug")
+			      + "  --threads " + to_string (threads_max )
 			      + " > " + logFName
 			      , logFName
 			      );
diff --git a/common.cpp b/common.cpp
index b02fb32..304ca7c 100644
--- a/common.cpp
+++ b/common.cpp
@@ -297,7 +297,7 @@ string getStack ()
   char** strings = backtrace_symbols (buffer, nptrs);
   if (strings /*&& ! which ("addr2line"). empty ()*/) 
   {
-    FOR_REV_END (int, i, 1, nptrs)
+    FOR_START /*FOR_REV_END*/ (int, i, 1, nptrs)  // From top to bottom of the stack
       s += string (strings [i]) + "\n";  
     s += "Use: addr2line -f -C -e " + programArgs [0] + "  -a <address>";
   //free (strings);
@@ -1918,6 +1918,7 @@ void Root::saveFile (const string &fName) const
 
 
 
+#if 0
 void Root::trace (ostream& os,
                   const string& title) const
 { 
@@ -1927,6 +1928,7 @@ void Root::trace (ostream& os,
   os << title << ": ";
   saveText (os);
 }
+#endif
 
 
 
diff --git a/common.hpp b/common.hpp
index d03164d..603cd63 100644
--- a/common.hpp
+++ b/common.hpp
@@ -116,7 +116,7 @@ constexpr size_t no_index = numeric_limits<size_t>::max ();
 static_assert ((size_t) 0 - 1 == no_index);
 
 constexpr double NaN = numeric_limits<double>::quiet_NaN ();  
-
+  
 
 
 // Global variables
@@ -165,6 +165,11 @@ void beep ();
     
 
 
+template <typename T> 
+  inline bool isNan (T x)
+    { return x != x; }
+
+
 // Comparison templates
 
 template <typename T> 
@@ -465,10 +470,14 @@ template <typename T /*container*/>
 typedef  map<string/*key*/,string/*value*/>  KeyValue;
 
 inline string find (const KeyValue& kv,
-                    const string& key)
+                    const string& key,
+                    bool force)
   { const auto& it = kv. find (key);
     if (it == kv. end ())
+    { if (force)
+        return key;
       throw runtime_error ("Key \"" + key + "\" is not found");
+    }
     return it->second;
   }
 
@@ -2087,15 +2096,17 @@ struct Root
       saveText (oss);
       return oss. str ();
     }
+#if 0
   void trace (ostream& os,
               const string& title) const;
+#endif
   virtual void saveXml (Xml::File& /*f*/) const 
     { throwf ("Root::saveXml() is not implemented"); }
   virtual Json* toJson (JsonContainer* /*parent_arg*/,
                         const string& /*name_arg*/) const
     { throwf ("Root::toJson() is not implemented"); }
 	virtual bool empty () const
-	  { return true; }
+	  { throwf ("Root::empty() is not implemented"); }
   virtual void clear ()
     { throwf ("Root::clear() is not implemented"); }
     // Postcondition: empty()
diff --git a/stx b/stx
index 1fd945e..fc3dab3 160000
--- a/stx
+++ b/stx
@@ -1 +1 @@
-Subproject commit 1fd945e52028234b8b2ba89475dbe62aac17167e
+Subproject commit fc3dab30e1143cd8a7afc3a3664882a7bcaef786
diff --git a/version.txt b/version.txt
index d13e837..43beb40 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-4.0.6
+4.0.7