--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/include/mash/CommandScreen.h	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,171 @@
+// Copyright © 2015, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
+
+#ifndef INCLUDED_CommandScreen
+#define INCLUDED_CommandScreen
+
+#include "Command.h"
+#include "Sketch.h"
+#include <list>
+#include <string>
+#include <vector>
+#include <atomic>
+#include "robin_hood.h"
+#include "MinHashHeap.h"
+
+namespace mash {
+
+struct HashTableEntry
+{
+	HashTableEntry() : count(0) {}
+	
+	uint32_t count;
+	robin_hood::unordered_set<uint64_t> indices;
+};
+
+//typedef robin_hood::unordered_map< uint64_t, HashTableEntry > HashTable;
+typedef robin_hood::unordered_map< uint64_t, robin_hood::unordered_set<uint64_t> > HashTable;
+
+static const robin_hood::unordered_map< std::string, char > codons =
+{
+	{"AAA",	'K'},
+	{"AAC",	'N'},
+	{"AAG",	'K'},
+	{"AAT",	'N'},
+	{"ACA",	'T'},
+	{"ACC",	'T'},
+	{"ACG",	'T'},
+	{"ACT",	'T'},
+	{"AGA",	'R'},
+	{"AGC",	'S'},
+	{"AGG",	'R'},
+	{"AGT",	'S'},
+	{"ATA",	'I'},
+	{"ATC",	'I'},
+	{"ATG",	'M'},
+	{"ATT",	'I'},
+	{"CAA",	'Q'},
+	{"CAC",	'H'},
+	{"CAG",	'Q'},
+	{"CAT",	'H'},
+	{"CCA",	'P'},
+	{"CCC",	'P'},
+	{"CCG",	'P'},
+	{"CCT",	'P'},
+	{"CGA",	'R'},
+	{"CGC",	'R'},
+	{"CGG",	'R'},
+	{"CGT",	'R'},
+	{"CTA",	'L'},
+	{"CTC",	'L'},
+	{"CTG",	'L'},
+	{"CTT",	'L'},
+	{"GAA",	'E'},
+	{"GAC",	'D'},
+	{"GAG",	'E'},
+	{"GAT",	'D'},
+	{"GCA",	'A'},
+	{"GCC",	'A'},
+	{"GCG",	'A'},
+	{"GCT",	'A'},
+	{"GGA",	'G'},
+	{"GGC",	'G'},
+	{"GGG",	'G'},
+	{"GGT",	'G'},
+	{"GTA",	'V'},
+	{"GTC",	'V'},
+	{"GTG",	'V'},
+	{"GTT",	'V'},
+	{"TAA",	'*'},
+	{"TAC",	'Y'},
+	{"TAG",	'*'},
+	{"TAT",	'Y'},
+	{"TCA",	'S'},
+	{"TCC",	'S'},
+	{"TCG",	'S'},
+	{"TCT",	'S'},
+	{"TGA",	'*'},
+	{"TGC",	'C'},
+	{"TGG",	'W'},
+	{"TGT",	'C'},
+	{"TTA",	'L'},
+	{"TTC",	'F'},
+	{"TTG",	'L'},
+	{"TTT",	'F'}
+};
+
+class CommandScreen : public Command
+{
+public:
+    
+    struct HashInput
+    {
+    	HashInput(robin_hood::unordered_map<uint64_t, std::atomic<uint32_t> > & hashCountsNew, MinHashHeap * minHashHeapNew, char * seqNew, uint64_t lengthNew, const Sketch::Parameters & parametersNew, bool transNew)
+    	:
+    	hashCounts(hashCountsNew),
+    	minHashHeap(minHashHeapNew),
+    	seq(seqNew),
+    	length(lengthNew),
+    	parameters(parametersNew),
+    	trans(transNew)
+    	{}
+    	
+    	~HashInput()
+    	{
+    		if ( seq != 0 )
+    		{
+	    		delete [] seq;
+	    	}
+    	}
+    	
+    	std::string fileName;
+    	
+    	char * seq;
+    	uint64_t length;
+    	bool trans;
+    	
+    	Sketch::Parameters parameters;
+		robin_hood::unordered_map<uint64_t, std::atomic<uint32_t> > & hashCounts;
+		MinHashHeap * minHashHeap;
+    };
+    
+    struct HashOutput
+    {
+    	HashOutput(MinHashHeap * minHashHeapNew)
+    	:
+    	minHashHeap(minHashHeapNew)
+    	{}
+    	
+		MinHashHeap * minHashHeap;
+    };
+    
+    CommandScreen();
+    
+    int run() const; // override
+
+private:
+	
+	struct Reference
+	{
+		Reference(uint64_t amerCountNew, std::string nameNew, std::string commentNew)
+		: amerCount(amerCountNew), name(nameNew), comment(commentNew) {}
+		
+		uint64_t amerCount;
+		std::string name;
+		std::string comment;
+	};
+};
+
+char aaFromCodon(const char * codon);
+double estimateIdentity(uint64_t common, uint64_t denom, int kmerSize, double kmerSpace);
+CommandScreen::HashOutput * hashSequence(CommandScreen::HashInput * input);
+double pValueWithin(uint64_t x, uint64_t setSize, double kmerSpace, uint64_t sketchSize);
+void translate(const char * src, char * dst, uint64_t len);
+void useThreadOutput(CommandScreen::HashOutput * output, robin_hood::unordered_set<MinHashHeap *> & minHashHeaps);
+
+} // namespace mash
+
+#endif