New upstream version 4.6.4 (54e22815) · Commits · Debian Med / seaview

FL/Fl_Native_File_Chooser.H

+0 −4

Original line number	Diff line number	Diff line
		@@ -2,10 +2,6 @@
		#define FL_NATIVE_FILE_CHOOSER_H

		#include <FL/Enumerations.H>
		#if defined(USE_NEW_FLTK_FEATURES) && FL_PATCH_VERSION < 3
		#undef FL_PATCH_VERSION
		#define FL_PATCH_VERSION 3
		#endif
		#define SEAVIEW_FLTK_VERSION 100FL_MAJOR_VERSION + 10FL_MINOR_VERSION + FL_PATCH_VERSION
		#if SEAVIEW_FLTK_VERSION < 133 && !(defined(__APPLE__) \|\| defined(WIN32))
		#define Fl_Native_File_Chooser mgFl_Native_File_Chooser

csrc/misc_acnuc.c

+162 −35

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@ void *mycalloc(int nbr, size_t taille);
		char complementer_base(char nucl);
		void complementer_seq(char *deb_ch, int l);
		char init_codon_to_aa(char *codon, int gc);
		char stop_codon_to_aa(char *codon, int gc);
		int notrail2(char *chaine, int len);
		int prepch(char chaine, char *posmot);
		int compch(char cible, int lcible, char *posmot, int nbrmots);
		@@ -53,31 +54,36 @@ for(i=(int)strlen(pname);i<length;i++) pname[i]=' ';
		}


		#define TOTCODES 20 /* nbre total de codes definis, 0 inclus */
		#define TOTCODES 25 /* nbre total de codes definis, 0 inclus */
		int totcodes=TOTCODES;

		char aminoacids[]="RLSTPAGVKNQHEDYCFIMW*X";

		struct genetic_code_libel { /* definition d'un code genetique */
		char libel[61]; /* nom du code decrivant ses variants % code standard */
		char* target;
		int code[65]; /* tableau codon->acide amine */
		int ncbi_gc; /* numero NCBI du meme code */
		int codon_init[64]; /* tableau codon initiateur -> acide amine */
		int codon_init[64]; /* tableau codon initiateur ou stop -> acide amine */
		};

		/*
		les codons sont numerotes de 1 a 64 selon ordre alphabetique;
		le numero 65 est attribue a tout codon avec base hors AcCcGgTtUu
		les acides amines sont numerotes selon l'ordre de la variable aminoacids
		de un a 20 + * pour stop et X pour inconnu
		de un a 20 + * pour stop et X pour inconnu.
		Table codon_init gives 19 (=M) for initiation codons and 21 (=*) for stop codons.
		In some genetic codes, the same codon corresponds to an aa in table code
		and to a stop in table codon_init.
		*/

		/* initialisation de tous les codes genetiques */
		struct genetic_code_libel genetic_code[TOTCODES] =
		{

		{ /* 0: universel */
		{"Universal genetic code"},
		{ /* 0: standard */
		{"Standard genetic code"},
		"Standard",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -86,11 +92,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* CUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		21,0,21,0,0,0,0,0,21,0,0,0,0,0,19,0} /* UUG */
		}
		,
		{ /* 1: yeast mt */
		{"CUN=T AUA=M UGA=W"},
		"Yeast Mitochondrial",
		{9,10,9,10,4,4,4,4,1,3,1,3,19,18,19,18,
		11,12,11,12,5,5,5,5,1,1,1,1,4,4,4,4,
		13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -99,23 +106,25 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,19,0,19,0, /* AUA, AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,0,0}
		}
		,
		{ /* 2: : MITOCHONDRIAL CODE OF VERTEBRATES */
		{"AGR=* AUA=M UGA=W"},
		"Vertebrate Mitochondrial",
		{9,10,9,10,4,4,4,4,21,3,21,3,19,18,19,18,11,12,11,12,
		5,5,5,5,1,1,1,1,2,2,2,2,13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,21,15,
		21,15,3,3,3,3,20,16,20,16,2,17,2,17,22},
		2,
		{0,0,0,0,0,0,0,0,0,0,0,0,19,19,19,19, /* AUN */
		{0,0,0,0,0,0,0,0,21,0,21,0,19,19,19,19, /* AUN */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,0,0}
		}
		,
		{ /* 3: MITOCHONDRIAL CODE OF FILAMENTOUS FUNGI */
		{"UGA=W"},
		"Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma",
		{9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,11,12,11,12,5,5,5,
		5,1,1,1,1,2,2,2,2,13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,21,15,21,
		15,3,3,3,3,20,16,20,16,2,17,2,17,22},
		@@ -123,11 +132,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,19,19,19,19, /* AUN */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* CUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		0,0,0,0,0,0,0,0,0,0,0,0,19,0,19,0} /* UUR */
		21,0,21,0,0,0,0,0,0,0,0,0,19,0,19,0} /* UUR */
		}
		,
		{ /* 4: MITOCHONDRIAL CODE OF INSECT AND PLATYHELMINTHES */
		{"AUA=M UGA=W AGR=S"},
		"Invertebrate Mitochondrial",
		{9,10,9,10,4,4,4,4,3,3,3,3,19,18,19,18,11,12,11,12,5,5,5,
		5,1,1,1,1,2,2,2,2,13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,21,15,21,
		15,3,3,3,3,20,16,20,16,2,17,2,17,22},
		@@ -135,11 +145,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,19,19,19,19, /* AUN */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		}
		,
		{ /* 5: Nuclear code of Candida cylindracea (see nature 341:164) */
		{"CUG=S"},
		"Alternative Yeast Nuclear",
		{9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		11,12,11,12,5,5,5,5,1,1,1,1,2,2,3,2,
		13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -148,11 +159,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* CUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,21,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 6: NUCLEAR CODE OF CILIATA: UAR = Gln = Q */
		{"UAR=Q"},
		"Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear",
		{9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,11,12,11,12,5,5,5,
		5,1,1,1,1,2,2,2,2,13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,11,15,11,
		15,3,3,3,3,21,16,20,16,2,17,2,17,22},
		@@ -160,11 +172,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		0,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 7: NUCLEAR CODE OF EUPLOTES */
		{"UGA=C"},
		"Euplotid Nuclear",
		{9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,11,12,11,12,5,5,5,
		5,1,1,1,1,2,2,2,2,13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,21,15,21,
		15,3,3,3,3,16,16,20,16,2,17,2,17,22},
		@@ -172,11 +185,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,0,0}
		}
		,
		{ /* 8: MITOCHONDRIAL CODE OF ECHINODERMS */
		{"UGA=W AGR=S AAA=N"},
		"Echinoderm Mitochondrial; Flatworm Mitochondrial",
		{10,10,9,10,4,4,4,4,3,3,3,3,18,18,19,18,
		11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -184,25 +198,27 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		9,
		{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,0,0}
		}
		,
		{ /* 9: MITOCHONDRIAL CODE OF ASCIDIACEA */
		{"UGA=W AGR=G AUA=M"},
		"Ascidian Mitochondrial",
		{9,10,9,10,4,4,4,4,7,3,7,3,19,18,19,18,
		11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		21,15,21,15,3,3,3,3,20,16,20,16,2,17,2,17,22},
		13,
		{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		{0,0,0,0,0,0,0,0,0,0,0,0,19,0,19,0, /* AUA,AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		}
		,
		{ /* 10: MITOCHONDRIAL CODE OF PLATYHELMINTHES */
		{"UGA=W AGR=S UAA=Y AAA=N"},
		"Alternative Flatworm Mitochondrial",
		{10,10,9,10,4,4,4,4,3,3,3,3,18,18,19,18,
		11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -211,11 +227,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		0,0,21,0,0,0,0,0,0,0,0,0,0,0,0,0}
		}
		,
		{ /* 11: NUCLEAR CODE OF BLEPHARISMA */
		{"UAG=Q"},
		"Blepharisma Macronuclear",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -224,11 +241,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 12: NUCLEAR CODE OF BACTERIA: differs only for initiation codons */
		{"NUG=AUN=M when initiation codon"},
		"Bacterial, Archaeal and Plant Plastid",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -237,11 +255,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,19,19,19,19, /* AUN */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* CUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		21,0,21,0,0,0,0,0,21,0,0,0,0,0,19,0} /* UUG */
		}
		,
		{ /* 13: Chlorophycean Mitochondrial */
		{"UAG=Leu"},
		"Chlorophycean Mitochondrial",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -250,11 +269,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 14: MITOCHONDRIAL CODE OF TREMATODE */
		{"AUA=M UGA=W AGR=S AAA=N"},
		"Trematode Mitochondrial",
		{10,10,9,10,4,4,4,4,3,3,3,3,19,18,19,18,11,12,11,12,5,5,5,
		5,1,1,1,1,2,2,2,2,13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,21,15,21,
		15,3,3,3,3,20,16,20,16,2,17,2,17,22},
		@@ -262,11 +282,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,0,0}
		}
		,
		{ /* 15: TAG-Leu,TCA-stop */
		{"UAG=L UCA=*"},
		"Scenedesmus obliquus mitochondrial",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -275,11 +296,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,0,0,21,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 16: Thraustochytrium-mt */
		{"UUA=*"},
		"Thraustochytrium mitochondrial",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -288,11 +310,12 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,19, /* AUG AUU */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
		21,0,21,0,0,0,0,0,21,0,0,0,21,0,0,0}
		}
		,
		{ /* 17: MITOCHONDRIAL CODE OF Pterobranchia */
		{"UGA=W AGA=S AGG=K"},
		"Pterobranchia Mitochondrial",
		/ANN/ {9,10,9,10,4,4,4,4,3,3,9,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -300,25 +323,27 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		/ncbi/24,
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* CUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		}
		,
		{ /* 18: Candidate Division SR1 and Gracilibacteria */
		{"UGA=G"},
		"Candidate Division SR1 and Gracilibacteria",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		/TNN/ 21,15,21,15,3,3,3,3,7,16,20,16,2,17,2,17,22},
		/ncbi/25,
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* CUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* GUG */
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,19,0} /* UUG */
		}
		,
		{ /* 19: Pachysolen tannophilus */
		{"CUG=A"},
		"Pachysolen tannophilus Nuclear",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,6,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		@@ -327,7 +352,77 @@ struct genetic_code_libel genetic_code[TOTCODES] =
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* CUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0} /* UUG */
		21,0,21,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 20: Karyorelict Nuclear */
		{"UAR=Q, UGA=W, CUG=A"},
		"Karyorelict Nuclear",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,6,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		/TNN/ 11,15,11,15,3,3,3,3,20,16,20,16,2,17,2,17,22},
		/ncbi/27,
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 21: Condylostoma Nuclear */
		{"UAR=Q, UGA=W, CUG=A"},
		"Condylostoma Nuclear",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,6,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		/TNN/ 11,15,11,15,3,3,3,3,20,16,20,16,2,17,2,17,22},
		/ncbi/28,
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		21,0,21,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 22: Mesodinium Nuclear */
		{"UAR=Y, CUG=A"},
		"Mesodinium Nuclear",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,6,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		/TNN/ 15,15,15,15,3,3,3,3,21,16,20,16,2,17,2,17,22},
		/ncbi/29,
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 23: Peritrich Nuclear */
		{"UAR=E, CUG=A"},
		"Peritrich Nuclear",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,6,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		/TNN/ 13,15,13,15,3,3,3,3,21,16,20,16,2,17,2,17,22},
		/ncbi/30,
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0}
		}
		,
		{ /* 24: Blastocrithidia Nuclear */
		{"UAR=E, UGA=W"},
		"Blastocrithidia Nuclear",
		/ANN/ {9,10,9,10,4,4,4,4,1,3,1,3,18,18,19,18,
		/CNN/ 11,12,11,12,5,5,5,5,1,1,1,1,2,2,2,2,
		/GNN/ 13,14,13,14,6,6,6,6,7,7,7,7,8,8,8,8,
		/TNN/ 13,15,13,15,3,3,3,3,20,16,20,16,2,17,2,17,22},
		/ncbi/31,
		/init/{0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0, /* AUG */
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		21,0,21,0,0,0,0,0,0,0,0,0,0,0,0,0}
		}


		@@ -352,6 +447,19 @@ else
		}


		char *get_code_target(int code)
		/*
		get a description of target organisms of a variant genetic code
		return value pointer to the description, not to be altered!
		*/
		{
		if(code >= 0 && code < totcodes)
		return genetic_code[code].target ;
		else
		return "Unknown genetic code. Standard code is used.";
		}


		int calc_codon_number(char *codon)
		{
		static char nucleotides[] = "AaCcGgTtUu";
		@@ -537,7 +645,6 @@ void complementer_seq(char *deb_ch, int l)
		}



		char init_codon_to_aa(char *codon, int gc)
		{
		int num, aa;
		@@ -550,7 +657,27 @@ if(gc < 0 \|\| gc >= totcodes) gc = 0;
		pdata = &genetic_code[gc];
		aa = pdata->codon_init[num];
		/* if not listed in expected init codons */
		if(aa == 0) aa = pdata->code[num];
		if(aa == 0 \|\| aa == 21) aa = pdata->code[num];
		return aminoacids[aa - 1];
		}


		char stop_codon_to_aa(char *codon, int gc)
		{
		int num, aa;
		struct genetic_code_libel *pdata;

		num = calc_codon_number(codon);
		if(num >= 64) return 'X';
		/* use regular code if unknown number */
		if(gc < 0 \|\| gc >= totcodes) gc = 0;
		pdata = &genetic_code[gc];
		aa = pdata->code[num];
		if (aa != 21) {
		aa = pdata->codon_init[num];
		/* if not listed in expected stop codons */
		if (aa != 21) aa = pdata->code[num];
		}
		return aminoacids[aa - 1];
		}

macos_extras.mm

+68 −11

Original line number	Diff line number	Diff line
		@@ -5,9 +5,6 @@
		#include <FL/x.H>
		#include <FL/Fl_Sys_Menu_Bar.H>
		#include <FL/Fl_Help_View.H>
		#if 100FL_MAJOR_VERSION + 10FL_MINOR_VERSION + FL_PATCH_VERSION >= 140
		#include <src/drivers/Quartz/Fl_Quartz_Graphics_Driver.H>
		#endif
		#include <FL/filename.H>
		#include <FL/fl_draw.H>
		#include <sys/stat.h>
		@@ -20,11 +17,13 @@ static void file_receive_cb(const char *fname);
		static void show_apropos(Fl_Widget , void unused);
		void MG_apple_inits(void);
		void set_seaview_modified(SEA_VIEW *view, int ismodified);
		#if 100*FL_MAJOR_VERSION + FL_MINOR_VERSION < 104
		void windowmenuitem_callback(Fl_Widget o, void data);
		int find_windowmenuitem(Fl_Window *w);
		int add_windowmenuitem(const char name, Fl_Window w);
		void rename_windowmenuitem(const char *name, int rank);
		void delete_windowmenuitem(int rank);
		#endif
		char mac_GetOutputFName_Plus(const char dfault, const char message, int, const char directory);

		/* extern functions */
		@@ -181,7 +180,7 @@ char mac_GetOutputFName_Plus(const char dfault, const char *message, int use_o
		[key makeKeyWindow];
		[preset release];
		[dir release];
		if ( retval == NSOKButton ) {//read accessory view state
		if ( retval == NSFileHandlingPanelOKButton ) {//read accessory view state
		printout_block = [blockview intValue];
		printout_fontsize = [fontview intValue];
		printout_black = [pdfmatrix selectedRow];
		@@ -191,10 +190,11 @@ char mac_GetOutputFName_Plus(const char dfault, const char *message, int use_o
		strcpy(pathname, [[[_panel URL] path] UTF8String]);
		}
		[_panel setAccessoryView:nil];
		if ( retval == NSCancelButton ) return NULL;
		if ( retval == NSFileHandlingPanelCancelButton ) return NULL;
		return pathname;
		}

		#if 100*FL_MAJOR_VERSION + FL_MINOR_VERSION < 104

		void windowmenuitem_callback(Fl_Widget o, void data)
		{
		@@ -239,6 +239,9 @@ void delete_windowmenuitem(int rank)
		fl_sys_menu_bar->remove(rank);
		}

		#endif


		static void file_receive_cb(const char *fname)
		{
		SEA_VIEW *view;
		@@ -293,10 +296,56 @@ static void show_apropos(Fl_Widget w, void unused)
		about->show();
		}

		#if 100*FL_MAJOR_VERSION + FL_MINOR_VERSION >= 104

		static Fl_Window *merged;

		static bool merge_windows_for_class(Fl_Window *first)
		{
		bool retval = false;
		Fl_Window *win = first;
		NSWindow nsw = (NSWindow)fl_xid(first), *nsw2;
		while ((win = Fl::next_window(win)) != NULL) {
		int diff = strcmp(win->xclass(), first->xclass());
		if (win->parent() \|\| diff) continue;
		nsw2 = (NSWindow*)fl_xid(win);
		[nsw2 addTabbedWindow:nsw ordered:NSWindowAbove];
		retval = true;
		if (!merged) merged = win;
		}
		return retval;
		}

		static void merge_windows_by_class_cb(Fl_Widget , void )
		{
		merged = NULL;
		more:
		Fl_Window *win = Fl::first_window();
		NSWindow *nsw;
		while (win) {
		nsw = (NSWindow*)fl_xid(win);
		if (!win->parent() && ![nsw tabbedWindows] && strcmp(win->xclass(), Fl_Window::default_xclass())) {
		if (merge_windows_for_class(win)) goto more;
		}
		win = Fl::next_window(win);
		}
		if (merged) merged->show();
		}
		#endif // FLTK ≥ 1.4

		void MG_apple_inits(void)
		{
		fl_open_callback(file_receive_cb);
		fl_mac_set_about(show_apropos, NULL, 0);
		#if 100*FL_MAJOR_VERSION + FL_MINOR_VERSION >= 104
		Fl_Sys_Menu_Bar::create_window_menu();
		int merge = fl_sys_menu_bar->find_index("Window/Merge All Windows");
		if (merge >= 0) {
		fl_sys_menu_bar->replace(merge, "Merge Windows by Class");
		Fl_Menu_Item item = (Fl_Menu_Item)fl_sys_menu_bar->menu() + merge;
		item->callback(merge_windows_by_class_cb);
		}
		#endif
		Fl::set_font(FL_COURIER,"Courier");
		Fl::set_font(FL_COURIER_BOLD, (fl_mac_os_version >= 100500 ? "Courier-Bold" : "Courier Bold") );
		if (fl_mac_os_version >= 100500) { // it seems that Courier Oblique is not present on older OS
		@@ -463,9 +512,17 @@ Copy_Surface::Copy_Surface(bool pict, int w, int h) : Fl_Surface_Device(NULL)
		}
		else {
		prepare_copy_pdf_and_pict(w, h);
		#if 100FL_MAJOR_VERSION + 10FL_MINOR_VERSION + FL_PATCH_VERSION >= 140
		driver(Fl_Graphics_Driver::newMainGraphicsDriver());
		#else
		driver(new Fl_Quartz_Graphics_Driver());
		#endif
		oldgc = fl_gc;
		#if 100FL_MAJOR_VERSION + 10FL_MINOR_VERSION + FL_PATCH_VERSION >= 140
		driver()->gc(gc);
		#else
		fl_gc = gc;
		#endif
		}
		}

		@@ -558,7 +615,7 @@ void Copy_Surface::init_PDF_context(int w, int h)
		CGRect bounds = CGRectMake(0, 0, w, h );
		pdfdata = CFDataCreateMutable(NULL, 0);
		CGDataConsumerRef myconsumer;
		if (CGDataConsumerCreateWithCFData != NULL) { // true from 10.4
		if (CGDataConsumerCreateWithCFData) { // true from 10.4
		myconsumer = CGDataConsumerCreateWithCFData (pdfdata);
		}
		else {

pdf_or_ps.h

+28 −9

Original line number	Diff line number	Diff line
		@@ -6,6 +6,10 @@
		#include <FL/Fl_Graphics_Driver.H>
		#endif

		#if defined(WIN32)
		#include <windows.h>
		#endif

		#if !(defined(__APPLE__) \|\| defined(WIN32)) && 100FL_MAJOR_VERSION + 10FL_MINOR_VERSION + FL_PATCH_VERSION == 130
		// for X11 under 1.3.0 only
		#include <FL/Fl_Printer.H>
		@@ -161,10 +165,8 @@ typedef Fl_PDF_File_Device Fl_PDF_or_PS_File_Device;
		#endif
		#endif

		#if (defined(__APPLE__) \|\| defined(WIN32))

		#if defined(__APPLE__)
		class Copy_Surface : public Fl_Surface_Device {
		#ifdef __APPLE__
		bool use_pict;
		CFMutableDataRef pdfdata;
		CGContextRef oldgc;
		@@ -178,18 +180,35 @@ class Copy_Surface : public Fl_Surface_Device {
		void prepare_copy_pdf_and_pict(int w, int h);
		void complete_copy_pdf_and_pict();
		void init_PDF_context(int w, int h);
		#else
		HDC oldflgc;
		#endif
		public:
		#ifdef __APPLE__
		Copy_Surface(bool use_pict, int w, int h);
		~Copy_Surface();
		};
		#endif // __APPLE__

		#if defined(WIN32)

		#if 100FL_MAJOR_VERSION + 10FL_MINOR_VERSION + FL_PATCH_VERSION >= 134 // FLTK after 1.3.4

		#include <FL/Fl_Copy_Surface.H>
		class Copy_Surface : public Fl_Copy_Surface {
		public:
		Copy_Surface(int w, int h) : Fl_Copy_Surface(w, h) {}
		~Copy_Surface() {}
		};

		#else

		class Copy_Surface : public Fl_Surface_Device {
		HDC oldflgc;
		public:
		Copy_Surface(int w, int h);
		#endif
		~Copy_Surface();
		};
		#endif

		#endif // FLTK after 1.4

		#endif // WIN32


		#endif // PDF_OR_PS_H

seaview.cxx

+78 −35

File changed.

Preview size limit exceeded, changes collapsed.