New upstream version 2.3.0

1 files changed, 0 insertions, 199 deletions

diff --git a/alphabet.cpp b/alphabet.cpp
index 630a3bb..c31aeed 100644
--- a/alphabet.cpp
+++ b/alphabet.cpp
@@ -115,164 +115,6 @@ uint8_t asc2dnamask[] = {
 };
 
 /**
- * Convert a pair of DNA masks to a color mask
- *
- * 
- */ 
-uint8_t dnamasks2colormask[16][16] = {
-	         /* 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15 */
-	/*  0 */ {  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0 },
-	/*  1 */ {  0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15 },
-	/*  2 */ {  0,  2,  1,  3,  8, 10,  9, 11,  4,  6,  5,  7, 12, 14, 13, 15 },
-	/*  3 */ {  0,  3,  3,  3, 12, 15, 15, 15, 12, 15, 15, 15, 12, 15, 15, 15 },
-	/*  4 */ {  0,  4,  8, 12,  1,  5,  9, 13,  2,  6, 10, 14,  3,  7, 11, 15 },
-	/*  5 */ {  0,  5, 10, 15,  5,  5, 15, 15, 10, 15, 10, 15, 15, 15, 15, 15 },
-	/*  6 */ {  0,  6,  9, 15,  9, 15,  9, 15,  6,  6, 15, 15, 15, 15, 15, 15 },
-	/*  7 */ {  0,  7, 11, 15, 13, 15, 15, 15, 14, 15, 15, 15, 15, 15, 15, 15 },
-	/*  8 */ {  0,  8,  4, 12,  2, 10,  6, 14,  1,  9,  5, 13,  3, 11,  7, 15 },
-	/*  9 */ {  0,  9,  6, 15,  6, 15,  6, 15,  9,  9, 15, 15, 15, 15, 15, 15 },
-	/* 10 */ {  0, 10,  5, 15, 10, 10, 15, 15,  5, 15,  5, 15, 15, 15, 15, 15 },
-	/* 11 */ {  0, 11,  7, 15, 14, 15, 15, 15, 13, 15, 15, 15, 15, 15, 15, 15 },
-	/* 12 */ {  0, 12, 12, 12,  3, 15, 15, 15,  3, 15, 15, 15,  3, 15, 15, 15 },
-	/* 13 */ {  0, 13, 14, 15,  7, 15, 15, 15, 11, 15, 15, 15, 15, 15, 15, 15 },
-	/* 14 */ {  0, 14, 13, 15, 11, 15, 15, 15,  7, 15, 15, 15, 15, 15, 15, 15 },
-	/* 15 */ {  0, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15 }
-};
-
-/**
- * Mapping from ASCII characters for ambiguous nucleotides into masks:
- */
-char asc2dnacomp[] = {
-	/*   0 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  16 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  32 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,'-',  0,  0,
-	/*  48 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  64 */ 0,'T','V','G','H',  0,  0,'C','D',  0,  0,'M',  0,'K','N',  0,
-	       /*    A   B   C   D           G   H           K       M   N */
-	/*  80 */ 0,  0,'Y','S','A',  0,'B','W',  0,'R',  0,  0,  0,  0,  0,  0,
-	       /*        R   S   T       V   W       Y */
-	/*  96 */ 0,'T','V','G','H',  0,  0,'C','D',  0,  0,'M',  0,'K','N',  0,
-	        /*   a   b   c   d           g   h           k       m   n */
-	/* 112 */ 0,  0,'Y','S','A',  0,'B','W',  0,'R',  0,  0,  0,  0,  0,  0,
-	       /*        r   s   t       v   w       y */
-	/* 128 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 144 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 160 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 176 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 192 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 208 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 224 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 240 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
-};
-
-/**
- * Mapping from ASCII characters for ambiguous nucleotides into masks:
- */
-char col2dna[] = {
-	/*   0 */  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  16 */  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  32 */  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,'-','N',  0,
-	       /*                                                     -   . */
-	/*  48 */'A','C','G','T','N',  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	       /* 0   1   2   3   4  */
-	/*  64 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  80 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  96 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 112 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 128 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 144 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 160 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 176 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 192 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 208 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 224 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 240 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
-};
-
-/**
- * Mapping from ASCII characters for ambiguous nucleotides into masks:
- */
-char dna2col[] = {
-	/*   0 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  16 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  32 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,'-',  0,  0,
-	/*  48 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/*  64 */ 0,'0',  0,'1',  0,  0,  0,'2',  0,  0,  0,  0,  0,  0,'.',  0,
-	       /*    A       C               G                           N */
-	/*  80 */ 0,  0,  0,  0,'3',  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	       /*                T */
-	/*  92 */ 0,'0',  0,'1',  0,  0,  0,'2',  0,  0,  0,  0,  0,  0,'.',  0,
-	       /*    a       c               g                           n */
-	/* 112 */ 0,  0,  0,  0,'3',  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	       /*                t */
-	/* 128 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 144 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 160 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 176 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 192 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 208 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 224 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-	/* 240 */ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
-};
-
-/**
- * Mapping from ASCII characters for ambiguous nucleotides into masks:
- */
-const char* dna2colstr[] = {
-	/*   0 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/*  16 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/*  32 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "-",  "?",  "?",
-	/*  48 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/*  64 */ "?",  "0","1|2|3","1","0|2|3","?",  "?",  "2","0|1|3","?",  "?", "2|3", "?", "0|1", ".",  "?",
-	/*               A     B     C     D                 G     H                 K           M     N */
-	/*  80 */ "?",  "?", "0|2","1|2", "3",  "?","0|1|2","0|3","?", "1|3", "?",  "?",  "?",  "?",  "?",  "?",
-	/*                     R     S     T           V     W           Y */
-	/*  92 */ "?",  "?","1|2|3","1","0|2|3","?",  "?",  "2","0|1|3","?",  "?", "2|3", "?", "0|1", ".",  "?",
-	/*               a     b     c     d                 g     h                 k           m     n */
-	/* 112 */ "?",  "0", "0|2","1|2", "3",  "?","0|1|2","0|3","?", "1|3", "?",  "?",  "?",  "?",  "?",  "?",
-	/*                     r     s     t           v     w           y */
-	/* 128 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/* 144 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/* 160 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/* 176 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/* 192 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/* 208 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/* 224 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",
-	/* 240 */ "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?",  "?"
-};
-
-/**
- * Mapping from ASCII characters to color categories:
- *
- * 0 = invalid - error
- * 1 = valid color
- * 2 = IUPAC (ambiguous DNA) - there is no such thing for colors to my
- *     knowledge
- * 3 = not an error, but unmatchable; alignments containing this
- *     character are invalid
- */
-uint8_t asc2colcat[] = {
-	/*   0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*  16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*  32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 0,
-	       /*                                        -  . */
-	/*  48 */ 1, 1, 1, 1, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	       /* 0  1  2  3  4  */
-	/*  64 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*  80 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*  96 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 112 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-};
-
-/**
  * Set the category for all IUPAC codes.  By default they're in
  * category 2 (IUPAC), but sometimes we'd like to put them in category
  * 3 (unmatchable), for example.
@@ -321,33 +163,6 @@ uint8_t asc2dna[] = {
 	/* 240 */ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
 };
 
-/// Convert an ascii char representing a base or a color to a 2-bit
-/// code: 0=A,0; 1=C,1; 2=G,2; 3=T,3; 4=N,.
-uint8_t asc2dnaOrCol[] = {
-	/*   0 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*  16 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*  32 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 4, 0,
-	/*                                               -  . */
-	/*  48 */ 0, 1, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*        0  1  2  3 */
-	/*  64 */ 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 4, 0,
-	/*           A     C           G                    N */
-	/*  80 */ 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*                    T */
-	/*  96 */ 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 4, 0,
-	/*           a     c           g                    n */
-	/* 112 */ 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/*                    t */
-	/* 128 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 144 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 160 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 176 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 192 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 208 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 224 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	/* 240 */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-};
-
 /// For converting from ASCII to the Dna5 code where A=0, C=1, G=2,
 /// T=3, N=4
 uint8_t asc2col[] = {
@@ -372,20 +187,6 @@ uint8_t asc2col[] = {
 };
 
 /**
- * Convert a nucleotide and a color to the paired nucleotide.  Indexed
- * first by nucleotide then by color.  Note that this is exactly the
- * same as the dinuc2color array.
- */
-uint8_t nuccol2nuc[5][5] = {
-	/*       B  G  O  R  . */
-	/* A */ {0, 1, 2, 3, 4},
-	/* C */ {1, 0, 3, 2, 4},
-	/* G */ {2, 3, 0, 1, 4},
-	/* T */ {3, 2, 1, 0, 4},
-	/* N */ {4, 4, 4, 4, 4}
-};
-
-/**
  * Convert a pair of nucleotides to a color.
  */
 uint8_t dinuc2color[5][5] = {