Lines Matching refs:Gaplen
60 } Gaplen; typedef
908 static void cleargaplens( Gaplen ****gaplens ) in cleargaplens()
912 Gaplen ****ptptptpt, ***ptptpt, ***ptptptmv, **ptptmv, **ptpt; in cleargaplens()
922 while( *(ptpt=ptptmv++)!=(Gaplen *)1 ) in cleargaplens()
938 static void cleargaplens( Gaplen ****gaplens ) in cleargaplens()
945 for( k=0; gaplens[i][j][k]!=(Gaplen *)1; k++ ) in cleargaplens()
958 static void FreeGaplenMtxReport( Gaplen **mtx ) in FreeGaplenMtxReport()
968 if( mtx[i] == (Gaplen *)1 ) break; in FreeGaplenMtxReport()
978 static void FreeGaplenMtx( Gaplen **mtx, int inclfreq ) in FreeGaplenMtx()
987 if( mtx[i] == (Gaplen *)1 ) break; in FreeGaplenMtx()
1014 static void FreeGaplenCubgaplenReport( Gaplen ***cub ) in FreeGaplenCubgaplenReport()
1030 static void FreeGaplenCub( Gaplen ***cub ) in FreeGaplenCub()
1057 static void fillgaplen( Gaplen **mtx, int l ) in fillgaplen()
1076 mtx[pos] = calloc( 2, sizeof( Gaplen ) ); in fillgaplen()
1092 mtx[pos] = realloc( mtx[pos], sizeof( Gaplen ) * ( k + 2 ) ); in fillgaplen()
1156 static void gaplencount( int n, int l, Gaplen **mtx, char **seq, double *eff ) in gaplencount()
1166 if( mtx[j] == (Gaplen *)1 ) break; in gaplencount()
1210 mtx[j] = realloc( mtx[j], sizeof( Gaplen ) * (nknown+2) ); in gaplencount()
1251 static void showgaplen( Gaplen **mtx, int seqlen ) in showgaplen()
1262 if( mtx[i] == (Gaplen *)1 ) break; in showgaplen()
1329 static double calcpfac_gap_noidatend( Gaplen **gaplen1, Gaplen **gaplen2, int newgaplen, int i, int… in calcpfac_gap_noidatend()
1334 Gaplen *gaplen1i, *gaplen2j, *g1, *g2; in calcpfac_gap_noidatend()
1428 Gaplen *gaplen1i, *gaplen2j; in calcpfac_gap_noidatend()
1523 static double calcpfac_gap_incomplete( Gaplen **gaplen1, Gaplen **gaplen2, int newgaplen, int i, in… in calcpfac_gap_incomplete()
1527 Gaplen *gapend1, *gapend2; in calcpfac_gap_incomplete()
1528 Gaplen *gaplen1i, *gaplen2j; in calcpfac_gap_incomplete()
1625 static double calcpfac_gapex( Gaplen **gaplen1, Gaplen **gaplen2, int i, int j, int newgaplen, char… in calcpfac_gapex()
1629 Gaplen *gapend1, *gapend2; in calcpfac_gapex()
1630 Gaplen *gaplen1i, *gaplen2j; in calcpfac_gapex()
1682 static double calcpfac( Gaplen **gaplen1, Gaplen **gaplen2, int i, int j, char *seq1, char *seq2, i… in calcpfac()
1686 Gaplen *gapend1, *gapend2; in calcpfac()
1687 Gaplen *gaplen1i, *gaplen2j; in calcpfac()
1763 static double calcpfac_gapex_noidatend( Gaplen **gaplen1, Gaplen **gaplen2, int i, int j, int newga… in calcpfac_gapex_noidatend()
1768 Gaplen *gaplen1i, *gaplen2j, *g1, *g2; in calcpfac_gapex_noidatend()
1817 Gaplen *gaplen1i, *gaplen2j; in calcpfac_gapex_noidatend()
1869 static double calcpfacnoidatend( Gaplen **gaplen1, Gaplen **gaplen2, int i, int j, char *seq1, char… in calcpfacnoidatend()
1873 Gaplen *gaplen1i, *gaplen2j, *g1, *g2; in calcpfacnoidatend()
1979 static void extendgaplencompactx( Gaplen **cpy, Gaplen **orig, int start ) in extendgaplencompactx()
1981 Gaplen *opt, *cpt; in extendgaplencompactx()
1984 Gaplen cpybk; in extendgaplencompactx()
2010 cpy[start] = realloc( cpy[start], (l+2) * sizeof( Gaplen ) ); in extendgaplencompactx()
2053 cptplus = cpy[posplus] = realloc( cpy[posplus], (k+2) * sizeof( Gaplen ) ); in extendgaplencompactx()
2106 static void extendgaplenpartly( Gaplen **cpy, Gaplen **orig, int start, int end ) in extendgaplenpartly()
2109 Gaplen *pt; in extendgaplenpartly()
2164 cpy[i] = realloc( cpy[i], (l+2) * sizeof( Gaplen ) ); in extendgaplenpartly()
2188 static void duplicategaplencompactx( Gaplen **cpy, Gaplen **orig, int maxlen, int start, int end ) in duplicategaplencompactx()
2197 if( cpy[i] == (Gaplen *)1 ) in duplicategaplencompactx()
2224 cpy[i] = realloc( cpy[i], (l+2) * sizeof( Gaplen ) ); in duplicategaplencompactx()
2243 static void duplicategaplenpartly( Gaplen **cpy, Gaplen **orig, int start, int end ) in duplicategaplenpartly()
2246 Gaplen *pt; in duplicategaplenpartly()
2251 if( cpy[i] == (Gaplen *)1 ) in duplicategaplenpartly()
2299 cpy[i] = realloc( cpy[i], (l+2) * sizeof( Gaplen ) ); in duplicategaplenpartly()
2324 static void gaplenextendnoidatend( Gaplen **cpy, int gapstartpos, int insertionlen ) in gaplenextendnoidatend()
2361 static void gaplenextend( Gaplen **cpy, int gapstartpos, int insertionlen ) in gaplenextend()
2396 static void copygaplencompactx( Gaplen **cpy, Gaplen **orig, int seqlen, int gapstartpos, int inser… in copygaplencompactx()
2398 Gaplen *pt, *cpt; in copygaplencompactx()
2454 static void copygaplenrestricted_zurasu( Gaplen **cpy, Gaplen **orig, int seqlen, int gapstartpos, … in copygaplenrestricted_zurasu()
2458 Gaplen *pt, *cpt; in copygaplenrestricted_zurasu()
2570 static void copygaplenrestricted( Gaplen **cpy, Gaplen **orig, int seqlen, int gapstartpos, int ins… in copygaplenrestricted()
2573 Gaplen *pt, *cpt; in copygaplenrestricted()
2675 static void freegaplenpartly( Gaplen **mtx, int startpos, int endpos ) in freegaplenpartly()
2678 Gaplen **pt; in freegaplenpartly()
2683 if( *(pt=mtx+i) == (Gaplen *)1 ) break; in freegaplenpartly()
2689 static void freegaplenpartly( Gaplen **mtx, int startpos, int endpos ) in freegaplenpartly()
2696 if( mtx[i] == (Gaplen *)1 ) break; in freegaplenpartly()
2746 Gaplen ****gaplen1half = NULL; // NULL ga iru to omou. in D__align()
2747 Gaplen ****gaplen2half = NULL; // NULL ga iru to omou. in D__align()
2750 Gaplen ****gaplen1mtx = NULL; // NULL ga iru to omou. in D__align()
2751 Gaplen ****gaplen2mtx = NULL; // NULL ga iru to omou. in D__align()
2753 static TLS Gaplen **gaplen1 = NULL; // NULL ga iru to omou. in D__align()
2754 static TLS Gaplen **gaplen2 = NULL; // NULL ga iru to omou. in D__align()
2755 static TLS Gaplen ***gaplen1jprev = NULL; in D__align()
2756 static TLS Gaplen ***gaplen2jprev = NULL; in D__align()
2757 static TLS Gaplen ***gaplen1jcurr = NULL; in D__align()
2758 static TLS Gaplen ***gaplen2jcurr = NULL; in D__align()
2759 static TLS Gaplen ***gaplen1icurr = NULL; in D__align()
2760 static TLS Gaplen ***gaplen2icurr = NULL; in D__align()
2761 static TLS Gaplen ***gaplen1jbestkamo = NULL; in D__align()
2762 static TLS Gaplen ***gaplen2jbestkamo = NULL; in D__align()
2763 static TLS Gaplen ***gaplen1ibestkamo = NULL; in D__align()
2764 static TLS Gaplen ***gaplen2ibestkamo = NULL; in D__align()
2765 static TLS Gaplen ***gaplen1jbest = NULL; in D__align()
2766 static TLS Gaplen ***gaplen2jbest = NULL; in D__align()
2769 static TLS Gaplen ****gaplens = NULL; in D__align()
2771 Gaplen ***gaplentmp = NULL; in D__align()
3026 gaplen1 = (Gaplen ** )calloc( ll1+2, sizeof( Gaplen * ) ); in D__align()
3027 gaplen1[ll1+1] = (Gaplen *)1; in D__align()
3028 gaplen2 = (Gaplen ** )calloc( ll2+2, sizeof( Gaplen * ) ); in D__align()
3029 gaplen2[ll2+1] = (Gaplen *)1; in D__align()
3033 gaplen1ibestkamo = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) ); in D__align()
3034 gaplen2ibestkamo = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) ); in D__align()
3035 gaplen1icurr = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) ); in D__align()
3036 gaplen2icurr = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) ); in D__align()
3037 gaplen1jbestkamo = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align()
3038 gaplen2jbestkamo = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align()
3039 gaplen1jbest = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align()
3040 gaplen2jbest = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align()
3041 gaplen1jcurr = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align()
3042 gaplen2jcurr = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align()
3043 gaplen1jprev = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align()
3044 gaplen2jprev = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align()
3046 gaplens = calloc( sizeof( Gaplen ***), 12 ); in D__align()
3069 gaplen1ibestkamo[i] = (Gaplen **)calloc( ll1+2-i, sizeof( Gaplen * ) ); in D__align()
3071 gaplen1ibestkamo[i][k] = (Gaplen *)1; in D__align()
3073 gaplen2ibestkamo[i] = (Gaplen **)calloc( ll2+2, sizeof( Gaplen * ) ); in D__align()
3075 gaplen2ibestkamo[i][k] = (Gaplen *)1; in D__align()
3077 gaplen1icurr[i] = (Gaplen **)calloc( ll1+2-i, sizeof( Gaplen * ) ); in D__align()
3079 gaplen1icurr[i][k] = (Gaplen *)1; in D__align()
3081 gaplen2icurr[i] = (Gaplen **)calloc( ll2+2, sizeof( Gaplen * ) ); in D__align()
3083 gaplen2icurr[i][k] = (Gaplen *)1; in D__align()
3093 gaplen1jbestkamo[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) ); in D__align()
3095 gaplen1jbestkamo[i][k] = (Gaplen *)1; in D__align()
3097 gaplen2jbestkamo[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) ); in D__align()
3099 gaplen2jbestkamo[i][k] = (Gaplen *)1; in D__align()
3101 gaplen1jbest[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) ); in D__align()
3103 gaplen1jbest[i][k] = (Gaplen *)1; in D__align()
3105 gaplen2jbest[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) ); in D__align()
3107 gaplen2jbest[i][k] = (Gaplen *)1; in D__align()
3109 gaplen1jcurr[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) ); in D__align()
3111 gaplen1jcurr[i][k] = (Gaplen *)1; in D__align()
3113 gaplen2jcurr[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) ); in D__align()
3115 gaplen2jcurr[i][k] = (Gaplen *)1; in D__align()
3117 gaplen1jprev[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) ); in D__align()
3119 gaplen1jprev[i][k] = (Gaplen *)1; in D__align()
3121 gaplen2jprev[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) ); in D__align()
3123 gaplen2jprev[i][k] = (Gaplen *)1; in D__align()
3141 gaplen1mtx = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) ); in D__align()
3142 for(i=0; i<lgth1+1; i++ ) gaplen1mtx[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) ); in D__align()
3147 gaplen1mtx[i][j] = (Gaplen **)calloc( lgth1+2, sizeof( Gaplen * ) ); in D__align()
3149 gaplen1mtx[i][j][k] = (Gaplen *)1; in D__align()
3156 gaplen2mtx = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) ); in D__align()
3157 for(i=0; i<lgth1+1; i++ ) gaplen2mtx[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) ); in D__align()
3162 gaplen2mtx[i][j] = (Gaplen **)calloc( lgth2+2, sizeof( Gaplen * ) ); in D__align()
3164 gaplen2mtx[i][j][k] = (Gaplen *)1; in D__align()
3174 gaplen1half = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) ); in D__align()
3175 for(i=0; i<lgth1+1; i++ ) gaplen1half[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) ); in D__align()
3180 gaplen1half[i][j] = (Gaplen **)calloc( lgth1+2 - i, sizeof( Gaplen * ) ); in D__align()
3182 gaplen1half[i][j][k] = (Gaplen *)1; in D__align()
3189 gaplen2half = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) ); in D__align()
3190 for(i=0; i<lgth1+1; i++ ) gaplen2half[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) ); in D__align()
3195 gaplen2half[i][j] = (Gaplen **)calloc( lgth2+2 - j, sizeof( Gaplen * ) ); in D__align()
3197 gaplen2half[i][j][k] = (Gaplen *)1; in D__align()
4582 Gaplen ****gaplen1half = NULL; // NULL ga iru to omou. in D__align_variousdist()
4583 Gaplen ****gaplen2half = NULL; // NULL ga iru to omou. in D__align_variousdist()
4586 Gaplen ****gaplen1mtx = NULL; // NULL ga iru to omou. in D__align_variousdist()
4587 Gaplen ****gaplen2mtx = NULL; // NULL ga iru to omou. in D__align_variousdist()
4589 static TLS Gaplen **gaplen1 = NULL; // NULL ga iru to omou. in D__align_variousdist()
4590 static TLS Gaplen **gaplen2 = NULL; // NULL ga iru to omou. in D__align_variousdist()
4591 static TLS Gaplen ***gaplen1jprev = NULL; in D__align_variousdist()
4592 static TLS Gaplen ***gaplen2jprev = NULL; in D__align_variousdist()
4593 static TLS Gaplen ***gaplen1jcurr = NULL; in D__align_variousdist()
4594 static TLS Gaplen ***gaplen2jcurr = NULL; in D__align_variousdist()
4595 static TLS Gaplen ***gaplen1icurr = NULL; in D__align_variousdist()
4596 static TLS Gaplen ***gaplen2icurr = NULL; in D__align_variousdist()
4597 static TLS Gaplen ***gaplen1jbestkamo = NULL; in D__align_variousdist()
4598 static TLS Gaplen ***gaplen2jbestkamo = NULL; in D__align_variousdist()
4599 static TLS Gaplen ***gaplen1ibestkamo = NULL; in D__align_variousdist()
4600 static TLS Gaplen ***gaplen2ibestkamo = NULL; in D__align_variousdist()
4601 static TLS Gaplen ***gaplen1jbest = NULL; in D__align_variousdist()
4602 static TLS Gaplen ***gaplen2jbest = NULL; in D__align_variousdist()
4605 static TLS Gaplen ****gaplens = NULL; in D__align_variousdist()
4607 Gaplen ***gaplentmp = NULL; in D__align_variousdist()
4890 gaplen1 = (Gaplen ** )calloc( ll1+2, sizeof( Gaplen * ) ); in D__align_variousdist()
4891 gaplen1[ll1+1] = (Gaplen *)1; in D__align_variousdist()
4892 gaplen2 = (Gaplen ** )calloc( ll2+2, sizeof( Gaplen * ) ); in D__align_variousdist()
4893 gaplen2[ll2+1] = (Gaplen *)1; in D__align_variousdist()
4897 gaplen1ibestkamo = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) ); in D__align_variousdist()
4898 gaplen2ibestkamo = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) ); in D__align_variousdist()
4899 gaplen1icurr = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) ); in D__align_variousdist()
4900 gaplen2icurr = (Gaplen ***)calloc( (ll1+2), sizeof( Gaplen **) ); in D__align_variousdist()
4901 gaplen1jbestkamo = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align_variousdist()
4902 gaplen2jbestkamo = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align_variousdist()
4903 gaplen1jbest = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align_variousdist()
4904 gaplen2jbest = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align_variousdist()
4905 gaplen1jcurr = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align_variousdist()
4906 gaplen2jcurr = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align_variousdist()
4907 gaplen1jprev = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align_variousdist()
4908 gaplen2jprev = (Gaplen ***)calloc( (ll2+2), sizeof( Gaplen **) ); in D__align_variousdist()
4910 gaplens = calloc( sizeof( Gaplen ***), 12 ); in D__align_variousdist()
4933 gaplen1ibestkamo[i] = (Gaplen **)calloc( ll1+2-i, sizeof( Gaplen * ) ); in D__align_variousdist()
4935 gaplen1ibestkamo[i][k] = (Gaplen *)1; in D__align_variousdist()
4937 gaplen2ibestkamo[i] = (Gaplen **)calloc( ll2+2, sizeof( Gaplen * ) ); in D__align_variousdist()
4939 gaplen2ibestkamo[i][k] = (Gaplen *)1; in D__align_variousdist()
4941 gaplen1icurr[i] = (Gaplen **)calloc( ll1+2-i, sizeof( Gaplen * ) ); in D__align_variousdist()
4943 gaplen1icurr[i][k] = (Gaplen *)1; in D__align_variousdist()
4945 gaplen2icurr[i] = (Gaplen **)calloc( ll2+2, sizeof( Gaplen * ) ); in D__align_variousdist()
4947 gaplen2icurr[i][k] = (Gaplen *)1; in D__align_variousdist()
4957 gaplen1jbestkamo[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) ); in D__align_variousdist()
4959 gaplen1jbestkamo[i][k] = (Gaplen *)1; in D__align_variousdist()
4961 gaplen2jbestkamo[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) ); in D__align_variousdist()
4963 gaplen2jbestkamo[i][k] = (Gaplen *)1; in D__align_variousdist()
4965 gaplen1jbest[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) ); in D__align_variousdist()
4967 gaplen1jbest[i][k] = (Gaplen *)1; in D__align_variousdist()
4969 gaplen2jbest[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) ); in D__align_variousdist()
4971 gaplen2jbest[i][k] = (Gaplen *)1; in D__align_variousdist()
4973 gaplen1jcurr[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) ); in D__align_variousdist()
4975 gaplen1jcurr[i][k] = (Gaplen *)1; in D__align_variousdist()
4977 gaplen2jcurr[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) ); in D__align_variousdist()
4979 gaplen2jcurr[i][k] = (Gaplen *)1; in D__align_variousdist()
4981 gaplen1jprev[i] = (Gaplen **)calloc( ll1+2, sizeof( Gaplen * ) ); in D__align_variousdist()
4983 gaplen1jprev[i][k] = (Gaplen *)1; in D__align_variousdist()
4985 gaplen2jprev[i] = (Gaplen **)calloc( ll2+2-i, sizeof( Gaplen * ) ); in D__align_variousdist()
4987 gaplen2jprev[i][k] = (Gaplen *)1; in D__align_variousdist()
5005 gaplen1mtx = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) ); in D__align_variousdist()
5006 for(i=0; i<lgth1+1; i++ ) gaplen1mtx[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) ); in D__align_variousdist()
5011 gaplen1mtx[i][j] = (Gaplen **)calloc( lgth1+2, sizeof( Gaplen * ) ); in D__align_variousdist()
5013 gaplen1mtx[i][j][k] = (Gaplen *)1; in D__align_variousdist()
5020 gaplen2mtx = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) ); in D__align_variousdist()
5021 for(i=0; i<lgth1+1; i++ ) gaplen2mtx[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) ); in D__align_variousdist()
5026 gaplen2mtx[i][j] = (Gaplen **)calloc( lgth2+2, sizeof( Gaplen * ) ); in D__align_variousdist()
5028 gaplen2mtx[i][j][k] = (Gaplen *)1; in D__align_variousdist()
5038 gaplen1half = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) ); in D__align_variousdist()
5039 for(i=0; i<lgth1+1; i++ ) gaplen1half[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) ); in D__align_variousdist()
5044 gaplen1half[i][j] = (Gaplen **)calloc( lgth1+2 - i, sizeof( Gaplen * ) ); in D__align_variousdist()
5046 gaplen1half[i][j][k] = (Gaplen *)1; in D__align_variousdist()
5053 gaplen2half = (Gaplen ****)calloc( (lgth1+2), sizeof( Gaplen ***) ); in D__align_variousdist()
5054 for(i=0; i<lgth1+1; i++ ) gaplen2half[i] = (Gaplen ***)calloc( lgth2+2, sizeof( Gaplen ** ) ); in D__align_variousdist()
5059 gaplen2half[i][j] = (Gaplen **)calloc( lgth2+2 - j, sizeof( Gaplen * ) ); in D__align_variousdist()
5061 gaplen2half[i][j][k] = (Gaplen *)1; in D__align_variousdist()