source: tags/svn.1.5.4/NTREE/AP_consensus.cxx

/* -----------------------------------------------------------------
 * Project:                       ARB
 *
 * Module:                        consensus [abbrev.:CON]
 *
 * Exported Classes:              x
 *
 * Global Functions:              x
 *
 * Global Variables:              AWARS:
 *                  AW_STRING, "tmp/con/alignment"     : name of alignment
 *                  AW_STRING, "tmp/con/which_species" : only marked species ?
 *                  AW_STRING, "con/group"         : allow Sgrouping ?
 *                  AW_STRING, "con/countgaps"
 *                  AW_DOUBLE, "con/fupper"
 *                  AW_INT, "con/lower"
 *                  AW_INT, "con/gapbound"  : result is '-' if more than
 *                                            'gapbound' per cent gaps
 *                  AW_DOUBLE, "con/fconsidbound" : if frequency of character is
 *                                     more than 'fconsidbound' per cent, this
 *                                     character can contribute to groups
 *                  AW_STRING, "tmp/con/name"   : save with this name
 *                  AW_STRING, "con/result" : result has one or more lines ?
 *
 * Global Structures:             x
 *
 * Private Classes:               .
 *
 * Private Functions:             .
 *
 * Private Variables:             .
 *
 * Dependencies:       Needs consens.fig and CON_groups.fig
 *
 * Description: This module calculates the consensus of sequences of
 *              bases or amino acids. The result can be one or more lines
 *              of characters and it is written to the extended data of
 *              the alignment.
 *
 * Integration Notes: To use this module the main function must have a
 *                    callback to the function
 *                    AW_window *AP_open_consensus_window( AW_root *aw_root)
 *                    and the function void AP_create_consensus_var
 *                    (AW_root *aw_root, AW_default aw_def) has to be called.
 *
 * -----------------------------------------------------------------
 */

#include <awt_sel_boxes.hxx>
#include <aw_window.hxx>
#include <arb_progress.h>
#include <aw_root.hxx>
#include <aw_msg.hxx>
#include <aw_awar.hxx>
#include <arbdbt.h>
#include <arb_strbuf.h>

// AISC_MKPT_PROMOTE:#ifndef AW_BASE_HXX
// AISC_MKPT_PROMOTE:#include <aw_base.hxx>
// AISC_MKPT_PROMOTE:#endif

#define AWAR_MAX_FREQ   "tmp/CON_MAX_FREQ/"

#define AWAR_MAX_FREQ_NO_GAPS AWAR_MAX_FREQ "no_gaps"
#define AWAR_MAX_FREQ_SAI_NAME AWAR_MAX_FREQ "sai_name"


extern GBDATA *GLOBAL_gb_main;
enum {
    BAS_GAP,
    BAS_A,  BAS_C,  BAS_G,  BAS_T, BAS_N,

    MAX_BASES,
    MAX_AMINOS  = 27,
    MAX_GROUPS  = 40
};

/* -----------------------------------------------------------------
 * Function:                     CON_evaluatestatistic
 *
 * Arguments:                    int **statistic,char **groupflags,
 *                               char *groupnames
 * Returns:                      char *result
 *
 * Description:       This function creates one or more result strings out
 *                    of table statistic. Memory for result is allocated
 *                    and later freed in function CON_calculate_cb
 *
 * NOTE:              Usage of groupflags and groupnames see function
 *                    CON_makegrouptable.
 *
 * Global Variables referenced:  .
 *
 * Global Variables modified:    x
 *
 * AWARs referenced:             .
 *
 * AWARs modified:               x
 *
 * Dependencies:                 Always check that behavior is identical to that
 *                               of ED4_char_table::build_consensus_string()
 * -----------------------------------------------------------------
 */
static void CON_evaluatestatistic(char   *&result, int **statistic, char **groupflags,
                           char    *groupnames, int alignlength, double fupper, int lower,
                           double   fconsidbound, int gapbound, int countgap, int numgroups)
{
    int row=0;
    int j = 0;
    int groupfr[MAX_GROUPS]; // frequency of group
    int highestfr, highestgr;
    long numentries;

    arb_progress progress("calculating result", alignlength);

    result=(char *)GB_calloc(alignlength+1, 1);

    for (int column=0; column<alignlength; column++) {
        numentries=0;
        for (row=0; statistic[row]; row++) numentries+=statistic[row][column];
        if (numentries==0) {
            result[column]='.';
        }
        else {
            if (numentries-statistic[0][column]==0) {
                result[column]='='; // 100 per cent `-` -> `=` 
            }
            else {
                if (!countgap) {
                    numentries -= statistic[0][column];
                    statistic[0][column]=0;
                }

                if ((statistic[0][column]*100/numentries)>gapbound) {
                    result[column]='-';
                }
                else {
                    for (j=0; j<numgroups; j++) {
                        groupfr[j]=0;
                    }

                    row=0;
                    while (statistic[row]) {
                        if ((statistic[row][column]*100.0)>=fconsidbound*numentries) {
                            for (j=numgroups-1; j>=0; j--) {
                                if (groupflags[j][row]) {
                                    groupfr[j] += statistic[row][column];
                                }
                            }
                        }
                        row++;
                    }

                    highestfr=0;
                    highestgr=0;
                    for (j=0; j<numgroups; j++) {
                        if (groupfr[j] > highestfr) {
                            highestfr=groupfr[j];
                            highestgr=j;
                        }
                    }

                    if ((highestfr*100.0/numentries)>=fupper) {
                        result[column]=groupnames[highestgr];
                    }
                    else if ((highestfr*100/numentries)>=lower) {
                        char c=groupnames[highestgr];
                        if (c>='A' && c<='Z') {
                            c=c-'A'+'a';
                        }
                        result[column]=c;
                    }
                    else {
                        result[column]='.';
                    }
                }
            }
        }
        ++progress;
    }
}



/* -----------------------------------------------------------------
 * Function:                     CON_makegrouptable
 *
 * Arguments:                    .
 *
 * Returns:                      char **gf [groupflags],char *groupnames
 *
 * Description:       Creates table groupflags that is used in function
 *                    CON_evaluatestatistic. E.g. gf[10][3]=1 means, that
 *                    all characters c with convtable[c]==3 are members
 *                    of group 10.
 *                    Table groupnames is also created.
 *                    E.g. c=groupnames[5] gives abbrev of 5th group.
 *
 * NOTE:                         .
 *
 * Global Variables referenced:  .
 *
 * Global Variables modified:    x
 *
 * AWARs referenced:             .
 *
 * AWARs modified:               x
 *
 * Dependencies:                 .
 * -----------------------------------------------------------------
 */
static int CON_makegrouptable(char **gf, char *groupnames,
                       int isamino, int groupallowed)
{
    for (int j=0; j<MAX_GROUPS; j++) {
        gf[j]=(char *)GB_calloc(MAX_GROUPS, 1); }

    if (!isamino)
    {
        strcpy(groupnames, "-ACGUMRWSYKVHDBN\0");
        for (int i=1; i<MAX_BASES; i++) {
            gf[i][i]=1; }
        if (groupallowed)
        {
            gf[5][BAS_A]=1; gf[5][BAS_C]=1;
            gf[6][BAS_A]=1; gf[6][BAS_G]=1;
            gf[7][BAS_A]=1; gf[7][BAS_T]=1;
            gf[8][BAS_C]=1; gf[8][BAS_G]=1;
            gf[9][BAS_C]=1; gf[9][BAS_T]=1;
            gf[10][BAS_G]=1; gf[10][BAS_T]=1;
            gf[11][BAS_A]=1; gf[11][BAS_C]=1; gf[11][BAS_G]=1;
            gf[12][BAS_A]=1; gf[12][BAS_C]=1; gf[12][BAS_T]=1;
            gf[13][BAS_A]=1; gf[13][BAS_G]=1; gf[13][BAS_T]=1;
            gf[14][BAS_C]=1; gf[14][BAS_G]=1; gf[14][BAS_T]=1;
            gf[15][BAS_A]=1; gf[15][BAS_C]=1;
            gf[15][BAS_G]=1; gf[15][BAS_T]=1;
            return (16);
        }
        return (5);
    }
    else
    {
        strcpy(groupnames, "-ABCDEFGHI*KLMN.PQRST.VWXYZADHIF\0");
        for (int i=1; i<MAX_AMINOS; i++) {
            gf[i][i]=1; }
        if (groupallowed)
#define SC(x, P) gf[x][P-'A'+1] = 1
        {
            SC(27, 'P'); SC(27, 'A'); SC(27, 'G'); SC(27, 'S'); SC(27, 'T');
            // PAGST
            SC(28, 'Q'); SC(28, 'N'); SC(28, 'E'); SC(28, 'D'); SC(28, 'B');
            SC(28, 'Z');   // QNEDBZ
            SC(29, 'H'); SC(29, 'K'); SC(29, 'R');
            // HKR
            SC(30, 'L'); SC(30, 'I'); SC(30, 'V'); SC(30, 'M');
            // LIVM
            SC(31, 'F'); SC(31, 'Y'); SC(31, 'W');
            // FYW
            return (32);
        }
#undef SC
        return (27);
    }
}


/* -----------------------------------------------------------------
 * Function:                     CON_makestatistic
 *
 * Arguments:                    int *convtable
 *
 * Returns:                      int **statistic
 *
 * Description:       This function fills the table statistic, that is used
 *                    later by function CON_evaluatestatistic. The filling
 *                    is done depending on table convtable, that is created
 *                    in function CON_maketables. Memory for statistic is
 *                    allocated also in function CON_maketables.
 *
 *
 * NOTE:                         .
 *
 * Global Variables referenced:  .
 *
 * Global Variables modified:    x
 *
 * AWARs referenced:             .
 *
 * AWARs modified:               x
 *
 * Dependencies:                 .
 * -----------------------------------------------------------------
 */


static long CON_makestatistic(int **statistic, int *convtable, char *align, int onlymarked)
{
    long maxalignlen=GBT_get_alignment_len(GLOBAL_gb_main, align);
    GBDATA *gb_species, *alidata;
    int i, nrofspecies=0;

    if (onlymarked) {
        nrofspecies = GBT_count_marked_species(GLOBAL_gb_main);
    }
    else {
        nrofspecies = GBT_get_species_count(GLOBAL_gb_main);
    }

    arb_progress progress(nrofspecies);
    progress.auto_subtitles("Examining sequence");

    if (onlymarked) {
        gb_species = GBT_first_marked_species(GLOBAL_gb_main);
    }
    else {
        gb_species = GBT_first_species(GLOBAL_gb_main);
    }

    while (gb_species) {
        if ((alidata=GBT_read_sequence(gb_species, align))) {
            unsigned char        c;
            const unsigned char *data = (const unsigned char *)GB_read_char_pntr(alidata);

            i = 0;
            while ((c=data[i])) {
                if ((c=='-') || ((c>='a')&&(c<='z')) || ((c>='A')&&(c<='Z'))
                    || (c=='*')) {
                    if (i > maxalignlen) break;
                    statistic[convtable[c]][i] += 1;
                }
                i++;
            }
        }
        if (onlymarked) {
            gb_species = GBT_next_marked_species(gb_species);
        }
        else {
            gb_species = GBT_next_species(gb_species);
        }
        ++progress;
    }
    return (nrofspecies);
}


/* -----------------------------------------------------------------
 * Function:          CON_maketables
 *
 * Arguments:         long maxalignlen,int isamino
 *
 * Returns:           return parameters: int *convtable,int **statistic
 *
 * Description:       Creates tables convtable and statistic, that are
 *                    used by function CON_makestatistic. The memory
 *                    allocated for both tables is freed in the
 *                    function CON_calculate_cb.
 *                    E.g. convtable['c']=k means that the character c
 *                    is counted in table statistic in row k.
 *
 * NOTE:                         .
 *
 * Global Variables referenced:  .
 *
 * Global Variables modified:    x
 *
 * AWARs referenced:             .
 *
 * AWARs modified:               x
 *
 * Dependencies:                 .
 * -----------------------------------------------------------------
 */
static void CON_maketables(int *convtable, int **statistic, long maxalignlen, int isamino)
{
    int i;
    for (i=0; i<256; i++) { convtable[i]=0; }
    if (!isamino) {
        for (i='a'; i <= 'z'; i++) convtable[i] = BAS_N;
        for (i='A'; i <= 'Z'; i++) convtable[i] = BAS_N;

        convtable['a']=BAS_A;   convtable['A']=BAS_A;
        convtable['c']=BAS_C;   convtable['C']=BAS_C;
        convtable['g']=BAS_G;   convtable['G']=BAS_G;
        convtable['t']=BAS_T;   convtable['T']=BAS_T;
        convtable['u']=BAS_T;   convtable['U']=BAS_T;


        for (i=0; i<MAX_BASES; i++) {
            statistic[i]=(int*)GB_calloc((unsigned int)maxalignlen, sizeof(int));
        }
        statistic[MAX_BASES]=NULL;
    }
    else {
        for (i=0; i<MAX_AMINOS-1; i++)
        {
            convtable['a'+i]=i+1;
            convtable['A'+i]=i+1;
        }
        for (i=0; i<MAX_AMINOS; i++) {
            statistic[i]=(int*)GB_calloc((unsigned int)maxalignlen, sizeof(int));
        }
        statistic[MAX_AMINOS]=NULL;
        convtable['*']=10; // 'J'
    }
}

// export results into database
static GB_ERROR CON_export(char *savename, char *align, int **statistic, char *result, int *convtable, char *groupnames, int onlymarked, long nrofspecies, long maxalignlen, int countgaps, int gapbound, int groupallowed, double fconsidbound, double fupper, int lower, int resultiscomplex)
{
    GB_ERROR    err;
    const char *off    = "off";
    const char *on     = "on";
    char       *buffer = (char *)GB_calloc(2000, sizeof(char));

    GBDATA *gb_extended = GBT_find_or_create_SAI(GLOBAL_gb_main, savename);
    GBDATA *gb_data     = GBT_add_data(gb_extended, align, "data", GB_STRING);
    err                 = GB_write_string(gb_data, result);
    GBDATA *gb_options  = GBT_add_data(gb_extended, align, "_TYPE", GB_STRING);

    const char *allvsmarked    = "all";
    if (onlymarked) allvsmarked = "marked";

    const char *countgapsstring   = off;
    if (countgaps) countgapsstring = on;

    const char *simplifystring      = off;
    if (groupallowed) simplifystring = on;

    sprintf(buffer, "CON: [species: %s]  [number: %ld]  [count gaps: %s] "
            "[threshold for gaps: %d]  [simplify: %s] "
            "[threshold for character: %f]  [upper: %f]  [lower: %d]",
            allvsmarked, nrofspecies, countgapsstring,
            gapbound, simplifystring,
            fconsidbound, fupper, lower);

    err=GB_write_string(gb_options, buffer);

    GBDATA *gb_names = GB_search(GB_get_father(gb_options), "_SPECIES", GB_FIND);
    if (gb_names) GB_delete(gb_names); // delete old entry

    if (nrofspecies<20) {
        GBDATA        *gb_species;
        GBS_strstruct *strstruct = GBS_stropen(1000);

        if (onlymarked) gb_species = GBT_first_marked_species(GLOBAL_gb_main);
        else gb_species            = GBT_first_species(GLOBAL_gb_main);

        while (gb_species) {
            if (GBT_read_sequence(gb_species, align)) {
                GBDATA     *gb_speciesname = GB_search(gb_species, "name", GB_FIND);
                const char *name           = GB_read_char_pntr(gb_speciesname);

                GBS_strcat(strstruct, name);
                GBS_chrcat(strstruct, ' ');
            }
            if (onlymarked) gb_species = GBT_next_marked_species(gb_species);
            else gb_species            = GBT_next_species(gb_species);
        }

        char *allnames = GBS_strclose(strstruct);
        err            = GBT_write_string(GB_get_father(gb_options), "_SPECIES", allnames);
        free(allnames);
    }

    {
        char buffer2[256];
        sprintf(buffer2, "%s/FREQUENCIES", align);
        GBDATA *gb_graph = GB_search(gb_extended, buffer2, GB_FIND);
        if (gb_graph) GB_delete(gb_graph);  // delete old entry
    }
    // export additional information
    if (resultiscomplex)
    {
        GBDATA *gb_graph = GBT_add_data(gb_extended, align, "FREQUENCIES", GB_DB);
        char *charname=(char *)GB_calloc(5, sizeof(char));

        float **additional=0;
        // problem : aminos, especially '*' -> new order

        int *allreadycounted=(int*)GB_calloc((unsigned int)256, sizeof(char));
        int *neworder=(int*)GB_calloc((unsigned int)256, sizeof(int));
        int k;
        int numdiffchars=1;  // first additional row (nr. 0) is max-row
        for (int c=0; c<256; c++)
        {
            if ((k=convtable[c]))
            {
                if (!(allreadycounted[k]))
                {
                    allreadycounted[k]=1;
                    neworder[numdiffchars++]=k;
                }
            }
        }

        additional=(float**)GB_calloc((unsigned int)numdiffchars, sizeof(float*));
        int group;
        for (group=0; group<numdiffchars; group++)
        {
            additional[group]=(float*)GB_calloc((unsigned int)maxalignlen,
                                                sizeof(float));
        }

        int *absolutrow=(int*)GB_calloc((unsigned int)maxalignlen, sizeof(int));
        long col;
        for (col=0; col<maxalignlen; col++)
        {
            int group2=1;
            int colsum=0;
            while (neworder[group2])
            {
                colsum+=statistic[neworder[group2++]][col];
            }
            if (countgaps) colsum+=statistic[0][col];
            absolutrow[col]=colsum;
        }

        for (col=0; col<maxalignlen; col++)
        {
            int group2=1;
            float highest=0, relative;
            int diffchar;
            if (absolutrow[col]) {
                while ((diffchar=neworder[group2++])) {
                    relative=(float)statistic[diffchar][col]
                        /(float)absolutrow[col];
                    if (relative>highest) highest=relative;
                    additional[diffchar][col]=relative;
                }
                additional[0][col]=highest;
            }
            else {
                additional[0][col]=0.0;
            }
        }

        GBDATA *gb_relative=GB_search(gb_graph, "MAX", GB_FLOATS);
        err=GB_write_floats(gb_relative, additional[0], maxalignlen);

        for (group=1; group<numdiffchars; group++)
        {
            char ch = groupnames[neworder[group]];
            if (ch <'A' || ch>'Z') continue;
            sprintf(charname, "N%c", ch);
            gb_relative=GB_search(gb_graph, charname, GB_FLOATS);
            err=GB_write_floats(gb_relative, additional[group], maxalignlen);
        }

        free(charname);
        free(neworder);
        free(allreadycounted);
        for (group=0; group<numdiffchars; group++) free(additional[group]);
        free(additional);
    }
    free(buffer);
    return err;
}


static void CON_cleartables(int **statistic, int isamino) {
    int i;
    int no_of_tables = isamino ? MAX_AMINOS : MAX_BASES;

    for (i = 0; i<no_of_tables; ++i) {
        free(statistic[i]);
    }
}

/* -----------------------------------------------------------------
 * Function:                     void CON_calculate_cb(AW_window *aw )
 *
 * Arguments:                    .
 *
 * Returns:                      .
 *
 * Description:                  main callback
 *                               This function calculates the consensus.
 *                               Function CON_makestatistic creates the
 *                               statistic and function CON_evaluatestatistic
 *                               evaluates the statistic. Then the result
 *                               string(s) are written to the extended data of
 *                               the alignment.
 * NOTE:                         .
 *
 * Global Variables referenced:  .
 *
 * Global Variables modified:    x
 *
 * AWARs referenced:
 *                  AW_STRING, "tmp/con/alignment"     : name of alignment
 *                  AW_STRING, "tmp/con/which_species" : only marked species ?
 *                  AW_STRING, "con/group"         : allow grouping ?
 *                  AW_STRING, "con/countgaps"
 *                  AW_DOUBLE, "con/fupper"
 *                  AW_INT, "con/lower"
 *                  AW_INT, "con/gapbound"  : result is '-' if more than
 *                                            'gapbound' per cent gaps
 *                  AW_DOUBLE, "con/fconsidbound" : if frequency of character is
 *                                     more than 'considbound' per cent, this
 *                                     character can contribute to groups
 *                  AW_STRING, "tmp/intcon/name"   : save with this name
 *                  AW_STRING, "con/result" : result has one or more lines ?
 *
 * AWARs modified:               x
 *
 * Dependencies:                 CON_maketables
 *                               CON_makestatistic
 *                               CON_makegrouptable
 *                               CON_evaluatestatistic
 * -----------------------------------------------------------------
 */
static void CON_calculate_cb(AW_window *aw)
{
    AW_root  *awr   = aw->get_root();
    char     *align = awr->awar("tmp/con/alignment")->read_string();
    GB_ERROR  error = 0;

    GB_push_transaction(GLOBAL_gb_main);

    long maxalignlen = GBT_get_alignment_len(GLOBAL_gb_main, align);
    if (maxalignlen <= 0) error = GB_export_errorf("alignment '%s' doesn't exist", align);

    if (!error) {
        int isamino         = GBT_is_alignment_protein(GLOBAL_gb_main, align);
        int onlymarked      = 1;
        int resultiscomplex = 1;

        {
            char *marked        = awr->awar("tmp/con/which_species")->read_string();
            char *complexresult = awr->awar("con/result")->read_string();

            if (strcmp("marked", marked)        != 0) onlymarked = 0;
            if (strcmp("complex", complexresult) != 0) resultiscomplex = 0;

            free(complexresult);
            free(marked);
        }


        // creating the table for characters and allocating memory for 'statistic'
        int *statistic[MAX_AMINOS+1];
        int  convtable[256];
        CON_maketables(convtable, statistic, maxalignlen, isamino);

        // filling the statistic table
        arb_progress progress("Calculating consensus");

        long   nrofspecies = CON_makestatistic(statistic, convtable, align, onlymarked);
        double fupper      = awr->awar("con/fupper")->read_float();
        int    lower       = (int)awr->awar("con/lower")->read_int();

        if (fupper>100.0)   fupper = 100;
        if (fupper<0)       fupper = 0;
        if (lower<0)        lower  = 0;

        if (lower>fupper) {
            error = "fault: lower greater than upper";
        }
        else {

            double fconsidbound                = awr->awar("con/fconsidbound")->read_float();
            if (fconsidbound>100) fconsidbound = 100;
            if (fconsidbound<0)   fconsidbound = 0;

            int gapbound               = (int)awr->awar("con/gapbound")->read_int();
            if (gapbound<0)   gapbound = 0;
            if (gapbound>100) gapbound = 100;

            int groupallowed, countgap;
            {
                char *group     = awr->awar("con/group")->read_string();
                char *countgaps = awr->awar("con/countgaps")->read_string();

                groupallowed = strcmp("on", group) == 0;
                countgap     = strcmp("on", countgaps) == 0;

                free(countgaps);
                free(group);
            }

            // creating the table for groups
            char *groupflags[40];
            char  groupnames[40];
            int   numgroups = CON_makegrouptable(groupflags, groupnames, isamino, groupallowed);

            // calculate and export the result strings
            char *result = 0;
            CON_evaluatestatistic(result, statistic, groupflags, groupnames, (int)maxalignlen, fupper, lower, fconsidbound, gapbound, countgap, numgroups);

            char *savename = awr->awar("tmp/con/name")->read_string();

            error = CON_export(savename, align, statistic, result, convtable, groupnames,
                               onlymarked, nrofspecies, maxalignlen, countgap, gapbound, groupallowed,
                               fconsidbound, fupper, lower, resultiscomplex);

            // freeing allocated memory
            free(savename);
            free(result);
            for (int i=0; i<MAX_GROUPS; i++) free(groupflags[i]);
        }

        CON_cleartables(statistic, isamino);
    }

    free(align);
    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
}

void AP_create_consensus_var(AW_root *aw_root, AW_default aw_def)
{
    GB_transaction dummy(GLOBAL_gb_main);
    {
        char *defali = GBT_get_default_alignment(GLOBAL_gb_main);
        aw_root->awar_string("tmp/con/alignment", defali, aw_def);
        free(defali);
    }
    aw_root->awar_string("tmp/con/which_species", "marked", aw_def);
    aw_root->awar_string("con/group", "off", aw_def);
    aw_root->awar_string("con/countgaps", "on", aw_def);
    aw_root->awar_float("con/fupper", 95, aw_def);
    aw_root->awar_int("con/lower", 70, aw_def);
    aw_root->awar_int("con/gapbound", 60, aw_def);
    aw_root->awar_float("con/fconsidbound", 30, aw_def);
    aw_root->awar_string("tmp/con/name", "CONSENSUS", aw_def);
    aw_root->awar_string("con/result", "single line", aw_def);

    aw_root->awar_string(AWAR_MAX_FREQ_SAI_NAME, "MAX_FREQUENCY", aw_def);
    aw_root->awar_int(AWAR_MAX_FREQ_NO_GAPS, 1, aw_def);

}

// Open window to show IUPAC tables
static AW_window * CON_showgroupswin_cb(AW_root *aw_root)
{
    AW_window_simple *aws = new AW_window_simple;
    aws->init(aw_root, "SHOW_IUPAC", "Show IUPAC");
    aws->load_xfig("consensus/groups.fig");
    aws->button_length(7);

    aws->at("ok"); aws->callback((AW_CB0)AW_POPDOWN);
    aws->create_button("CLOSE", "CLOSE", "O");

    return (AW_window *)aws;
}

AW_window *
AP_open_con_expert_window(AW_root *aw_root)
{
    AW_window_simple *aws = new AW_window_simple;
    aws->init(aw_root, "BUILD_CONSENSUS", "CONSENSUS OF SEQUENCES");
    aws->load_xfig("consensus/expert.fig");
    aws->button_length(6);

    aws->at("cancel"); aws->callback((AW_CB0)AW_POPDOWN);
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->at("help"); aws->callback(AW_POPUP_HELP, (AW_CL)"consensus.hlp");
    aws->create_button("HELP", "HELP", "H");

    aws->button_length(10);
    aws->at("showgroups"); aws->callback(AW_POPUP, (AW_CL)CON_showgroupswin_cb, 0);
    aws->create_button("SHOW_IUPAC", "show\nIUPAC...", "s");
    aws->button_length(10);

    aws->at("which_species");
    aws->create_toggle_field("tmp/con/which_species", NULL, "");
    aws->insert_toggle("all", "1", "all");
    aws->insert_default_toggle("marked",   "1", "marked");
    aws->update_toggle_field();

    aws->at("which_alignment");
    awt_create_selection_list_on_alignments(GLOBAL_gb_main, (AW_window *)aws, "tmp/con/alignment", "*=");

    aws->button_length(15);

    // activation of consensus calculation by button ...
    aws->at("calculate"); aws->callback((AW_CB0)CON_calculate_cb);
    aws->create_button("GO", "GO", "G");

    aws->at("group");
    aws->create_toggle_field("con/group", NULL, "");
    aws->insert_toggle("on", "1", "on");
    aws->insert_default_toggle("off", "1", "off");
    aws->update_toggle_field();

    aws->at("countgaps");
    aws->create_toggle_field("con/countgaps", NULL, "");
    aws->insert_toggle("on", "1", "on");
    aws->insert_default_toggle("off", "1", "off");
    aws->update_toggle_field();

    aws->at("upper");
    aws->create_input_field("con/fupper", 4);

    aws->at("lower");
    aws->create_input_field("con/lower", 4);

    aws->at("considbound");
    aws->create_input_field("con/fconsidbound", 4);

    aws->at("gapbound");
    aws->create_input_field("con/gapbound", 4);

    aws->at("name");
    aws->create_input_field("tmp/con/name", 10);

    aws->at("result");
    aws->create_toggle_field("con/result", NULL, "");
    aws->insert_toggle("single line", "1", "single line");
    aws->insert_default_toggle("complex", "1", "complex");
    aws->update_toggle_field();

    aws->at("save_box");
    awt_create_selection_list_on_extendeds(GLOBAL_gb_main, aws, "tmp/con/name");

    return aws;
}

/* -----------------------------------------------------------------
 * Function:           CON_calc_max_freq_cb( AW_window *aw)
 *
 * Description:       Gets the maximum frequency for each columns.
 *
 * NOTE:
 *
 * -----------------------------------------------------------------
 */

static void CON_calc_max_freq_cb(AW_window *aw) {

    AW_root *awr=aw->get_root();
    long maxalignlen, i;
    int *statistic[MAX_AMINOS+1];
    int convtable[256];
    int onlymarked=1, isamino=1;
    long no_gaps;

    GB_ERROR  error       = 0;
    GB_push_transaction(GLOBAL_gb_main);

    char *align = GBT_get_default_alignment(GLOBAL_gb_main);
    maxalignlen = GBT_get_alignment_len(GLOBAL_gb_main, align);
    no_gaps     = awr->awar(AWAR_MAX_FREQ_NO_GAPS)->read_int();

    if (maxalignlen<=0) {
        GB_pop_transaction(GLOBAL_gb_main);
        aw_message("alignment doesn't exist!");
        delete align;
        return;
    }
    isamino = GBT_is_alignment_protein(GLOBAL_gb_main, align);

    arb_progress progress("Calculating max. frequency");
    long nrofspecies;

    CON_maketables(convtable, statistic, maxalignlen, isamino);
    nrofspecies = CON_makestatistic(statistic, convtable, align, onlymarked);

    int   end            = MAX_BASES;
    if (isamino) end     = MAX_AMINOS;
    int   pos;
    char *result         = new char[maxalignlen+1];
    char *result2        = new char[maxalignlen+1];
    result[maxalignlen]  = 0;
    result2[maxalignlen] = 0;

    for (pos = 0;  pos < maxalignlen; pos++) {
        int sum                               = 0;
        int max                               = 0;
        for (i=0; i<end; i++) {
            if (no_gaps && (i == convtable[(unsigned char)'-'])) continue;
            sum                              += statistic[i][pos];
            if (statistic[i][pos] > max) max  = statistic[i][pos];
        }
        if (sum == 0) {
            result[pos] = '=';
            result2[pos] = '=';
        }
        else {
            result[pos] = "01234567890"[((10*max)/sum)%11];
            result2[pos] = "01234567890"[((100*max)/sum)%10];
        }
    }

    char   *savename    = awr->awar(AWAR_MAX_FREQ_SAI_NAME)->read_string();
    GBDATA *gb_extended = GBT_find_or_create_SAI(GLOBAL_gb_main, savename);
    free(savename);
    GBDATA *gb_data     = GBT_add_data(gb_extended, align, "data", GB_STRING);
    GBDATA *gb_data2    = GBT_add_data(gb_extended, align, "dat2", GB_STRING);
    error               = GB_write_string(gb_data, result);
    if (!error) error   = GB_write_string(gb_data2, result2);
    GBDATA *gb_options  = GBT_add_data(gb_extended, align, "_TYPE", GB_STRING);
    delete [] result;
    delete [] result2;

    if (!error) {
        char    buffer[2000];
        sprintf (buffer, "MFQ: [species: %li] [exclude gaps: %li]",
                 nrofspecies, no_gaps);
        error=GB_write_string(gb_options, buffer);
    }

    GB_pop_transaction(GLOBAL_gb_main);

    CON_cleartables(statistic, isamino);
    free(align);
    if (error) aw_message(error);
}

AW_window *
AP_open_max_freq_window(AW_root *aw_root)
{
    AW_window_simple *aws = new AW_window_simple;
    aws->init(aw_root, "MAX_FREQUENCY", "MAX FREQUENCY");
    aws->load_xfig("consensus/max_freq.fig");

    GB_push_transaction(GLOBAL_gb_main);

    aws->button_length(6);

    aws->at("cancel"); aws->callback((AW_CB0)AW_POPDOWN);
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->at("help"); aws->callback(AW_POPUP_HELP, (AW_CL)"max_freq.hlp");
    aws->create_button("HELP", "HELP", "H");

    // activation of consensus calculation by button ...
    aws->at("go"); aws->callback((AW_CB0)CON_calc_max_freq_cb);
    aws->create_button("GO", "GO", "C");

    aws->at("save");
    aws->create_input_field(AWAR_MAX_FREQ_SAI_NAME, 1);

    aws->at("sai");
    awt_create_selection_list_on_extendeds(GLOBAL_gb_main, aws, AWAR_MAX_FREQ_SAI_NAME);

    aws->at("gaps");
    aws->create_toggle(AWAR_MAX_FREQ_NO_GAPS);

    GB_pop_transaction(GLOBAL_gb_main);

    return (AW_window *)aws;
}