source: tags/arb_5.3/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 sequencies 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 create_consensus_var
 *                    (AW_root *aw_root, AW_default aw_def) has to be called.
 *
 * -----------------------------------------------------------------
 */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <arbdb.h>
#include <arbdbt.h>
// #include <malloc.h>
#include <aw_root.hxx>
#include <aw_device.hxx>
#include <aw_window.hxx>
#include <awt.hxx>
#include <awt_sel_boxes.hxx>

#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 freeded 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()
 * -----------------------------------------------------------------
 */
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;

    aw_status("calculating result");

    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]='.';
            continue;
        }

        if(numentries-statistic[0][column]==0) {
            result[column]='=';
            continue;   /* 100 per cent `-` -> `=` */
        }

        if(!countgap)  {
            numentries -= statistic[0][column];
            statistic[0][column]=0;
        }

        if((statistic[0][column]*100/numentries)>gapbound) {
            result[column]='-';
            continue;
        }

        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]='.';
        }
    }
}



/* -----------------------------------------------------------------
 * 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:                 .
 * -----------------------------------------------------------------
 */
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:                 .
 * -----------------------------------------------------------------
 */


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;

    aw_status("reading database");

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

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

    long count = 0;
    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);

            aw_status((double)count++/(double)nrofspecies);
            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);
        }
    }
    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:                 .
 * -----------------------------------------------------------------
 */
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 */
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));
//     GB_push_transaction(GLOBAL_gb_main);

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

        GBDATA *gb_relativ=GB_search(gb_graph,"MAX",GB_FLOATS);
        err=GB_write_floats(gb_relativ,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_relativ=GB_search(gb_graph,charname,GB_FLOATS);
            err=GB_write_floats(gb_relativ,additional[group],maxalignlen);
        }

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


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
 * -----------------------------------------------------------------
 */
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 'statistc' */
        int *statistic[MAX_AMINOS+1];
        int  convtable[256];
        CON_maketables(convtable,statistic,maxalignlen,isamino);

        /* filling the statistic table */
        aw_openstatus("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]);
        }

        aw_closestatus();
        CON_cleartables(statistic,isamino);
    }

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

void 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 */
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_ad(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 (AW_window *)aws;
}


/* -----------------------------------------------------------------
 * Function:           AP_open_consensus_window( AW_root *aw_root)
 *
 * Arguments:
 *
 * Returns:
 *
 * Description:       Draws window, initializes callback for most important
 *                    function, CON_calculate_cb.
 *
 * NOTE:
 *
 * Global Variables referenced:
 *
 * Global Variables modified:
 *
 * AWARs referenced:
 *
 * AWARs modified:
 *
 * Dependencies:      Needs xfig files consens.fig and CON_groups.fig
 * -----------------------------------------------------------------
 */
AW_window *
AP_open_consensus_window( AW_root *aw_root)
{
    AW_window_simple *aws = new AW_window_simple;
    aws->init( aw_root, "SIMPLE_CONSENSUS", "SIMPLE CONSENSUS");
    aws->load_xfig("consensus/main.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)"consensus.hlp");
    aws->create_button("HELP","HELP","H");

    aws->button_length( 15);
    aws->at("showgroups");aws->callback(AW_POPUP,(AW_CL)CON_showgroupswin_cb,0);
    aws->create_button("SHOW_IUPAC", "show IUPAC...","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_ad(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("CALCULATE","CALCULATE","C");

    aws->at("expert");aws->callback(AW_POPUP,(AW_CL)AP_open_con_expert_window,0);
    aws->create_button("EXPERT", "expert...","e");

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

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

    GB_pop_transaction(GLOBAL_gb_main);

    return (AW_window *)aws;
}


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

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);

    aw_openstatus("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);
    aw_closestatus();
    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;
}