root/trunk/AWT/AWT_seq_colors.cxx

// ================================================================ //
//                                                                  //
//   File      : AWT_seq_colors.cxx                                 //
//   Purpose   :                                                    //
//                                                                  //
//   Institute of Microbiology (Technical University Munich)        //
//   http://www.arb-home.de/                                        //
//                                                                  //
// ================================================================ //

#include "awt_seq_colors.hxx"
#include "awt.hxx"

#include <aw_root.hxx>
#include <aw_awar.hxx>
#include <aw_msg.hxx>
#include <arbdbt.h>

#include <cctype>

static int default_NUC_set = 0;     // number of default nucleotide set
static int default_AMI_set = 3;     // number of default amino acid set

#define SEQ_COLOR_SETS      8
#define SEQ_COLOR_SET_ELEMS 28 // has to be a even number!

static const char *default_sets[SEQ_COLOR_SETS] = {
    //A B C D E F G H I J K L M N O P Q R S T U V W X Y Z * -
    "=2=0=3=0=0=0=4=0=0=0=0=0=0=6=0=0=0=0=0=5=5=0=0=0=0=0=0=6", // A, C, G, TU and N in 5 colors
    "R2=0Y3=0=0=0R2=0=0=0=0=0=0=0=0=0=0=2=0Y3Y3=0=0=0=3=0=0=6", // AG and CTU in 2 colors
    "=0=5=0=5=7=7=0=5=7=7=3=7=3=9=7=7=7=3=3=0=0=5=3=7=3=7=0=6", // ambiguity
    "=7=0=7=8=2=9=8=9=3=0=2=3=7=8=0=8=2=2=2=2=0=3=9=6=9=0=0=6", // Protein colors

    "=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=6",
    "o9=0|2=0=0=0o5=0=0=0=0=0=0=0=0=0=0=0=0|8|8=0=0=0=0=0=0=6", // ambiguity (symbols)
    "=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=6",
    "=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=0=6",
};

static bool seq_color_awars_created = false;

// --------------------------------------------------------------------------------

static const char *default_characters(int elem) {
    static char result[3] = "xX";

    if (elem<26) { //  first 26 elements (0-25) are characters
        result[0] = 'a'+elem;
        result[1] = 'A'+elem;
    }
    else if (elem == 26) { // stop codon
        result[0] = '*';
        result[1] = 0;
    }
    else if (elem == 27) { // gaps
        result[0] = '-';
        result[1] = '.';
    }

    return result;
}
static const char *default_color(int cset, int elem) {
    // returns default color numbers for seq-color-set
    static char result[3] = "=0";
    const char *pos       = default_sets[cset]+2*elem;

    result[0] = pos[0];
    result[1] = pos[1];

    if (result[0] == '=' && result[1] == '0') result[0] = 0;

    return result;
}

static void awt_awar_changed_cb(AW_root *, AW_CL cl_sc) {
    AWT_seq_colors *sc = (AWT_seq_colors *)cl_sc;
    sc->reload();
}

static void create_seq_color_awars(AW_root *awr, AWT_seq_colors *asc) {
    awt_assert(!seq_color_awars_created);

    awr->awar_int(AWAR_SEQ_NAME_SELECTOR_NA, default_NUC_set, AW_ROOT_DEFAULT)->add_callback(awt_awar_changed_cb, (AW_CL)asc);
    awr->awar_int(AWAR_SEQ_NAME_SELECTOR_AA, default_AMI_set, AW_ROOT_DEFAULT)->add_callback(awt_awar_changed_cb, (AW_CL)asc);

    for (int elem = 0; elem<SEQ_COLOR_SET_ELEMS; ++elem) {
        const char *awar_name = GBS_global_string(AWAR_SEQ_NAME_STRINGS_TEMPLATE, elem);
        awr->awar_string(awar_name, default_characters(elem))->add_callback(awt_awar_changed_cb, (AW_CL)asc);

        for (int cset = 0; cset<SEQ_COLOR_SETS; ++cset) {
            awar_name         = GBS_global_string(AWAR_SEQ_NAME_TEMPLATE, cset, elem);
            AW_awar *awar_col = awr->awar_string(awar_name, default_color(cset, elem))->add_callback(awt_awar_changed_cb, (AW_CL)asc);

            if (strcmp(awar_col->read_char_pntr(), "=0") == 0) { // translate old->new default
                awar_col->write_string("");
            }
        }
    }

    seq_color_awars_created = true;
}

AW_window *create_seq_colors_window(AW_root *awr, AWT_seq_colors *asc) {
    char                     buf[256];
    static AW_window_simple *aws = 0;
    if (aws) return aws;

    if (!seq_color_awars_created) create_seq_color_awars(awr, asc);

    aws = new AW_window_simple;
    aws->init(awr, "SEQUENCE_MAPPING", "Sequence color mapping");

    aws->at(10, 10);
    aws->auto_space(0, 3);

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

    aws->callback(AW_POPUP_HELP, (AW_CL)"sequence_colors.hlp");
    aws->create_button("HELP", "HELP");
    
    aws->at_newline();

    for (int seqType=0; seqType<2; seqType++) {
        if (seqType==0) {
            aws->label("Select color-set for Nucleotides (NA):");
            aws->create_toggle_field(AWAR_SEQ_NAME_SELECTOR_NA, 1);
        }
        else {
            aws->label("Select color-set for Amino Acids (AA):");
            aws->create_toggle_field(AWAR_SEQ_NAME_SELECTOR_AA, 1);
        }

        for (int cset = 0; cset < SEQ_COLOR_SETS; cset++) {
            sprintf(buf, "%i", cset+1);
            aws->insert_toggle(buf, " ", cset);
        }
        aws->update_toggle_field();
        aws->at_newline();
    }

    const int BIG_COLUMNS    = 2;
    const int CHAR_COL_WIDTH = 4;
    const int SET_COL_WIDTH  = 2;

    int col_x_off[BIG_COLUMNS][SEQ_COLOR_SETS+1];

    aws->auto_space(3, 2);

    for (int bcol = 0; bcol<BIG_COLUMNS; ++bcol) {
        col_x_off[bcol][0] = aws->get_at_xposition();
        aws->button_length(CHAR_COL_WIDTH);
        aws->create_button(0, "Chars");
        
        aws->button_length(SET_COL_WIDTH);
        for (int cset = 0; cset < SEQ_COLOR_SETS; cset++) {
            sprintf(buf, "  %i", cset+1);
            col_x_off[bcol][cset+1] = aws->get_at_xposition();
            aws->create_button(0, buf);
        }

        if (!bcol) {
            int set_col_pixel_width = col_x_off[0][1]-col_x_off[0][0];
            aws->at_x(aws->get_at_xposition()+set_col_pixel_width);
        }
    }

    aws->at_newline();

    const int ROWS = SEQ_COLOR_SET_ELEMS/2;
    for (int r = 0; r<ROWS; r++) {
        for (int bcol = 0; bcol<BIG_COLUMNS; ++bcol) {
            int elem = bcol*ROWS+r;

            sprintf(buf, AWAR_SEQ_NAME_STRINGS_TEMPLATE, elem);
            aws->at_x(col_x_off[bcol][0]);
            aws->create_input_field(buf, CHAR_COL_WIDTH);

            for (int cset = 0; cset < SEQ_COLOR_SETS; cset++) {
                sprintf(buf, AWAR_SEQ_NAME_TEMPLATE, cset, elem);
                aws->at_x(col_x_off[bcol][cset+1]);
                aws->create_input_field(buf, SET_COL_WIDTH);
            }
        }
        aws->at_newline();
    }

    aws->window_fit();
    
    return aws;
}

void AWT_seq_colors::reload() {
    for (int i=0; i<256; i++) {
        char_2_gc[i]   = char_2_gc_aa[i]   = base_gc;
        char_2_char[i] = char_2_char_aa[i] = i;
    }

    AW_root *aw_root = AW_root::SINGLETON;

    if (!seq_color_awars_created) create_seq_color_awars(aw_root, this);

    const char *selector_awar[2] = { AWAR_SEQ_NAME_SELECTOR_NA, AWAR_SEQ_NAME_SELECTOR_AA };

    for (int selector = 0; selector<2; selector++) {
        long def_set = selector == 0 ? default_NUC_set : default_AMI_set;
        long cset    = aw_root->awar(selector_awar[selector])->read_int();

        if (cset < 0 || cset >= SEQ_COLOR_SETS) {
            cset = def_set;
        }

        for (int elem = 0; elem < SEQ_COLOR_SET_ELEMS; elem++) {
            char awar_name[256];

            sprintf(awar_name, AWAR_SEQ_NAME_STRINGS_TEMPLATE, elem);
            unsigned char *sc = (unsigned char *)aw_root->awar(awar_name)->read_string();

            sprintf(awar_name, AWAR_SEQ_NAME_TEMPLATE, (int)cset, elem);
            char *val = aw_root->awar(awar_name)->read_string();
            if (!val[0]) freedup(val, "=0"); // interpret '' as '  = 0'

            if (strlen(val) != 2 || val[1] >'9' || val[1] < '0') {
                aw_message(GB_export_errorf("Error in Color Lookup Table: '%s' is not of type X#", val));
            }
            else {
                if (selector == 0) { // Nucleotide colors
                    for (int i=0; sc[i]; i++) {
                        char_2_gc[sc[i]] = val[1]-'0' + base_gc;
                        if (val[0] != '=') char_2_char[sc[i]] = val[0];
                    }
                }
                else {
                    for (int i=0; sc[i]; i++) {
                        char_2_gc_aa[sc[i]] = val[1]-'0' + base_gc;
                        if (val[0] != '=') char_2_char_aa[sc[i]] = val[0];
                    }
                }
            }
            free(val);
            free(sc);
        }
    }

    run_cb();
}

AWT_seq_colors::AWT_seq_colors(int baseGC, void (*changed_cb)()) {
    cb      = changed_cb;
    base_gc = baseGC;

    this->reload();
}



AWT_reference::AWT_reference(GBDATA *_gb_main) {
    reference = 0;
    ref_len = 0;
    gb_main = _gb_main;
    init_species_name = 0;
}

void AWT_reference::init() {
    free(reference);
    reference = 0;
    ref_len = 0;
    delete init_species_name;
    init_species_name = 0;
}

void AWT_reference::expand_to_length(int len) {
    if (len > ref_len) {
        char *ref2 = (char *)GB_calloc(sizeof(char), len+1);

        if (reference) {
            strcpy(ref2, reference);
            free(reference);
        }
        reference = ref2;
        ref_len   = len;
    }
}

void AWT_reference::init(const char *species_name, const char *alignment_name) {

    awt_assert(species_name);
    awt_assert(alignment_name);

    GB_transaction dummy(gb_main);
    GBDATA *gb_species = GBT_find_species(gb_main, species_name);

    init();
    if (gb_species) {
        GBDATA *gb_data = GBT_read_sequence(gb_species, alignment_name);
        if (gb_data) {
            reference = GB_read_as_string(gb_data);
            if (reference) {
                ref_len = strlen(reference);
                init_species_name = strdup(species_name);
            }
        }
    }
}

void AWT_reference::init(const char *name, const char *sequence_data, int len) {

    awt_assert(name);
    awt_assert(sequence_data);
    awt_assert(len>0);

    init();

    reference = (char*)GB_calloc(sizeof(char), len+1);
    memcpy(reference, sequence_data, len);
    reference[len] = 0;
    ref_len = len;
    init_species_name = strdup(name);
}

AWT_reference::~AWT_reference() {
    delete reference;
}