ED4_naligner.cxx

Go to the documentation of this file.

// =============================================================== //
//                                                                 //
//   File      : ED4_naligner.cxx                                  //
//   Purpose   :                                                   //
//                                                                 //
//   Institute of Microbiology (Technical University Munich)       //
//   http://www.arb-home.de/                                       //
//                                                                 //
// =============================================================== //

#include "ed4_naligner.hxx"

#include <aw_window.hxx>
#include <aw_awars.hxx>
#include <aw_root.hxx>
#include <awt_sel_boxes.hxx>
#include <arbdbt.h>
#include <arb_strbuf.h>

#include <iostream>

static void aed_start_naligning(AW_window *aw, GBDATA *gb_main) {
    AW_root *root = aw->get_root();
    int      i, j;

    GBS_strstruct cmd(1000);
    cmd.cat("xterm -sl 1000 -sb -e sh -c 'LD_LIBRARY_PATH=\"");
    cmd.cat(GB_getenv("LD_LIBRARY_PATH"));
    cmd.cat("\";export LD_LIBRARY_PATH;for i in ");
    if (root->awar("naligner/what")->read_int()) {
        GB_transaction  ta(gb_main);

        for (GBDATA *gb_species = GBT_first_marked_species(gb_main);
             gb_species;
             gb_species = GBT_next_marked_species(gb_species))
        {
            cmd.put('\"');
            cmd.cat(GBT_get_name_or_description(gb_species));
            cmd.cat("\" ");
        }
    }
    else {
        const char *species_name = root->awar(AWAR_SPECIES_NAME)->read_char_pntr();
        cmd.put('\"');
        cmd.cat(species_name);
        cmd.cat("\" ");
    }


    cmd.cat("; do arb_naligner");


    if (root->awar("naligner/against")->read_int()) {
        cmd.cat(" -PARB_PT_SERVER");
        cmd.putlong(root->awar("naligner/pt_server")->read_int());
    }
    else {
        const char *family = root->awar("naligner/sagainst")->read_char_pntr();
        cmd.cat(" \"-f");
        cmd.cat(family);
        cmd.put('\"');
    }
    cmd.cat(" \"-s$i\" ");

    if (root->awar("naligner/mark_profile")->read_int()) cmd.cat(" -mf");
    if (root->awar("naligner/unmark_sequence")->read_int()) cmd.cat(" -us");

    cmd.cat(" -minf");  cmd.putlong (root->awar("naligner/minf")->read_int());
    cmd.cat(" -maxf");  cmd.putlong (root->awar("naligner/maxf")->read_int());
    cmd.cat(" -minw");  cmd.putfloat(root->awar("naligner/minw")->read_float());
    cmd.cat(" -maxew"); cmd.putfloat(root->awar("naligner/maxew")->read_float());
    cmd.cat(" -ib");    cmd.putlong (root->awar("naligner/det/ib")->read_int());
    cmd.cat(" -ic");    cmd.putlong (root->awar("naligner/det/ic")->read_int());
    cmd.cat(" -cl");    cmd.putfloat(root->awar("naligner/det/cl")->read_float());

    cmd.cat(" -cm");    cmd.putfloat(root->awar("naligner/det/cm")->read_float());
    cmd.cat(" -ch");    cmd.putfloat(root->awar("naligner/det/ch")->read_float());
    cmd.cat(" -mgf");   cmd.putfloat(root->awar("naligner/igap_panelty")->read_float());
    cmd.cat(" -mma1");
    cmd.cat(" -msub");

    for (i=0; i<5; i++) {
        for (j=0; j<5; j++) {
            if (i==4 || j==4) {                 // gap panelty
                if (i==4 && j==4) {
                    cmd.putfloat(0.0);
                }
                else {
                    cmd.putfloat(root->awar("naligner/gap_panelty")->read_float());
                    cmd.put(',');
                }
            }
            else {
                char var[100];
                if (i<j) sprintf(var, "naligner/%c%c", "acgt-"[i], "acgt-"[j]);
                else     sprintf(var, "naligner/%c%c", "acgt-"[j], "acgt-"[i]);
                cmd.putfloat(root->awar(var)->read_float());
                if (i<4 || j<4) cmd.put(',');
            }
        }
    }
    cmd.cat(" || echo \"Aligner failed\";done;");
    cmd.cat("echo press \"(return)\" to close window;read a' &");

    GB_ERROR error = GBK_system(cmd.get_data());
    if (error) fputs(error, stderr);
}


void create_naligner_variables(AW_root *root, AW_default db1) {
    root->awar_int("naligner/what", 0, db1);

    root->awar_int   ("naligner/against",   0,  db1);
    root->awar_string("naligner/sagainst",  "", db1);
    root->awar_int   ("naligner/pt_server", -1, db1);

    root->awar_int("naligner/mark_profile",    1, db1);
    root->awar_int("naligner/unmark_sequence", 0, db1);

    root->awar_float("naligner/aa",           0.0, db1);
    root->awar_float("naligner/ac",           3.0, db1);
    root->awar_float("naligner/ag",           1.0, db1);
    root->awar_float("naligner/at",           3.0, db1);
    root->awar_float("naligner/cc",           0.0, db1);
    root->awar_float("naligner/cg",           3.0, db1);
    root->awar_float("naligner/ct",           1.0, db1);
    root->awar_float("naligner/gg",           0.0, db1);
    root->awar_float("naligner/gt",           3.0, db1);
    root->awar_float("naligner/tt",           0.0, db1);
    root->awar_float("naligner/gap_panelty",  5.0, db1);
    root->awar_float("naligner/igap_panelty", 0.2, db1);
    root->awar_int  ("naligner/minf",         3,   db1);
    root->awar_int  ("naligner/maxf",         30,  db1);

    root->awar_float("naligner/minw",  .7, db1);
    root->awar_float("naligner/maxew", .2, db1);

    root->awar_float("naligner/det/cl", .25, db1);
    root->awar_float("naligner/det/cm", .5,  db1);
    root->awar_float("naligner/det/ch", .8,  db1);
    root->awar_int  ("naligner/det/ib", 5,   db1);
    root->awar_int  ("naligner/det/ic", 5,   db1);
}

static AW_window *create_expert_naligner_window(AW_root *root) {
    const       int     mwidth = 5;
    AW_window_simple *aws = new AW_window_simple;
    aws->init(root, "ALIGNER_V2_EXPERT2", "ALIGNER V2.0 EXPERT 2");
    aws->load_xfig("ed_al_ex.fig");

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

    aws->at("minw"); aws->create_input_field("naligner/minw", mwidth);
    aws->at("maxew"); aws->create_input_field("naligner/maxew", mwidth);

    aws->at("ib"); aws->create_input_field("naligner/det/ib", mwidth);
    aws->at("ic"); aws->create_input_field("naligner/det/ic", mwidth);
    aws->at("cl"); aws->create_input_field("naligner/det/cl", mwidth);
    aws->at("cm"); aws->create_input_field("naligner/det/cm", mwidth);
    aws->at("ch"); aws->create_input_field("naligner/det/ch", mwidth);

    return aws;
}

static AW_window *create_special_naligner_window(AW_root *root) {
    AW_window_simple *aws    = new AW_window_simple;
    const       int   mwidth = 3;

    aws->init(root, "ALIGNER_V2_EXPERT", "ALIGNER V2.0 EXPERT");
    aws->load_xfig("ed_al_sp.fig");

    aws->label_length(22);

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

    aws->at("minr"); aws->create_input_field("naligner/minf", 6);
    aws->at("maxr"); aws->create_input_field("naligner/maxf", 6);

    aws->at("aa"); aws->create_input_field("naligner/aa", mwidth);
    aws->at("ac"); aws->create_input_field("naligner/ac", mwidth);
    aws->at("ag"); aws->create_input_field("naligner/ag", mwidth);
    aws->at("at"); aws->create_input_field("naligner/at", mwidth);

    aws->at("ca"); aws->create_input_field("naligner/ac", mwidth);
    aws->at("cc"); aws->create_input_field("naligner/cc", mwidth);
    aws->at("cg"); aws->create_input_field("naligner/cg", mwidth);
    aws->at("ct"); aws->create_input_field("naligner/ct", mwidth);

    aws->at("ga"); aws->create_input_field("naligner/ag", mwidth);
    aws->at("gc"); aws->create_input_field("naligner/cg", mwidth);
    aws->at("gg"); aws->create_input_field("naligner/gg", mwidth);
    aws->at("gt"); aws->create_input_field("naligner/gt", mwidth);

    aws->at("ta"); aws->create_input_field("naligner/at", mwidth);
    aws->at("tc"); aws->create_input_field("naligner/ct", mwidth);
    aws->at("tg"); aws->create_input_field("naligner/gt", mwidth);
    aws->at("tt"); aws->create_input_field("naligner/tt", mwidth);

    aws->at("gap");  aws->create_input_field("naligner/gap_panelty",  4);
    aws->at("igap"); aws->create_input_field("naligner/igap_panelty", 4);

    aws->at("expert");
    aws->callback(create_expert_naligner_window);
    aws->create_button("EXPERT_OPTIONS", "EXPERT2", "E");

    return aws;
}

AW_window *create_naligner_window(AW_root *root, GBDATA *gb_main) {
    AW_window_simple *aws = new AW_window_simple;
    aws->init(root, "ALIGNER_V2", "ALIGNER V2.0");
    aws->load_xfig("awt/align.fig");

    aws->label_length(10);
    aws->button_length(10);

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

    aws->at("help");
    aws->callback(makeHelpCallback("ne_align_seq.hlp"));
    aws->create_button("HELP", "HELP");

    aws->at("align");
    aws->callback(makeWindowCallback(aed_start_naligning, gb_main));
    aws->highlight();
    aws->create_button("GO", "GO", "G");

    aws->at("expert");
    aws->callback(create_special_naligner_window);
    aws->create_button("OPTIONS", "PARAMETERS", "E");

    aws->at("what");
    aws->create_toggle_field("naligner/what", "Align");
    aws->insert_toggle("Selected Species:", "S", 0);
    aws->insert_default_toggle("Marked Species", "M", 1);
    aws->update_toggle_field();

    aws->at("swhat");
    aws->create_input_field(AWAR_SPECIES_NAME, 2);

    aws->at("against");
    aws->create_toggle_field("naligner/against", "Reference");
    aws->insert_toggle("Species by name", "S", 0);
    aws->insert_default_toggle("Auto search by pt_server", "S", 1);
    aws->update_toggle_field();

    aws->at("sagainst");
    aws->create_input_field("naligner/sagainst", 2);

    aws->label_length(25);

    aws->at("pt_server");
    aws->label("PT_SERVER:");
    awt_create_PTSERVER_selection_button(aws, "naligner/pt_server");

    aws->at("mark");
    aws->label_length(40);
    aws->label("Mark sequences found by the pt_server");
    aws->create_toggle("naligner/mark_profile");

    return aws;
}