1.1 --- a/pair_cores/web/approot/locales/pair-cores-web.xml	Wed Nov 28 17:15:45 2012 +0400
     1.2 +++ b/pair_cores/web/approot/locales/pair-cores-web.xml	Wed Nov 28 17:16:10 2012 +0400
     1.3 @@ -41,6 +41,27 @@
     1.4  PDYLLKGD
     1.5          </pre>
     1.6      </message>
     1.7 +    <message id='pair.main.Example_fasta_compare'>
     1.8 +        <pre>
     1.9 +>1PER_L
    1.10 +SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVS
    1.11 +>1PER_R
    1.12 +SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVS
    1.13 +>1ADR_A_1
    1.14 +LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCS
    1.15 +>1ADR_A_2
    1.16 +LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCS
    1.17 +
    1.18 +>1PER_L
    1.19 +SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVS-
    1.20 +>1PER_R
    1.21 +SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVS-
    1.22 +>1ADR_A_1
    1.23 +LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCS
    1.24 +>1ADR_A_2
    1.25 +LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCS
    1.26 +        </pre>
    1.27 +    </message>
    1.28      <message id='pair.main.Rfbr'>
    1.29          The work was partly supported by
    1.30          the Russian Foundation for Basic Research, grant 09-04-92743.
    1.31 @@ -57,6 +78,7 @@
    1.32      <message id='pair.out.Pair_blocks'>Pair cores file</message>
    1.33      <message id='pair.out.Pair_html'>Pair cores HTML file</message>
    1.34      <message id='pair.out.Pymol'>Pair cores PyMol file</message>
    1.35 +    <message id='pair.out.Result'>Result</message>
    1.36  
    1.37  </messages>
    1.38  

     2.1 --- a/pair_cores/web/approot/locales/pair-cores-web_ru.xml	Wed Nov 28 17:15:45 2012 +0400
     2.2 +++ b/pair_cores/web/approot/locales/pair-cores-web_ru.xml	Wed Nov 28 17:16:10 2012 +0400
     2.3 @@ -47,6 +47,7 @@
     2.4      <message id='pair.out.Pair_blocks'>Парные блоки (текст)</message>
     2.5      <message id='pair.out.Pair_html'>Парные блоки (HTML)</message>
     2.6      <message id='pair.out.Pymol'>Парные блоки (PyMol-скрипт)</message>
     2.7 +    <message id='pair.out.Result'>Результат</message>
     2.8  
     2.9  </messages>
    2.10  

     3.1 --- a/pair_cores/web/compare-aln-3d.cpp	Wed Nov 28 17:15:45 2012 +0400
     3.2 +++ b/pair_cores/web/compare-aln-3d.cpp	Wed Nov 28 17:16:10 2012 +0400
     3.3 @@ -25,7 +25,7 @@
     3.4      std::string file = input->file_upload()->clientFileName().toUTF8();
     3.5      std::string without_extension = file.substr(0, file.find_last_of("."));
     3.6      if (without_extension.empty()) {
     3.7 -        without_extension = "pair-cores";
     3.8 +        without_extension = "compare-aln-3d";
     3.9      }
    3.10      return without_extension + "." + extension;
    3.11  }
    3.12 @@ -68,10 +68,15 @@
    3.13      //
    3.14      TableTask* task = new TableTask(root());
    3.15      //
    3.16 -    TextFileInput* input_aln = new TextFileInput("-i");
    3.17 -    input_aln->text_area()->setColumns(60);
    3.18 -    input_aln->text_area()->setRows(12);
    3.19 -    task->add_input(input_aln, tr("pair.in.Alignment"));
    3.20 +    TextFileInput* a = new TextFileInput("-a");
    3.21 +    a->text_area()->setColumns(60);
    3.22 +    a->text_area()->setRows(12);
    3.23 +    task->add_input(a, tr("pair.in.Alignment") + " A");
    3.24 +    //
    3.25 +    TextFileInput* b = new TextFileInput("-b");
    3.26 +    b->text_area()->setColumns(60);
    3.27 +    b->text_area()->setRows(12);
    3.28 +    task->add_input(b, tr("pair.in.Alignment") + " B");
    3.29      //
    3.30      WLineEdit* delta_edit = new WLineEdit("2.0");
    3.31      delta_edit->setValidator(new WDoubleValidator(0, 10));
    3.32 @@ -79,85 +84,27 @@
    3.33      LineEditInput* delta = new LineEditInput(delta_edit, "-d");
    3.34      task->add_input(delta, tr("pair.in.Delta"));
    3.35      //
    3.36 -    WLineEdit* width_edit = new WLineEdit("3");
    3.37 -    width_edit->setValidator(new WIntValidator(3, 9999));
    3.38 -    width_edit->validator()->setMandatory(true);
    3.39 -    LineEditInput* width = new LineEditInput(width_edit, "-w");
    3.40 -    task->add_input(width, tr("pair.in.Width"));
    3.41 -    //
    3.42 -    BoolInput* blocks3d = new BoolInput(new WCheckBox(), "--blocks3d");
    3.43 -    task->add_input(blocks3d, tr("pair.in.Blocks3D"));
    3.44 -    //
    3.45 -    BoolInput* ioss = new BoolInput(new WCheckBox(), "-e");
    3.46 -    ioss->set_value_if_true("True");
    3.47 -    task->add_input(ioss, tr("pair.in.SS"));
    3.48 -    //
    3.49 -    WLineEdit* pair_timeout_edit = new WLineEdit("10");
    3.50 -    pair_timeout_edit->setValidator(new WIntValidator(-1, 30 * 24 * 3600));
    3.51 -    pair_timeout_edit->validator()->setMandatory(true);
    3.52 -    LineEditInput* pair_timeout = new LineEditInput(pair_timeout_edit,
    3.53 -            "--pair-timeout");
    3.54 -    task->add_input(pair_timeout, tr("pair.in.Pair_timeout"));
    3.55 -    //
    3.56 -    WLineEdit* blocks3d_timeout_edit = new WLineEdit("-1");
    3.57 -    blocks3d_timeout_edit->setValidator(new WIntValidator(-1, 30 * 24 * 3600));
    3.58 -    blocks3d_timeout_edit->validator()->setMandatory(true);
    3.59 -    LineEditInput* blocks3d_timeout = new LineEditInput(blocks3d_timeout_edit,
    3.60 -            "--blocks3d-timeout");
    3.61 -    task->add_input(blocks3d_timeout, tr("pair.in.Blocks3D_timeout"));
    3.62 -    //
    3.63      // outputs
    3.64      //
    3.65      boost::function<std::string(std::string)> name_gen2 = boost::bind(name_gen,
    3.66 -            input_aln, _1);
    3.67 +            a, _1);
    3.68      //
    3.69 -    ViewFileOutput* homology = new ViewFileOutput("-y");
    3.70 -    homology->set_suggested_gen(boost::bind(name_gen2, "hom"));
    3.71 -    homology->set_selectable(false);
    3.72 -    task->add_output(homology, tr("pair.out.Homology"));
    3.73 -    //
    3.74 -    ViewFileOutput* pair_blocks = new ViewFileOutput("-b");
    3.75 -    pair_blocks->set_suggested_gen(boost::bind(name_gen2, "blocks"));
    3.76 -    task->add_output(pair_blocks, tr("pair.out.Pair_blocks"));
    3.77 -    //
    3.78 -    ViewFileOutput* pair_html = new ViewFileOutput("-H",
    3.79 -            &FileOutput::unique_name,
    3.80 -            "application/octet-stream",
    3.81 -            "text/html");
    3.82 -    pair_html->set_suggested_gen(boost::bind(name_gen2, "html"));
    3.83 -    task->add_output(pair_html, tr("pair.out.Pair_html"));
    3.84 -    //
    3.85 -    ViewFileOutput* pymol = new ViewFileOutput("-p");
    3.86 -    pymol->set_suggested_gen(boost::bind(name_gen2, "pml"));
    3.87 -    task->add_output(pymol, tr("pair.out.Pymol"));
    3.88 -    //
    3.89 -    ViewFileOutput* high_pymol = new ViewFileOutput("--high-blocks-pymol");
    3.90 -    high_pymol->set_suggested_gen(boost::bind(name_gen2, "pml"));
    3.91 -    task->add_output(high_pymol, tr("pair.out.High_pymol"));
    3.92 -    //
    3.93 -    ViewFileOutput* high_blocks = new ViewFileOutput("--high-blocks");
    3.94 -    high_blocks->set_suggested_gen(boost::bind(name_gen2, "blocks"));
    3.95 -    task->add_output(high_blocks, tr("pair.out.High_blocks"));
    3.96 -    //
    3.97 -    ViewFileOutput* high_html = new ViewFileOutput("--high-blocks-html",
    3.98 -            &FileOutput::unique_name,
    3.99 -            "application/octet-stream",
   3.100 -            "text/html");
   3.101 -    high_html->set_suggested_gen(boost::bind(name_gen2, "html"));
   3.102 -    task->add_output(high_html, tr("pair.out.High_html"));
   3.103 -    //
   3.104 -    PrintFileOutput* execution_log = new PrintFileOutput("&>");
   3.105 +    ViewFileOutput* execution_log = new ViewFileOutput("2>");
   3.106      execution_log->set_suggested_gen(boost::bind(name_gen2, "log"));
   3.107 -    execution_log->set_selectable(false);
   3.108      task->add_output(execution_log, tr("pair.out.Log"));
   3.109      //
   3.110 -    task->set_runner(new ForkingRunner("pair-cores --no-read-local"));
   3.111 +    PrintFileOutput* result = new PrintFileOutput("| sed \"s@^@<br/>@\" >");
   3.112 +    result->set_suggested_gen(boost::bind(name_gen2, "out"));
   3.113 +    result->set_selectable(false);
   3.114 +    task->add_output(result, tr("pair.out.Result"));
   3.115 +    //
   3.116 +    task->set_runner(new ForkingRunner("compare-aln-3d"));
   3.117      task->set_queue(&queue);
   3.118      new TaskCountup(task, root());
   3.119      //
   3.120      new WBreak(root());
   3.121      new Wt::WTemplate(tr("pair.main.Example"), root());
   3.122 -    new Wt::WTemplate(tr("pair.main.Example_fasta"), root());
   3.123 +    new Wt::WTemplate(tr("pair.main.Example_fasta_compare"), root());
   3.124      new Wt::WTemplate(tr("pair.main.Rfbr"), root());
   3.125  }
   3.126