# -*-Perl-*-
## Bioperl Test Harness Script for Modules

use strict;
BEGIN {
    use Bio::Root::Test;
    test_begin(-tests => 7);

    use_ok('Bio::Tools::Run::Vista');
    use_ok('Bio::AlignIO');
}

SKIP: {
    #Java and java version check
    my $v;
    if (-d "java") {
        skip("Skipping because no java present to run vista", 5);
    }

    open(PIPE,"java -version 2>&1 |");
    while (<PIPE>) {
        if (/Java\sVersion\:\s(\d+\.\d+)/) {
            $v = $1;
            last;
        }
        elsif (/java version\s.(\d+\.\d+)/) {
            $v = $1;
            last;
        }
        elsif (/java version\s\"(\d\.\d)"/) {
            $v = $1;
            last;
        }
    }
    if ($v < 1.2) {
        skip("Skipping due to old java version", 5);
    }

    open (PIPE ,'java Vista 2>&1 |');
    while(<PIPE>){
        if (   /NoClassDefFoundError/
            # For JRE 1.7.0_25 - Win7 - Spanish, the message is:
            # "Error: no se ha encontrado o cargado la clase principal Vista"
            or /^Error\:/
            ){
            diag('Vista.jar is not in your class path: '.$_);
            skip("Vista.jar is not in your class path",5);
        }
    }
    my $inputfilename= test_input_file("vista.cls");
    my $gff_file = test_input_file("vista.gff");
    my $aio = Bio::AlignIO->new(-file   => $inputfilename,
                                -format => 'clustalw');
    my $aln = $aio->next_aln;

    my $out= test_output_file();
    my $vis = Bio::Tools::Run::Vista->new('outfile'           => $out,
                                          'title'             => "My Vista Plot",
                                          'annotation'        => $gff_file,
                                          'annotation_format' => 'GFF',
                                          'min_perc_id'       => 75,
                                          'min_length'        => 100,
                                          'plotmin'           => 50,
                                          'tickdist'          => 2000,
                                          'window'            => 40,
                                          'numwindows'        => 4,
                                          'start'             => 50,
                                          'end'               => 1500,
                                          'tickdist'          => 100,
                                          'bases'             => 1000,
                                          'color'             => {'EXON'=>'45 25 54','CNS'=>'0 0 100'},
                                          'quiet'             =>1);
    isa_ok $vis,'Bio::Tools::Run::Vista';
    is $vis->plotmin, 50;
    is $vis->annotation, $gff_file;

    $vis->run($aln,1);
    ok -e $out;
    $vis->run($aln,'mouse');
    ok -e $out;
}