use warnings;
use strict;
use Data::Dumper;
+use Maasha::Common;
use Maasha::Calc;
use vars qw( @ISA @EXPORT );
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-sub entries_sort
+sub track_ruler
{
- my ( $entries, # list of KISS entries
+ my ( $draw_metrics, # hashref with image draw metrics
+ $cookie, # browser cookie
) = @_;
- # Returns nothing.
+ my ( $beg, $end, $factor, $step, $i, $txt, $x, @ruler );
- @{ $entries } = sort { $a->{ 'S_BEG' } <=> $b->{ 'S_BEG' } or
- $a->{ 'S_END' } <=> $b->{ 'S_END' } } @{ $entries };
+ $beg = $cookie->{ 'NAV_START' };
+ $end = $cookie->{ 'NAV_END' };
+
+ $factor = $draw_metrics->{ 'IMG_WIDTH' } / ( $end - $beg );
+
+ $step = 10;
+
+ while ( ( $end - $beg ) / $step > 20 )
+ {
+ $step *= 5;
+ }
+
+ for ( $i = $beg; $i < $end; $i++ )
+ {
+ if ( ( $i % $step ) == 0 )
+ {
+ $txt = Maasha::Calc::commify( $i ) . "|";
+ $x = sprintf( "%.0f", ( $i - $beg - length $txt ) * $factor );
+
+ if ( $x > 0 and $x + ( $draw_metrics->{ 'RULER_FONT_SIZE' } * length $txt ) < $draw_metrics->{ 'IMG_WIDTH' } )
+ {
+ push @ruler, {
+ type => 'text',
+ txt => $txt,
+ font_size => $draw_metrics->{ 'RULER_FONT_SIZE' },
+ color => $draw_metrics->{ 'RULER_COLOR' },
+ x1 => $x,
+ y1 => $draw_metrics->{ 'TRACK_OFFSET' },
+ };
+ }
+ }
+ }
+
+ $draw_metrics->{ 'TRACK_OFFSET' } += $draw_metrics->{ 'TRACK_SPACE' };
+
+ return wantarray ? @ruler : \@ruler;
+}
+
+
+sub track_seq
+{
+ my ( $draw_metrics, # hashref with image draw metrics
+ $cookie, # browser cookie
+ ) = @_;
+
+ my ( $file, $fh, $seq, @chars, $factor, $i, @seq_list );
+
+ if ( $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 <= 220 )
+ {
+ $file = path_seq( $cookie );
+ $fh = Maasha::Filesys::file_read_open( $file );
+ $seq = Maasha::Filesys::file_read( $fh, $cookie->{ 'NAV_START' } - 1, $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 );
+ close $fh;
+
+ @chars = split //, $seq;
+
+ $factor = $draw_metrics->{ 'IMG_WIDTH' } / @chars;
+
+ for ( $i = 0; $i < @chars; $i++ ) {
+ push @seq_list, {
+ type => 'text',
+ txt => $chars[ $i ],
+ font_size => $draw_metrics->{ 'SEQ_FONT_SIZE' },
+ color => $draw_metrics->{ 'SEQ_COLOR' },
+ x1 => sprintf( "%.0f", $i * $factor ),
+ y1 => $draw_metrics->{ 'TRACK_OFFSET' },
+ };
+ }
+
+ $draw_metrics->{ 'TRACK_OFFSET' } += $draw_metrics->{ 'TRACK_SPACE' };
+
+ return wantarray ? @seq_list : \@seq_list;
+ }
+ else
+ {
+ return;
+ }
}
sub track_feature
{
- my ( $width, # draw window width
- $y_offset, # y axis draw offset
- $beg, # base window beg
- $end, # base window end
- $entries, # list of sorted KISS entries
+ my ( $track,
+ $draw_metrics,
+ $cookie,
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $index, $count, $track_name, $start, $end, $entries, $features );
+
+ $start = $cookie->{ 'NAV_START' };
+ $end = $cookie->{ 'NAV_END' };
+
+ $index = Maasha::KISS::IO::kiss_index_retrieve( "$track/track_data.kiss.index" );
+ $count = Maasha::KISS::IO::kiss_index_count( $index, $start, $end );
+
+ $track_name = ( split "/", $track )[ -1 ];
+ $track_name =~ s/^\d+_//;
+ $track_name =~ s/_/ /g;
+
+ $features = [ {
+ type => 'text',
+ txt => $track_name,
+ font_size => $draw_metrics->{ 'SEQ_FONT_SIZE' },
+ color => $draw_metrics->{ 'SEQ_COLOR' },
+ x1 => 0,
+ y1 => $draw_metrics->{ 'TRACK_OFFSET' },
+ } ];
+
+ $draw_metrics->{ 'TRACK_OFFSET' } += 10;
+
+ if ( $count > 5000 )
+ {
+ $entries = Maasha::KISS::IO::kiss_index_get_blocks( $index, $start, $end );
+ push @{ $features }, Maasha::KISS::Track::track_feature_histogram( $draw_metrics, $start, $end, $entries );
+ }
+ else
+ {
+ $entries = Maasha::KISS::IO::kiss_index_get_entries( "$track/track_data.kiss", $index, $start, $end );
+ push @{ $features }, Maasha::KISS::Track::track_feature_linear( $draw_metrics, $start, $end, $entries );
+ }
+
+ return wantarray ? @{ $features } : $features;
+}
+
+
+sub track_feature_linear
+{
+ my ( $draw_metrics, # hashref with image draw metrics
+ $beg, # base window beg
+ $end, # base window end
+ $entries, # list of unsorted KISS entries
) = @_;
# Returns a list.
- my ( $factor, $entry, $y_step, @ladder, $i, $x, $y, $w, @features );
+ my ( $factor, $entry, $y_step, @ladder, $y_max, $w, $x1, $y1, $x2, $y2, @features );
- $factor = $width / ( $end - $beg );
+ @{ $entries } = sort { $a->{ 'S_BEG' } <=> $b->{ 'S_BEG' } or $a->{ 'S_END' } <=> $b->{ 'S_END' } } @{ $entries };
+
+ $factor = $draw_metrics->{ 'IMG_WIDTH' } / ( $end - $beg );
$y_step = 0;
+ $y_max = 0;
foreach $entry ( @{ $entries } )
{
if ( $w >= 1 )
{
- $x = sprintf( "%.0f", $entry->{ 'S_BEG' } * $factor );
+ $x1 = sprintf( "%.0f", ( $entry->{ 'S_BEG' } - $beg ) * $factor );
+
+ for ( $y_step = 0; $y_step < @ladder; $y_step++ ) {
+ last if $x1 >= $ladder[ $y_step ] + 1;
+ }
+
+ $y1 = $draw_metrics->{ 'TRACK_OFFSET' } + ( $draw_metrics->{ 'FEAT_WIDTH' } * $y_step );
+
+ push @features, {
+ type => 'rect',
+ line_width => $draw_metrics->{ 'FEAT_WIDTH' },
+ color => $draw_metrics->{ 'FEAT_COLOR' },
+ title => "Q_ID: $entry->{ 'Q_ID' } S_BEG: $entry->{ 'S_BEG' } S_END: $entry->{ 'S_END' } STRAND: $entry->{ 'STRAND' }",
+ id => $entry->{ 'Q_ID' },
+ x1 => $x1,
+ y1 => $y1,
+ x2 => $x1 + $w,
+ y2 => $y1 + $draw_metrics->{ 'FEAT_WIDTH' },
+ };
+
+ $y_max = Maasha::Calc::max( $y_max, $y_step * $draw_metrics->{ 'FEAT_WIDTH' } );
+
+ push @features, feature_align( $entry, $beg, $y1, $factor, $draw_metrics->{ 'FEAT_WIDTH' } ) if $entry->{ 'ALIGN' } ne '.';
+
+ $ladder[ $y_step ] = $x1 + $w;
+ }
+ }
+
+ $draw_metrics->{ 'TRACK_OFFSET' } += $y_max + $draw_metrics->{ 'TRACK_SPACE' };
+
+ return wantarray ? @features : \@features;
+}
+
+
+sub feature_align
+{
+ # 17:A>T
+
+ my ( $entry, # Partial KISS entry
+ $beg, # base window beg
+ $y_offset, # y axis draw offset
+ $factor, # scale factor
+ $feat_height, # hight of feature in pixels
+ ) = @_;
+
+ # Returns a list.
- for ( $y_step = 0; $y_step < @ladder; $y_step++ )
+ my ( $w, $align, $pos, $nt_before, $nt_after, $x1, @features );
+
+ $w = sprintf( "%.0f", 1 * $factor );
+
+ if ( $w >= 1 )
+ {
+ foreach $align ( split /,/, $entry->{ 'ALIGN' } )
+ {
+ if ( $align =~ /(\d+):([ATCGN-])>([ATCGN-])/ )
{
- last if $x >= $ladder[ $y_step ] + 1;
+ $pos = $1;
+ $nt_before = $2;
+ $nt_after = $3;
+ }
+ else
+ {
+ Maasha::Common::error( qq(BAD align descriptor: "$align") );
}
- $y = $y_offset + ( 5 * $y_step );
+ $x1 = sprintf( "%.0f", ( $entry->{ 'S_BEG' } + $pos - $beg ) * $factor );
push @features, {
- id => $entry->{ 'Q_ID' },
- x => $x,
- y => $y,
- height => 5,
- width => $w,
+ type => 'rect',
+ line_width => $feat_height,
+ color => [ 1, 0, 0 ],
+ title => $align,
+ x1 => $x1,
+ y1 => $y_offset,
+ x2 => $x1 + $w,
+ y2 => $y_offset + $feat_height,
};
- $ladder[ $y_step ] = $x + $w;
+ if ( $w > $feat_height )
+ {
+ push @features, {
+ type => 'text',
+ font_size => $feat_height + 2,
+ color => [ 0, 0, 0 ],
+ txt => $nt_after,
+ x1 => $x1 + sprintf( "%.0f", ( $w / 2 ) ) - $feat_height / 2,
+ y1 => $y_offset + $feat_height,
+ };
+ }
}
}
}
+sub track_feature_histogram
+{
+ my ( $draw_metrics, # hashref with image draw metrics
+ $min, # minimum base position
+ $max, # maximum base position
+ $blocks, # list of blocks
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $hist_height, $bucket_width, $bucket_count, $min_bucket, $factor, $factor_heigth, $max_height, $block, $bucket_beg, $bucket_end, $i, @buckets, $h, $x, @hist );
+
+ return if $max <= $min;
+
+ $hist_height = 100; # pixels
+ $bucket_width = 5;
+ $bucket_count = $draw_metrics->{ 'IMG_WIDTH' } / $bucket_width;
+ $factor = ( $draw_metrics->{ 'IMG_WIDTH' } / $bucket_width ) / ( $max - $min + 1 );
+
+ $min_bucket = 999999999;
+ $max_height = 0;
+
+ foreach $block ( @{ $blocks } )
+ {
+ $bucket_beg = int( $block->{ 'BEG' } * $factor );
+ $bucket_end = int( $block->{ 'END' } * $factor );
+
+ $min_bucket = Maasha::Calc::min( $min_bucket, $bucket_beg );
+
+ for ( $i = $bucket_beg; $i <= $bucket_end; $i++ )
+ {
+ $buckets[ $i ] += $block->{ 'COUNT' };
+
+ $max_height = Maasha::Calc::max( $max_height, $buckets[ $i ] );
+ }
+ }
+
+ if ( $max_height > 0 )
+ {
+ $factor_heigth = $hist_height / $max_height;
+
+ $x = 0;
+
+ for ( $i = $min_bucket; $i < @buckets; $i++ )
+ {
+ if ( defined $buckets[ $i ] )
+ {
+ $h = sprintf( "%.0f", $buckets[ $i ] * $factor_heigth );
+
+ if ( $h >= 1 )
+ {
+ push @hist, {
+ type => 'line',
+ line_width => $bucket_width,
+ color => $draw_metrics->{ 'FEAT_COLOR' },
+ title => "Features: $buckets[ $i ]",
+ x1 => $x,
+ y1 => $draw_metrics->{ 'TRACK_OFFSET' } + $hist_height,
+ x2 => $x,
+ y2 => $draw_metrics->{ 'TRACK_OFFSET' } + $hist_height - $h,
+ };
+ }
+ }
+
+ $x += $bucket_width;
+ }
+ }
+
+ $draw_metrics->{ 'TRACK_OFFSET' } += $hist_height + $draw_metrics->{ 'TRACK_SPACE' };
+
+ return wantarray ? @hist : \@hist;
+}
+
+
+sub path_seq
+{
+ my ( $cookie,
+ ) = @_;
+
+ # Returns a string.
+
+ my ( $path );
+
+ die qq(ERROR: no USER in cookie.\n) if not $cookie->{ 'USER' };
+ die qq(ERROR: no CLADE in cookie.\n) if not $cookie->{ 'CLADE' };
+ die qq(ERROR: no GENOME in cookie.\n) if not $cookie->{ 'GENOME' };
+ die qq(ERROR: no ASSEMBLY in cookie.\n) if not $cookie->{ 'ASSEMBLY' };
+ die qq(ERROR: no CONTIG in cookie.\n) if not $cookie->{ 'CONTIG' };
+
+ $path = join( "/",
+ $cookie->{ 'DATA_DIR' },
+ "Users",
+ $cookie->{ 'USER' },
+ $cookie->{ 'CLADE' },
+ $cookie->{ 'GENOME' },
+ $cookie->{ 'ASSEMBLY' },
+ $cookie->{ 'CONTIG' },
+ "Sequence",
+ "sequence.txt"
+ );
+
+ die qq(ERROR: no such file: "$path".\n) if not -e $path;
+
+ return $path;
+}
+
+
+sub path_tracks
+{
+ my ( $cookie,
+ ) = @_;
+
+ # Returns a list.
+ #
+ my ( $path, @tracks );
+
+ die qq(ERROR: no USER in cookie.\n) if not $cookie->{ 'USER' };
+ die qq(ERROR: no CLADE in cookie.\n) if not $cookie->{ 'CLADE' };
+ die qq(ERROR: no GENOME in cookie.\n) if not $cookie->{ 'GENOME' };
+ die qq(ERROR: no ASSEMBLY in cookie.\n) if not $cookie->{ 'ASSEMBLY' };
+ die qq(ERROR: no CONTIG in cookie.\n) if not $cookie->{ 'CONTIG' };
+
+ $path = join( "/",
+ $cookie->{ 'DATA_DIR' },
+ "Users",
+ $cookie->{ 'USER' },
+ $cookie->{ 'CLADE' },
+ $cookie->{ 'GENOME' },
+ $cookie->{ 'ASSEMBLY' },
+ $cookie->{ 'CONTIG' },
+ "Tracks",
+ );
+
+ if ( -d $path )
+ {
+ @tracks = Maasha::Filesys::ls_dirs( $path );
+
+ @tracks = grep { $_ !~ /\/\.\.?$/ } @tracks;
+
+ return wantarray ? @tracks : \@tracks;
+ }
+ else
+ {
+ return wantarray ? () : [];
+ }
+}
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
1;
-
projects / biopieces.git / blobdiff