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removing defined @ which is deprecated and throws an error
package Observation;
#use lib '/vol/ontologies';
use DBMaster;
use Data::Dumper;
require Exporter;
@EXPORT_OK = qw(get_objects get_sims_objects);
use WebColors;
use WebConfig;
use FIG_Config;
use LWP::Simple;
#use strict;
#use warnings;
use HTML;
use FFs;
1;
=head1 NAME
Observation -- A presentation layer for observations in SEED.
=head1 DESCRIPTION
The SEED environment contains various sources of information for sequence features. The purpose of this library is to provide a
single interface to this data.
The data can be used to display information for a given sequence feature (protein or other, but primarily information is computed for proteins).
=cut
=head1 BACKGROUND
=head2 Data incorporated in the Observations
As the goal of this library is to provide an integrated view, we combine diverse sources of evidence.
=head3 SEED core evidence
The core SEED data structures provided by FIG.pm. These are Similarities, BBHs and PCHs.
=head3 Attribute based Evidence
We use the SEED attribute infrastructure to store information computed by a variety of computational procedures.
These are e.g. InterPro hits via InterProScan (ipr), NCBI Conserved Domain Database Hits via PSSM(cdd),
PFAM hits via HMM(pfam), SignalP results(signalp), and various others.
=head1 METHODS
The public methods this package provides are listed below:
=head3 context()
Returns close or diverse for purposes of displaying genomic context
=cut
sub context {
my ($self) = @_;
return $self->{context};
}
=head3 rows()
each row in a displayed table
=cut
sub rows {
my ($self) = @_;
return $self->{rows};
}
=head3 acc()
A valid accession or remote ID (in the style of a db_xref) or a valid local ID (FID) in case this is supported.
=cut
sub acc {
my ($self) = @_;
return $self->{acc};
}
=head3 query()
The query id
=cut
sub query {
my ($self) = @_;
return $self->{query};
}
=head3 class()
The class of evidence (required). This is usually simply the name of the tool or the name of the SEED data structure.
B<Please note> the connection of class and display_method and URL.
Current valid classes are:
=over 9
=item IDENTICAL (seq)
=item SIM (seq)
=item BBH (seq)
=item PCH (fc)
=item FIGFAM (seq)
=item IPR (dom)
=item CDD (dom)
=item PFAM (dom)
=item SIGNALP_CELLO_TMPRED (loc)
=item PDB (seq)
=item TMHMM (loc)
=item HMMTOP (loc)
=back
=cut
sub class {
my ($self) = @_;
return $self->{class};
}
=head3 type()
The type of evidence (required).
Where type is one of the following:
=over 8
=item seq=Sequence similarity
=item dom=domain based match
=item loc=Localization of the feature
=item fc=Functional coupling.
=back
=cut
sub type {
my ($self) = @_;
return $self->{type};
}
=head3 start()
Start of hit in query sequence.
=cut
sub start {
my ($self) = @_;
return $self->{start};
}
=head3 end()
End of the hit in query sequence.
=cut
sub stop {
my ($self) = @_;
return $self->{stop};
}
=head3 start()
Start of hit in query sequence.
=cut
sub qstart {
my ($self) = @_;
return $self->{qstart};
}
=head3 qstop()
End of the hit in query sequence.
=cut
sub qstop {
my ($self) = @_;
return $self->{qstop};
}
=head3 hstart()
Start of hit in hit sequence.
=cut
sub hstart {
my ($self) = @_;
return $self->{hstart};
}
=head3 end()
End of the hit in hit sequence.
=cut
sub hstop {
my ($self) = @_;
return $self->{hstop};
}
=head3 qlength()
length of the query sequence in similarities
=cut
sub qlength {
my ($self) = @_;
return $self->{qlength};
}
=head3 hlength()
length of the hit sequence in similarities
=cut
sub hlength {
my ($self) = @_;
return $self->{hlength};
}
=head3 evalue()
E-value or P-Value if present.
=cut
sub evalue {
my ($self) = @_;
return $self->{evalue};
}
=head3 score()
Score if present.
=cut
sub score {
my ($self) = @_;
return $self->{score};
}
=head3 display()
will be different for each type
=cut
sub display {
die "Abstract Method Called\n";
}
=head3 display_table()
will be different for each type
=cut
sub display_table {
die "Abstract Table Method Called\n";
}
=head3 get_objects()
This is the B<REAL WORKHORSE> method of this Package.
=cut
sub get_objects {
my ($self,$fid,$fig,$parameters,$scope) = @_;
my $objects = [];
my @matched_datasets=();
# call function that fetches attribute based observations
# returns an array of arrays of hashes
if($scope){
get_cluster_observations($fid,\@matched_datasets,$scope);
}
else{
my %domain_classes;
my @attributes = $fig->get_attributes($fid);
#$domain_classes{'CDD'} = 1;
$domain_classes{'PFAM'} = 1;
get_identical_proteins($fid,\@matched_datasets,$fig);
get_attribute_based_domain_observations($fid,\%domain_classes,\@matched_datasets,\@attributes,$fig);
get_sims_observations($fid,\@matched_datasets,$fig,$parameters);
get_functional_coupling($fid,\@matched_datasets,$fig);
get_attribute_based_location_observations($fid,\@matched_datasets,\@attributes,$fig);
get_pdb_observations($fid,\@matched_datasets,\@attributes,$fig);
}
foreach my $dataset (@matched_datasets) {
my $object;
if($dataset->{'type'} eq "dom"){
$object = Observation::Domain->new($dataset);
}
elsif($dataset->{'class'} eq "PCH"){
$object = Observation::FC->new($dataset);
}
elsif ($dataset->{'class'} eq "IDENTICAL"){
$object = Observation::Identical->new($dataset);
}
elsif ($dataset->{'class'} eq "SIGNALP_CELLO_TMPRED"){
$object = Observation::Location->new($dataset);
}
elsif ($dataset->{'class'} eq "SIM"){
$object = Observation::Sims->new($dataset);
}
elsif ($dataset->{'class'} eq "CLUSTER"){
$object = Observation::Cluster->new($dataset);
}
elsif ($dataset->{'class'} eq "PDB"){
$object = Observation::PDB->new($dataset);
}
push (@$objects, $object);
}
return $objects;
}
=head3 get_attributes
provides layer of abstraction between tools and underlying access method to Attribute Server
=cut
sub get_attributes{
my ($self,$fig,$search_set,$search_term,$value_array_ref) = @_;
my @attributes = $fig->get_attributes($search_set,$search_term,@$value_array_ref);
return @attributes;
}
=head3 get_sims_objects()
This is the B<REAL WORKHORSE> method of this Package.
=cut
sub get_sims_objects {
my ($self,$fid,$fig,$parameters) = @_;
my $objects = [];
my @matched_datasets=();
# call function that fetches attribute based observations
# returns an array of arrays of hashes
get_sims_observations($fid,\@matched_datasets,$fig,$parameters);
foreach my $dataset (@matched_datasets) {
my $object;
if ($dataset->{'class'} eq "SIM"){
$object = Observation::Sims->new($dataset);
}
push (@$objects, $object);
}
return $objects;
}
=head3 display_housekeeping
This method returns the housekeeping data for a given peg in a table format
=cut
sub display_housekeeping {
my ($self,$fid,$fig) = @_;
my $content = [];
my $row = [];
my $org_name = "Data not available";
if ( $fig->org_of($fid)){
$org_name = $fig->org_of($fid);
}
my $org_id = $fig->genome_of($fid);
my $function = $fig->function_of($fid);
#my $taxonomy = $fig->taxonomy_of($org_id);
my $length = $fig->translation_length($fid);
push (@$row, $org_name);
push (@$row, $fid);
push (@$row, $length);
push (@$row, $function);
# initialize the table for commentary and annotations
#$content .= qq(<b>My Sequence Data</b><br><table border="0">);
#$content .= qq(<tr width=15%><td >FIG ID</td><td>$fid</td></tr>\n);
#$content .= qq(<tr width=15%><td >Organism Name</td><td>$org_name</td></tr>\n);
#$content .= qq(<tr><td width=15%>Taxonomy</td><td>$taxonomy</td></tr>\n);
#$content .= qq(<tr width=15%><td>Function</td><td>$function</td></tr>\n);
#$content .= qq(<tr width=15%><td>Sequence Length</td><td>$length aa</td></tr>\n);
#$content .= qq(</table><p>\n);
push(@$content, $row);
return ($content);
}
=head3 get_sims_summary
This method uses as input the similarities of a peg and creates a tree view of their taxonomy
=cut
sub get_sims_summary {
my ($observation, $dataset, $fig) = @_;
my %families;
my $taxes = $fig->taxonomy_list();
foreach my $thing (@$dataset) {
my ($id, $evalue);
if ($thing =~ /fig\|/){
$id = $thing;
$evalue = -1;
}
else{
next if ($thing->class ne "SIM");
$id = $thing->acc;
$evalue = $thing->evalue;
}
next if ($id !~ /fig\|/);
next if ($fig->is_deleted_fid($id));
my $genome = $fig->genome_of($id);
#my ($genome1) = ($genome) =~ /(.*)\./;
my $taxonomy = $taxes->{$genome};
my $parent_tax = "Root";
my @currLineage = ($parent_tax);
push (@{$families{figs}{$parent_tax}}, $id);
my $level = 2;
foreach my $tax (split(/\; /, $taxonomy),$id){
next if ($tax eq $parent_tax);
push (@{$families{children}{$parent_tax}}, $tax) if ($tax ne $parent_tax);
push (@{$families{figs}{$tax}}, $id) if ($tax ne $parent_tax);
$families{level}{$tax} = $level;
push (@currLineage, $tax);
$families{parent}{$tax} = $parent_tax;
$families{lineage}{$tax} = join(";", @currLineage);
if (defined ($families{evalue}{$tax})){
if ($evalue < $families{evalue}{$tax}){
$families{evalue}{$tax} = $evalue;
$families{color}{$tax} = &get_taxcolor($evalue);
}
}
else{
$families{evalue}{$tax} = $evalue;
$families{color}{$tax} = &get_taxcolor($evalue);
}
$parent_tax = $tax;
$level++;
}
}
foreach my $key (keys %{$families{children}}){
$families{count}{$key} = @{$families{children}{$key}};
my %saw;
my @out = grep(!$saw{$_}++, @{$families{children}{$key}});
$families{children}{$key} = \@out;
}
return \%families;
}
=head1 Internal Methods
These methods are not meant to be used outside of this package.
B<Please do not use them outside of this package!>
=cut
sub get_taxcolor{
my ($evalue) = @_;
my $color;
if ($evalue == -1){ $color = "black"; }
elsif (($evalue <= 1e-170) && ($evalue >= 0)){ $color = "#FF2000"; }
elsif (($evalue <= 1e-120) && ($evalue > 1e-170)){ $color = "#FF3300"; }
elsif (($evalue <= 1e-90) && ($evalue > 1e-120)){ $color = "#FF6600"; }
elsif (($evalue <= 1e-70) && ($evalue > 1e-90)){ $color = "#FF9900"; }
elsif (($evalue <= 1e-40) && ($evalue > 1e-70)){ $color = "#FFCC00"; }
elsif (($evalue <= 1e-20) && ($evalue > 1e-40)){ $color = "#FFFF00"; }
elsif (($evalue <= 1e-5) && ($evalue > 1e-20)){ $color = "#CCFF00"; }
elsif (($evalue <= 1) && ($evalue > 1e-5)){ $color = "#66FF00"; }
elsif (($evalue <= 10) && ($evalue > 1)){ $color = "#00FF00"; }
else{ $color = "#6666FF"; }
return ($color);
}
sub get_attribute_based_domain_observations{
# we read a FIG ID and a reference to an array (of arrays of hashes, see above)
my ($fid,$domain_classes,$datasets_ref,$attributes_ref,$fig) = (@_);
my $seen = {};
foreach my $attr_ref (@$attributes_ref) {
my $key = @$attr_ref[1];
my @parts = split("::",$key);
my $class = $parts[0];
my $name = $parts[1];
next if ($seen->{$name});
$seen->{$name}++;
#next if (($class eq "PFAM") && ($name !~ /interpro/));
if($domain_classes->{$parts[0]}){
my $val = @$attr_ref[2];
if($val =~/^(\d+\.\d+|0\.0);(\d+)-(\d+)/){
my $raw_evalue = $1;
my $from = $2;
my $to = $3;
my $evalue;
if(($raw_evalue =~/(\d+)\.(\d+)/) && ($class ne "PFAM")){
my $part2 = 1000 - $1;
my $part1 = $2/100;
$evalue = $part1."e-".$part2;
}
elsif(($raw_evalue =~/(\d+)\.(\d+)/) && ($class eq "PFAM")){
#$evalue=$raw_evalue;
my $part2 = 1000 - $1;
my $part1 = $2/100;
$evalue = $part1."e-".$part2;
}
else{
$evalue = "0.0";
}
my $dataset = {'class' => $class,
'acc' => $key,
'type' => "dom" ,
'evalue' => $evalue,
'start' => $from,
'stop' => $to,
'fig_id' => $fid,
'score' => $raw_evalue
};
push (@{$datasets_ref} ,$dataset);
}
}
}
}
sub get_attribute_based_location_observations{
my ($fid,$datasets_ref, $attributes_ref,$fig) = (@_);
#my $fig = new FIG;
my $location_attributes = ['SignalP','CELLO','TMPRED','Phobius'];
my $dataset = {'type' => "loc",
'class' => 'SIGNALP_CELLO_TMPRED',
'fig_id' => $fid
};
foreach my $attr_ref (@$attributes_ref){
my $key = @$attr_ref[1];
next if (($key !~ /SignalP/) && ($key !~ /CELLO/) && ($key !~ /TMPRED/) && ($key !~/Phobius/) );
my @parts = split("::",$key);
my $sub_class = $parts[0];
my $sub_key = $parts[1];
my $value = @$attr_ref[2];
if($sub_class eq "SignalP"){
if($sub_key eq "cleavage_site"){
my @value_parts = split(";",$value);
$dataset->{'cleavage_prob'} = $value_parts[0];
$dataset->{'cleavage_loc'} = $value_parts[1];
}
elsif($sub_key eq "signal_peptide"){
$dataset->{'signal_peptide_score'} = $value;
}
}
elsif($sub_class eq "CELLO"){
$dataset->{'cello_location'} = $sub_key;
$dataset->{'cello_score'} = $value;
}
elsif($sub_class eq "Phobius"){
if($sub_key eq "transmembrane"){
$dataset->{'phobius_tm_locations'} = $value;
}
elsif($sub_key eq "signal"){
$dataset->{'phobius_signal_location'} = $value;
}
}
elsif($sub_class eq "TMPRED"){
my @value_parts = split(/\;/,$value);
$dataset->{'tmpred_score'} = $value_parts[0];
$dataset->{'tmpred_locations'} = $value_parts[1];
}
}
push (@{$datasets_ref} ,$dataset);
}
=head3 get_pdb_observations() (internal)
This methods sets the type and class for pdb observations
=cut
sub get_pdb_observations{
my ($fid,$datasets_ref, $attributes_ref,$fig) = (@_);
#my $fig = new FIG;
foreach my $attr_ref (@$attributes_ref){
my $key = @$attr_ref[1];
next if ( ($key !~ /PDB/));
my($key1,$key2) =split("::",$key);
my $value = @$attr_ref[2];
my ($evalue,$location) = split(";",$value);
if($evalue =~/(\d+)\.(\d+)/){
my $part2 = 1000 - $1;
my $part1 = $2/100;
$evalue = $part1."e-".$part2;
}
my($start,$stop) =split("-",$location);
my $url = @$attr_ref[3];
my $dataset = {'class' => 'PDB',
'type' => 'seq' ,
'acc' => $key2,
'evalue' => $evalue,
'start' => $start,
'stop' => $stop,
'fig_id' => $fid
};
push (@{$datasets_ref} ,$dataset);
}
}
=head3 get_cluster_observations() (internal)
This methods sets the type and class for cluster observations
=cut
sub get_cluster_observations{
my ($fid,$datasets_ref,$scope) = (@_);
my $dataset = {'class' => 'CLUSTER',
'type' => 'fc',
'context' => $scope,
'fig_id' => $fid
};
push (@{$datasets_ref} ,$dataset);
}
=head3 get_sims_observations() (internal)
This methods retrieves sims fills the internal data structures.
=cut
sub get_sims_observations{
my ($fid,$datasets_ref,$fig,$parameters) = (@_);
my ($max_sims, $max_expand, $max_eval, $sim_order, $db_filter, $sim_filters);
if ( (defined $parameters->{flag}) && ($parameters->{flag})){
$max_sims = $parameters->{max_sims};
$max_expand = $parameters->{max_expand};
$max_eval = $parameters->{max_eval};
$db_filter = $parameters->{db_filter};
$sim_filters->{ sort_by } = $parameters->{sim_order};
#$sim_order = $parameters->{sim_order};
$group_by_genome = 1 if (defined ($parameters->{group_genome}));
}
elsif ( (defined $parameters->{sims_db}) && ($parameters->{sims_db} eq 'all')){
$max_sims = 50;
$max_expand = 5;
$max_eval = 1e-5;
$db_filter = "all";
$sim_filters->{ sort_by } = 'id';
}
else{
$max_sims = 50;
$max_expand = 5;
$max_eval = 1e-5;
$db_filter = "figx";
$sim_filters->{ sort_by } = 'id';
#$sim_order = "id";
}
my($id, $genome, @genomes, %sims);
# my @tmp= $fig->sims($fid,$max_sims,$max_eval,$db_filter,$max_expand,$sim_filters);
my @tmp= $fig->sims($fid,1000000,$max_eval,$db_filter,$max_expand,$sim_filters);
@tmp = grep { !($_->id2 =~ /^fig\|/ and $fig->is_deleted_fid($_->id2)) } @tmp;
my ($dataset);
if ($group_by_genome){
# Collect all sims from genome with the first occurance of the genome:
foreach $sim ( @tmp ){
$id = $sim->id2;
$genome = ($id =~ /^fig\|(\d+\.\d+)\.peg\.\d+/) ? $1 : $id;
if (! defined( $sims{ $genome } ) ) { push @genomes, $genome }
push @{ $sims{ $genome } }, $sim;
}
@tmp = map { @{ $sims{$_} } } @genomes;
}
my $seen_sims={};
my $count=1;
foreach my $sim (@tmp){
my $hit = $sim->[1];
next if ($seen_sims->{$hit});
next if ($hit =~ /nmpdr\||gnl\|md5\|/);
$seen_sims->{$hit}++;
last if ($count>$max_sims);
$count++;
my $percent = $sim->[2];
my $evalue = $sim->[10];
my $qfrom = $sim->[6];
my $qto = $sim->[7];
my $hfrom = $sim->[8];
my $hto = $sim->[9];
my $qlength = $sim->[12];
my $hlength = $sim->[13];
my $db = get_database($hit);
my $func = $fig->function_of($hit);
my $organism;
if ($fig->org_of($hit)){
$organism = $fig->org_of($hit);
}
else{
$organism = "Data not available";
}
$dataset = {'class' => 'SIM',
'query' => $sim->[0],
'acc' => $hit,
'identity' => $percent,
'type' => 'seq',
'evalue' => $evalue,
'qstart' => $qfrom,
'qstop' => $qto,
'hstart' => $hfrom,
'hstop' => $hto,
'database' => $db,
'organism' => $organism,
'function' => $func,
'qlength' => $qlength,
'hlength' => $hlength,
'fig_id' => $fid
};
push (@{$datasets_ref} ,$dataset);
}
}
=head3 get_database (internal)
This method gets the database association from the sequence id
=cut
sub get_database{
my ($id) = (@_);
my ($db);
if ($id =~ /^fig\|/) { $db = "SEED" }
elsif ($id =~ /^gi\|/) { $db = "NCBI" }
elsif ($id =~ /^gb\|/) { $db = "GenBank" }
elsif ($id =~ /^^[NXYZA]P_/) { $db = "RefSeq" }
elsif ($id =~ /^ref\|/) { $db = "RefSeq" }
elsif ($id =~ /^sp\|/) { $db = "SwissProt" }
elsif ($id =~ /^uni\|/) { $db = "UniProt" }
elsif ($id =~ /^tigr\|/) { $db = "TIGR" }
elsif ($id =~ /^pir\|/) { $db = "PIR" }
elsif (($id =~ /^kegg\|/) || ($id =~ /Spy/)) { $db = "KEGG" }
elsif ($id =~ /^tr\|/) { $db = "TrEMBL" }
elsif ($id =~ /^eric\|/) { $db = "ASAP" }
elsif ($id =~ /^img\|/) { $db = "JGI" }
elsif ($id =~ /^pdb\|/) { $db = "PDB" }
elsif ($id =~ /^img\|/) { $db = "IMG" }
elsif ($id =~ /^cmr\|/) { $db = "CMR" }
elsif ($id =~ /^dbj\|/) { $db = "DBJ" }
return ($db);
}
=head3 get_identical_proteins() (internal)
This methods retrieves sims fills the internal data structures.
=cut
sub get_identical_proteins{
my ($fid,$datasets_ref,$fig) = (@_);
#my $fig = new FIG;
my $funcs_ref;
my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
foreach my $id (@maps_to) {
my ($tmp, $who);
if (($id ne $fid) && ($tmp = $fig->function_of($id))) {
$who = &get_database($id);
push(@$funcs_ref, [$id,$who,$tmp]);
}
}
my $dataset = {'class' => 'IDENTICAL',
'type' => 'seq',
'fig_id' => $fid,
'rows' => $funcs_ref
};
push (@{$datasets_ref} ,$dataset);
}
=head3 get_functional_coupling() (internal)
This methods retrieves the functional coupling of a protein given a peg ID
=cut
sub get_functional_coupling{
my ($fid,$datasets_ref,$fig) = (@_);
#my $fig = new FIG;
my @funcs = ();
# initialize some variables
my($sc,$neigh);
# set default parameters for coupling and evidence
my ($bound,$sim_cutoff,$coupling_cutoff) = (5000, 1.0e-10, 4);
# get the fc data
my @fc_data = $fig->coupling_and_evidence($fid,$bound,$sim_cutoff,$coupling_cutoff);
# retrieve data
my @rows = map { ($sc,$neigh) = @$_;
[$sc,$neigh,scalar $fig->function_of($neigh)]
} @fc_data;
my $dataset = {'class' => 'PCH',
'type' => 'fc',
'fig_id' => $fid,
'rows' => \@rows
};
push (@{$datasets_ref} ,$dataset);
}
=head3 new (internal)
Instantiate a new object.
=cut
sub new {
my ($class,$dataset) = @_;
my $self = { class => $dataset->{'class'},
type => $dataset->{'type'},
fig_id => $dataset->{'fig_id'},
score => $dataset->{'score'},
};
bless($self,$class);
return $self;
}
=head3 identity (internal)
Returns the % identity of the similar sequence
=cut
sub identity {
my ($self) = @_;
return $self->{identity};
}
=head3 fig_id (internal)
=cut
sub fig_id {
my ($self) = @_;
return $self->{fig_id};
}
=head3 feature_id (internal)
=cut
sub feature_id {
my ($self) = @_;
return $self->{feature_id};
}
=head3 id (internal)
Returns the ID of the identical sequence
=cut
sub id {
my ($self) = @_;
return $self->{id};
}
=head3 organism (internal)
Returns the organism of the identical sequence
=cut
sub organism {
my ($self) = @_;
return $self->{organism};
}
=head3 function (internal)
Returns the function of the identical sequence
=cut
sub function {
my ($self) = @_;
return $self->{function};
}
=head3 database (internal)
Returns the database of the identical sequence
=cut
sub database {
my ($self) = @_;
return $self->{database};
}
############################################################
############################################################
package Observation::PDB;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{acc} = $dataset->{'acc'};
$self->{evalue} = $dataset->{'evalue'};
$self->{start} = $dataset->{'start'};
$self->{stop} = $dataset->{'stop'};
bless($self,$class);
return $self;
}
=head3 display()
displays data stored in best_PDB attribute and in Ontology server for given PDB id
=cut
sub display{
my ($self,$gd,$fig) = @_;
my $fid = $self->fig_id;
my $dbmaster = DBMaster->new(-database =>'Ontology',
-host => $WebConfig::DBHOST,
-user => $WebConfig::DBUSER,
-password => $WebConfig::DBPWD);
my $acc = $self->acc;
my ($pdb_description,$pdb_source,$pdb_ligand);
my $pdb_objs = $dbmaster->pdb->get_objects( { 'id' => $acc } );
if(!scalar(@$pdb_objs)){
$pdb_description = "not available";
$pdb_source = "not available";
$pdb_ligand = "not available";
}
else{
my $pdb_obj = $pdb_objs->[0];
$pdb_description = $pdb_obj->description;
$pdb_source = $pdb_obj->source;
$pdb_ligand = $pdb_obj->ligand;
}
my $lines = [];
my $line_data = [];
my $line_config = { 'title' => "PDB hit for $fid",
'hover_title' => 'PDB',
'short_title' => "best PDB",
'basepair_offset' => '1' };
#my $fig = new FIG;
my $seq = $fig->get_translation($fid);
my $fid_stop = length($seq);
my $fid_element_hash = {
"title" => $fid,
"start" => '1',
"end" => $fid_stop,
"color"=> '1',
"zlayer" => '1'
};
push(@$line_data,$fid_element_hash);
my $links_list = [];
my $descriptions = [];
my $name;
$name = {"title" => 'id',
"value" => $acc};
push(@$descriptions,$name);
my $description;
$description = {"title" => 'pdb description',
"value" => $pdb_description};
push(@$descriptions,$description);
my $score;
$score = {"title" => "score",
"value" => $self->evalue};
push(@$descriptions,$score);
my $start_stop;
my $start_stop_value = $self->start."_".$self->stop;
$start_stop = {"title" => "start-stop",
"value" => $start_stop_value};
push(@$descriptions,$start_stop);
my $source;
$source = {"title" => "source",
"value" => $pdb_source};
push(@$descriptions,$source);
my $ligand;
$ligand = {"title" => "pdb ligand",
"value" => $pdb_ligand};
push(@$descriptions,$ligand);
my $link;
my $link_url ="http://www.rcsb.org/pdb/explore/explore.do?structureId=".$acc;
$link = {"link_title" => $acc,
"link" => $link_url};
push(@$links_list,$link);
my $pdb_element_hash = {
"title" => "PDB homology",
"start" => $self->start,
"end" => $self->stop,
"color"=> '6',
"zlayer" => '3',
"links_list" => $links_list,
"description" => $descriptions};
push(@$line_data,$pdb_element_hash);
$gd->add_line($line_data, $line_config);
return $gd;
}
1;
############################################################
############################################################
package Observation::Identical;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{rows} = $dataset->{'rows'};
bless($self,$class);
return $self;
}
=head3 display_table()
If available use the function specified here to display the "raw" observation.
This code will display a table for the identical protein
B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
dence.
=cut
sub display_table{
my ($self,$fig) = @_;
#my $fig = new FIG;
my $fid = $self->fig_id;
my $rows = $self->rows;
my $cgi = new CGI;
my $all_domains = [];
my $count_identical = 0;
my $content;
foreach my $row (@$rows) {
my $id = $row->[0];
my $who = $row->[1];
my $assignment = $row->[2];
my $organism = "Data not available";
if ($fig->org_of($id)){
$organism = $fig->org_of($id);
}
my $single_domain = [];
push(@$single_domain,$who);
push(@$single_domain,$self->get_url_for_id($id));
push(@$single_domain,$organism);
push(@$single_domain,$assignment);
push(@$all_domains,$single_domain);
$count_identical++;
}
if ($count_identical >0){
$content = $all_domains;
}
else{
$content = "<p>This PEG does not have any essentially identical proteins</p>";
}
return ($content);
}
sub get_url_for_id {
my ($self, $id) = @_;
my $copy = $id;
if ($copy =~ s/^kegg\|//) {
return "<a href='http://www.genome.jp/dbget-bin/www_bget?$copy'>$id</a>";
}
elsif ($copy =~ s/^sp\|//) {
return "<a href='http://www.uniprot.org/entry/$copy'>$id</a>";
}
elsif ($copy =~ s/^tr\|//) {
return "<a href='http://www.uniprot.org/entry/$copy'>$id</a>";
}
elsif ($copy =~ s/^uni\|//) {
return "<a href='http://www.uniprot.org/entry/$copy'>$id</a>";
}
elsif ($copy =~ s/^gi\|//) {
return "<a href='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$copy'>$id</a>";
}
elsif ($copy =~ s/^ref\|//) {
return "<a href='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$copy'>$id</a>";
}
elsif ($copy =~ s/^gb\|//) {
return "<a href='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$copy'>$id</a>";
}
elsif ($copy =~ s/^cmr\|// or $copy =~ s/^tigrcmr\|//) {
return "<a href='http://cmr.tigr.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=$copy'>$id</a>";
}
elsif ($copy =~ /^fig\|/) {
return "<a href='http://seed-viewer.theseed.org/linkin.cgi?id=$id'>$id</a>";
}
elsif ($copy =~ s/^img\|//) {
return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=$copy'>$id</a>";
}
else {
return $id;
}
}
1;
#########################################
#########################################
package Observation::FC;
1;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{rows} = $dataset->{'rows'};
bless($self,$class);
return $self;
}
=head3 display_table()
If available use the function specified here to display the "raw" observation.
This code will display a table for the identical protein
B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
dence.
=cut
sub display_table {
my ($self,$dataset,$fig) = @_;
my $fid = $self->fig_id;
my $rows = $self->rows;
my $cgi = new CGI;
my $functional_data = [];
my $count = 0;
my $content;
foreach my $row (@$rows) {
my $single_domain = [];
$count++;
# construct the score link
my $score = $row->[0];
my $toid = $row->[1];
my $link = $cgi->url(-relative => 1) . "?page=Annotation&feature=$fid";
my $sc_link = "<a href='$link'>$score</a>";
push(@$single_domain,$sc_link);
push(@$single_domain,$row->[1]);
push(@$single_domain,$row->[2]);
push(@$functional_data,$single_domain);
}
if ($count >0){
$content = $functional_data;
}
else
{
$content = "<p>This PEG does not have any functional coupling</p>";
}
return ($content);
}
#########################################
#########################################
package Observation::Domain;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{evalue} = $dataset->{'evalue'};
$self->{acc} = $dataset->{'acc'};
$self->{start} = $dataset->{'start'};
$self->{stop} = $dataset->{'stop'};
bless($self,$class);
return $self;
}
sub display {
my ($thing,$gd) = @_;
my $lines = [];
# my $line_config = { 'title' => $thing->acc,
# 'short_title' => $thing->type,
# 'basepair_offset' => '1' };
my $color = "4";
my $line_data = [];
my $links_list = [];
my $descriptions = [];
my $db_and_id = $thing->acc;
my ($db,$id) = split("::",$db_and_id);
my $dbmaster = DBMaster->new(-database =>'Ontology',
-host => $WebConfig::DBHOST,
-user => $WebConfig::DBUSER,
-password => $WebConfig::DBPWD);
my ($name_title,$name_value,$description_title,$description_value);
if($db =~ /PFAM/){
my $new_id;
if ($id =~ /_/){
($new_id) = ($id) =~ /(.*?)_/;
}
else{
$new_id = $id;
}
my $pfam_objs = $dbmaster->pfam->get_objects( { 'id' => $new_id } );
if(!scalar(@$pfam_objs)){
$name_title = "name";
$name_value = "not available";
$description_title = "description";
$description_value = "not available";
}
else{
my $pfam_obj = $pfam_objs->[0];
$name_title = "name";
$name_value = $pfam_obj->term;
#$description_title = "description";
#$description_value = $pfam_obj->description;
}
}
my $short_title = $thing->acc;
$short_title =~ s/::/ - /ig;
my $new_short_title=$short_title;
if ($short_title =~ /interpro/){
($new_short_title) = ($short_title) =~ /(.*?)_/;
}
my $line_config = { 'title' => $name_value,
'hover_title', => 'Domain',
'short_title' => $new_short_title,
'basepair_offset' => '1' };
my $name;
my ($new_id) = ($id) =~ /(.*?)_/;
$name = {"title" => $db,
"value" => $new_id};
push(@$descriptions,$name);
# my $description;
# $description = {"title" => $description_title,
# "value" => $description_value};
# push(@$descriptions,$description);
my $score;
$score = {"title" => "score",
"value" => $thing->evalue};
push(@$descriptions,$score);
my $location;
$location = {"title" => "location",
"value" => $thing->start . " - " . $thing->stop};
push(@$descriptions,$location);
my $link_id;
if ($thing->acc =~/::(.*)/){
$link_id = $1;
}
my $link;
my $link_url;
# if ($thing->class eq "CDD"){$link_url = "http://0-www.ncbi.nlm.nih.gov.library.vu.edu.au:80/Structure/cdd/cddsrv.cgi?uid=$link_id"}
if($thing->class eq "PFAM"){$link_url = "http://pfam.sanger.ac.uk/family?acc=$link_id"}
else{$link_url = "NO_URL"}
$link = {"link_title" => $thing->acc,
"link" => $link_url};
push(@$links_list,$link);
my $element_hash = {
"title" => $name_value,
"start" => $thing->start,
"end" => $thing->stop,
"color"=> $color,
"zlayer" => '2',
"links_list" => $links_list,
"description" => $descriptions};
push(@$line_data,$element_hash);
$gd->add_line($line_data, $line_config);
return $gd;
}
sub display_table {
my ($self,$dataset) = @_;
my $cgi = new CGI;
my $data = [];
my $count = 0;
my $content;
my $seen = {};
foreach my $thing (@$dataset) {
next if ($thing->type !~ /dom/);
my $single_domain = [];
$count++;
my $db_and_id = $thing->acc;
my ($db,$id) = split("::",$db_and_id);
my $dbmaster = DBMaster->new(-database =>'Ontology',
-host => $WebConfig::DBHOST,
-user => $WebConfig::DBUSER,
-password => $WebConfig::DBPWD);
my ($name_title,$name_value,$description_title,$description_value);
my $new_id;
if($db =~ /PFAM/){
if ($id =~ /_/){
($new_id) = ($id) =~ /(.*?)_/;
}
else{
$new_id = $id;
}
next if ($seen->{$new_id});
$seen->{$new_id}=1;
my $pfam_objs = $dbmaster->pfam->get_objects( { 'id' => $new_id } );
# print STDERR "VALUES: " . $pfam_objs . "\n";
if(!scalar(@$pfam_objs)){
$name_title = "name";
$name_value = "not available";
$description_title = "description";
$description_value = "not available";
}
else{
my $pfam_obj = $pfam_objs->[0];
$name_title = "name";
$name_value = $pfam_obj->term;
#$description_title = "description";
#$description_value = $pfam_obj->description;
}
}
my $location = $thing->start . " - " . $thing->stop;
push(@$single_domain,$db);
push(@$single_domain,$new_id);
push(@$single_domain,$name_value);
push(@$single_domain,$location);
push(@$single_domain,$thing->evalue);
push(@$single_domain,$description_value);
push(@$data,$single_domain);
}
if ($count >0){
$content = $data;
}
else
{
$content = "<p>This PEG does not have any similarities to domains</p>";
}
}
#########################################
#########################################
package Observation::Location;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{cleavage_prob} = $dataset->{'cleavage_prob'};
$self->{cleavage_loc} = $dataset->{'cleavage_loc'};
$self->{signal_peptide_score} = $dataset->{'signal_peptide_score'};
$self->{cello_location} = $dataset->{'cello_location'};
$self->{cello_score} = $dataset->{'cello_score'};
$self->{tmpred_score} = $dataset->{'tmpred_score'};
$self->{tmpred_locations} = $dataset->{'tmpred_locations'};
$self->{phobius_signal_location} = $dataset->{'phobius_signal_location'};
$self->{phobius_tm_locations} = $dataset->{'phobius_tm_locations'};
bless($self,$class);
return $self;
}
sub display_cello {
my ($thing) = @_;
my $html;
my $cello_location = $thing->cello_location;
my $cello_score = $thing->cello_score;
if($cello_location){
$html .= "<p><font type=verdana size=-2>Subcellular location prediction: $cello_location, score: $cello_score</font> </p>";
#$html .= "<p>CELLO score: $cello_score </p>";
}
return ($html);
}
sub display {
my ($thing,$gd,$fig) = @_;
my $fid = $thing->fig_id;
#my $fig= new FIG;
my $length = length($fig->get_translation($fid));
my $cleavage_prob;
if($thing->cleavage_prob){$cleavage_prob = $thing->cleavage_prob;}
my ($cleavage_loc_begin,$cleavage_loc_end) = split("-",$thing->cleavage_loc);
my $signal_peptide_score = $thing->signal_peptide_score;
my $cello_location = $thing->cello_location;
my $cello_score = $thing->cello_score;
my $tmpred_score = $thing->tmpred_score;
my @tmpred_locations = split(",",$thing->tmpred_locations);
my $phobius_signal_location = $thing->phobius_signal_location;
my @phobius_tm_locations = split(",",$thing->phobius_tm_locations);
my $lines = [];
#color is
my $color = "6";
# if($cello_location){
# my $cello_descriptions = [];
# my $line_data =[];
#
# my $line_config = { 'title' => 'Localization Evidence',
# 'short_title' => 'CELLO',
# 'hover_title' => 'Localization',
# 'basepair_offset' => '1' };
#
# my $description_cello_location = {"title" => 'Best Cello Location',
# "value" => $cello_location};
#
# push(@$cello_descriptions,$description_cello_location);
#
# my $description_cello_score = {"title" => 'Cello Score',
# "value" => $cello_score};
#
# push(@$cello_descriptions,$description_cello_score);
#
# my $element_hash = {
# "title" => "CELLO",
# "color"=> $color,
# "start" => "1",
# "end" => $length + 1,
# "zlayer" => '1',
# "description" => $cello_descriptions};
#
# push(@$line_data,$element_hash);
# $gd->add_line($line_data, $line_config);
# }
#
# $color = "2";
# if($tmpred_score){
# my $line_data =[];
# my $line_config = { 'title' => 'Localization Evidence',
# 'short_title' => 'Transmembrane',
# 'basepair_offset' => '1' };
#
# foreach my $tmpred (@tmpred_locations){
# my $descriptions = [];
# my ($begin,$end) =split("-",$tmpred);
# my $description_tmpred_score = {"title" => 'TMPRED score',
# "value" => $tmpred_score};
#
# push(@$descriptions,$description_tmpred_score);
#
# my $element_hash = {
# "title" => "transmembrane location",
# "start" => $begin + 1,
# "end" => $end + 1,
# "color"=> $color,
# "zlayer" => '5',
# "type" => 'box',
# "description" => $descriptions};
#
# push(@$line_data,$element_hash);
#
# }
# $gd->add_line($line_data, $line_config);
# }
if((scalar(@phobius_tm_locations) > 0) || $phobius_signal_location){
my $line_data =[];
my $line_config = { 'title' => 'Localization Evidence, Transmembrane and Signal Peptide',
'short_title' => 'TM and SP',
'hover_title' => 'Localization',
'basepair_offset' => '1' };
foreach my $tm_loc (@phobius_tm_locations){
my $descriptions = [];
my $description_phobius_tm_locations = {"title" => 'transmembrane location',
"value" => $tm_loc};
push(@$descriptions,$description_phobius_tm_locations);
my ($begin,$end) =split("-",$tm_loc);
my $element_hash = {
"title" => "Phobius",
"start" => $begin + 1,
"end" => $end + 1,
"color"=> '6',
"zlayer" => '4',
"type" => 'bigbox',
"description" => $descriptions};
push(@$line_data,$element_hash);
}
if($phobius_signal_location){
my $descriptions = [];
my $description_phobius_signal_location = {"title" => 'Phobius Signal Location',
"value" => $phobius_signal_location};
push(@$descriptions,$description_phobius_signal_location);
my ($begin,$end) =split("-",$phobius_signal_location);
my $element_hash = {
"title" => "phobius signal locations",
"start" => $begin + 1,
"end" => $end + 1,
"color"=> '1',
"zlayer" => '5',
"type" => 'box',
"description" => $descriptions};
push(@$line_data,$element_hash);
}
$gd->add_line($line_data, $line_config);
}
# $color = "1";
# if($signal_peptide_score){
# my $line_data = [];
# my $descriptions = [];
#
# my $line_config = { 'title' => 'Localization Evidence',
# 'short_title' => 'SignalP',
# 'hover_title' => 'Localization',
# 'basepair_offset' => '1' };
#
# my $description_signal_peptide_score = {"title" => 'signal peptide score',
# "value" => $signal_peptide_score};
#
# push(@$descriptions,$description_signal_peptide_score);
#
# my $description_cleavage_prob = {"title" => 'cleavage site probability',
# "value" => $cleavage_prob};
#
# push(@$descriptions,$description_cleavage_prob);
#
# my $element_hash = {
# "title" => "SignalP",
# "start" => $cleavage_loc_begin - 2,
# "end" => $cleavage_loc_end + 1,
# "type" => 'bigbox',
# "color"=> $color,
# "zlayer" => '10',
# "description" => $descriptions};
#
# push(@$line_data,$element_hash);
# $gd->add_line($line_data, $line_config);
# }
return ($gd);
}
sub cleavage_loc {
my ($self) = @_;
return $self->{cleavage_loc};
}
sub cleavage_prob {
my ($self) = @_;
return $self->{cleavage_prob};
}
sub signal_peptide_score {
my ($self) = @_;
return $self->{signal_peptide_score};
}
sub tmpred_score {
my ($self) = @_;
return $self->{tmpred_score};
}
sub tmpred_locations {
my ($self) = @_;
return $self->{tmpred_locations};
}
sub cello_location {
my ($self) = @_;
return $self->{cello_location};
}
sub cello_score {
my ($self) = @_;
return $self->{cello_score};
}
sub phobius_signal_location {
my ($self) = @_;
return $self->{phobius_signal_location};
}
sub phobius_tm_locations {
my ($self) = @_;
return $self->{phobius_tm_locations};
}
#########################################
#########################################
package Observation::Sims;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{identity} = $dataset->{'identity'};
$self->{acc} = $dataset->{'acc'};
$self->{query} = $dataset->{'query'};
$self->{evalue} = $dataset->{'evalue'};
$self->{qstart} = $dataset->{'qstart'};
$self->{qstop} = $dataset->{'qstop'};
$self->{hstart} = $dataset->{'hstart'};
$self->{hstop} = $dataset->{'hstop'};
$self->{database} = $dataset->{'database'};
$self->{organism} = $dataset->{'organism'};
$self->{function} = $dataset->{'function'};
$self->{qlength} = $dataset->{'qlength'};
$self->{hlength} = $dataset->{'hlength'};
bless($self,$class);
return $self;
}
=head3 display()
If available use the function specified here to display a graphical observation.
This code will display a graphical view of the similarities using the genome drawer object
=cut
sub display {
my ($self,$gd,$thing,$fig,$base_start,$in_subs,$cgi) = @_;
# declare variables
my $window_size = $gd->window_size;
my $peg = $thing->acc;
my $query_id = $thing->query;
my $organism = $thing->organism;
my $abbrev_name = $fig->abbrev($organism);
if (!$organism){
$organism = $peg;
$abbrev_name = $peg;
}
my $genome = $fig->genome_of($peg);
my ($org_tax) = ($genome) =~ /(.*)\./;
my $function = $thing->function;
my $query_start = $thing->qstart;
my $query_stop = $thing->qstop;
my $hit_start = $thing->hstart;
my $hit_stop = $thing->hstop;
my $ln_query = $thing->qlength;
my $ln_hit = $thing->hlength;
my $query_color = match_color($query_start, $query_stop, abs($query_stop-$query_start)+1, 1);
my $hit_color = match_color($hit_start, $hit_stop, abs($query_stop-$query_start)+1, 1);
my $tax_link = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" . $org_tax;
# hit sequence title
my $line_config = { 'title' => "$organism [$org_tax]",
'short_title' => "$abbrev_name",
'title_link' => '$tax_link',
'basepair_offset' => '0',
'no_middle_line' => '1'
};
# query sequence title
my $replace_id = $peg;
$replace_id =~ s/\|/_/ig;
my $anchor_name = "anchor_". $replace_id;
my $query_config = { 'title' => "Query",
'short_title' => "Query",
'title_link' => "changeSimsLocation('$replace_id', 1)",
'basepair_offset' => '0',
'no_middle_line' => '1'
};
my $line_data = [];
my $query_data = [];
my $element_hash;
my $hit_links_list = [];
my $hit_descriptions = [];
my $query_descriptions = [];
# get sequence information
# evidence link
my $evidence_link;
if ($peg =~ /^fig\|/){
$evidence_link = "?page=Annotation&feature=".$peg;
}
else{
my $db = &Observation::get_database($peg);
my ($link_id) = ($peg) =~ /\|(.*)/;
$evidence_link = &HTML::alias_url($link_id, $db);
#print STDERR "LINK: $db $evidence_link";
}
my $link = {"link_title" => $peg,
"link" => $evidence_link};
push(@$hit_links_list,$link) if ($evidence_link);
# subsystem link
my $subs = $in_subs->{$peg} if (defined $in_subs->{$peg});
my @subsystems;
foreach my $array (@$subs){
my $subsystem = $$array[0];
push(@subsystems,$subsystem);
my $link = {"link" => "?page=Subsystems&subsystem=$subsystem",
"link_title" => $subsystem};
push(@$hit_links_list,$link);
}
# blast alignment
$link = {"link_title" => "view blast alignment",
"link" => "$FIG_Config::cgi_url/seedviewer.cgi?page=ToolResult&tool=bl2seq&peg1=$query_id&peg2=$peg"};
push (@$hit_links_list,$link) if ($peg =~ /^fig\|/);
# description data
my $description_function;
$description_function = {"title" => "function",
"value" => $function};
push(@$hit_descriptions,$description_function);
# subsystem description
my $ss_string = join (",", @subsystems);
$ss_string =~ s/_/ /ig;
my $description_ss = {"title" => "subsystems",
"value" => $ss_string};
push(@$hit_descriptions,$description_ss);
# location description
# hit
my $description_loc;
$description_loc = {"title" => "Hit Location",
"value" => $hit_start . " - " . $hit_stop};
push(@$hit_descriptions, $description_loc);
$description_loc = {"title" => "Sequence Length",
"value" => $ln_hit};
push(@$hit_descriptions, $description_loc);
# query
$description_loc = {"title" => "Hit Location",
"value" => $query_start . " - " . $query_stop};
push(@$query_descriptions, $description_loc);
$description_loc = {"title" => "Sequence Length",
"value" => $ln_query};
push(@$query_descriptions, $description_loc);
# evalue score description
my $evalue = $thing->evalue;
while ($evalue =~ /-0/)
{
my ($chunk1, $chunk2) = split(/-/, $evalue);
$chunk2 = substr($chunk2,1);
$evalue = $chunk1 . "-" . $chunk2;
}
my $color = &color($evalue);
my $description_eval = {"title" => "E-Value",
"value" => $evalue};
push(@$hit_descriptions, $description_eval);
push(@$query_descriptions, $description_eval);
my $identity = $self->identity;
my $description_identity = {"title" => "Identity",
"value" => $identity};
push(@$hit_descriptions, $description_identity);
push(@$query_descriptions, $description_identity);
my $number = $base_start + ($query_start-$hit_start);
#print STDERR "START: $number";
$element_hash = {
"title" => $query_id,
"start" => $base_start,
"end" => $base_start+$ln_query,
"type"=> 'box',
"color"=> $color,
"zlayer" => "2",
"links_list" => $query_links_list,
"description" => $query_descriptions
};
push(@$query_data,$element_hash);
$element_hash = {
"title" => $query_id . ': HIT AREA',
"start" => $base_start + $query_start,
"end" => $base_start + $query_stop,
"type"=> 'smallbox',
"color"=> $query_color,
"zlayer" => "3",
"links_list" => $query_links_list,
"description" => $query_descriptions
};
push(@$query_data,$element_hash);
$gd->add_line($query_data, $query_config);
$element_hash = {
"title" => $peg,
"start" => $base_start + ($query_start-$hit_start),
"end" => $base_start + (($query_start-$hit_start)+$ln_hit),
"type"=> 'box',
"color"=> $color,
"zlayer" => "2",
"links_list" => $hit_links_list,
"description" => $hit_descriptions
};
push(@$line_data,$element_hash);
$element_hash = {
"title" => $peg . ': HIT AREA',
"start" => $base_start + $query_start,
"end" => $base_start + $query_stop,
"type"=> 'smallbox',
"color"=> $hit_color,
"zlayer" => "3",
"links_list" => $hit_links_list,
"description" => $hit_descriptions
};
push(@$line_data,$element_hash);
$gd->add_line($line_data, $line_config);
my $breaker = [];
my $breaker_hash = {};
my $breaker_config = { 'no_middle_line' => "1" };
push (@$breaker, $breaker_hash);
$gd->add_line($breaker, $breaker_config);
return ($gd);
}
=head3 display_domain_composition()
If available use the function specified here to display a graphical observation of the CDD(later Pfam or selected) domains that occur in the set of similar proteins
=cut
sub display_domain_composition {
my ($self,$gd,$fig) = @_;
#$fig = new FIG;
my $peg = $self->acc;
my $line_data = [];
my $links_list = [];
my $descriptions = [];
my @domain_query_results =$fig->get_attributes($peg,"CDD");
#my @domain_query_results = ();
foreach $dqr (@domain_query_results){
my $key = @$dqr[1];
my @parts = split("::",$key);
my $db = $parts[0];
my $id = $parts[1];
my $val = @$dqr[2];
my $from;
my $to;
my $evalue;
if($val =~/^(\d+\.\d+|0\.0);(\d+)-(\d+)/){
my $raw_evalue = $1;
$from = $2;
$to = $3;
if($raw_evalue =~/(\d+)\.(\d+)/){
my $part2 = 1000 - $1;
my $part1 = $2/100;
$evalue = $part1."e-".$part2;
}
else{
$evalue = "0.0";
}
}
my $dbmaster = DBMaster->new(-database =>'Ontology',
-host => $WebConfig::DBHOST,
-user => $WebConfig::DBUSER,
-password => $WebConfig::DBPWD);
my ($name_value,$description_value);
if($db eq "CDD"){
my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
if(!scalar(@$cdd_objs)){
$name_title = "name";
$name_value = "not available";
$description_title = "description";
$description_value = "not available";
}
else{
my $cdd_obj = $cdd_objs->[0];
$name_value = $cdd_obj->term;
$description_value = $cdd_obj->description;
}
}
my $domain_name;
$domain_name = {"title" => "name",
"value" => $name_value};
push(@$descriptions,$domain_name);
my $description;
$description = {"title" => "description",
"value" => $description_value};
push(@$descriptions,$description);
my $score;
$score = {"title" => "score",
"value" => $evalue};
push(@$descriptions,$score);
my $link_id = $id;
my $link;
my $link_url;
if ($db eq "CDD"){$link_url = "http://0-www.ncbi.nlm.nih.gov.library.vu.edu.au:80/Structure/cdd/cddsrv.cgi?uid=$link_id"}
elsif($db eq "PFAM"){$link_url = "http://pfam.sanger.ac.uk/family?acc=$link_id"}
else{$link_url = "NO_URL"}
$link = {"link_title" => $name_value,
"link" => $link_url};
push(@$links_list,$link);
my $domain_element_hash = {
"title" => $peg,
"start" => $from,
"end" => $to,
"type"=> 'box',
"zlayer" => '4',
"links_list" => $links_list,
"description" => $descriptions
};
push(@$line_data,$domain_element_hash);
#just one CDD domain for now, later will add option for multiple domains from selected DB
last;
}
my $line_config = { 'title' => $peg,
'hover_title' => 'Domain',
'short_title' => $peg,
'basepair_offset' => '1' };
$gd->add_line($line_data, $line_config);
return ($gd);
}
=head3 display_table()
If available use the function specified here to display the "raw" observation.
This code will display a table for the similarities protein
B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evidence.
=cut
sub display_table {
my ($self,$dataset, $show_columns, $query_fid, $fig, $application, $cgi) = @_;
my ($count, $data, $content, %box_column, $subsystems_column, $evidence_column, %e_identical, $function_color, @ids);
my $scroll_list;
foreach my $col (@$show_columns){
push (@$scroll_list, $col->{key});
}
push (@ids, $query_fid);
foreach my $thing (@$dataset) {
next if ($thing->class ne "SIM");
push (@ids, $thing->acc);
}
$lineages = $fig->taxonomy_list() if (grep /lineage/, @$scroll_list);
my @attributes = $fig->get_attributes(\@ids) if ( (grep /evidence/, @$scroll_list) || (grep /(pfam|mw)/, @$scroll_list) );
# get the column for the subsystems
$subsystems_column = &get_subsystems_column(\@ids,$fig,$cgi,'hash');
# get the column for the evidence codes
$evidence_column = &get_evidence_column(\@ids, \@attributes, $fig, $cgi, 'hash');
# get the column for pfam_domain
$pfam_column = &get_attrb_column(\@ids, \@attributes, $fig, $cgi, 'pfam', 'PFAM', 'hash') if (grep /^pfam$/, @$scroll_list);
# get the column for molecular weight
$mw_column = &get_attrb_column(\@ids, \@attributes, $fig, $cgi, 'mw', 'molecular_weight', 'hash') if (grep /^mw$/, @$scroll_list);
# get the column for organism's habitat
my $habitat_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'habitat', 'Habitat', 'hash') if (grep /^habitat$/, @$scroll_list);
# get the column for organism's temperature optimum
my $temperature_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'temperature', 'Optimal_Temperature', 'hash') if (grep /^temperature$/, @$scroll_list);
# get the column for organism's temperature range
my $temperature_range_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'temp_range', 'Temperature_Range', 'hash') if (grep /^temp_range$/, @$scroll_list);
# get the column for organism's oxygen requirement
my $oxygen_req_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'oxygen', 'Oxygen_Requirement', 'hash') if (grep /^oxygen$/, @$scroll_list);
# get the column for organism's pathogenicity
my $pathogenic_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'pathogenic', 'Pathogenic', 'hash') if (grep /^pathogenic$/, @$scroll_list);
# get the column for organism's pathogenicity host
my $pathogenic_in_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'pathogenic_in', 'Pathogenic_In', 'hash') if (grep /^pathogenic_in$/, @$scroll_list);
# get the column for organism's salinity
my $salinity_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'salinity', 'Salinity', 'hash') if (grep /^salinity$/, @$scroll_list);
# get the column for organism's motility
my $motility_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'motility', 'Motility', 'hash') if (grep /^motility$/, @$scroll_list);
# get the column for organism's gram stain
my $gram_stain_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'gram_stain', 'Gram_Stain', 'hash') if (grep /^gram_stain$/, @$scroll_list);
# get the column for organism's endospores
my $endospores_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'endospores', 'Endospores', 'hash') if (grep /^endospores$/, @$scroll_list);
# get the column for organism's shape
my $shape_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'shape', 'Shape', 'hash') if (grep /^shape$/, @$scroll_list);
# get the column for organism's disease
my $disease_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'disease', 'Disease', 'hash') if (grep /^disease$/, @$scroll_list);
# get the column for organism's disease
my $gc_content_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'gc_content', 'GC_Content', 'hash') if (grep /^gc_content$/, @$scroll_list);
# get the column for transmembrane domains
my $transmembrane_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'transmembrane', 'Phobius::transmembrane', 'hash') if (grep /^transmembrane$/, @$scroll_list);
# get the column for similar to human
my $similar_to_human_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'similar_to_human', 'similar_to_human', 'hash') if (grep /^similar_to_human$/, @$scroll_list);
# get the column for signal peptide
my $signal_peptide_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'signal_peptide', 'Phobius::signal', 'hash') if (grep /^signal_peptide$/, @$scroll_list);
# get the column for transmembrane domains
my $isoelectric_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'isoelectric', 'isoelectric_point', 'hash') if (grep /^isoelectric$/, @$scroll_list);
# get the column for conserved neighborhood
my $cons_neigh_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'conserved_neighborhood', undef, 'hash') if (grep /^conserved_neighborhood$/, @$scroll_list);
# get the column for cellular location
my $cell_location_column = &get_attrb_column(\@ids, undef, $fig, $cgi, 'cellular_location', 'PSORT::', 'hash') if (grep /^isoelectric$/, @$scroll_list);
# get the aliases
my $alias_col;
if ( (grep /asap_id/, @$scroll_list) || (grep /ncbi_id/, @$scroll_list) ||
(grep /refseq_id/, @$scroll_list) || (grep /swissprot_id/, @$scroll_list) ||
(grep /uniprot_id/, @$scroll_list) || (grep /tigr_id/, @$scroll_list) ||
(grep /kegg_id/, @$scroll_list) || (grep /pir_id/, @$scroll_list) ||
(grep /trembl_id/, @$scroll_list) || (grep /jgi_id/, @$scroll_list) ) {
$alias_col = &get_db_aliases(\@ids,$fig,'all',$cgi,'hash');
}
# get the colors for the function cell
my $functions = $fig->function_of_bulk(\@ids,1);
$functional_color = &get_function_color_cell($functions, $fig);
my $query_function = $fig->function_of($query_fid);
my %e_identical = &get_essentially_identical($query_fid,$dataset,$fig);
my $figfam_data = &FIG::get_figfams_data();
my $figfams = new FFs($figfam_data);
my $same_genome_flag = 0;
my $func_color_offset=0;
unshift(@$dataset, $query_fid);
for (my $thing_count=0;$thing_count<scalar @$dataset;$thing_count++){
# foreach my $thing ( @$dataset){
my $thing = $dataset->[$thing_count];
my $next_thing = $dataset->[$thing_count+1] if (defined $dataset->[$thing_count+1]);
my ($id, $taxid, $iden, $ln1,$ln2,$b1,$b2,$e1,$e2,$d1,$d2,$color1,$color2,$reg1,$reg2, $next_org);
if ($thing eq $query_fid){
$id = $thing;
$taxid = $fig->genome_of($id);
$organism = $fig->genus_species($taxid);
$current_function = $fig->function_of($id);
}
else{
next if ($thing->class ne "SIM");
$id = $thing->acc;
$evalue = $thing->evalue;
$taxid = $fig->genome_of($id);
$iden = $thing->identity;
$organism= $thing->organism;
$ln1 = $thing->qlength;
if ($ln1 < 1) { $ln1 = 1; }
$ln2 = $thing->hlength;
if ($ln2 < 1) { $ln2 = 1; }
$b1 = $thing->qstart;
$e1 = $thing->qstop;
$b2 = $thing->hstart;
$e2 = $thing->hstop;
$d1 = abs($e1 - $b1) + 1;
$d2 = abs($e2 - $b2) + 1;
$color1 = match_color( $b1, $e1, $ln1 );
$color2 = match_color( $b2, $e2, $ln2 );
$reg1 = {'data'=> "$b1-$e1 (<b>$d1/$ln1</b>)", 'highlight' => $color1};
$reg2 = {'data'=> "$b2-$e2 (<b>$d2/$ln2</b>)", 'highlight' => $color2};
$current_function = $thing->function;
$next_org = $next_thing->organism if (defined $next_thing);
}
next if ($id =~ /nmpdr\||gnl\|md5\|/);
my $single_domain = [];
$count++;
# organisms cell
my ($org, $org_color) = $fig->org_and_color_of($id);
my $org_cell;
if ( ($next_org ne $organism) && ($same_genome_flag == 0) ){
$org_cell = { 'data' => $organism, 'highlight' => $org_color};
}
elsif ($next_org eq $organism){
$org_cell = { 'data' => "<b>" . $organism . "</b>", 'highlight' => $org_color};
$same_genome_flag = 1;
}
elsif ($same_genome_flag == 1){
$org_cell = { 'data' => "<b>" . $organism . "</b>", 'highlight' => $org_color};
$same_genome_flag = 0;
}
# checkbox cell
my ($box_cell,$tax, $radio_cell);
my $field_name = "tables_" . $id;
my $pair_name = "visual_" . $id;
my $cell_name = "cell_". $id;
my $replace_id = $id;
$replace_id =~ s/\|/_/ig;
my $white = '#ffffff';
$white = '#999966' if ($id eq $query_fid);
$org_color = '#999966' if ($id eq $query_fid);
my $anchor_name = "anchor_". $replace_id;
my $checked = "";
#$checked = "checked" if ($id eq $query_fid);
# if ($id =~ /^fig\|/){
my $box = qq~<a name="$anchor_name"></a><input type="checkbox" name="seq" value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name','$cell_name');" $checked>~;
$box_cell = { 'data'=>$box, 'highlight'=>$org_color};
$tax = $fig->genome_of($id) if ($id =~ /^fig\|/);
# }
# else{
# my $box = qq(<a name="$anchor_name"></a>);
# $box_cell = { 'data'=>$box, 'highlight'=>$org_color};
# }
# create the radio cell for any sequence, not just fig ids
my $radio = qq(<input type="radio" name="function_select" value="$current_function" id="$field_name" onClick="clearText('new_text_function')">);
$radio_cell = { 'data'=>$radio, 'highlight'=>$white};
# get the linked fig id
my $anchor_link = "graph_" . $replace_id;
my $fig_data;
if ($id =~ /^fig\|/)
{
$fig_data = "<table><tr><td><a href='?page=Annotation&feature=$id'>$id</a></td>" . " " x 2;
}
else
{
my $url_link = &HTML::set_prot_links($cgi,$id);
$fig_data = "<table><tr><td>$url_link</td>". " " x 2;
}
$fig_data .= qq(<td><img height='10px' width='20px' src='$FIG_Config::cgi_url/Html/anchor_alignment.png' alt='View Graphic View of Alignment' onClick='changeSimsLocation("$anchor_link", 0)'/></td></tr></table>);
my $fig_col = {'data'=> $fig_data,
'highlight'=>$white};
$replace_id = $peg;
$replace_id =~ s/\|/_/ig;
$anchor_name = "anchor_". $replace_id;
my $query_config = { 'title' => "Query",
'short_title' => "Query",
'title_link' => "changeSimsLocation('$replace_id')",
'basepair_offset' => '0'
};
# function cell
my $function_cell_colors = {0=>"#ffffff", 1=>"#eeccaa", 2=>"#ffaaaa",
3=>"#ffcc66", 4=>"#ffff00", 5=>"#aaffaa",
6=>"#bbbbff", 7=>"#ffaaff", 8=>"#dddddd"};
my $function_color;
if ( (defined($functional_color->{$query_function})) && ($functional_color->{$query_function} == 1) ){
$function_color = $function_cell_colors->{ $functional_color->{$current_function} - $func_color_offset};
}
else{
$function_color = $function_cell_colors->{ $functional_color->{$current_function}};
}
my $function_cell;
if ($current_function){
if ($current_function eq $query_function){
$function_cell = {'data'=>$current_function, 'highlight'=>$function_cell_colors->{0}};
$func_color_offset=1;
}
else{
$function_cell = {'data'=>$current_function,'highlight' => $function_color};
}
}
else{
$function_cell = {'data'=>$current_function,'highlight' => "#dddddd"};
}
if ($id eq $query_fid){
push (@$single_domain, $box_cell, {'data'=>qq~<i>Query Sequence: </i>~ . qq~<b>$id</b>~ , 'highlight'=>$white}, {'data'=> 'n/a', 'highlight'=>$white},
{'data'=>'n/a', 'highlight'=>$white}, {'data'=>'n/a', 'highlight'=>$white}, {'data'=>'n/a', 'highlight'=>$white},
{'data' => $organism, 'highlight'=> $white}, {'data'=>$current_function, 'highlight'=>$white},
{'data'=>$subsystems_column->{$id},'highlight'=>$white},
{'data'=>$evidence_column->{$id},'highlight'=>$white}); # permanent columns
}
else{
push (@$single_domain, $box_cell, $fig_col, {'data'=> $evalue, 'highlight'=>"#ffffff"},
{'data'=>"$iden\%", 'highlight'=>"#ffffff"}, $reg1, $reg2, $org_cell, $function_cell,
{'data'=>$subsystems_column->{$id},'highlight'=>"#ffffff"},
{'data'=>$evidence_column->{$id},'highlight'=>"#ffffff"}); # permanent columns
}
if ( ( $application->session->user) ){
my $user = $application->session->user;
if ($user && $user->has_right(undef, 'annotate', 'genome')) {
push (@$single_domain,$radio_cell);
}
}
my ($ff) = $figfams->families_containing_peg($id);
foreach my $col (@$scroll_list){
if ($id eq $query_fid) { $highlight_color = "#999966"; }
else { $highlight_color = "#ffffff"; }
if ($col =~ /pfam/) {push(@$single_domain,{'data'=>$pfam_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /mw/) {push(@$single_domain,{'data'=>$mw_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /habitat/) {push(@$single_domain,{'data'=>$habitat_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /temperature/) {push(@$single_domain,{'data'=>$temperature_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /temp_range/) {push(@$single_domain,{'data'=>$temperature_range_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /oxygen/) {push(@$single_domain,{'data'=>$oxygen_req_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /^pathogenic$/) {push(@$single_domain,{'data'=>$pathogenic_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /^pathogenic_in$/) {push(@$single_domain,{'data'=>$pathogenic_in_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /salinity/) {push(@$single_domain,{'data'=>$salinity_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /motility/) {push(@$single_domain,{'data'=>$motility_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /gram_stain/) {push(@$single_domain,{'data'=>$gram_stain_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /endospores/) {push(@$single_domain,{'data'=>$endospores_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /shape/) {push(@$single_domain,{'data'=>$shape_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /disease/) {push(@$single_domain,{'data'=>$disease_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /gc_content/) {push(@$single_domain,{'data'=>$gc_content_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /transmembrane/) {push(@$single_domain,{'data'=>$transmembrane_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /signal_peptide/) {push(@$single_domain,{'data'=>$signal_peptide_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /isoelectric/) {push(@$single_domain,{'data'=>$isoelectric_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /conerved_neighborhood/) {push(@$single_domain,{'data'=>$cons_neigh_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /cellular_location/) {push(@$single_domain,{'data'=>$cell_location_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /ncbi_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"NCBI"},'highlight'=>$highlight_color});}
elsif ($col =~ /refseq_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"RefSeq"},'highlight'=>$highlight_color});}
elsif ($col =~ /swissprot_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"SwissProt"},'highlight'=>$highlight_color});}
elsif ($col =~ /uniprot_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"UniProt"},'highlight'=>$highlight_color});}
elsif ($col =~ /tigr_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"TIGR"},'highlight'=>$highlight_color});}
elsif ($col =~ /pir_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"PIR"},'highlight'=>$highlight_color});}
elsif ($col =~ /kegg_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"KEGG"},'highlight'=>$highlight_color});}
elsif ($col =~ /trembl_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"TrEMBL"},'highlight'=>$highlight_color});}
elsif ($col =~ /asap_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"ASAP"},'highlight'=>$highlight_color});}
elsif ($col =~ /jgi_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"JGI"},'highlight'=>$highlight_color});}
elsif ($col =~ /lineage/) {push(@$single_domain,{'data'=>$lineages->{$tax},'highlight'=>$highlight_color});}
elsif ($col =~ /figfam/) {push(@$single_domain,{'data'=>"<a href='?page=FigFamViewer&figfam=" . $ff . "' target='_new'>" . $ff . "</a>",'highlight'=>$highlight_color});}
}
push(@$data,$single_domain);
}
if ($count >0 ){
$content = $data;
}
else{
$content = "<p>This PEG does not have any similarities</p>";
}
shift(@$dataset);
return ($content);
}
=head3 display_figfam_table()
If available use the function specified here to display the "raw" observation.
This code will display a table for the similarities protein
B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evidence.
=cut
sub display_figfam_table {
my ($self,$ids, $show_columns, $fig, $application, $cgi) = @_;
my ($count, $data, $content, %box_column, $subsystems_column, $evidence_column, %e_identical, $function_color, @ids);
my $scroll_list;
foreach my $col (@$show_columns){
push (@$scroll_list, $col->{key});
}
$lineages = $fig->taxonomy_list() if (grep /lineage/, @$scroll_list);
my @attributes = $fig->get_attributes($ids) if ( (grep /evidence/, @$scroll_list) || (grep /(pfam|mw)/, @$scroll_list) );
# get the column for the subsystems
$subsystems_column = &get_subsystems_column($ids,$fig,$cgi,'hash');
# get the column for the evidence codes
$evidence_column = &get_evidence_column($ids, \@attributes, $fig, $cgi, 'hash') if (grep /^evidence$/, @$scroll_list);
# get the column for pfam_domain
$pfam_column = &get_attrb_column($ids, \@attributes, $fig, $cgi, 'pfam', 'PFAM', 'hash') if (grep /^pfam$/, @$scroll_list);
# get the column for molecular weight
$mw_column = &get_attrb_column($ids, \@attributes, $fig, $cgi, 'mw', 'molecular_weight', 'hash') if (grep /^mw$/, @$scroll_list);
# get the column for organism's habitat
my $habitat_column = &get_attrb_column($ids, undef, $fig, $cgi, 'habitat', 'Habitat', 'hash') if (grep /^habitat$/, @$scroll_list);
# get the column for organism's temperature optimum
my $temperature_column = &get_attrb_column($ids, undef, $fig, $cgi, 'temperature', 'Optimal_Temperature', 'hash') if (grep /^temperature$/, @$scroll_list);
# get the column for organism's temperature range
my $temperature_range_column = &get_attrb_column($ids, undef, $fig, $cgi, 'temp_range', 'Temperature_Range', 'hash') if (grep /^temp_range$/, @$scroll_list);
# get the column for organism's oxygen requirement
my $oxygen_req_column = &get_attrb_column($ids, undef, $fig, $cgi, 'oxygen', 'Oxygen_Requirement', 'hash') if (grep /^oxygen$/, @$scroll_list);
# get the column for organism's pathogenicity
my $pathogenic_column = &get_attrb_column($ids, undef, $fig, $cgi, 'pathogenic', 'Pathogenic', 'hash') if (grep /^pathogenic$/, @$scroll_list);
# get the column for organism's pathogenicity host
my $pathogenic_in_column = &get_attrb_column($ids, undef, $fig, $cgi, 'pathogenic_in', 'Pathogenic_In', 'hash') if (grep /^pathogenic_in$/, @$scroll_list);
# get the column for organism's salinity
my $salinity_column = &get_attrb_column($ids, undef, $fig, $cgi, 'salinity', 'Salinity', 'hash') if (grep /^salinity$/, @$scroll_list);
# get the column for organism's motility
my $motility_column = &get_attrb_column($ids, undef, $fig, $cgi, 'motility', 'Motility', 'hash') if (grep /^motility$/, @$scroll_list);
# get the column for organism's gram stain
my $gram_stain_column = &get_attrb_column($ids, undef, $fig, $cgi, 'gram_stain', 'Gram_Stain', 'hash') if (grep /^gram_stain$/, @$scroll_list);
# get the column for organism's endospores
my $endospores_column = &get_attrb_column($ids, undef, $fig, $cgi, 'endospores', 'Endospores', 'hash') if (grep /^endospores$/, @$scroll_list);
# get the column for organism's shape
my $shape_column = &get_attrb_column($ids, undef, $fig, $cgi, 'shape', 'Shape', 'hash') if (grep /^shape$/, @$scroll_list);
# get the column for organism's disease
my $disease_column = &get_attrb_column($ids, undef, $fig, $cgi, 'disease', 'Disease', 'hash') if (grep /^disease$/, @$scroll_list);
# get the column for organism's disease
my $gc_content_column = &get_attrb_column($ids, undef, $fig, $cgi, 'gc_content', 'GC_Content', 'hash') if (grep /^gc_content$/, @$scroll_list);
# get the column for transmembrane domains
my $transmembrane_column = &get_attrb_column($ids, undef, $fig, $cgi, 'transmembrane', 'Phobius::transmembrane', 'hash') if (grep /^transmembrane$/, @$scroll_list);
# get the column for similar to human
my $similar_to_human_column = &get_attrb_column($ids, undef, $fig, $cgi, 'similar_to_human', 'similar_to_human', 'hash') if (grep /^similar_to_human$/, @$scroll_list);
# get the column for signal peptide
my $signal_peptide_column = &get_attrb_column($ids, undef, $fig, $cgi, 'signal_peptide', 'Phobius::signal', 'hash') if (grep /^signal_peptide$/, @$scroll_list);
# get the column for transmembrane domains
my $isoelectric_column = &get_attrb_column($ids, undef, $fig, $cgi, 'isoelectric', 'isoelectric_point', 'hash') if (grep /^isoelectric$/, @$scroll_list);
# get the column for conserved neighborhood
my $cons_neigh_column = &get_attrb_column($ids, undef, $fig, $cgi, 'conserved_neighborhood', undef, 'hash') if (grep /^conserved_neighborhood$/, @$scroll_list);
# get the column for cellular location
my $cell_location_column = &get_attrb_column($ids, undef, $fig, $cgi, 'cellular_location', 'PSORT::', 'hash') if (grep /^isoelectric$/, @$scroll_list);
# get the aliases
my $alias_col;
if ( (grep /asap_id/, @$scroll_list) || (grep /ncbi_id/, @$scroll_list) ||
(grep /refseq_id/, @$scroll_list) || (grep /swissprot_id/, @$scroll_list) ||
(grep /uniprot_id/, @$scroll_list) || (grep /tigr_id/, @$scroll_list) ||
(grep /kegg_id/, @$scroll_list) || (grep /pir_id/, @$scroll_list) ||
(grep /trembl_id/, @$scroll_list) || (grep /jgi_id/, @$scroll_list) ) {
$alias_col = &get_db_aliases($ids,$fig,'all',$cgi,'hash');
}
foreach my $id ( @$ids){
my $current_function = $fig->function_of($id);
my $organism = $fig->org_of($id);
my $single_domain = [];
# organisms cell comehere2
my ($org, $org_color) = $fig->org_and_color_of($id);
my $org_cell = { 'data' => $organism, 'highlight' => $org_color};
# get the linked fig id
my $fig_data;
if ($id =~ /^fig\|/)
{
$fig_data = "<a href='?page=Annotation&feature=$id'>$id</a>";
}
else
{
my $url_link = &HTML::set_prot_links($cgi,$id);
$fig_data = "<table><tr><td>$url_link</td>". " " x 2;
}
my $fig_col = {'data'=> $fig_data,
'highlight'=>"#ffffff"};
# get sequence length
my $length_col = {'data'=> $fig->translation_length($id),
'highlight'=>"#ffffff"};
# function cell
$function_cell = {'data'=>$current_function, 'highlight'=> "#ffffff"};
# insert data
push (@$single_domain, $fig_col, $length_col, $org_cell, {'data'=>$subsystems_column->{$id},'highlight'=>"#ffffff"}, $function_cell);
foreach my $col (@$scroll_list){
my $highlight_color = "#ffffff";
if ($col =~ /evidence/) {push(@$single_domain,{'data'=>$evidence_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /pfam/) {push(@$single_domain,{'data'=>$pfam_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /mw/) {push(@$single_domain,{'data'=>$mw_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /habitat/) {push(@$single_domain,{'data'=>$habitat_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /temperature/) {push(@$single_domain,{'data'=>$temperature_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /temp_range/) {push(@$single_domain,{'data'=>$temperature_range_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /oxygen/) {push(@$single_domain,{'data'=>$oxygen_req_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /^pathogenic$/) {push(@$single_domain,{'data'=>$pathogenic_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /^pathogenic_in$/) {push(@$single_domain,{'data'=>$pathogenic_in_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /salinity/) {push(@$single_domain,{'data'=>$salinity_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /motility/) {push(@$single_domain,{'data'=>$motility_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /gram_stain/) {push(@$single_domain,{'data'=>$gram_stain_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /endospores/) {push(@$single_domain,{'data'=>$endospores_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /shape/) {push(@$single_domain,{'data'=>$shape_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /disease/) {push(@$single_domain,{'data'=>$disease_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /gc_content/) {push(@$single_domain,{'data'=>$gc_content_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /transmembrane/) {push(@$single_domain,{'data'=>$transmembrane_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /signal_peptide/) {push(@$single_domain,{'data'=>$signal_peptide_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /isoelectric/) {push(@$single_domain,{'data'=>$isoelectric_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /conerved_neighborhood/) {push(@$single_domain,{'data'=>$cons_neigh_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /cellular_location/) {push(@$single_domain,{'data'=>$cell_location_column->{$id},'highlight'=>$highlight_color});}
elsif ($col =~ /ncbi_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"NCBI"},'highlight'=>$highlight_color});}
elsif ($col =~ /refseq_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"RefSeq"},'highlight'=>$highlight_color});}
elsif ($col =~ /swissprot_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"SwissProt"},'highlight'=>$highlight_color});}
elsif ($col =~ /uniprot_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"UniProt"},'highlight'=>$highlight_color});}
elsif ($col =~ /tigr_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"TIGR"},'highlight'=>$highlight_color});}
elsif ($col =~ /pir_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"PIR"},'highlight'=>$highlight_color});}
elsif ($col =~ /kegg_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"KEGG"},'highlight'=>$highlight_color});}
elsif ($col =~ /trembl_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"TrEMBL"},'highlight'=>$highlight_color});}
elsif ($col =~ /asap_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"ASAP"},'highlight'=>$highlight_color});}
elsif ($col =~ /jgi_id/) {push(@$single_domain,{'data'=>$alias_col->{$id}->{"JGI"},'highlight'=>$highlight_color});}
elsif ($col =~ /lineage/) {push(@$single_domain,{'data'=>$lineages->{$tax},'highlight'=>$highlight_color});}
elsif ($col =~ /figfam/) {push(@$single_domain,{'data'=>"<a href='?page=FigFamViewer&figfam=" . $ff . "' target='_new'>" . $ff . "</a>",'highlight'=>$highlight_color});}
}
push(@$data,$single_domain);
}
$content = $data;
return ($content);
}
sub get_box_column{
my ($ids) = @_;
my %column;
foreach my $id (@$ids){
my $field_name = "tables_" . $id;
my $pair_name = "visual_" . $id;
my $cell_name = "cell_" . $id;
$column{$id} = qq(<input type=checkbox name=seq value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name', '$cell_name');">);
}
return (%column);
}
sub get_figfam_column{
my ($ids, $fig, $cgi) = @_;
my $column;
my $figfam_data = &FIG::get_figfams_data();
my $figfams = new FFs($figfam_data);
foreach my $id (@$ids){
my ($ff);
if ($id =~ /\.peg\./){
($ff) = $figfams->families_containing_peg($id);
}
if ($ff){
push (@$column, "<a href='?page=FigFamViewer&figfam=" . $ff . "' target='_new'>" . $ff . "</a>");
}
else{
push (@$column, " ");
}
}
return $column;
}
sub get_subsystems_column{
my ($ids,$fig,$cgi,$returnType) = @_;
my %in_subs = $fig->subsystems_for_pegs($ids,1);
my ($column, $ss);
foreach my $id (@$ids){
my @in_sub = @{$in_subs{$id}} if (defined $in_subs{$id});
my @subsystems;
if (scalar(@in_sub)) {
foreach my $array (@in_sub){
my $ss_name = $array->[0];
$ss_name =~ s/_/ /ig;
push (@subsystems, "-" . $ss_name);
}
my $in_sub_line = join ("<br>", @subsystems);
$ss->{$id} = $in_sub_line;
} else {
$ss->{$id} = "None added";
}
push (@$column, $ss->{$id});
}
if ($returnType eq 'hash') { return $ss; }
elsif ($returnType eq 'array') { return $column; }
}
sub get_lineage_column{
my ($ids, $fig, $cgi) = @_;
my $lineages = $fig->taxonomy_list();
foreach my $id (@$ids){
my $genome = $fig->genome_of($id);
if ($lineages->{$genome}){
# push (@$column, qq~<table style='border-style:hidden;'><tr><td style='background-color: #ffffff;'>~ . $lineages->{$genome} . qq~</td></tr</table>~);
push (@$column, $lineages->{$genome});
}
else{
push (@$column, " ");
}
}
return $column;
}
sub match_color {
my ( $b, $e, $n , $rgb) = @_;
my ( $l, $r ) = ( $e > $b ) ? ( $b, $e ) : ( $e, $b );
my $hue = 5/6 * 0.5*($l+$r)/$n - 1/12;
my $cov = ( $r - $l + 1 ) / $n;
my $sat = 1 - 10 * $cov / 9;
my $br = 1;
if ($rgb){
return html2rgb( rgb2html( hsb2rgb( $hue, $sat, $br ) ) );
}
else{
rgb2html( hsb2rgb( $hue, $sat, $br ) );
}
}
sub hsb2rgb {
my ( $h, $s, $br ) = @_;
$h = 6 * ($h - floor($h));
if ( $s > 1 ) { $s = 1 } elsif ( $s < 0 ) { $s = 0 }
if ( $br > 1 ) { $br = 1 } elsif ( $br < 0 ) { $br = 0 }
my ( $r, $g, $b ) = ( $h <= 3 ) ? ( ( $h <= 1 ) ? ( 1, $h, 0 )
: ( $h <= 2 ) ? ( 2 - $h, 1, 0 )
: ( 0, 1, $h - 2 )
)
: ( ( $h <= 4 ) ? ( 0, 4 - $h, 1 )
: ( $h <= 5 ) ? ( $h - 4, 0, 1 )
: ( 1, 0, 6 - $h )
);
( ( $r * $s + 1 - $s ) * $br,
( $g * $s + 1 - $s ) * $br,
( $b * $s + 1 - $s ) * $br
)
}
sub html2rgb {
my ($hex) = @_;
my ($r,$g,$b) = ($hex) =~ /^\#(\w\w)(\w\w)(\w\w)/;
my $code = { 'A'=>10, 'B'=>11, 'C'=>12, 'D'=>13, 'E'=>14, 'F'=>15,
1=>1, 2=>2, 3=>3, 4=>4, 5=>5, 6=>6, 7=>7, 8=>8, 9=>9};
my @R = split(//, $r);
my @G = split(//, $g);
my @B = split(//, $b);
my $red = ($code->{uc($R[0])}*16)+$code->{uc($R[1])};
my $green = ($code->{uc($G[0])}*16)+$code->{uc($G[1])};
my $blue = ($code->{uc($B[0])}*16)+$code->{uc($B[1])};
my $rgb = [$red, $green, $blue];
return $rgb;
}
sub rgb2html {
my ( $r, $g, $b ) = @_;
if ( $r > 1 ) { $r = 1 } elsif ( $r < 0 ) { $r = 0 }
if ( $g > 1 ) { $g = 1 } elsif ( $g < 0 ) { $g = 0 }
if ( $b > 1 ) { $b = 1 } elsif ( $b < 0 ) { $b = 0 }
sprintf("#%02x%02x%02x", int(255.999*$r), int(255.999*$g), int(255.999*$b) )
}
sub floor {
my $x = $_[0];
defined( $x ) || return undef;
( $x >= 0 ) || ( int($x) == $x ) ? int( $x ) : -1 - int( - $x )
}
sub get_function_color_cell{
my ($functions, $fig) = @_;
# figure out the quantity of each function
my %hash;
foreach my $key (keys %$functions){
my $func = $functions->{$key};
$hash{$func}++;
}
my %func_colors;
my $count = 1;
foreach my $key (sort {$hash{$b}<=>$hash{$a}} keys %hash){
$func_colors{$key}=$count;
$count++;
}
return \%func_colors;
}
sub get_essentially_identical{
my ($fid,$dataset,$fig) = @_;
#my $fig = new FIG;
my %id_list;
#my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
foreach my $thing (@$dataset){
if($thing->class eq "IDENTICAL"){
my $rows = $thing->rows;
my $count_identical = 0;
foreach my $row (@$rows) {
my $id = $row->[0];
if (($id ne $fid) && ($fig->function_of($id))) {
$id_list{$id} = 1;
}
}
}
}
# foreach my $id (@maps_to) {
# if (($id ne $fid) && ($fig->function_of($id))) {
# $id_list{$id} = 1;
# }
# }
return(%id_list);
}
sub get_evidence_column{
my ($ids,$attributes,$fig,$cgi,$returnType) = @_;
my ($column, $code_attributes);
if (! defined $attributes) {
my @attributes_array = $fig->get_attributes($ids);
$attributes = \@attributes_array;
}
my @codes = grep { $_->[1] =~ /^evidence_code/i } @$attributes;
foreach my $key (@codes){
push (@{$code_attributes->{$key->[0]}}, $key);
}
foreach my $id (@$ids){
# add evidence code with tool tip
my $ev_codes=" ";
my @codes = @{$code_attributes->{$id}} if (defined @{$code_attributes->{$id}});
my @ev_codes = ();
foreach my $code (@codes) {
my $pretty_code = $code->[2];
if ($pretty_code =~ /;/) {
my ($cd, $ss) = split(";", $code->[2]);
if ($cd =~ /ilit|dlit/){
my ($type,$pubmed_id) = ($cd) =~ /(.*?)\((.*)\)/;
my $publink = &HTML::alias_url($pubmed_id,'PMID');
$cd = $type . "(<a href='" . $publink . "'>" . $pubmed_id . "</a>)";
}
$ss =~ s/_/ /g;
$pretty_code = $cd;# . " in " . $ss;
}
push(@ev_codes, $pretty_code);
}
if (scalar(@ev_codes) && $ev_codes[0]) {
my $ev_code_help=join("<br />", map {&HTML::evidence_codes_explain($_)} @ev_codes);
$ev_codes = $cgi->a(
{
id=>"evidence_codes", onMouseover=>"javascript:if(!this.tooltip) this.tooltip=new Popup_Tooltip(this, 'Evidence Codes', '$ev_code_help', ''); this.tooltip.addHandler(); return false;"}, join("<br />", @ev_codes));
}
if ($returnType eq 'hash') { $column->{$id}=$ev_codes; }
elsif ($returnType eq 'array') { push (@$column, $ev_codes); }
}
return $column;
}
sub get_attrb_column{
my ($ids, $attributes, $fig, $cgi, $colName, $attrbName, $returnType) = @_;
my ($column, %code_attributes, %attribute_locations);
my $dbmaster = DBMaster->new(-database =>'Ontology',
-host => $WebConfig::DBHOST,
-user => $WebConfig::DBUSER,
-password => $WebConfig::DBPWD);
if ($colName eq "pfam"){
if (! defined $attributes) {
my @attributes_array = $fig->get_attributes($ids);
$attributes = \@attributes_array;
}
my @codes = grep { $_->[1] =~ /^$attrbName/i } @$attributes;
foreach my $key (@codes){
my $name = $key->[1];
if ($name =~ /_/){
($name) = ($key->[1]) =~ /(.*?)_/;
}
push (@{$code_attributes{$key->[0]}}, $name);
push (@{$attribute_location{$key->[0]}{$name}}, $key->[2]);
}
foreach my $id (@$ids){
# add pfam code
my $pfam_codes=" ";
my @pfam_codes = "";
my %description_codes;
if ($id =~ /^fig\|\d+\.\d+\.peg\.\d+$/) {
my @ncodes = @{$code_attributes{$id}} if (@{$code_attributes{$id}});
@pfam_codes = ();
# get only unique values
my %saw;
foreach my $key (@ncodes) {$saw{$key}=1;}
@ncodes = keys %saw;
foreach my $code (@ncodes) {
my @parts = split("::",$code);
my $pfam_link = "<a href=http://pfam.sanger.ac.uk/family?acc=" . $parts[1] . ">$parts[1]</a>";
# # get the locations for the domain
# my @locs;
# foreach my $part (@{$attribute_location{$id}{$code}}){
# my ($loc) = ($part) =~ /\;(.*)/;
# push (@locs,$loc);
# }
# my %locsaw;
# foreach my $key (@locs) {$locsaw{$key}=1;}
# @locs = keys %locsaw;
#
# my $locations = join (", ", @locs);
#
if (defined ($description_codes{$parts[1]})){
push(@pfam_codes, "$parts[1]");
}
else {
my $description = $dbmaster->pfam->get_objects( { 'id' => $parts[1] } );
$description_codes{$parts[1]} = $description->[0]->{term};
push(@pfam_codes, "$pfam_link");
}
}
if ($returnType eq 'hash') { $column->{$id} = join("<br><br>", @pfam_codes); }
elsif ($returnType eq 'array') { push (@$column, join("<br><br>", @pfam_codes)); }
}
}
}
elsif ($colName eq 'cellular_location'){
if (! defined $attributes) {
my @attributes_array = $fig->get_attributes($ids);
$attributes = \@attributes_array;
}
my @codes = grep { $_->[1] =~ /^$attrbName/i } @$attributes;
foreach my $key (@codes){
my ($loc) = ($key->[1]) =~ /::(.*)/;
my ($new_loc, @all);
@all = split (//, $loc);
my $count = 0;
foreach my $i (@all){
if ( ($i eq uc($i)) && ($count > 0) ){
$new_loc .= " " . $i;
}
else{
$new_loc .= $i;
}
$count++;
}
push (@{$code_attributes{$key->[0]}}, [$new_loc, $key->[2]]);
}
foreach my $id (@$ids){
my (@values, $entry);
#@values = (" ");
if (@{$code_attributes{$id}}){
my @ncodes = @{$code_attributes{$id}};
foreach my $code (@ncodes){
push (@values, $code->[0] . ", " . $code->[1]);
}
}
else{
@values = ("Not available");
}
if ($returnType eq 'hash') { $column->{$id} = join ("<BR>", @values); }
elsif ($returnType eq 'array') { push (@$column, join ("<BR>", @values)); }
}
}
elsif ( ($colName eq 'mw') || ($colName eq 'transmembrane') || ($colName eq 'similar_to_human') ||
($colName eq 'signal_peptide') || ($colName eq 'isoelectric') ){
if (! defined $attributes) {
my @attributes_array = $fig->get_attributes($ids);
$attributes = \@attributes_array;
}
my @codes = grep { $_->[1] =~ /^$attrbName/i } @$attributes;
foreach my $key (@codes){
push (@{$code_attributes{$key->[0]}}, $key->[2]);
}
foreach my $id (@$ids){
my (@values, $entry);
#@values = (" ");
if (@{$code_attributes{$id}}){
my @ncodes = @{$code_attributes{$id}};
foreach my $code (@ncodes){
push (@values, $code);
}
}
else{
@values = ("Not available");
}
if ($returnType eq 'hash') { $column->{$id} = join ("<BR>", @values); }
elsif ($returnType eq 'array') { push (@$column, join ("<BR>", @values)); }
}
}
elsif ( ($colName eq 'habitat') || ($colName eq 'temperature') || ($colName eq 'temp_range') ||
($colName eq 'oxygen') || ($colName eq 'pathogenic') || ($colName eq 'pathogenic_in') ||
($colName eq 'salinity') || ($colName eq 'motility') || ($colName eq 'gram_stain') ||
($colName eq 'endospores') || ($colName eq 'shape') || ($colName eq 'disease') ||
($colName eq 'gc_content') ) {
if (! defined $attributes) {
my @attributes_array = $fig->get_attributes(undef,$attrbName);
$attributes = \@attributes_array;
}
my $genomes_with_phenotype;
foreach my $attribute (@$attributes){
my $genome = $attribute->[0];
$genomes_with_phenotype->{$genome} = $attribute->[2];
}
foreach my $id (@$ids){
my $genome = $fig->genome_of($id);
my @values = (' ');
if (defined $genomes_with_phenotype->{$genome}){
push (@values, $genomes_with_phenotype->{$genome});
}
if ($returnType eq 'hash') { $column->{$id} = join ("<BR>", @values); }
elsif ($returnType eq 'array') { push (@$column, join ("<BR>", @values)); }
}
}
return $column;
}
sub get_aclh_aliases {
my ($ids,$fig,$db,$cgi,$returnType) = @_;
my $db_array;
my $id_line = join (",", @$ids);
my $aclh_url = "http://clearinghouse.nmpdr.org/aclh.cgi?page=SearchResults&raw_dump=1&query=" . $id_line;
}
sub get_id_aliases {
my ($id, $fig) = @_;
my $aliases = {};
my $org = $fig->org_of($id);
my $url = "http://clearinghouse.nmpdr.org/aclh.cgi?page=SearchResults&raw_dump=1&query=$id";
if ( my $form = &LWP::Simple::get($url) ) {
my ($block) = ($form) =~ /<pre>(.*)<\/pre>/s;
foreach my $line (split /\n/, $block){
my @values = split /\t/, $line;
next if ($values[3] eq "Expert");
if (($values[1] =~ /$org/) || ($org =~ /$values[1]/) && (! defined $aliases->{$values[4]}) ){
$aliases->{$values[4]} = $values[0];
}
}
}
return $aliases;
}
sub get_db_aliases {
my ($ids,$fig,$db,$cgi,$returnType) = @_;
my $db_array;
my $all_aliases = $fig->feature_aliases_bulk($ids);
foreach my $id (@$ids){
# my @all_aliases = grep { $_ ne $id and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($id);
my $id_org = $fig->org_of($id);
foreach my $alias (@{$$all_aliases{$id}}){
# foreach my $alias (@all_aliases){
my $id_db = &Observation::get_database($alias);
next if ( ($id_db ne $db) && ($db ne 'all') );
next if ($aliases->{$id}->{$db});
my $alias_org = $fig->org_of($alias);
# if (($id ne $peg) && ( ($alias_org =~ /$id_org/) || ($id_org =~ /$alias_org/)) ) {
#push(@funcs, [$id,$id_db,$tmp]);
$aliases->{$id}->{$id_db} = &HTML::set_prot_links($cgi,$alias);
# }
}
if (!defined( $aliases->{$id}->{$db})){
$aliases->{$id}->{$db} = " ";
}
#push (@$db_array, {'data'=> $aliases->{$id}->{$db},'highlight'=>"#ffffff"});
push (@$db_array, $aliases->{$id}->{$db});
}
if ($returnType eq 'hash') { return $aliases; }
elsif ($returnType eq 'array') { return $db_array; }
}
sub html_enc { $_ = $_[0]; s/\&/&/g; s/\>/>/g; s/\</</g; $_ }
sub color {
my ($evalue) = @_;
my $palette = WebColors::get_palette('vitamins');
my $color;
if ($evalue <= 1e-170){ $color = $palette->[0]; }
elsif (($evalue <= 1e-120) && ($evalue > 1e-170)){ $color = $palette->[1]; }
elsif (($evalue <= 1e-90) && ($evalue > 1e-120)){ $color = $palette->[2]; }
elsif (($evalue <= 1e-70) && ($evalue > 1e-90)){ $color = $palette->[3]; }
elsif (($evalue <= 1e-40) && ($evalue > 1e-70)){ $color = $palette->[4]; }
elsif (($evalue <= 1e-20) && ($evalue > 1e-40)){ $color = $palette->[5]; }
elsif (($evalue <= 1e-5) && ($evalue > 1e-20)){ $color = $palette->[6]; }
elsif (($evalue <= 1) && ($evalue > 1e-5)){ $color = $palette->[7]; }
elsif (($evalue <= 10) && ($evalue > 1)){ $color = $palette->[8]; }
else{ $color = $palette->[9]; }
return ($color);
}
############################
package Observation::Cluster;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{context} = $dataset->{'context'};
bless($self,$class);
return $self;
}
sub display {
my ($self,$gd,$selected_taxonomies,$taxes,$sims_array,$fig) = @_;
$taxes = $fig->taxonomy_list();
my $fid = $self->fig_id;
my $compare_or_coupling = $self->context;
my $gd_window_size = $gd->window_size;
my $range = $gd_window_size;
my $all_regions = [];
my $gene_associations={};
#get the organism genome
my $target_genome = $fig->genome_of($fid);
$gene_associations->{$fid}->{"organism"} = $target_genome;
$gene_associations->{$fid}->{"main_gene"} = $fid;
$gene_associations->{$fid}->{"reverse_flag"} = 0;
# get location of the gene
my $data = $fig->feature_location($fid);
my ($contig, $beg, $end);
my %reverse_flag;
if ($data =~ /(.*)_(\d+)_(\d+)$/){
$contig = $1;
$beg = $2;
$end = $3;
}
my $offset;
my ($region_start, $region_end);
if ($beg < $end)
{
$region_start = $beg - ($range);
$region_end = $end+ ($range);
$offset = ($2+(($3-$2)/2))-($gd_window_size/2);
}
else
{
$region_start = $end-($range);
$region_end = $beg+($range);
$offset = ($3+(($2-$3)/2))-($gd_window_size/2);
$reverse_flag{$target_genome} = $fid;
$gene_associations->{$fid}->{"reverse_flag"} = 1;
}
# call genes in region
my ($target_gene_features, $reg_beg, $reg_end) = $fig->genes_in_region($target_genome, $contig, $region_start, $region_end);
#foreach my $feat (@$target_gene_features){
# push (@$all_regions, $feat) if ($feat =~ /peg/);
#}
push(@$all_regions,$target_gene_features);
my (@start_array_region);
push (@start_array_region, $offset);
my %all_genes;
my %all_genomes;
foreach my $feature (@$target_gene_features){
#if ($feature =~ /peg/){
$all_genes{$feature} = $fid; $gene_associations->{$feature}->{"main_gene"}=$fid;
#}
}
my @selected_sims;
if ($compare_or_coupling eq "sims"){
# get the selected boxes
my @selected_taxonomy = @$selected_taxonomies;
# get the similarities and store only the ones that match the lineages selected
if (@selected_taxonomy > 0){
foreach my $sim (@$sims_array){
next if ($sim->class ne "SIM");
next if ($sim->acc !~ /fig\|/);
#my $genome = $fig->genome_of($sim->[1]);
my $genome = $fig->genome_of($sim->acc);
#my ($genome1) = ($genome) =~ /(.*)\./;
my $lineage = $taxes->{$genome};
#my $lineage = $fig->taxonomy_of($fig->genome_of($genome));
foreach my $taxon(@selected_taxonomy){
if ($lineage =~ /$taxon/){
#push (@selected_sims, $sim->[1]);
push (@selected_sims, $sim->acc);
}
}
}
}
else{
my $simcount = 0;
foreach my $sim (@$sims_array){
next if ($sim->class ne "SIM");
next if ($sim->acc !~ /fig\|/);
push (@selected_sims, $sim->acc);
$simcount++;
last if ($simcount > 4);
}
}
my %saw;
@selected_sims = grep(!$saw{$_}++, @selected_sims);
# get the gene context for the sorted matches
foreach my $sim_fid(@selected_sims){
#get the organism genome
my $sim_genome = $fig->genome_of($sim_fid);
$gene_associations->{$sim_fid}->{"organism"} = $sim_genome;
$gene_associations->{$sim_fid}->{"main_gene"} = $sim_fid;
$gene_associations->{$sim_fid}->{"reverse_flag"} = 0;
# get location of the gene
my $data = $fig->feature_location($sim_fid);
my ($contig, $beg, $end);
if ($data =~ /(.*)_(\d+)_(\d+)$/){
$contig = $1;
$beg = $2;
$end = $3;
}
my $offset;
my ($region_start, $region_end);
if ($beg < $end)
{
$region_start = $beg - ($range/2);
$region_end = $end+($range/2);
$offset = ($beg+(($end-$beg)/2))-($gd_window_size/2);
}
else
{
$region_start = $end-($range/2);
$region_end = $beg+($range/2);
$offset = ($end+(($beg-$end)/2))-($gd_window_size/2);
$reverse_flag{$sim_genome} = $sim_fid;
$gene_associations->{$sim_fid}->{"reverse_flag"} = 1;
}
# call genes in region
my ($sim_gene_features, $reg_beg, $reg_end) = $fig->genes_in_region($sim_genome, $contig, $region_start, $region_end);
push(@$all_regions,$sim_gene_features);
push (@start_array_region, $offset);
foreach my $feature (@$sim_gene_features){ $all_genes{$feature} = $sim_fid;$gene_associations->{$feature}->{"main_gene"}=$sim_fid;}
$all_genomes{$sim_genome} = 1;
}
}
#print STDERR "START CLUSTER OF GENES IN COMP REGION: " . `date`;
# cluster the genes
my @all_pegs = keys %all_genes;
my $color_sets = &cluster_genes($fig,\@all_pegs,$fid);
#print STDERR "END CLUSTER OF GENES IN COMP REGION: ". `date`;
my %in_subs = $fig->subsystems_for_pegs(\@all_pegs,1);
foreach my $region (@$all_regions){
my $sample_peg = @$region[0];
my $region_genome = $fig->genome_of($sample_peg);
my $region_gs = $fig->genus_species($region_genome);
my $abbrev_name = $fig->abbrev($region_gs);
#my ($genome1) = ($region_genome) =~ /(.*?)\./;
my $lineage = $taxes->{$region_genome};
#my $lineage = $fig->taxonomy_of($region_genome);
#$region_gs .= "Lineage:$lineage";
my $line_config = { 'title' => $region_gs,
'short_title' => $abbrev_name,
'basepair_offset' => '0'
};
my $offsetting = shift @start_array_region;
my $second_line_config = { 'title' => "$lineage",
'short_title' => "",
'basepair_offset' => '0',
'no_middle_line' => '1'
};
my $line_data = [];
my $second_line_data = [];
# initialize variables to check for overlap in genes
my ($prev_start, $prev_stop, $prev_fig, $second_line_flag);
my $major_line_flag = 0;
my $prev_second_flag = 0;
foreach my $fid1 (@$region){
$second_line_flag = 0;
my $element_hash;
my $links_list = [];
my $descriptions = [];
my $color = $color_sets->{$fid1};
# get subsystem information
my $function = $fig->function_of($fid1);
my $url_link = "?page=Annotation&feature=".$fid1;
my $link;
$link = {"link_title" => $fid1,
"link" => $url_link};
push(@$links_list,$link);
my @subs = @{$in_subs{$fid1}} if (defined $in_subs{$fid1});
my @subsystems;
foreach my $array (@subs){
my $subsystem = $$array[0];
my $ss = $subsystem;
$ss =~ s/_/ /ig;
push (@subsystems, $ss);
my $link;
$link = {"link" => "?page=Subsystems&subsystem=$subsystem",
"link_title" => $ss};
push(@$links_list,$link);
}
if ($fid1 eq $fid){
my $link;
$link = {"link_title" => "Annotate this sequence",
"link" => "$FIG_Config::cgi_url/seedviewer.cgi?page=Commentary"};
push (@$links_list,$link);
}
my $description_function;
$description_function = {"title" => "function",
"value" => $function};
push(@$descriptions,$description_function);
my $description_ss;
my $ss_string = join (", ", @subsystems);
$description_ss = {"title" => "subsystems",
"value" => $ss_string};
push(@$descriptions,$description_ss);
my $fid_location = $fig->feature_location($fid1);
if($fid_location =~/(.*)_(\d+)_(\d+)$/){
my($start,$stop);
$start = $2 - $offsetting;
$stop = $3 - $offsetting;
if ( (($prev_start) && ($prev_stop) ) &&
( ($start < $prev_start) || ($start < $prev_stop) ||
($stop < $prev_start) || ($stop < $prev_stop) )){
if (($second_line_flag == 0) && ($prev_second_flag == 0)) {
$second_line_flag = 1;
$major_line_flag = 1;
}
}
$prev_start = $start;
$prev_stop = $stop;
$prev_fig = $fid1;
if ((defined($reverse_flag{$region_genome})) && ($reverse_flag{$region_genome} eq $all_gnes{$fid1})){
$start = $gd_window_size - $start;
$stop = $gd_window_size - $stop;
}
my $title = $fid1;
if ($fid1 eq $fid){
$title = "My query gene: $fid1";
}
$element_hash = {
"title" => $title,
"start" => $start,
"end" => $stop,
"type"=> 'arrow',
"color"=> $color,
"zlayer" => "2",
"links_list" => $links_list,
"description" => $descriptions
};
# if there is an overlap, put into second line
if ($second_line_flag == 1){ push(@$second_line_data,$element_hash); $prev_second_flag = 1;}
else{ push(@$line_data,$element_hash); $prev_second_flag = 0;}
if ($fid1 eq $fid){
$element_hash = {
"title" => 'Query',
"start" => $start,
"end" => $stop,
"type"=> 'bigbox',
"color"=> $color,
"zlayer" => "1"
};
# if there is an overlap, put into second line
if ($second_line_flag == 1){ push(@$second_line_data,$element_hash); $prev_second_flag = 1;}
else{ push(@$line_data,$element_hash); $prev_second_flag = 0;}
}
}
}
$gd->add_line($line_data, $line_config);
$gd->add_line($second_line_data, $second_line_config); # if ($major_line_flag == 1);
}
return ($gd, \@selected_sims);
}
sub cluster_genes {
my($fig,$all_pegs,$peg) = @_;
my(%seen,$i,$j,$k,$x,$cluster,$conn,$pegI,$red_set);
my @color_sets = ();
$conn = &get_connections_by_similarity($fig,$all_pegs);
for ($i=0; ($i < @$all_pegs); $i++) {
if ($all_pegs->[$i] eq $peg) { $pegI = $i }
if (! $seen{$i}) {
$cluster = [$i];
$seen{$i} = 1;
for ($j=0; ($j < @$cluster); $j++) {
$x = $conn->{$cluster->[$j]};
foreach $k (@$x) {
if (! $seen{$k}) {
push(@$cluster,$k);
$seen{$k} = 1;
}
}
}
if ((@$cluster > 1) || ($cluster->[0] eq $pegI)) {
push(@color_sets,$cluster);
}
}
}
for ($i=0; ($i < @color_sets) && (! &in($pegI,$color_sets[$i])); $i++) {}
$red_set = $color_sets[$i];
splice(@color_sets,$i,1);
@color_sets = sort { @$b <=> @$a } @color_sets;
unshift(@color_sets,$red_set);
my $color_sets = {};
for ($i=0; ($i < @color_sets); $i++) {
foreach $x (@{$color_sets[$i]}) {
$color_sets->{$all_pegs->[$x]} = $i;
}
}
return $color_sets;
}
sub get_connections_by_similarity {
my($fig,$all_pegs) = @_;
my($i,$j,$tmp,$peg,%pos_of);
my($sim,%conn,$x,$y);
for ($i=0; ($i < @$all_pegs); $i++) {
$tmp = $fig->maps_to_id($all_pegs->[$i]);
push(@{$pos_of{$tmp}},$i);
if ($tmp ne $all_pegs->[$i]) {
push(@{$pos_of{$all_pegs->[$i]}},$i);
}
}
foreach $y (keys(%pos_of)) {
$x = $pos_of{$y};
for ($i=0; ($i < @$x); $i++) {
for ($j=$i+1; ($j < @$x); $j++) {
push(@{$conn{$x->[$i]}},$x->[$j]);
push(@{$conn{$x->[$j]}},$x->[$i]);
}
}
}
for ($i=0; ($i < @$all_pegs); $i++) {
foreach $sim ($fig->sims($all_pegs->[$i],500,10,"raw")) {
if (defined($x = $pos_of{$sim->id2})) {
foreach $y (@$x) {
push(@{$conn{$i}},$y);
}
}
}
}
return \%conn;
}
sub in {
my($x,$xL) = @_;
my($i);
for ($i=0; ($i < @$xL) && ($x != $xL->[$i]); $i++) {}
return ($i < @$xL);
}
#############################################
#############################################
package Observation::Commentary;
use base qw(Observation);
=head3 display_protein_commentary()
=cut
sub display_protein_commentary {
my ($self,$dataset,$mypeg,$fig) = @_;
my $all_rows = [];
my $content;
#my $fig = new FIG;
my $cgi = new CGI;
my $count = 0;
my $peg_array = [];
my ($evidence_column, $subsystems_column, %e_identical);
if (@$dataset != 1){
foreach my $thing (@$dataset){
if ($thing->class eq "SIM"){
push (@$peg_array, $thing->acc);
}
}
# get the column for the evidence codes
$evidence_column = &Observation::Sims::get_evidence_column($peg_array, undef, $fig, $cgi, 'hash');
# get the column for the subsystems
$subsystems_column = &Observation::Sims::get_subsystems_column($peg_array,$fig, $cgi, 'array');
# get essentially identical seqs
%e_identical = &Observation::Sims::get_essentially_identical($mypeg,$dataset,$fig);
}
else{
push (@$peg_array, @$dataset);
}
my $selected_sims = [];
foreach my $id (@$peg_array){
last if ($count > 10);
my $row_data = [];
my ($set, $org, $ss, $ev, $function, $function_cell, $id_cell);
if ($fig->org_of($id)){
$org = $fig->org_of($id);
}
else{
$org = "Data not available";
}
$function = $fig->function_of($id);
if ($mypeg ne $id){
$function_cell = "<input type='radio' name='function' id='$id' value='$function' onClick=\"clearText('setAnnotation');\"> $function";
$id_cell .= "<a href='?page=Annotation&feature=$id'>$id</a>"; # &HTML::set_prot_links($cgi,$id);
if (defined($e_identical{$id})) { $id_cell .= "*";}
}
else{
$function_cell = " $function";
$id_cell = "<input type='checkbox' name='peg' id='peg$count' value='$id' checked='true'>";
$id_cell .= "<a href='?page=Annotation&feature=$id'>$id</a>"; # &HTML::set_prot_links($cgi,$id);
}
push(@$row_data,$id_cell);
push(@$row_data,$org);
push(@$row_data, $subsystems_column->{$id}) if ($mypeg ne $id);
push(@$row_data, $evidence_column->{$id}) if ($mypeg ne $id);
push(@$row_data, $fig->translation_length($id));
push(@$row_data,$function_cell);
push(@$all_rows,$row_data);
push (@$selected_sims, $id);
$count++;
}
if ($count >0){
$content = $all_rows;
}
else{
$content = "<p>This PEG does not have enough similarities to change the commentary</p>";
}
return ($content,$selected_sims);
}
sub display_protein_history {
my ($self, $id,$fig) = @_;
my $all_rows = [];
my $content;
my $cgi = new CGI;
my $count = 0;
foreach my $feat ($fig->feature_annotations($id)){
my $row = [];
my $col1 = $feat->[2];
my $col2 = $feat->[1];
#my $text = "<pre>" . $feat->[3] . "<\pre>";
my $text = $feat->[3];
push (@$row, $col1);
push (@$row, $col2);
push (@$row, $text);
push (@$all_rows, $row);
$count++;
}
if ($count > 0){
$content = $all_rows;
}
else {
$content = "There is no history for this PEG";
}
return($content);
}
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