Code Context $full_gene_info = $AnnotationModel->getFullGeneInfo($gene_id);
$this->GenomeBrowser->setController($controller);
$gene_id = 'CSS0041725'
$AnnotationModel = object(Annotation) {
name => 'Annotation'
useTable => 'annotation'
primaryKey => 'gene_id'
cacheQueries => false
cacheSources => false
belongsTo => array(
'AnnotSource' => array(
[maximum depth reached]
)
)
hasMany => array(
'GfDatum' => array(
[maximum depth reached]
)
)
useDbConfig => 'default'
id => false
data => array()
schemaName => 'db_plaza_public_dicots_05'
table => 'annotation'
validate => array()
validationErrors => array()
validationDomain => null
tablePrefix => ''
plugin => null
alias => 'Annotation'
tableToModel => array(
'annotation' => 'Annotation'
)
hasOne => array()
hasAndBelongsToMany => array()
actsAs => null
Behaviors => object(BehaviorCollection) {}
whitelist => array()
findQueryType => null
recursive => (int) 1
order => null
virtualFields => array()
__backAssociation => array()
__backInnerAssociation => array()
__backOriginalAssociation => array()
__backContainableAssociation => array()
__safeUpdateMode => false
useConsistentAfterFind => true
findMethods => array(
'all' => true,
'first' => true,
'count' => true,
'neighbors' => true,
'list' => true,
'threaded' => true
)
[protected] _schema => array(
'gene_id' => array(
[maximum depth reached]
),
'species' => array(
[maximum depth reached]
),
'transcript' => array(
[maximum depth reached]
),
'coord_cds' => array(
[maximum depth reached]
),
'start' => array(
[maximum depth reached]
),
'stop' => array(
[maximum depth reached]
),
'coord_transcript' => array(
[maximum depth reached]
),
'seq' => array(
[maximum depth reached]
),
'strand' => array(
[maximum depth reached]
),
'chr' => array(
[maximum depth reached]
),
'type' => array(
[maximum depth reached]
),
'check_transcript' => array(
[maximum depth reached]
),
'check_protein' => array(
[maximum depth reached]
),
'transl_table' => array(
[maximum depth reached]
)
)
[protected] _associationKeys => array(
'belongsTo' => array(
[maximum depth reached]
),
'hasOne' => array(
[maximum depth reached]
),
'hasMany' => array(
[maximum depth reached]
),
'hasAndBelongsToMany' => array(
[maximum depth reached]
)
)
[protected] _associations => array(
(int) 0 => 'belongsTo',
(int) 1 => 'hasOne',
(int) 2 => 'hasMany',
(int) 3 => 'hasAndBelongsToMany'
)
[protected] _insertID => null
[protected] _sourceConfigured => true
[protected] _eventManager => object(CakeEventManager) {}
[protected] _validator => null
}
$MsaModel = object(Msa) {
name => 'Msa'
useTable => 'msa'
primaryKey => 'msa_id'
useDbConfig => 'default'
id => null
data => array()
schemaName => null
table => 'msa'
validate => array()
validationErrors => array()
validationDomain => null
plugin => null
alias => 'Msa'
tableToModel => array(
'msa' => 'Msa'
)
cacheQueries => false
belongsTo => array()
hasOne => array()
hasMany => array()
hasAndBelongsToMany => array()
actsAs => null
Behaviors => object(BehaviorCollection) {}
whitelist => array()
cacheSources => true
findQueryType => null
recursive => (int) 1
order => null
virtualFields => array()
__backAssociation => array()
__backInnerAssociation => array()
__backOriginalAssociation => array()
__backContainableAssociation => array()
__safeUpdateMode => false
useConsistentAfterFind => true
findMethods => array(
'all' => true,
'first' => true,
'count' => true,
'neighbors' => true,
'list' => true,
'threaded' => true
)
[protected] _schema => null
[protected] _associationKeys => array(
'belongsTo' => array(
[maximum depth reached]
),
'hasOne' => array(
[maximum depth reached]
),
'hasMany' => array(
[maximum depth reached]
),
'hasAndBelongsToMany' => array(
[maximum depth reached]
)
)
[protected] _associations => array(
(int) 0 => 'belongsTo',
(int) 1 => 'hasOne',
(int) 2 => 'hasMany',
(int) 3 => 'hasAndBelongsToMany'
)
[protected] _insertID => null
[protected] _sourceConfigured => false
[protected] _eventManager => null
[protected] _validator => null
}
$TreesModel = object(Trees) {
name => 'Trees'
useTable => 'trees'
useDbConfig => 'default'
id => null
data => array()
schemaName => null
table => 'trees'
primaryKey => 'id'
validate => array()
validationErrors => array()
validationDomain => null
plugin => null
alias => 'Trees'
tableToModel => array(
'trees' => 'Trees'
)
cacheQueries => false
belongsTo => array()
hasOne => array()
hasMany => array()
hasAndBelongsToMany => array()
actsAs => null
Behaviors => object(BehaviorCollection) {}
whitelist => array()
cacheSources => true
findQueryType => null
recursive => (int) 1
order => null
virtualFields => array()
__backAssociation => array()
__backInnerAssociation => array()
__backOriginalAssociation => array()
__backContainableAssociation => array()
__safeUpdateMode => false
useConsistentAfterFind => true
findMethods => array(
'all' => true,
'first' => true,
'count' => true,
'neighbors' => true,
'list' => true,
'threaded' => true
)
[protected] _schema => null
[protected] _associationKeys => array(
'belongsTo' => array(
[maximum depth reached]
),
'hasOne' => array(
[maximum depth reached]
),
'hasMany' => array(
[maximum depth reached]
),
'hasAndBelongsToMany' => array(
[maximum depth reached]
)
)
[protected] _associations => array(
(int) 0 => 'belongsTo',
(int) 1 => 'hasOne',
(int) 2 => 'hasMany',
(int) 3 => 'hasAndBelongsToMany'
)
[protected] _insertID => null
[protected] _sourceConfigured => false
[protected] _eventManager => null
[protected] _validator => null
}
$gene_families_info = array(
'HOMFAM' => array(
'gf_id' => 'HOM05D000834',
'order' => '1',
'is_valid' => true,
'info' => array(
'name' => 'Homologous gene family'
),
'profile' => array(
'num_genes' => '714',
'num_species' => '100'
)
),
'ORTHOFAM' => array(
'gf_id' => 'ORTHO05D000909',
'order' => '2',
'is_valid' => true,
'info' => array(
'name' => 'Orthologous gene family'
),
'profile' => array(
'num_genes' => '559',
'num_species' => '99'
)
)
)
$default_hom_gf_type_id = 'HOMFAM'
$full_gene_info = array(
'gene_id' => 'CSS0041725',
'species' => 'camsi',
'transcript' => 'CSS0041725.1',
'coord_cds' => 'join(326375..326921,327006..327114,327603..327853,327917..328323)',
'start' => '326375',
'stop' => '328323',
'coord_transcript' => 'join(326375..326921,327006..327114,327603..327853,327917..328323)',
'seq' => 'ATGGGTAGTCTCAAAGCTGACCCTGAACTCGAAAATGGTTCAACCTCAATGTTGAACTTGAACCCACTAGACCCTGATGAATTCAGGAGGCAAGCCCATAAGATGGTAGATTTTCTAGCTGATTACCACCAAAACATTGAAAAATACCCGGTTCGAAGCCAAGTCGAGCCGGGTTATCTCTCAAAATGTCTTCCTGGGTCTGCTCCGTATGACCCAGAACCAATAGAGAAAATTCTCTATGATGTGGAGAGGCATATTATCCCTGGTATCACACATTGGCAAAGTCCTAACCACTTTGCTTTTTTCCCATCAAGTGGAAGCATTACCGGGTTCCTCGGAGAAATGCTTAGCACCGGCTTTAATGTGGTCGGTTTTAATTGGATGTCATCACCTGTGGCAACTGAACTAGAAAGCATTGTCATGGATTGGCTTGGGAAAATGCTTCAACTTCCCAACTCTTTTCTTTTCTCCGGTGGTGGTGGTGGTGTGTTACAGGGAACCACTTGTGAGGCCGTTTTATGTACTCTAGCCACGGCGAGAGATCATTCCAGAATCGCTGGAATCAACCTAGATAATTTCCGAGCCATCACAACCACAAAAGCTACTGCATTGGGGTTATCTCTGAACTCACTTGAATCAGCGATAGTGTCGGATGTACCACTATGTGATGTTGCTAAACGGTACAATATGTGGGTCCACGTGGACGCTGCATACGCAGGAAGTGCATGCATATGCCAAGAATTCCGACATTTCATTGATGGTGTTGAGGATGCAAACTCATTTAGTCTCAATGCACACAAGTGGTTCTTCACTAACTTGGATTGTTGCTGTCTTTGGGTTAAAGACCCAAATGCCCTCATCAAAGCTCTATCAACAAGCACACCTGAGTACTTGAAAAACAAGGCTACAATGAAGCTATGGCTCGTTCTCCGAACCTACGGTGTGGTGAACCTGAGAAATTTCATTAGAGGACATGTCAATATGGCAAAGCATTTTGAAGGGCTTGTTGCAATGGACCATAGGTTTGAGCTTGTTGTCCCTAGAAACTTTGCTATGGTTTGTTTTAGGGTTTCACCATCCGCCCTTCGTGTTCATCGCGAGCCGACCGATGAAAATTGTGTGAAAAAATTCAATAGTAAGTTGCTGGAGTCCATCAATTCATTAGGACGCATATACATGACTCATGCTGTGGTGGAAGGAGTGTATGTGATTAGATTTGCTGTGGGTGCAAGTCTTACTAACTATCAACATGTGAACATGGCTTGGAAGGTGGTCCAGACGTTGAGATCCTCTAGAGTGTTAATGGTAGAGTGA',
'strand' => '+',
'chr' => 'Contig859',
'type' => 'coding',
'check_transcript' => 'eq',
'check_protein' => 'eq',
'transl_table' => '1'
)
DataUtilsComponent::getSidebarToolsInfo() - APP/Controller/Component/DataUtilsComponent.php, line 65
AppController::beforeRender() - APP/Controller/AppController.php, line 94
CakeEventManager::dispatch() - CORE/Cake/Event/CakeEventManager.php, line 243
Controller::render() - CORE/Cake/Controller/Controller.php, line 936
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 151