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Tripal 0.3b
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Tripal 0.3b
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Functions | |
| tripal_core_gff3_load_form () | |
| tripal_core_gff3_load_form_validate ($form, &$form_state) | |
| tripal_core_gff3_load_form_submit ($form, &$form_state) | |
| tripal_core_load_gff3 ($gff_file, $organism_id, $analysis_id, $add_only=0, $update=0, $refresh=0, $remove=0, $job=NULL) | |
| tripal_core_load_gff3_parents ($feature, $cvterm, $parents, &$gff_features, $organism_id, $fmin) | |
| tripal_core_load_gff3_dbxref ($feature, $dbxrefs) | |
| tripal_core_load_gff3_ontology ($feature, $dbxrefs) | |
| tripal_core_load_gff3_alias ($feature, $aliases) | |
| tripal_core_load_gff3_feature ($organism, $analysis_id, $cvterm, $uniquename, $name, $residues, $is_analysis='f', $is_obsolete='f', $add_only) | |
| tripal_core_load_gff3_featureloc ($feature, $organism, $landmark, $fmin, $fmax, $strand, $phase, $is_fmin_partial, $is_fmax_partial, $residue_info, $locgroup) | |
Provides gff3 loading functionality. Creates features based on their specification in a GFF3 file.
| tripal_core_gff3_load_form | ( | ) |
Definition at line 20 of file gff_loader.php.
References tripal_db_set_active().
| tripal_core_gff3_load_form_submit | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 168 of file gff_loader.php.
References $args, $user, and tripal_add_job().
| tripal_core_gff3_load_form_validate | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 136 of file gff_loader.php.
References $_SERVER.
| tripal_core_load_gff3 | ( | $ | gff_file, |
| $ | organism_id, | ||
| $ | analysis_id, | ||
| $ | add_only = 0, |
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| $ | update = 0, |
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| $ | refresh = 0, |
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| $ | remove = 0, |
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| $ | job = NULL |
||
| ) |
Definition at line 204 of file gff_loader.php.
References $_SERVER, $job, tripal_core_chado_select(), tripal_core_chado_update(), tripal_core_load_gff3_alias(), tripal_core_load_gff3_dbxref(), tripal_core_load_gff3_feature(), tripal_core_load_gff3_featureloc(), tripal_core_load_gff3_ontology(), tripal_core_load_gff3_parents(), tripal_db_set_active(), and tripal_job_set_progress().
| tripal_core_load_gff3_alias | ( | $ | feature, |
| $ | aliases | ||
| ) |
Definition at line 748 of file gff_loader.php.
References tripal_cv_obo_add_cv_term(), and tripal_cv_obo_quiterror().
Referenced by tripal_core_load_gff3().
| tripal_core_load_gff3_dbxref | ( | $ | feature, |
| $ | dbxrefs | ||
| ) |
Definition at line 600 of file gff_loader.php.
References $ret, tripal_core_chado_insert(), and tripal_core_chado_select().
Referenced by tripal_core_load_gff3().
| tripal_core_load_gff3_feature | ( | $ | organism, |
| $ | analysis_id, | ||
| $ | cvterm, | ||
| $ | uniquename, | ||
| $ | name, | ||
| $ | residues, | ||
| $ | is_analysis = 'f', |
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| $ | is_obsolete = 'f', |
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| $ | add_only | ||
| ) |
Definition at line 848 of file gff_loader.php.
References tripal_core_chado_insert(), and tripal_core_chado_select().
Referenced by tripal_core_load_gff3().
| tripal_core_load_gff3_featureloc | ( | $ | feature, |
| $ | organism, | ||
| $ | landmark, | ||
| $ | fmin, | ||
| $ | fmax, | ||
| $ | strand, | ||
| $ | phase, | ||
| $ | is_fmin_partial, | ||
| $ | is_fmax_partial, | ||
| $ | residue_info, | ||
| $ | locgroup | ||
| ) |
Definition at line 917 of file gff_loader.php.
Referenced by tripal_core_load_gff3().
| tripal_core_load_gff3_ontology | ( | $ | feature, |
| $ | dbxrefs | ||
| ) |
Definition at line 671 of file gff_loader.php.
References $ret, tripal_core_chado_insert(), and tripal_core_chado_select().
Referenced by tripal_core_load_gff3().
| tripal_core_load_gff3_parents | ( | $ | feature, |
| $ | cvterm, | ||
| $ | parents, | ||
| &$ | gff_features, | ||
| $ | organism_id, | ||
| $ | fmin | ||
| ) |
Definition at line 537 of file gff_loader.php.
Referenced by tripal_core_load_gff3().
1.7.4 
