Revision 1083804e
Added by Andreas Kohlbecker over 10 years ago
| 7.x/modules/cdm_dataportal/includes/occurrences.inc | ||
|---|---|---|
| 389 | 389 |
$groups = array(); |
| 390 | 390 |
|
| 391 | 391 |
// -- retrieve additional data if neesscary |
| 392 |
// TODO bellow call disabled since sequences are not yet supported,
|
|
| 392 |
// TODO below call disabled since sequences are not yet supported, |
|
| 393 | 393 |
// see #3347 (services and REST service controller for molecular classes implemented) |
| 394 | 394 |
// |
| 395 | 395 |
// cdm_load_annotations($sequence); |
| ... | ... | |
| 400 | 400 |
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
| 401 | 401 |
switch ($field) {
|
| 402 | 402 |
|
| 403 |
case 'genBankAccession';
|
|
| 403 |
case 'geneticAccessionNumber';
|
|
| 404 | 404 |
$dd_elements = array(); |
| 405 | 405 |
foreach ($value as $accession) {
|
| 406 | 406 |
if (isset($accession->uri) ){
|
| ... | ... | |
| 412 | 412 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 1); |
| 413 | 413 |
break; |
| 414 | 414 |
|
| 415 |
case 'length': |
|
| 416 |
@_description_list_group_add($groups, t('Sequence length'), $value , ' ' . t('Nucleotites'), 2);
|
|
| 417 |
break; |
|
| 418 | 415 |
|
| 419 |
case 'locus': |
|
| 416 |
case 'locus': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
|
| 420 | 417 |
if (isset($value->name)) {
|
| 421 | 418 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3); |
| 422 | 419 |
} |
| ... | ... | |
| 425 | 422 |
} |
| 426 | 423 |
break; |
| 427 | 424 |
|
| 428 |
case 'sequence':
|
|
| 425 |
case 'consensusSequence':
|
|
| 429 | 426 |
// format in genbank style, force linebreaks after each 70 nucleotites |
| 430 | 427 |
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and |
| 431 | 428 |
@_description_list_group_add( |
| ... | ... | |
| 433 | 430 |
cdm_occurrence_field_name_label($field), |
| 434 | 431 |
array( |
| 435 | 432 |
array( |
| 436 |
'#markup' => '<div>' . wordwrap($value, 70, '</br>', TRUE) . '</div>',
|
|
| 433 |
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb'). '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
|
| 437 | 434 |
'#wrapper_attributes' => array('class'=>'dna-sequence')
|
| 438 | 435 |
) |
| 439 | 436 |
), |
| 440 | 437 |
5); |
| 441 | 438 |
break; |
| 442 | 439 |
|
| 443 |
case 'dateSequenced': |
|
| 440 |
case 'dnaSample': // FIXME 3.3 implement |
|
| 441 |
break; |
|
| 442 |
case 'singleReads': // FIXME 3.3 implement |
|
| 443 |
break; |
|
| 444 |
case 'contigFile': // FIXME 3.3 implement - Media |
|
| 445 |
break; |
|
| 446 |
case 'pherograms': // FIXME 3.3 implement - Media |
|
| 447 |
break; |
|
| 448 |
case 'haplotype': // FIXME 3.3 implement |
|
| 449 |
break; |
|
| 450 |
case 'dateSequenced': // FIXME 3.3 now in SingelRead |
|
| 444 | 451 |
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
| 445 | 452 |
break; |
| 446 | 453 |
|
| 447 | 454 |
case 'barcode': // boolean |
| 448 | 455 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes': 'No', NULL, 7); |
| 449 | 456 |
break; |
| 457 |
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence |
|
| 458 |
break; |
|
| 450 | 459 |
|
| 451 | 460 |
case 'citation': |
| 452 | 461 |
@_description_list_group_add($groups, |
| ... | ... | |
| 515 | 524 |
|
| 516 | 525 |
return $sequence_elements; |
| 517 | 526 |
} |
| 527 |
|
|
| 528 |
|
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Also available in: Unified diff
showing consensusSequence and adding TODO comments - #3749 (Check if all molecular data is shown correctly in data portal)