Lines Matching refs:already_processed
419 already_processed = []
420 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Phyloxml')
428 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Phyloxml'): argument
445 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
465 def buildAttributes(self, node, attrs, already_processed): argument
558 already_processed = []
559 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Phylogeny')
567 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Phylogeny'… argument
568 if self.rerootable is not None and 'rerootable' not in already_processed:
569 already_processed.append('rerootable')
571 if self.branch_length_unit is not None and 'branch_length_unit' not in already_processed:
572 already_processed.append('branch_length_unit')
574 if self.type_ is not None and 'type_' not in already_processed:
575 already_processed.append('type_')
577 if self.rooted is not None and 'rooted' not in already_processed:
578 already_processed.append('rooted')
622 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
623 if self.rerootable is not None and 'rerootable' not in already_processed:
624 already_processed.append('rerootable')
627 if self.branch_length_unit is not None and 'branch_length_unit' not in already_processed:
628 already_processed.append('branch_length_unit')
631 if self.type_ is not None and 'type_' not in already_processed:
632 already_processed.append('type_')
635 if self.rooted is not None and 'rooted' not in already_processed:
636 already_processed.append('rooted')
714 def buildAttributes(self, node, attrs, already_processed): argument
716 if value is not None and 'rerootable' not in already_processed:
717 already_processed.append('rerootable')
725 if value is not None and 'branch_length_unit' not in already_processed:
726 already_processed.append('branch_length_unit')
730 if value is not None and 'type' not in already_processed:
731 already_processed.append('type')
735 if value is not None and 'rooted' not in already_processed:
736 already_processed.append('rooted')
897 already_processed = []
898 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Clade')
906 def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Clade'): argument
907 if self.id_source is not None and 'id_source' not in already_processed:
908 already_processed.append('id_source')
910 if self.branch_length_attr is not None and 'branch_length_attr' not in already_processed:
911 already_processed.append('branch_length_attr')
973 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
974 if self.id_source is not None and 'id_source' not in already_processed:
975 already_processed.append('id_source')
978 if self.branch_length_attr is not None and 'branch_length_attr' not in already_processed:
979 already_processed.append('branch_length_attr')
1111 def buildAttributes(self, node, attrs, already_processed): argument
1113 if value is not None and 'id_source' not in already_processed:
1114 already_processed.append('id_source')
1117 if value is not None and 'branch_length_attr' not in already_processed:
1118 already_processed.append('branch_length_attr')
1259 already_processed = []
1260 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Taxonomy')
1268 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Taxonomy'): argument
1269 if self.id_source is not None and 'id_source' not in already_processed:
1270 already_processed.append('id_source')
1314 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
1315 if self.id_source is not None and 'id_source' not in already_processed:
1316 already_processed.append('id_source')
1367 def buildAttributes(self, node, attrs, already_processed): argument
1369 if value is not None and 'id_source' not in already_processed:
1370 already_processed.append('id_source')
1482 already_processed = []
1483 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Sequence')
1491 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Sequence'): argument
1492 if self.id_source is not None and 'id_source' not in already_processed:
1493 already_processed.append('id_source')
1495 if self.id_ref is not None and 'id_ref' not in already_processed:
1496 already_processed.append('id_ref')
1498 if self.type_ is not None and 'type_' not in already_processed:
1499 already_processed.append('type_')
1540 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
1541 if self.id_source is not None and 'id_source' not in already_processed:
1542 already_processed.append('id_source')
1545 if self.id_ref is not None and 'id_ref' not in already_processed:
1546 already_processed.append('id_ref')
1549 if self.type_ is not None and 'type_' not in already_processed:
1550 already_processed.append('type_')
1604 def buildAttributes(self, node, attrs, already_processed): argument
1606 if value is not None and 'id_source' not in already_processed:
1607 already_processed.append('id_source')
1610 if value is not None and 'id_ref' not in already_processed:
1611 already_processed.append('id_ref')
1614 if value is not None and 'type' not in already_processed:
1615 already_processed.append('type')
1682 already_processed = []
1683 self.exportAttributes(outfile, level, already_processed, namespace_, name_='MolSeq')
1691 … def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='MolSeq'): argument
1692 if self.is_aligned is not None and 'is_aligned' not in already_processed:
1693 already_processed.append('is_aligned')
1711 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
1712 if self.is_aligned is not None and 'is_aligned' not in already_processed:
1713 already_processed.append('is_aligned')
1724 def buildAttributes(self, node, attrs, already_processed): argument
1726 if value is not None and 'is_aligned' not in already_processed:
1727 already_processed.append('is_aligned')
1761 already_processed = []
1762 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Accession')
1770 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Accession'… argument
1771 if self.source is not None and 'source' not in already_processed:
1772 already_processed.append('source')
1790 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
1791 if self.source is not None and 'source' not in already_processed:
1792 already_processed.append('source')
1803 def buildAttributes(self, node, attrs, already_processed): argument
1805 if value is not None and 'source' not in already_processed:
1806 already_processed.append('source')
1840 already_processed = []
1841 … self.exportAttributes(outfile, level, already_processed, namespace_, name_='DomainArchitecture')
1849 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='DomainArch… argument
1850 if self.length is not None and 'length' not in already_processed:
1851 already_processed.append('length')
1868 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
1869 if self.length is not None and 'length' not in already_processed:
1870 already_processed.append('length')
1891 def buildAttributes(self, node, attrs, already_processed): argument
1893 if value is not None and 'length' not in already_processed:
1894 already_processed.append('length')
1940 already_processed = []
1941 self.exportAttributes(outfile, level, already_processed, namespace_, name_='ProteinDomain')
1949 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='ProteinDom… argument
1950 if self.to is not None and 'to' not in already_processed:
1951 already_processed.append('to')
1953 if self.confidence is not None and 'confidence' not in already_processed:
1954 already_processed.append('confidence')
1956 if self.fromxx is not None and 'fromxx' not in already_processed:
1957 already_processed.append('fromxx')
1959 if self.id is not None and 'id' not in already_processed:
1960 already_processed.append('id')
1978 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
1979 if self.to is not None and 'to' not in already_processed:
1980 already_processed.append('to')
1983 if self.confidence is not None and 'confidence' not in already_processed:
1984 already_processed.append('confidence')
1987 if self.fromxx is not None and 'fromxx' not in already_processed:
1988 already_processed.append('fromxx')
1991 if self.id is not None and 'id' not in already_processed:
1992 already_processed.append('id')
2003 def buildAttributes(self, node, attrs, already_processed): argument
2005 if value is not None and 'to' not in already_processed:
2006 already_processed.append('to')
2014 if value is not None and 'confidence' not in already_processed:
2015 already_processed.append('confidence')
2021 if value is not None and 'from' not in already_processed:
2022 already_processed.append('from')
2030 if value is not None and 'id' not in already_processed:
2031 already_processed.append('id')
2071 already_processed = []
2072 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Events')
2080 … def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Events'): argument
2113 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
2139 def buildAttributes(self, node, attrs, already_processed): argument
2227 already_processed = []
2228 … self.exportAttributes(outfile, level, already_processed, namespace_, name_='BinaryCharacters')
2236 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='BinaryChar… argument
2237 if self.lost_count is not None and 'lost_count' not in already_processed:
2238 already_processed.append('lost_count')
2240 if self.absent_count is not None and 'absent_count' not in already_processed:
2241 already_processed.append('absent_count')
2243 if self.present_count is not None and 'present_count' not in already_processed:
2244 already_processed.append('present_count')
2246 if self.type_ is not None and 'type_' not in already_processed:
2247 already_processed.append('type_')
2249 if self.gained_count is not None and 'gained_count' not in already_processed:
2250 already_processed.append('gained_count')
2276 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
2277 if self.lost_count is not None and 'lost_count' not in already_processed:
2278 already_processed.append('lost_count')
2281 if self.absent_count is not None and 'absent_count' not in already_processed:
2282 already_processed.append('absent_count')
2285 if self.present_count is not None and 'present_count' not in already_processed:
2286 already_processed.append('present_count')
2289 if self.type_ is not None and 'type_' not in already_processed:
2290 already_processed.append('type_')
2293 if self.gained_count is not None and 'gained_count' not in already_processed:
2294 already_processed.append('gained_count')
2327 def buildAttributes(self, node, attrs, already_processed): argument
2329 if value is not None and 'lost_count' not in already_processed:
2330 already_processed.append('lost_count')
2338 if value is not None and 'absent_count' not in already_processed:
2339 already_processed.append('absent_count')
2347 if value is not None and 'present_count' not in already_processed:
2348 already_processed.append('present_count')
2356 if value is not None and 'type' not in already_processed:
2357 already_processed.append('type')
2361 if value is not None and 'gained_count' not in already_processed:
2362 already_processed.append('gained_count')
2410 already_processed = []
2411 … self.exportAttributes(outfile, level, already_processed, namespace_, name_='BinaryCharacterList')
2419 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='BinaryChar… argument
2437 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
2454 def buildAttributes(self, node, attrs, already_processed): argument
2487 already_processed = []
2488 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Reference')
2496 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Reference'… argument
2497 if self.doi is not None and 'doi' not in already_processed:
2498 already_processed.append('doi')
2516 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
2517 if self.doi is not None and 'doi' not in already_processed:
2518 already_processed.append('doi')
2530 def buildAttributes(self, node, attrs, already_processed): argument
2532 if value is not None and 'doi' not in already_processed:
2533 already_processed.append('doi')
2597 already_processed = []
2598 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Annotation')
2606 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Annotation… argument
2607 if self.source is not None and 'source' not in already_processed:
2608 already_processed.append('source')
2610 if self.type_ is not None and 'type_' not in already_processed:
2611 already_processed.append('type_')
2613 if self.ref is not None and 'ref' not in already_processed:
2614 already_processed.append('ref')
2616 if self.evidence is not None and 'evidence' not in already_processed:
2617 already_processed.append('evidence')
2644 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
2645 if self.source is not None and 'source' not in already_processed:
2646 already_processed.append('source')
2649 if self.type_ is not None and 'type_' not in already_processed:
2650 already_processed.append('type_')
2653 if self.ref is not None and 'ref' not in already_processed:
2654 already_processed.append('ref')
2657 if self.evidence is not None and 'evidence' not in already_processed:
2658 already_processed.append('evidence')
2694 def buildAttributes(self, node, attrs, already_processed): argument
2696 if value is not None and 'source' not in already_processed:
2697 already_processed.append('source')
2701 if value is not None and 'type' not in already_processed:
2702 already_processed.append('type')
2706 if value is not None and 'ref' not in already_processed:
2707 already_processed.append('ref')
2710 if value is not None and 'evidence' not in already_processed:
2711 already_processed.append('evidence')
2790 already_processed = []
2791 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Property')
2797 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Property'): argument
2798 if self.datatype is not None and 'datatype' not in already_processed:
2799 already_processed.append('datatype')
2801 if self.id_ref is not None and 'id_ref' not in already_processed:
2802 already_processed.append('id_ref')
2804 if self.ref is not None and 'ref' not in already_processed:
2805 already_processed.append('ref')
2807 if self.applies_to is not None and 'applies_to' not in already_processed:
2808 already_processed.append('applies_to')
2810 if self.unit is not None and 'unit' not in already_processed:
2811 already_processed.append('unit')
2829 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
2830 if self.datatype is not None and 'datatype' not in already_processed:
2831 already_processed.append('datatype')
2834 if self.id_ref is not None and 'id_ref' not in already_processed:
2835 already_processed.append('id_ref')
2838 if self.ref is not None and 'ref' not in already_processed:
2839 already_processed.append('ref')
2842 if self.applies_to is not None and 'applies_to' not in already_processed:
2843 already_processed.append('applies_to')
2846 if self.unit is not None and 'unit' not in already_processed:
2847 already_processed.append('unit')
2862 def buildAttributes(self, node, attrs, already_processed): argument
2864 if value is not None and 'datatype' not in already_processed:
2865 already_processed.append('datatype')
2868 if value is not None and 'id_ref' not in already_processed:
2869 already_processed.append('id_ref')
2872 if value is not None and 'ref' not in already_processed:
2873 already_processed.append('ref')
2876 if value is not None and 'applies_to' not in already_processed:
2877 already_processed.append('applies_to')
2880 if value is not None and 'unit' not in already_processed:
2881 already_processed.append('unit')
2918 already_processed = []
2919 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Uri')
2927 def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Uri'): argument
2928 if self.type_ is not None and 'type_' not in already_processed:
2929 already_processed.append('type_')
2931 if self.desc is not None and 'desc' not in already_processed:
2932 already_processed.append('desc')
2950 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
2951 if self.type_ is not None and 'type_' not in already_processed:
2952 already_processed.append('type_')
2955 if self.desc is not None and 'desc' not in already_processed:
2956 already_processed.append('desc')
2967 def buildAttributes(self, node, attrs, already_processed): argument
2969 if value is not None and 'type' not in already_processed:
2970 already_processed.append('type')
2974 if value is not None and 'desc' not in already_processed:
2975 already_processed.append('desc')
3005 already_processed = []
3006 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Confidence')
3014 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Confidence… argument
3015 if self.type_ is not None and 'type_' not in already_processed:
3016 already_processed.append('type_')
3034 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3035 if self.type_ is not None and 'type_' not in already_processed:
3036 already_processed.append('type_')
3047 def buildAttributes(self, node, attrs, already_processed): argument
3049 if value is not None and 'type' not in already_processed:
3050 already_processed.append('type')
3079 already_processed = []
3080 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Id')
3088 def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Id'): argument
3089 if self.provider is not None and 'provider' not in already_processed:
3090 already_processed.append('provider')
3108 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3109 if self.provider is not None and 'provider' not in already_processed:
3110 already_processed.append('provider')
3121 def buildAttributes(self, node, attrs, already_processed): argument
3123 if value is not None and 'provider' not in already_processed:
3124 already_processed.append('provider')
3170 already_processed = []
3171 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Distribution')
3179 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Distributi… argument
3203 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3238 def buildAttributes(self, node, attrs, already_processed): argument
3291 already_processed = []
3292 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Point')
3300 def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Point'): argument
3301 if self.geodetic_datum is not None and 'geodetic_datum' not in already_processed:
3302 already_processed.append('geodetic_datum')
3304 if self.alt_unit is not None and 'alt_unit' not in already_processed:
3305 already_processed.append('alt_unit')
3331 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3332 if self.geodetic_datum is not None and 'geodetic_datum' not in already_processed:
3333 already_processed.append('geodetic_datum')
3336 if self.alt_unit is not None and 'alt_unit' not in already_processed:
3337 already_processed.append('alt_unit')
3355 def buildAttributes(self, node, attrs, already_processed): argument
3357 if value is not None and 'geodetic_datum' not in already_processed:
3358 already_processed.append('geodetic_datum')
3362 if value is not None and 'alt_unit' not in already_processed:
3363 already_processed.append('alt_unit')
3417 already_processed = []
3418 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Polygon')
3426 … def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Polygon'): argument
3443 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3463 def buildAttributes(self, node, attrs, already_processed): argument
3508 already_processed = []
3509 self.exportAttributes(outfile, level, already_processed, namespace_, name_='Date')
3517 def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Date'): argument
3518 if self.unit is not None and 'unit' not in already_processed:
3519 already_processed.append('unit')
3549 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3550 if self.unit is not None and 'unit' not in already_processed:
3551 already_processed.append('unit')
3572 def buildAttributes(self, node, attrs, already_processed): argument
3574 if value is not None and 'unit' not in already_processed:
3575 already_processed.append('unit')
3636 already_processed = []
3637 self.exportAttributes(outfile, level, already_processed, namespace_, name_='BranchColor')
3645 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='BranchColo… argument
3671 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3688 def buildAttributes(self, node, attrs, already_processed): argument
3749 already_processed = []
3750 … self.exportAttributes(outfile, level, already_processed, namespace_, name_='SequenceRelation')
3758 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='SequenceRe… argument
3759 if self.id_ref_0 is not None and 'id_ref_0' not in already_processed:
3760 already_processed.append('id_ref_0')
3762 if self.id_ref_1 is not None and 'id_ref_1' not in already_processed:
3763 already_processed.append('id_ref_1')
3765 if self.type_ is not None and 'type_' not in already_processed:
3766 already_processed.append('type_')
3768 if self.distance is not None and 'distance' not in already_processed:
3769 already_processed.append('distance')
3786 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3787 if self.id_ref_0 is not None and 'id_ref_0' not in already_processed:
3788 already_processed.append('id_ref_0')
3791 if self.id_ref_1 is not None and 'id_ref_1' not in already_processed:
3792 already_processed.append('id_ref_1')
3795 if self.type_ is not None and 'type_' not in already_processed:
3796 already_processed.append('type_')
3799 if self.distance is not None and 'distance' not in already_processed:
3800 already_processed.append('distance')
3815 def buildAttributes(self, node, attrs, already_processed): argument
3817 if value is not None and 'id_ref_0' not in already_processed:
3818 already_processed.append('id_ref_0')
3821 if value is not None and 'id_ref_1' not in already_processed:
3822 already_processed.append('id_ref_1')
3825 if value is not None and 'type' not in already_processed:
3826 already_processed.append('type')
3829 if value is not None and 'distance' not in already_processed:
3830 already_processed.append('distance')
3874 already_processed = []
3875 self.exportAttributes(outfile, level, already_processed, namespace_, name_='CladeRelation')
3883 …def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='CladeRelat… argument
3884 if self.id_ref_0 is not None and 'id_ref_0' not in already_processed:
3885 already_processed.append('id_ref_0')
3887 if self.id_ref_1 is not None and 'id_ref_1' not in already_processed:
3888 already_processed.append('id_ref_1')
3890 if self.type_ is not None and 'type_' not in already_processed:
3891 already_processed.append('type_')
3893 if self.distance is not None and 'distance' not in already_processed:
3894 already_processed.append('distance')
3911 def exportLiteralAttributes(self, outfile, level, already_processed, name_): argument
3912 if self.id_ref_0 is not None and 'id_ref_0' not in already_processed:
3913 already_processed.append('id_ref_0')
3916 if self.id_ref_1 is not None and 'id_ref_1' not in already_processed:
3917 already_processed.append('id_ref_1')
3920 if self.type_ is not None and 'type_' not in already_processed:
3921 already_processed.append('type_')
3924 if self.distance is not None and 'distance' not in already_processed:
3925 already_processed.append('distance')
3940 def buildAttributes(self, node, attrs, already_processed): argument
3942 if value is not None and 'id_ref_0' not in already_processed:
3943 already_processed.append('id_ref_0')
3946 if value is not None and 'id_ref_1' not in already_processed:
3947 already_processed.append('id_ref_1')
3950 if value is not None and 'type' not in already_processed:
3951 already_processed.append('type')
3955 if value is not None and 'distance' not in already_processed:
3956 already_processed.append('distance')