biointerchange 0.1.3 → 0.2.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.md +17 -0
- data/VERSION +1 -1
- data/generators/GOxrefify.rb +41 -0
- data/generators/rdfxml.rb +6 -4
- data/lib/biointerchange/core.rb +94 -20
- data/lib/biointerchange/genomics/gff3_feature_set.rb +11 -3
- data/lib/biointerchange/genomics/gff3_pragmas.rb +3 -3
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +217 -12
- data/lib/biointerchange/genomics/gff3_reader.rb +78 -20
- data/lib/biointerchange/genomics/gvf_reader.rb +9 -3
- data/lib/biointerchange/gff3o.rb +69 -55
- data/lib/biointerchange/goxref.rb +867 -0
- data/lib/biointerchange/gvf1o.rb +546 -82
- data/lib/biointerchange/textmining/text_mining_reader.rb +9 -0
- data/spec/gff3_rdfwriter_spec.rb +1 -1
- data/spec/gvf_rdfwriter_spec.rb +1 -1
- data/spec/text_mining_pdfx_xml_reader_spec.rb +3 -0
- data/spec/text_mining_pubannos_json_reader_spec.rb +4 -1
- data/supplemental/java/biointerchange/pom.xml +1 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +93 -125
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +304 -205
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4044 -4290
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +3 -3
- data/supplemental/python/biointerchange/gff3o.py +1 -89
- data/supplemental/python/biointerchange/gvf1o.py +129 -147
- data/supplemental/python/biointerchange/sio.py +817 -46
- data/supplemental/python/biointerchange/sofa.py +543 -543
- data/supplemental/python/setup.py +1 -1
- data/web/ontologies.html +1 -3
- metadata +7 -2
data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java
CHANGED
@@ -14,11 +14,18 @@ import org.apache.commons.collections.Predicate;
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public class GVF1O {
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/**
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-
*
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*
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* Either:
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* Strand of the feature.
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* (http://www.biointerchange.org/gvf1o#GVF1_0010)
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* Or:
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* Strand of the breakpoint.
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* (http://www.biointerchange.org/gvf1o#GVF1_0083)
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* Or:
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* Strand of a target -- if applicable.
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* (http://www.biointerchange.org/gvf1o#GVF1_0091)
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*/
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public static Resource strand() {
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return _namespace_GVF1O("GVF1_0010");
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public static Set<Resource> strand() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0010"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0083"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0091") }));
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}
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/**
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@@ -26,7 +33,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0012)
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*/
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public static Resource attributes() {
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return _namespace_GVF1O("GVF1_0012");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0012");
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}
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/**
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@@ -34,7 +41,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0014)
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*/
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public static Resource parent() {
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return _namespace_GVF1O("GVF1_0014");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0014");
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}
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/**
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@@ -42,7 +49,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0015)
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*/
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public static Resource contains() {
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return _namespace_GVF1O("GVF1_0015");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0015");
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}
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/**
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@@ -52,9 +59,12 @@ public class GVF1O {
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* Or:
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* FALDO "Region" instance replacement for a breakpoint"s start, stop, strand properties.
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* (http://www.biointerchange.org/gvf1o#GVF1_0079)
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* Or:
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* FALDO "Region" instance replacement for a target"s start, stop, strand properties.
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* (http://www.biointerchange.org/gvf1o#GVF1_0090)
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*/
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public static Set<Resource> region() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0021"), _namespace_GVF1O("GVF1_0079") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0021"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0079"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0090") }));
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}
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/**
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@@ -62,7 +72,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0023)
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*/
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public static Resource species() {
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return _namespace_GVF1O("GVF1_0023");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0023");
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}
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/**
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@@ -70,7 +80,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0034)
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*/
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public static Resource variant() {
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return _namespace_GVF1O("GVF1_0034");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0034");
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}
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/**
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@@ -78,7 +88,15 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0036)
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*/
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public static Resource individual() {
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return _namespace_GVF1O("GVF1_0036");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0036");
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}
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/**
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* Zygosity of a variant.
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* (http://www.biointerchange.org/gvf1o#GVF1_0038)
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*/
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public static Resource zygosity() {
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0038");
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}
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/**
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@@ -86,7 +104,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0041)
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*/
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public static Resource effect() {
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return _namespace_GVF1O("GVF1_0041");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0041");
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}
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/**
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@@ -94,7 +112,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0042)
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*/
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public static Resource sequence_variant() {
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return _namespace_GVF1O("GVF1_0042");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0042");
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}
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/**
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@@ -102,7 +120,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0043)
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*/
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public static Resource feature_type() {
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return _namespace_GVF1O("GVF1_0043");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0043");
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}
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/**
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@@ -110,7 +128,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0044)
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public static Resource feature_id() {
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return _namespace_GVF1O("GVF1_0044");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0044");
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}
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/**
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@@ -118,7 +136,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0046)
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*/
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public static Resource start_range() {
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return _namespace_GVF1O("GVF1_0046");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0046");
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}
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/**
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@@ -126,7 +144,7 @@ public class GVF1O {
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* (http://www.biointerchange.org/gvf1o#GVF1_0047)
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*/
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public static Resource end_range() {
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return _namespace_GVF1O("GVF1_0047");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0047");
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}
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/**
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* (http://www.biointerchange.org/gvf1o#GVF1_0051)
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*/
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public static Resource chromosome() {
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return _namespace_GVF1O("GVF1_0051");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0051");
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}
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/**
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* (http://www.biointerchange.org/gvf1o#GVF1_0053)
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*/
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public static Resource genotype() {
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return _namespace_GVF1O("GVF1_0053");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0053");
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0059)
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public static Set<Resource> feature_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0066"), _namespace_GVF1O("GVF1_0059") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0066"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0059") }));
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}
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/**
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* (http://www.biointerchange.org/gvf1o#GVF1_0065)
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public static Set<Resource> sequencedindividual_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0067"), _namespace_GVF1O("GVF1_0065") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0067"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0065") }));
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0063)
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public static Set<Resource> set_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0068"), _namespace_GVF1O("GVF1_0063") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0068"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0063") }));
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0060)
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public static Set<Resource> variant_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0069"), _namespace_GVF1O("GVF1_0060") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0069"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0060") }));
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0070)
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public static Resource effect_properties() {
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return _namespace_GVF1O("GVF1_0070");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0070");
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0071)
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public static Set<Resource> breakpoint_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0075"), _namespace_GVF1O("GVF1_0071") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0075"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0071") }));
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0078)
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public static Resource dbxref() {
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return _namespace_GVF1O("GVF1_0078");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0078");
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}
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/**
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* Potential source or destination of zero-length sequence alterations.
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* (http://www.biointerchange.org/gvf1o#GVF1_0080)
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*/
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public static Resource breakpoint() {
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0080");
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}
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/**
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* Either:
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* Properties that are directly associated with Target class instances.
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* (http://www.biointerchange.org/gvf1o#GVF1_0089)
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* Or:
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* Properties that are directly associated with Target class instances.
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* (http://www.biointerchange.org/gvf1o#GVF1_0092)
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*/
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public static Set<Resource> target_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0089"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0092") }));
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0072)
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public static Set<Resource> seqid() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0004"), _namespace_GVF1O("GVF1_0072") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0004"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0072") }));
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}
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/**
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* (http://www.biointerchange.org/gvf1o#GVF1_0005)
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*/
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public static Resource source() {
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return _namespace_GVF1O("GVF1_0005");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0005");
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}
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/**
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* (http://www.biointerchange.org/gvf1o#GVF1_0006)
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public static Resource type() {
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return _namespace_GVF1O("GVF1_0006");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0006");
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}
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0007"), _namespace_GVF1O("GVF1_0048"), _namespace_GVF1O("GVF1_0073") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0007"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0048"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0073"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0094") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0008"), _namespace_GVF1O("GVF1_0049"), _namespace_GVF1O("GVF1_0074") }));
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0008"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0049"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0074"), _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0095") }));
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return _namespace_GVF1O("GVF1_0009");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0009");
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return _namespace_GVF1O("GVF1_0013");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0013");
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public static Resource
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return _namespace_GVF1O("GVF1_0022");
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public static Resource gvf_version() {
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0022");
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}
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public static Resource build() {
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return _namespace_GVF1O("GVF1_0024");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0024");
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}
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public static Resource variant_seq() {
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return _namespace_GVF1O("GVF1_0025");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0025");
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public static Resource id() {
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return _namespace_GVF1O("GVF1_0026");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0026");
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* (http://www.biointerchange.org/gvf1o#GVF1_0027)
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*/
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public static Resource alias() {
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return _namespace_GVF1O("GVF1_0027");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0027");
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0029)
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*/
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public static Resource name() {
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-
return _namespace_GVF1O("GVF1_0029");
|
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0029");
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}
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* (http://www.biointerchange.org/gvf1o#GVF1_0030)
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*/
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public static Resource xref() {
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return _namespace_GVF1O("GVF1_0030");
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return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0030");
|
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|
}
|
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|
@@ -356,7 +400,7 @@ public class GVF1O {
|
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* (http://www.biointerchange.org/gvf1o#GVF1_0031)
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*/
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public static Resource reference_seq() {
|
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-
return _namespace_GVF1O("GVF1_0031");
|
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+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0031");
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}
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|
@@ -364,7 +408,7 @@ public class GVF1O {
|
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* (http://www.biointerchange.org/gvf1o#GVF1_0032)
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*/
|
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public static Resource variant_reads() {
|
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|
-
return _namespace_GVF1O("GVF1_0032");
|
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+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0032");
|
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|
}
|
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|
@@ -372,15 +416,7 @@ public class GVF1O {
|
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* (http://www.biointerchange.org/gvf1o#GVF1_0037)
|
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*/
|
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|
public static Resource total_reads() {
|
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-
return _namespace_GVF1O("GVF1_0037");
|
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|
-
}
|
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|
-
|
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|
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/**
|
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* Zygosity of a feature locus.
|
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|
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* (http://www.biointerchange.org/gvf1o#GVF1_0038)
|
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|
-
*/
|
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|
-
public static Resource zygosity() {
|
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|
-
return _namespace_GVF1O("GVF1_0038");
|
419
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0037");
|
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|
}
|
385
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|
|
386
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|
/**
|
@@ -388,7 +424,7 @@ public class GVF1O {
|
|
388
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|
* (http://www.biointerchange.org/gvf1o#GVF1_0039)
|
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|
*/
|
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|
public static Resource variant_freq() {
|
391
|
-
return _namespace_GVF1O("GVF1_0039");
|
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|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0039");
|
392
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|
}
|
393
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|
|
394
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|
/**
|
@@ -396,7 +432,7 @@ public class GVF1O {
|
|
396
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|
* (http://www.biointerchange.org/gvf1o#GVF1_0050)
|
397
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|
*/
|
398
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|
public static Resource phased() {
|
399
|
-
return _namespace_GVF1O("GVF1_0050");
|
435
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0050");
|
400
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|
}
|
401
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|
|
402
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|
/**
|
@@ -404,7 +440,7 @@ public class GVF1O {
|
|
404
440
|
* (http://www.biointerchange.org/gvf1o#GVF1_0054)
|
405
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|
*/
|
406
442
|
public static Resource variant_codon() {
|
407
|
-
return _namespace_GVF1O("GVF1_0054");
|
443
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0054");
|
408
444
|
}
|
409
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|
|
410
446
|
/**
|
@@ -412,7 +448,7 @@ public class GVF1O {
|
|
412
448
|
* (http://www.biointerchange.org/gvf1o#GVF1_0055)
|
413
449
|
*/
|
414
450
|
public static Resource reference_codon() {
|
415
|
-
return _namespace_GVF1O("GVF1_0055");
|
451
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0055");
|
416
452
|
}
|
417
453
|
|
418
454
|
/**
|
@@ -420,7 +456,7 @@ public class GVF1O {
|
|
420
456
|
* (http://www.biointerchange.org/gvf1o#GVF1_0056)
|
421
457
|
*/
|
422
458
|
public static Resource variant_aa() {
|
423
|
-
return _namespace_GVF1O("GVF1_0056");
|
459
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0056");
|
424
460
|
}
|
425
461
|
|
426
462
|
/**
|
@@ -428,7 +464,7 @@ public class GVF1O {
|
|
428
464
|
* (http://www.biointerchange.org/gvf1o#GVF1_0057)
|
429
465
|
*/
|
430
466
|
public static Resource reference_aa() {
|
431
|
-
return _namespace_GVF1O("GVF1_0057");
|
467
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0057");
|
432
468
|
}
|
433
469
|
|
434
470
|
/**
|
@@ -436,7 +472,7 @@ public class GVF1O {
|
|
436
472
|
* (http://www.biointerchange.org/gvf1o#GVF1_0061)
|
437
473
|
*/
|
438
474
|
public static Resource range_properties() {
|
439
|
-
return _namespace_GVF1O("GVF1_0061");
|
475
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0061");
|
440
476
|
}
|
441
477
|
|
442
478
|
/**
|
@@ -444,7 +480,7 @@ public class GVF1O {
|
|
444
480
|
* (http://www.biointerchange.org/gvf1o#GVF1_0062)
|
445
481
|
*/
|
446
482
|
public static Resource dbxref_properties() {
|
447
|
-
return _namespace_GVF1O("GVF1_0062");
|
483
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0062");
|
448
484
|
}
|
449
485
|
|
450
486
|
/**
|
@@ -452,7 +488,7 @@ public class GVF1O {
|
|
452
488
|
* (http://www.biointerchange.org/gvf1o#GVF1_0064)
|
453
489
|
*/
|
454
490
|
public static Resource attribute_properties() {
|
455
|
-
return _namespace_GVF1O("GVF1_0064");
|
491
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0064");
|
456
492
|
}
|
457
493
|
|
458
494
|
/**
|
@@ -460,7 +496,31 @@ public class GVF1O {
|
|
460
496
|
* (http://www.biointerchange.org/gvf1o#GVF1_0076)
|
461
497
|
*/
|
462
498
|
public static Resource a_context() {
|
463
|
-
return _namespace_GVF1O("GVF1_0076");
|
499
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0076");
|
500
|
+
}
|
501
|
+
|
502
|
+
/**
|
503
|
+
* Version of the GFF specification that defines the feature set contents apart from GVF related definitions.
|
504
|
+
* (http://www.biointerchange.org/gvf1o#GVF1_0081)
|
505
|
+
*/
|
506
|
+
public static Resource gff_version() {
|
507
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0081");
|
508
|
+
}
|
509
|
+
|
510
|
+
/**
|
511
|
+
* Creation date of the GVF file that this set stems from.
|
512
|
+
* (http://www.biointerchange.org/gvf1o#GVF1_0082)
|
513
|
+
*/
|
514
|
+
public static Resource file_date() {
|
515
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0082");
|
516
|
+
}
|
517
|
+
|
518
|
+
/**
|
519
|
+
* ID or accession of the target alignment.
|
520
|
+
* (http://www.biointerchange.org/gvf1o#GVF1_0093)
|
521
|
+
*/
|
522
|
+
public static Resource target_id() {
|
523
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0093");
|
464
524
|
}
|
465
525
|
|
466
526
|
/**
|
@@ -468,7 +528,7 @@ public class GVF1O {
|
|
468
528
|
* (http://www.biointerchange.org/gvf1o#GVF1_0001)
|
469
529
|
*/
|
470
530
|
public static Resource Set() {
|
471
|
-
return _namespace_GVF1O("GVF1_0001");
|
531
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0001");
|
472
532
|
}
|
473
533
|
|
474
534
|
/**
|
@@ -476,11 +536,11 @@ public class GVF1O {
|
|
476
536
|
* (http://www.biointerchange.org/gvf1o#GVF1_0002)
|
477
537
|
*/
|
478
538
|
public static Resource Feature() {
|
479
|
-
return _namespace_GVF1O("GVF1_0002");
|
539
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0002");
|
480
540
|
}
|
481
541
|
|
482
542
|
public static Resource Attribute() {
|
483
|
-
return _namespace_GVF1O("GVF1_0003");
|
543
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0003");
|
484
544
|
}
|
485
545
|
|
486
546
|
/**
|
@@ -488,7 +548,7 @@ public class GVF1O {
|
|
488
548
|
* (http://www.biointerchange.org/gvf1o#GVF1_0016)
|
489
549
|
*/
|
490
550
|
public static Resource Strand() {
|
491
|
-
return _namespace_GVF1O("GVF1_0016");
|
551
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0016");
|
492
552
|
}
|
493
553
|
|
494
554
|
/**
|
@@ -496,7 +556,7 @@ public class GVF1O {
|
|
496
556
|
* (http://www.biointerchange.org/gvf1o#GVF1_0028)
|
497
557
|
*/
|
498
558
|
public static Resource DBXRef() {
|
499
|
-
return _namespace_GVF1O("GVF1_0028");
|
559
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0028");
|
500
560
|
}
|
501
561
|
|
502
562
|
/**
|
@@ -504,7 +564,7 @@ public class GVF1O {
|
|
504
564
|
* (http://www.biointerchange.org/gvf1o#GVF1_0033)
|
505
565
|
*/
|
506
566
|
public static Resource Variant() {
|
507
|
-
return _namespace_GVF1O("GVF1_0033");
|
567
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0033");
|
508
568
|
}
|
509
569
|
|
510
570
|
/**
|
@@ -512,7 +572,7 @@ public class GVF1O {
|
|
512
572
|
* (http://www.biointerchange.org/gvf1o#GVF1_0035)
|
513
573
|
*/
|
514
574
|
public static Resource SequencedIndividual() {
|
515
|
-
return _namespace_GVF1O("GVF1_0035");
|
575
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0035");
|
516
576
|
}
|
517
577
|
|
518
578
|
/**
|
@@ -520,7 +580,7 @@ public class GVF1O {
|
|
520
580
|
* (http://www.biointerchange.org/gvf1o#GVF1_0040)
|
521
581
|
*/
|
522
582
|
public static Resource Effect() {
|
523
|
-
return _namespace_GVF1O("GVF1_0040");
|
583
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0040");
|
524
584
|
}
|
525
585
|
|
526
586
|
/**
|
@@ -528,7 +588,7 @@ public class GVF1O {
|
|
528
588
|
* (http://www.biointerchange.org/gvf1o#GVF1_0045)
|
529
589
|
*/
|
530
590
|
public static Resource Range() {
|
531
|
-
return _namespace_GVF1O("GVF1_0045");
|
591
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0045");
|
532
592
|
}
|
533
593
|
|
534
594
|
/**
|
@@ -536,7 +596,7 @@ public class GVF1O {
|
|
536
596
|
* (http://www.biointerchange.org/gvf1o#GVF1_0052)
|
537
597
|
*/
|
538
598
|
public static Resource Chromosome() {
|
539
|
-
return _namespace_GVF1O("GVF1_0052");
|
599
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0052");
|
540
600
|
}
|
541
601
|
|
542
602
|
/**
|
@@ -544,7 +604,23 @@ public class GVF1O {
|
|
544
604
|
* (http://www.biointerchange.org/gvf1o#GVF1_0058)
|
545
605
|
*/
|
546
606
|
public static Resource Breakpoint() {
|
547
|
-
return _namespace_GVF1O("GVF1_0058");
|
607
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0058");
|
608
|
+
}
|
609
|
+
|
610
|
+
/**
|
611
|
+
* Denotes the zygosity of alleles.
|
612
|
+
* (http://www.biointerchange.org/gvf1o#GVF1_0084)
|
613
|
+
*/
|
614
|
+
public static Resource Zygosity() {
|
615
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0084");
|
616
|
+
}
|
617
|
+
|
618
|
+
/**
|
619
|
+
* Indicates a feature"s "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
|
620
|
+
* (http://www.biointerchange.org/gvf1o#GVF1_0088)
|
621
|
+
*/
|
622
|
+
public static Resource Target() {
|
623
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0088");
|
548
624
|
}
|
549
625
|
|
550
626
|
/**
|
@@ -552,7 +628,7 @@ public class GVF1O {
|
|
552
628
|
* (http://www.biointerchange.org/gvf1o#GVF1_0017)
|
553
629
|
*/
|
554
630
|
public static Resource Positive() {
|
555
|
-
return _namespace_GVF1O("GVF1_0017");
|
631
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0017");
|
556
632
|
}
|
557
633
|
|
558
634
|
/**
|
@@ -560,7 +636,7 @@ public class GVF1O {
|
|
560
636
|
* (http://www.biointerchange.org/gvf1o#GVF1_0018)
|
561
637
|
*/
|
562
638
|
public static Resource Negative() {
|
563
|
-
return _namespace_GVF1O("GVF1_0018");
|
639
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0018");
|
564
640
|
}
|
565
641
|
|
566
642
|
/**
|
@@ -568,7 +644,7 @@ public class GVF1O {
|
|
568
644
|
* (http://www.biointerchange.org/gvf1o#GVF1_0019)
|
569
645
|
*/
|
570
646
|
public static Resource UnknownStrand() {
|
571
|
-
return _namespace_GVF1O("GVF1_0019");
|
647
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0019");
|
572
648
|
}
|
573
649
|
|
574
650
|
/**
|
@@ -576,7 +652,31 @@ public class GVF1O {
|
|
576
652
|
* (http://www.biointerchange.org/gvf1o#GVF1_0020)
|
577
653
|
*/
|
578
654
|
public static Resource NotStranded() {
|
579
|
-
return _namespace_GVF1O("GVF1_0020");
|
655
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0020");
|
656
|
+
}
|
657
|
+
|
658
|
+
/**
|
659
|
+
* Denotes heterozygous alleles.
|
660
|
+
* (http://www.biointerchange.org/gvf1o#GVF1_0085)
|
661
|
+
*/
|
662
|
+
public static Resource Heterozygous() {
|
663
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0085");
|
664
|
+
}
|
665
|
+
|
666
|
+
/**
|
667
|
+
* Denotes homozygous alleles.
|
668
|
+
* (http://www.biointerchange.org/gvf1o#GVF1_0086)
|
669
|
+
*/
|
670
|
+
public static Resource Homozygous() {
|
671
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0086");
|
672
|
+
}
|
673
|
+
|
674
|
+
/**
|
675
|
+
* Denotes hemizygous alleles.
|
676
|
+
* (http://www.biointerchange.org/gvf1o#GVF1_0087)
|
677
|
+
*/
|
678
|
+
public static Resource Hemizygous() {
|
679
|
+
return _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0087");
|
580
680
|
}
|
581
681
|
|
582
682
|
/**
|
@@ -585,76 +685,94 @@ public class GVF1O {
|
|
585
685
|
* @param uri URI that is tested for being an object property
|
586
686
|
*/
|
587
687
|
public static boolean isObjectProperty(Resource uri) {
|
588
|
-
if (uri
|
688
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0010")) {
|
689
|
+
return true;
|
690
|
+
}
|
691
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0012")) {
|
692
|
+
return true;
|
693
|
+
}
|
694
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0014")) {
|
695
|
+
return true;
|
696
|
+
}
|
697
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0015")) {
|
698
|
+
return true;
|
699
|
+
}
|
700
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0021")) {
|
701
|
+
return true;
|
702
|
+
}
|
703
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0023")) {
|
704
|
+
return true;
|
705
|
+
}
|
706
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0034")) {
|
589
707
|
return true;
|
590
708
|
}
|
591
|
-
if (uri
|
709
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0036")) {
|
592
710
|
return true;
|
593
711
|
}
|
594
|
-
if (uri
|
712
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0038")) {
|
595
713
|
return true;
|
596
714
|
}
|
597
|
-
if (uri
|
715
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0041")) {
|
598
716
|
return true;
|
599
717
|
}
|
600
|
-
if (uri
|
718
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0042")) {
|
601
719
|
return true;
|
602
720
|
}
|
603
|
-
if (uri
|
721
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0043")) {
|
604
722
|
return true;
|
605
723
|
}
|
606
|
-
if (uri
|
724
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0044")) {
|
607
725
|
return true;
|
608
726
|
}
|
609
|
-
if (uri
|
727
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0046")) {
|
610
728
|
return true;
|
611
729
|
}
|
612
|
-
if (uri
|
730
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0047")) {
|
613
731
|
return true;
|
614
732
|
}
|
615
|
-
if (uri
|
733
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0051")) {
|
616
734
|
return true;
|
617
735
|
}
|
618
|
-
if (uri
|
736
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0053")) {
|
619
737
|
return true;
|
620
738
|
}
|
621
|
-
if (uri
|
739
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0066")) {
|
622
740
|
return true;
|
623
741
|
}
|
624
|
-
if (uri
|
742
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0067")) {
|
625
743
|
return true;
|
626
744
|
}
|
627
|
-
if (uri
|
745
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0068")) {
|
628
746
|
return true;
|
629
747
|
}
|
630
|
-
if (uri
|
748
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0069")) {
|
631
749
|
return true;
|
632
750
|
}
|
633
|
-
if (uri
|
751
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0070")) {
|
634
752
|
return true;
|
635
753
|
}
|
636
|
-
if (uri
|
754
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0075")) {
|
637
755
|
return true;
|
638
756
|
}
|
639
|
-
if (uri
|
757
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0078")) {
|
640
758
|
return true;
|
641
759
|
}
|
642
|
-
if (uri
|
760
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0079")) {
|
643
761
|
return true;
|
644
762
|
}
|
645
|
-
if (uri
|
763
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0080")) {
|
646
764
|
return true;
|
647
765
|
}
|
648
|
-
if (uri
|
766
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0083")) {
|
649
767
|
return true;
|
650
768
|
}
|
651
|
-
if (uri
|
769
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0089")) {
|
652
770
|
return true;
|
653
771
|
}
|
654
|
-
if (uri
|
772
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0090")) {
|
655
773
|
return true;
|
656
774
|
}
|
657
|
-
if (uri
|
775
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0091")) {
|
658
776
|
return true;
|
659
777
|
}
|
660
778
|
return false;
|
@@ -666,121 +784,136 @@ public class GVF1O {
|
|
666
784
|
* @param uri URI that is tested for being a datatype property
|
667
785
|
*/
|
668
786
|
public static boolean isDatatypeProperty(Resource uri) {
|
669
|
-
if (uri
|
787
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0004")) {
|
788
|
+
return true;
|
789
|
+
}
|
790
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0005")) {
|
791
|
+
return true;
|
792
|
+
}
|
793
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0006")) {
|
794
|
+
return true;
|
795
|
+
}
|
796
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0007")) {
|
670
797
|
return true;
|
671
798
|
}
|
672
|
-
if (uri
|
799
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0008")) {
|
673
800
|
return true;
|
674
801
|
}
|
675
|
-
if (uri
|
802
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0009")) {
|
676
803
|
return true;
|
677
804
|
}
|
678
|
-
if (uri
|
805
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0013")) {
|
679
806
|
return true;
|
680
807
|
}
|
681
|
-
if (uri
|
808
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0022")) {
|
682
809
|
return true;
|
683
810
|
}
|
684
|
-
if (uri
|
811
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0024")) {
|
685
812
|
return true;
|
686
813
|
}
|
687
|
-
if (uri
|
814
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0025")) {
|
688
815
|
return true;
|
689
816
|
}
|
690
|
-
if (uri
|
817
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0026")) {
|
691
818
|
return true;
|
692
819
|
}
|
693
|
-
if (uri
|
820
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0027")) {
|
694
821
|
return true;
|
695
822
|
}
|
696
|
-
if (uri
|
823
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0029")) {
|
697
824
|
return true;
|
698
825
|
}
|
699
|
-
if (uri
|
826
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0030")) {
|
700
827
|
return true;
|
701
828
|
}
|
702
|
-
if (uri
|
829
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0031")) {
|
703
830
|
return true;
|
704
831
|
}
|
705
|
-
if (uri
|
832
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0032")) {
|
706
833
|
return true;
|
707
834
|
}
|
708
|
-
if (uri
|
835
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0037")) {
|
709
836
|
return true;
|
710
837
|
}
|
711
|
-
if (uri
|
838
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0039")) {
|
712
839
|
return true;
|
713
840
|
}
|
714
|
-
if (uri
|
841
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0048")) {
|
715
842
|
return true;
|
716
843
|
}
|
717
|
-
if (uri
|
844
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0049")) {
|
718
845
|
return true;
|
719
846
|
}
|
720
|
-
if (uri
|
847
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0050")) {
|
721
848
|
return true;
|
722
849
|
}
|
723
|
-
if (uri
|
850
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0054")) {
|
724
851
|
return true;
|
725
852
|
}
|
726
|
-
if (uri
|
853
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0055")) {
|
727
854
|
return true;
|
728
855
|
}
|
729
|
-
if (uri
|
856
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0056")) {
|
730
857
|
return true;
|
731
858
|
}
|
732
|
-
if (uri
|
859
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0057")) {
|
733
860
|
return true;
|
734
861
|
}
|
735
|
-
if (uri
|
862
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0059")) {
|
736
863
|
return true;
|
737
864
|
}
|
738
|
-
if (uri
|
865
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0060")) {
|
739
866
|
return true;
|
740
867
|
}
|
741
|
-
if (uri
|
868
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0061")) {
|
742
869
|
return true;
|
743
870
|
}
|
744
|
-
if (uri
|
871
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0062")) {
|
745
872
|
return true;
|
746
873
|
}
|
747
|
-
if (uri
|
874
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0063")) {
|
748
875
|
return true;
|
749
876
|
}
|
750
|
-
if (uri
|
877
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0064")) {
|
751
878
|
return true;
|
752
879
|
}
|
753
|
-
if (uri
|
880
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0065")) {
|
754
881
|
return true;
|
755
882
|
}
|
756
|
-
if (uri
|
883
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0071")) {
|
757
884
|
return true;
|
758
885
|
}
|
759
|
-
if (uri
|
886
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0072")) {
|
760
887
|
return true;
|
761
888
|
}
|
762
|
-
if (uri
|
889
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0073")) {
|
763
890
|
return true;
|
764
891
|
}
|
765
|
-
if (uri
|
892
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0074")) {
|
766
893
|
return true;
|
767
894
|
}
|
768
|
-
if (uri
|
895
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0076")) {
|
769
896
|
return true;
|
770
897
|
}
|
771
|
-
if (uri
|
898
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0077")) {
|
772
899
|
return true;
|
773
900
|
}
|
774
|
-
if (uri
|
901
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0081")) {
|
775
902
|
return true;
|
776
903
|
}
|
777
|
-
if (uri
|
904
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0082")) {
|
778
905
|
return true;
|
779
906
|
}
|
780
|
-
if (uri
|
907
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0092")) {
|
781
908
|
return true;
|
782
909
|
}
|
783
|
-
if (uri
|
910
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0093")) {
|
911
|
+
return true;
|
912
|
+
}
|
913
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0094")) {
|
914
|
+
return true;
|
915
|
+
}
|
916
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0095")) {
|
784
917
|
return true;
|
785
918
|
}
|
786
919
|
return false;
|
@@ -792,37 +925,43 @@ public class GVF1O {
|
|
792
925
|
* @param uri URI that is tested for being a class
|
793
926
|
*/
|
794
927
|
public static boolean isClass(Resource uri) {
|
795
|
-
if (uri
|
928
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0001")) {
|
929
|
+
return true;
|
930
|
+
}
|
931
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0002")) {
|
796
932
|
return true;
|
797
933
|
}
|
798
|
-
if (uri
|
934
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0003")) {
|
799
935
|
return true;
|
800
936
|
}
|
801
|
-
if (uri
|
937
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0016")) {
|
802
938
|
return true;
|
803
939
|
}
|
804
|
-
if (uri
|
940
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0028")) {
|
805
941
|
return true;
|
806
942
|
}
|
807
|
-
if (uri
|
943
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0033")) {
|
808
944
|
return true;
|
809
945
|
}
|
810
|
-
if (uri
|
946
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0035")) {
|
811
947
|
return true;
|
812
948
|
}
|
813
|
-
if (uri
|
949
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0040")) {
|
814
950
|
return true;
|
815
951
|
}
|
816
|
-
if (uri
|
952
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0045")) {
|
817
953
|
return true;
|
818
954
|
}
|
819
|
-
if (uri
|
955
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0052")) {
|
820
956
|
return true;
|
821
957
|
}
|
822
|
-
if (uri
|
958
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0058")) {
|
823
959
|
return true;
|
824
960
|
}
|
825
|
-
if (uri
|
961
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0084")) {
|
962
|
+
return true;
|
963
|
+
}
|
964
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0088")) {
|
826
965
|
return true;
|
827
966
|
}
|
828
967
|
return false;
|
@@ -834,16 +973,25 @@ public class GVF1O {
|
|
834
973
|
* @param uri URI that is tested for being a named individual
|
835
974
|
*/
|
836
975
|
public static boolean isNamedIndividual(Resource uri) {
|
837
|
-
if (uri
|
976
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0017")) {
|
977
|
+
return true;
|
978
|
+
}
|
979
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0018")) {
|
980
|
+
return true;
|
981
|
+
}
|
982
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0019")) {
|
983
|
+
return true;
|
984
|
+
}
|
985
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0020")) {
|
838
986
|
return true;
|
839
987
|
}
|
840
|
-
if (uri
|
988
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0085")) {
|
841
989
|
return true;
|
842
990
|
}
|
843
|
-
if (uri
|
991
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0086")) {
|
844
992
|
return true;
|
845
993
|
}
|
846
|
-
if (uri
|
994
|
+
if (uri == _namespace_GVF1O("http://www.biointerchange.org/gvf1o#GVF1_0087")) {
|
847
995
|
return true;
|
848
996
|
}
|
849
997
|
return false;
|
@@ -867,7 +1015,7 @@ public class GVF1O {
|
|
867
1015
|
*/
|
868
1016
|
public static boolean hasParent(Resource uri, Resource parent) {
|
869
1017
|
if (__parent_properties.containsKey(uri)) {
|
870
|
-
if (__parent_properties.get(uri)
|
1018
|
+
if (__parent_properties.get(uri) == parent) {
|
871
1019
|
return true;
|
872
1020
|
}
|
873
1021
|
return hasParent((Resource)__parent_properties.get(uri), parent);
|
@@ -889,55 +1037,6 @@ public class GVF1O {
|
|
889
1037
|
private static Map<Resource, Resource> _init___parent_properties() {
|
890
1038
|
Map<Resource, Resource> map = new HashMap<Resource, Resource>();
|
891
1039
|
|
892
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0031"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
893
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0009"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
894
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0053"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0069"));
|
895
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0042"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
|
896
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0076"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
897
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0054"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
|
898
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0032"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
|
899
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0043"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
|
900
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0021"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
|
901
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0010"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075"));
|
902
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0077"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
903
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0055"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
|
904
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0022"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063"));
|
905
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0044"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
|
906
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0056"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
|
907
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0078"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
|
908
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0034"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
|
909
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0023"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068"));
|
910
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0012"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
|
911
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0057"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
|
912
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0024"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063"));
|
913
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0013"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0064"));
|
914
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0079"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075"));
|
915
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0046"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
|
916
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0025"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
|
917
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0047"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
|
918
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0036"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
|
919
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0014"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
|
920
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0048"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0061"));
|
921
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0037"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0065"));
|
922
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0026"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
923
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0004"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
924
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0015"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068"));
|
925
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0049"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0061"));
|
926
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0038"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
927
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0027"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
928
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0005"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
929
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0072"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0071"));
|
930
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0050"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
|
931
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0039"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
|
932
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0006"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
933
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0073"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0071"));
|
934
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0029"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0062"));
|
935
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0007"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
936
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0051"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0067"));
|
937
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0074"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0071"));
|
938
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0030"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0062"));
|
939
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0008"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
|
940
|
-
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0041"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0069"));
|
941
1040
|
|
942
1041
|
return map;
|
943
1042
|
}
|