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Rhollandandreasprlic
Rholland
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/* Writing */
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‎wiki/BioJava:BioJavaXDocs.md‎

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@@ -1062,10 +1062,10 @@ Table 8.11. UniProtFormat output field sources.
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| DE | getDescription() |
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| DT | For creation date: getNoteSet(Terms.getDateCreatedTerm()) and getNoteSet(Terms.getRelCreatedTerm()). For last updated date: getNoteSet(Terms.getDateUpdatedTerm()) and getNoteSetTerms.getRelUpdatedTerm()). For last annotation date: getNoteSet(Terms.getDateAnnotatedTerm()) and getNoteSetTerms.getRelAnnotatedTerm()). If date created or date annotated is null, then the update date is duplicated and used here as well. |
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| DR | getRankedCrossRef(), using getNoteSet(Terms.getAdditionalAccessionTerm()) to generate additional accessions. |
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| OS | getNCBITaxon().getDisplayName() followed by all synonyms from getNames(NCBITaxon.SYNONYM) in brackets. |
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| OC | getNCBITaxon().getNameHierarchy(). |
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| OS | getTaxon().getDisplayName() followed by all synonyms from getNames(NCBITaxon.SYNONYM) in brackets. |
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| OC | getTaxon().getNameHierarchy(). |
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| OG | getNoteSet(Terms.getOrganelleTerm()) |
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| OX | getNCBITaxon().getNCBITaxID() |
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| OX | getTaxon().getNCBITaxID() |
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| GN | Gene names are written from getNoteSet(Terms.getGeneNameTerm()). Gene synonyms are written from getNoteSet(Terms.getGeneSynonymTerm()). Ordered locus names are written from getNoteSet(Terms.getOrderedLocusNameTerm()). ORF names are written from getNoteSet(Terms.getORFNameTerm()). As the values have a number and a colon prefixed, where the number refers to the sequence order of the current gene, these values are used to keep the correct names grouped together. This prefix is not included in the output. |
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| RN | Each reference returned by getRankedDocRefs() is iterated over. The rank of the RankedDocRef object is output here. |
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| RP | The getRemark() from the DocRef. |

‎wiki/BioJava:BioJavaXDocs.mediawiki‎

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@@ -1222,16 +1222,16 @@ Table 8.11. UniProtFormat output field sources.
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|getRankedCrossRef(), using getNoteSet(Terms.getAdditionalAccessionTerm()) to generate additional accessions.
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|-
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|OS
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|getNCBITaxon().getDisplayName() followed by all synonyms from getNames(NCBITaxon.SYNONYM) in brackets.
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|getTaxon().getDisplayName() followed by all synonyms from getNames(NCBITaxon.SYNONYM) in brackets.
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|-
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|OC
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|getNCBITaxon().getNameHierarchy().
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|getTaxon().getNameHierarchy().
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|-
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|OG
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|getNoteSet(Terms.getOrganelleTerm())
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|-
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|OX
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|getNCBITaxon().getNCBITaxID()
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|getTaxon().getNCBITaxID()
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|-
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|GN
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|Gene names are written from getNoteSet(Terms.getGeneNameTerm()). Gene synonyms are written from getNoteSet(Terms.getGeneSynonymTerm()). Ordered locus names are written from getNoteSet(Terms.getOrderedLocusNameTerm()). ORF names are written from getNoteSet(Terms.getORFNameTerm()). As the values have a number and a colon prefixed, where the number refers to the sequence order of the current gene, these values are used to keep the correct names grouped together. This prefix is not included in the output.
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|Sequence counts are generated, then sequence is read directly as it is a SymbolList.
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|}
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=== INSDSeq (XML) ===
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For parsing files that conform to http://www.ebi.ac.uk/embl/Documentation/DTD/INSDSeq_v1.3.dtd.txt.

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