From 858b8c72db30a6fa7c92df91d9ee0e0cab0415e3 Mon Sep 17 00:00:00 2001 From: Chris Myers Date: Thu, 3 Dec 2015 16:29:43 -0700 Subject: [PATCH] Removed SBOLFactory. --- .../org/sbolstandard/core2/SBOLFactory.java | 82 ------------------- docs/javadocs/allclasses-frame.html | 3 +- docs/javadocs/allclasses-noframe.html | 3 +- docs/javadocs/constant-values.html | 2 +- docs/javadocs/deprecated-list.html | 2 +- docs/javadocs/help-doc.html | 2 +- docs/javadocs/index-files/index-1.html | 2 +- docs/javadocs/index-files/index-10.html | 2 +- docs/javadocs/index-files/index-11.html | 2 +- docs/javadocs/index-files/index-12.html | 2 +- docs/javadocs/index-files/index-13.html | 2 +- docs/javadocs/index-files/index-14.html | 2 +- docs/javadocs/index-files/index-15.html | 2 +- docs/javadocs/index-files/index-16.html | 6 +- docs/javadocs/index-files/index-17.html | 4 +- docs/javadocs/index-files/index-18.html | 2 +- docs/javadocs/index-files/index-19.html | 2 +- docs/javadocs/index-files/index-2.html | 2 +- docs/javadocs/index-files/index-20.html | 2 +- docs/javadocs/index-files/index-21.html | 6 +- docs/javadocs/index-files/index-3.html | 2 +- docs/javadocs/index-files/index-4.html | 2 +- docs/javadocs/index-files/index-5.html | 2 +- docs/javadocs/index-files/index-6.html | 2 +- docs/javadocs/index-files/index-7.html | 2 +- docs/javadocs/index-files/index-8.html | 2 +- docs/javadocs/index-files/index-9.html | 2 +- docs/javadocs/index.html | 2 +- .../org/sbolstandard/core2/AccessType.html | 2 +- .../org/sbolstandard/core2/Annotation.html | 2 +- .../org/sbolstandard/core2/Collection.html | 2 +- .../org/sbolstandard/core2/Component.html | 2 +- .../core2/ComponentDefinition.html | 2 +- .../sbolstandard/core2/ComponentInstance.html | 2 +- docs/javadocs/org/sbolstandard/core2/Cut.html | 2 +- .../org/sbolstandard/core2/DirectionType.html | 2 +- .../core2/FunctionalComponent.html | 2 +- .../sbolstandard/core2/GenericLocation.html | 2 +- .../sbolstandard/core2/GenericTopLevel.html | 2 +- .../org/sbolstandard/core2/Identified.html | 2 +- .../org/sbolstandard/core2/Interaction.html | 2 +- .../org/sbolstandard/core2/Location.html | 2 +- .../org/sbolstandard/core2/MapsTo.html | 2 +- .../org/sbolstandard/core2/Model.html | 2 +- .../org/sbolstandard/core2/Module.html | 2 +- .../sbolstandard/core2/ModuleDefinition.html | 2 +- .../sbolstandard/core2/OrientationType.html | 2 +- .../org/sbolstandard/core2/Participation.html | 2 +- .../org/sbolstandard/core2/Range.html | 2 +- .../sbolstandard/core2/RefinementType.html | 2 +- .../sbolstandard/core2/RestrictionType.html | 2 +- .../org/sbolstandard/core2/SBOLDocument.html | 6 +- .../org/sbolstandard/core2/SBOLReader.html | 6 +- .../org/sbolstandard/core2/SBOLValidate.html | 2 +- .../core2/SBOLValidationException.html | 2 +- .../org/sbolstandard/core2/SBOLWriter.html | 2 +- .../org/sbolstandard/core2/Sequence.html | 2 +- .../core2/SequenceAnnotation.html | 2 +- .../core2/SequenceConstraint.html | 2 +- .../sbolstandard/core2/SequenceOntology.html | 2 +- .../core2/SystemsBiologyOntology.html | 2 +- .../org/sbolstandard/core2/TopLevel.html | 2 +- .../core2/class-use/AccessType.html | 2 +- .../core2/class-use/Annotation.html | 2 +- .../core2/class-use/Collection.html | 2 +- .../core2/class-use/Component.html | 2 +- .../core2/class-use/ComponentDefinition.html | 2 +- .../core2/class-use/ComponentInstance.html | 2 +- .../org/sbolstandard/core2/class-use/Cut.html | 2 +- .../core2/class-use/DirectionType.html | 2 +- .../core2/class-use/FunctionalComponent.html | 2 +- .../core2/class-use/GenericLocation.html | 2 +- .../core2/class-use/GenericTopLevel.html | 2 +- .../core2/class-use/Identified.html | 2 +- .../core2/class-use/Interaction.html | 2 +- .../core2/class-use/Location.html | 2 +- .../sbolstandard/core2/class-use/MapsTo.html | 2 +- .../sbolstandard/core2/class-use/Model.html | 2 +- .../sbolstandard/core2/class-use/Module.html | 2 +- .../core2/class-use/ModuleDefinition.html | 2 +- .../core2/class-use/OrientationType.html | 2 +- .../core2/class-use/Participation.html | 2 +- .../sbolstandard/core2/class-use/Range.html | 2 +- .../core2/class-use/RefinementType.html | 2 +- .../core2/class-use/RestrictionType.html | 2 +- .../core2/class-use/SBOLDocument.html | 15 +--- .../core2/class-use/SBOLReader.html | 2 +- .../core2/class-use/SBOLValidate.html | 2 +- .../class-use/SBOLValidationException.html | 38 +-------- .../core2/class-use/SBOLWriter.html | 2 +- .../core2/class-use/Sequence.html | 2 +- .../core2/class-use/SequenceAnnotation.html | 2 +- .../core2/class-use/SequenceConstraint.html | 2 +- .../core2/class-use/SequenceOntology.html | 2 +- .../class-use/SystemsBiologyOntology.html | 2 +- .../core2/class-use/TopLevel.html | 2 +- .../org/sbolstandard/core2/package-frame.html | 3 +- .../sbolstandard/core2/package-summary.html | 22 ++--- .../org/sbolstandard/core2/package-tree.html | 9 +- .../org/sbolstandard/core2/package-use.html | 11 +-- docs/javadocs/overview-tree.html | 3 +- docs/javadocs/serialized-form.html | 2 +- 102 files changed, 120 insertions(+), 271 deletions(-) delete mode 100755 core2/src/main/java/org/sbolstandard/core2/SBOLFactory.java diff --git a/core2/src/main/java/org/sbolstandard/core2/SBOLFactory.java b/core2/src/main/java/org/sbolstandard/core2/SBOLFactory.java deleted file mode 100755 index e58cc8c9..00000000 --- a/core2/src/main/java/org/sbolstandard/core2/SBOLFactory.java +++ /dev/null @@ -1,82 +0,0 @@ -/* - * Copyright (c) 2012 Clark & Parsia, LLC. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.sbolstandard.core2; - -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; - -import javax.xml.stream.FactoryConfigurationError; -import javax.xml.stream.XMLStreamException; - -import uk.ac.ncl.intbio.core.io.CoreIoException; - -//import org.sbolstandard.core.impl.CollectionImpl; -//import org.sbolstandard.core.impl.DnaComponentImpl; -//import org.sbolstandard.core.impl.DnaSequenceImpl; -//import org.sbolstandard.core.impl.SBOLDocumentImpl; -//import org.sbolstandard.core.impl.SBOLReaderImpl; -//import org.sbolstandard.core.impl.SBOLValidatorImpl; -//import org.sbolstandard.core.impl.SBOLWriterImpl; -//import org.sbolstandard.core.impl.SequenceAnnotationImpl; - -public class SBOLFactory { - // This class only provides static fields, cannot be instantiated - private SBOLFactory() { - } - - /** - * Creates a fresh SBOL document instance and populates its contents from the given XML source. The reader will - * perform validation automatically. - * - * @throws SBOLValidationException if the contents of the document is not valid - * @throws FactoryConfigurationError - * @throws XMLStreamException - * @throws CoreIoException - */ - public static SBOLDocument read(InputStream in) throws IOException, SBOLValidationException, CoreIoException, XMLStreamException, FactoryConfigurationError { - return SBOLReader.read(in); - } - - /** - * Writes the contents of an SBOL document in XML format to the given output stream. The writer will - * perform validation automatically. - * - * @throws SBOLValidationException if the contents of the document is not valid - */ - public static void write(SBOLDocument doc, OutputStream out) throws IOException, SBOLValidationException { - try - { - SBOLWriter.write(doc, out); - } - catch (XMLStreamException e) - { - // TODO Auto-generated catch block - e.printStackTrace(); - } - catch (FactoryConfigurationError e) - { - // TODO Auto-generated catch block - e.printStackTrace(); - } - catch (CoreIoException e) - { - // TODO Auto-generated catch block - e.printStackTrace(); - } - } - -} diff --git a/docs/javadocs/allclasses-frame.html b/docs/javadocs/allclasses-frame.html index ad3d3df5..af8d2379 100644 --- a/docs/javadocs/allclasses-frame.html +++ b/docs/javadocs/allclasses-frame.html @@ -2,7 +2,7 @@ - + All Classes @@ -35,7 +35,6 @@

All Classes

  • RefinementType
  • RestrictionType
  • SBOLDocument
    • -
  • SBOLFactory
  • SBOLReader
  • SBOLValidate
  • SBOLValidationException
    • diff --git a/docs/javadocs/allclasses-noframe.html b/docs/javadocs/allclasses-noframe.html index eefb0970..7cd03c14 100644 --- a/docs/javadocs/allclasses-noframe.html +++ b/docs/javadocs/allclasses-noframe.html @@ -2,7 +2,7 @@ - + All Classes @@ -35,7 +35,6 @@

    All Classes

  • RefinementType
  • RestrictionType
  • SBOLDocument
    • -
  • SBOLFactory
  • SBOLReader
  • SBOLValidate
  • SBOLValidationException
    • diff --git a/docs/javadocs/constant-values.html b/docs/javadocs/constant-values.html index b541f3a9..a3567711 100644 --- a/docs/javadocs/constant-values.html +++ b/docs/javadocs/constant-values.html @@ -2,7 +2,7 @@ - + Constant Field Values diff --git a/docs/javadocs/deprecated-list.html b/docs/javadocs/deprecated-list.html index c2091a8f..c0a860bd 100644 --- a/docs/javadocs/deprecated-list.html +++ b/docs/javadocs/deprecated-list.html @@ -2,7 +2,7 @@ - + Deprecated List diff --git a/docs/javadocs/help-doc.html b/docs/javadocs/help-doc.html index f693bd15..7c68a340 100644 --- a/docs/javadocs/help-doc.html +++ b/docs/javadocs/help-doc.html @@ -2,7 +2,7 @@ - + API Help diff --git a/docs/javadocs/index-files/index-1.html b/docs/javadocs/index-files/index-1.html index 51e8f44e..fa92c0f8 100644 --- a/docs/javadocs/index-files/index-1.html +++ b/docs/javadocs/index-files/index-1.html @@ -2,7 +2,7 @@ - + A-Index diff --git a/docs/javadocs/index-files/index-10.html b/docs/javadocs/index-files/index-10.html index d53f2fa2..f2b98d2c 100644 --- a/docs/javadocs/index-files/index-10.html +++ b/docs/javadocs/index-files/index-10.html @@ -2,7 +2,7 @@ - + J-Index diff --git a/docs/javadocs/index-files/index-11.html b/docs/javadocs/index-files/index-11.html index 14e6b1d6..4439eb9b 100644 --- a/docs/javadocs/index-files/index-11.html +++ b/docs/javadocs/index-files/index-11.html @@ -2,7 +2,7 @@ - + L-Index diff --git a/docs/javadocs/index-files/index-12.html b/docs/javadocs/index-files/index-12.html index 13649356..720b39af 100644 --- a/docs/javadocs/index-files/index-12.html +++ b/docs/javadocs/index-files/index-12.html @@ -2,7 +2,7 @@ - + M-Index diff --git a/docs/javadocs/index-files/index-13.html b/docs/javadocs/index-files/index-13.html index d7c51c0a..0224a9a8 100644 --- a/docs/javadocs/index-files/index-13.html +++ b/docs/javadocs/index-files/index-13.html @@ -2,7 +2,7 @@ - + N-Index diff --git a/docs/javadocs/index-files/index-14.html b/docs/javadocs/index-files/index-14.html index 93efb89c..ffdfd983 100644 --- a/docs/javadocs/index-files/index-14.html +++ b/docs/javadocs/index-files/index-14.html @@ -2,7 +2,7 @@ - + O-Index diff --git a/docs/javadocs/index-files/index-15.html b/docs/javadocs/index-files/index-15.html index ccf4c879..106c3854 100644 --- a/docs/javadocs/index-files/index-15.html +++ b/docs/javadocs/index-files/index-15.html @@ -2,7 +2,7 @@ - + P-Index diff --git a/docs/javadocs/index-files/index-16.html b/docs/javadocs/index-files/index-16.html index e4fc5c34..787eba61 100644 --- a/docs/javadocs/index-files/index-16.html +++ b/docs/javadocs/index-files/index-16.html @@ -2,7 +2,7 @@ - + R-Index @@ -86,10 +86,6 @@

    R

    Takes in a given RDF InputStream and add the data read to this SBOLDocument.
    -
    read(InputStream) - Static method in class org.sbolstandard.core2.SBOLFactory
    -
    -
    Creates a fresh SBOL document instance and populates its contents from the given XML source.
    -
    read(String) - Static method in class org.sbolstandard.core2.SBOLReader
    Takes in the given RDF filename and converts the file to an SBOLDocument.
    diff --git a/docs/javadocs/index-files/index-17.html b/docs/javadocs/index-files/index-17.html index 656c8888..80be6044 100644 --- a/docs/javadocs/index-files/index-17.html +++ b/docs/javadocs/index-files/index-17.html @@ -2,7 +2,7 @@ - + S-Index @@ -80,8 +80,6 @@

    S

    and then adds the following namespaces: Sbol2Terms.sbol2, Sbol1Terms.rdf, Sbol2Terms.dc, and Sbol2Terms.prov.
    -
    SBOLFactory - Class in org.sbolstandard.core2
    -
     
    SBOLReader - Class in org.sbolstandard.core2
     
    SBOLReader() - Constructor for class org.sbolstandard.core2.SBOLReader
    diff --git a/docs/javadocs/index-files/index-18.html b/docs/javadocs/index-files/index-18.html index e1eddaca..edca242d 100644 --- a/docs/javadocs/index-files/index-18.html +++ b/docs/javadocs/index-files/index-18.html @@ -2,7 +2,7 @@ - + T-Index diff --git a/docs/javadocs/index-files/index-19.html b/docs/javadocs/index-files/index-19.html index bb61bdbe..82390508 100644 --- a/docs/javadocs/index-files/index-19.html +++ b/docs/javadocs/index-files/index-19.html @@ -2,7 +2,7 @@ - + U-Index diff --git a/docs/javadocs/index-files/index-2.html b/docs/javadocs/index-files/index-2.html index 72e83ce9..641bf94d 100644 --- a/docs/javadocs/index-files/index-2.html +++ b/docs/javadocs/index-files/index-2.html @@ -2,7 +2,7 @@ - + B-Index diff --git a/docs/javadocs/index-files/index-20.html b/docs/javadocs/index-files/index-20.html index e16185aa..baf0601d 100644 --- a/docs/javadocs/index-files/index-20.html +++ b/docs/javadocs/index-files/index-20.html @@ -2,7 +2,7 @@ - + V-Index diff --git a/docs/javadocs/index-files/index-21.html b/docs/javadocs/index-files/index-21.html index a62d3943..adcfe1f7 100644 --- a/docs/javadocs/index-files/index-21.html +++ b/docs/javadocs/index-files/index-21.html @@ -2,7 +2,7 @@ - + W-Index @@ -81,10 +81,6 @@

    W

    Serializes SBOLDocument and outputs the data from the serialization to the given output stream in RDF format
    -
    write(SBOLDocument, OutputStream) - Static method in class org.sbolstandard.core2.SBOLFactory
    -
    -
    Writes the contents of an SBOL document in XML format to the given output stream.
    -
    write(SBOLDocument, File) - Static method in class org.sbolstandard.core2.SBOLWriter
    Serializes a given SBOLDocument and outputs the data from the serialization to the given output file diff --git a/docs/javadocs/index-files/index-3.html b/docs/javadocs/index-files/index-3.html index 38d65e7a..0e6ee047 100644 --- a/docs/javadocs/index-files/index-3.html +++ b/docs/javadocs/index-files/index-3.html @@ -2,7 +2,7 @@ - + C-Index diff --git a/docs/javadocs/index-files/index-4.html b/docs/javadocs/index-files/index-4.html index c9f77fa0..e4087b48 100644 --- a/docs/javadocs/index-files/index-4.html +++ b/docs/javadocs/index-files/index-4.html @@ -2,7 +2,7 @@ - + D-Index diff --git a/docs/javadocs/index-files/index-5.html b/docs/javadocs/index-files/index-5.html index 420ae242..a3a83ea7 100644 --- a/docs/javadocs/index-files/index-5.html +++ b/docs/javadocs/index-files/index-5.html @@ -2,7 +2,7 @@ - + E-Index diff --git a/docs/javadocs/index-files/index-6.html b/docs/javadocs/index-files/index-6.html index cc1964c1..eb457c8d 100644 --- a/docs/javadocs/index-files/index-6.html +++ b/docs/javadocs/index-files/index-6.html @@ -2,7 +2,7 @@ - + F-Index diff --git a/docs/javadocs/index-files/index-7.html b/docs/javadocs/index-files/index-7.html index c8df5baf..be20ba44 100644 --- a/docs/javadocs/index-files/index-7.html +++ b/docs/javadocs/index-files/index-7.html @@ -2,7 +2,7 @@ - + G-Index diff --git a/docs/javadocs/index-files/index-8.html b/docs/javadocs/index-files/index-8.html index 81b1ac37..3f2b0e2d 100644 --- a/docs/javadocs/index-files/index-8.html +++ b/docs/javadocs/index-files/index-8.html @@ -2,7 +2,7 @@ - + H-Index diff --git a/docs/javadocs/index-files/index-9.html b/docs/javadocs/index-files/index-9.html index a6b0e0c2..b8b02e80 100644 --- a/docs/javadocs/index-files/index-9.html +++ b/docs/javadocs/index-files/index-9.html @@ -2,7 +2,7 @@ - + I-Index diff --git a/docs/javadocs/index.html b/docs/javadocs/index.html index 797e56cc..22b30f64 100644 --- a/docs/javadocs/index.html +++ b/docs/javadocs/index.html @@ -2,7 +2,7 @@ - + Generated Documentation (Untitled)