From 1184fa70f1cd3bf8856552de2495ac7bff023a8d Mon Sep 17 00:00:00 2001 From: kaitoii11 Date: Mon, 22 Aug 2016 02:48:05 +0900 Subject: [PATCH] updated license and readme, created util methods --- LICENSE | 2 +- README.md | 1 + .../sbml/wrapper/CompartmentAliasWrapper.java | 7 ++++ src/org/sbml/wrapper/CompartmentWrapper.java | 7 ++++ .../wrapper/ComplexSpeciesAliasWrapper.java | 36 +++++++++++++++++++ .../ModifierSpeciesReferenceWrapper.java | 7 ++++ src/org/sbml/wrapper/ReactionWrapper.java | 7 ++++ .../sbml/wrapper/SpeciesReferenceWrapper.java | 7 ++++ src/org/sbml/wrapper/SpeciesWrapper.java | 22 +++++++++++- 9 files changed, 94 insertions(+), 2 deletions(-) diff --git a/LICENSE b/LICENSE index 2b82bc8..8ec6a38 100644 --- a/LICENSE +++ b/LICENSE @@ -186,7 +186,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright {2016} {hogehoge} + Copyright {2016} {Kaito Ii, Akira Funahashi} Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/README.md b/README.md index 0adbf63..5c44742 100644 --- a/README.md +++ b/README.md @@ -118,6 +118,7 @@ Convert SBML Layout package to CellDesigner Annotation ## So, what's next? - Alter schema to add editPoints into reactant links and product links - Convert complex species and included species to [SBML Multi package](http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/multi) +- Convert Layers in CellDesigner Annotation ## License This content is licensed under the [Apache License](http://www.apache.org/licenses/LICENSE-2.0) . diff --git a/src/org/sbml/wrapper/CompartmentAliasWrapper.java b/src/org/sbml/wrapper/CompartmentAliasWrapper.java index 9cdd202..10ea0d1 100644 --- a/src/org/sbml/wrapper/CompartmentAliasWrapper.java +++ b/src/org/sbml/wrapper/CompartmentAliasWrapper.java @@ -303,4 +303,11 @@ public void setCompartmentAliased(Compartment compartment){ public CompartmentWrapper getCompartmentWrapperAliased(){ return compartmentWrapper; } + + /** + * @return the modelWrapper + */ + public ModelWrapper getModelWrapper() { + return modelWrapper; + } } diff --git a/src/org/sbml/wrapper/CompartmentWrapper.java b/src/org/sbml/wrapper/CompartmentWrapper.java index 5fde06d..0e0494d 100644 --- a/src/org/sbml/wrapper/CompartmentWrapper.java +++ b/src/org/sbml/wrapper/CompartmentWrapper.java @@ -133,4 +133,11 @@ public CompartmentWrapper getOutsideInstance(){ public CompartmentAliasWrapper getAliasWrapper() { return modelWrapper.getCompartmentAliasWrapperByCompartmentId(id); } + + /** + * @return the modelWrapper + */ + public ModelWrapper getModelWrapper() { + return modelWrapper; + } } diff --git a/src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java b/src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java index a3e8016..a27eadd 100644 --- a/src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java +++ b/src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java @@ -225,5 +225,41 @@ public void setListOfSpeciesTags(ListOfSpeciesTag value) { public ComplexSpeciesAlias getComplexSpeciesAliased() { return complexSpeciesAlias; } + + /** + * @return the speciesWrapper + */ + public SpeciesWrapper getSpeciesWrapper() { + return speciesWrapper; + } + + /** + * @param speciesWrapper the speciesWrapper to set + */ + public void setSpeciesWrapper(SpeciesWrapper speciesWrapper) { + this.speciesWrapper = speciesWrapper; + } + + /** + * @return the compartmentAliasWrapper + */ + public CompartmentAliasWrapper getCompartmentAliasWrapper() { + return compartmentAliasWrapper; + } + + /** + * @param compartmentAliasWrapper the compartmentAliasWrapper to set + */ + public void setCompartmentAliasWrapper( + CompartmentAliasWrapper compartmentAliasWrapper) { + this.compartmentAliasWrapper = compartmentAliasWrapper; + } + + /** + * @return the modelWrapper + */ + public ModelWrapper getModelWrapper() { + return modelWrapper; + } } diff --git a/src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java b/src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java index 7ef03da..b41f02f 100644 --- a/src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java +++ b/src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java @@ -251,4 +251,11 @@ public void setEditPointList(List editPointList) { System.out.println(modification.getEditPoints()); } + /** + * @return the modelWrapper + */ + public ModelWrapper getModelWrapper() { + return modelWrapper; + } + } diff --git a/src/org/sbml/wrapper/ReactionWrapper.java b/src/org/sbml/wrapper/ReactionWrapper.java index 50f2714..37020ae 100644 --- a/src/org/sbml/wrapper/ReactionWrapper.java +++ b/src/org/sbml/wrapper/ReactionWrapper.java @@ -934,4 +934,11 @@ public void createBaseProduct(SpeciesReferenceWrapper srw) { baseProducts.add(bp); } + /** + * @return the modelWrapper + */ + public ModelWrapper getModelWrapper() { + return modelWrapper; + } + } diff --git a/src/org/sbml/wrapper/SpeciesReferenceWrapper.java b/src/org/sbml/wrapper/SpeciesReferenceWrapper.java index f8ebf00..ab4f4ab 100644 --- a/src/org/sbml/wrapper/SpeciesReferenceWrapper.java +++ b/src/org/sbml/wrapper/SpeciesReferenceWrapper.java @@ -115,4 +115,11 @@ public SpeciesAliasWrapper getAliased(){ return modelWrapper.getSpeciesAliasWrapperById(getAlias()); } + /** + * @return the modelWrapper + */ + public ModelWrapper getModelWrapper() { + return modelWrapper; + } + } diff --git a/src/org/sbml/wrapper/SpeciesWrapper.java b/src/org/sbml/wrapper/SpeciesWrapper.java index 155d920..dd3434f 100644 --- a/src/org/sbml/wrapper/SpeciesWrapper.java +++ b/src/org/sbml/wrapper/SpeciesWrapper.java @@ -88,7 +88,6 @@ public SpeciesWrapper(Species species, ModelWrapper modelWrapper){ setAnnotations(); else initAnnotations(); - } /** @@ -318,4 +317,25 @@ public Catalyzed createCatalyzedReaction(String reaction){ return catalyzed; } + /** + * @return the modelWrapper + */ + public ModelWrapper getModelWrapper() { + return modelWrapper; + } + + /** + * @return the compartmentWrapper + */ + public CompartmentWrapper getCompartmentWrapper() { + return compartmentWrapper; + } + + /** + * @param compartmentWrapper the compartmentWrapper to set + */ + public void setCompartmentWrapper(CompartmentWrapper compartmentWrapper) { + this.compartmentWrapper = compartmentWrapper; + } + }