diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeRegulation.java b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeRegulation.java index ca1e444af259bc29127d71d8503a45c20bcbfcf1..220e738700f697574e8d73de3d2dab60af377d31 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeRegulation.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeRegulation.java @@ -9,16 +9,27 @@ package lcsb.mapviewer.reactome.model; * */ public class ReactomeRegulation extends ReactomeDatabaseObject { + /** - * Event param in reactome model. More information can be found <a - * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. + * Event param in reactome model. More information can be found + * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. */ - private ReactomeEvent regulatedEntity; + private ReactomeEvent regulatedEntity; + /** - * DatabaseObject param in reactome model. More information can be found <a - * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. + * DatabaseObject param in reactome model. More information can be found + * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. */ - private ReactomeDatabaseObject regulator; + private ReactomeDatabaseObject regulator; + + /** + * If a reaction is regulated in different ways in different pathway contexts, + * the containedInPathway allows curator to specify this. More information can + * be found <a href= + * "http://wiki.reactome.org/index.php/Glossary_Data_Model#Regulation">here + * </a>. + */ + private ReactomePathway containedInPathway; /** * @return the regulatedEntity @@ -54,4 +65,21 @@ public class ReactomeRegulation extends ReactomeDatabaseObject { this.regulator = regulator; } + /** + * @return the containedInPathway + * @see #containedInPathway + */ + public ReactomePathway getContainedInPathway() { + return containedInPathway; + } + + /** + * @param containedInPathway + * the containedInPathway to set + * @see #containedInPathway + */ + public void setContainedInPathway(ReactomePathway containedInPathway) { + this.containedInPathway = containedInPathway; + } + } diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/RegulationColumnParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/RegulationColumnParser.java index 39f16dfb7c555c3f1277105d43f43ecff0cdce3b..08beeb87dd59efc88ffc5e97a89a8a8eec4416bd 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/RegulationColumnParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/RegulationColumnParser.java @@ -26,6 +26,8 @@ public class RegulationColumnParser extends ColumnParser<ReactomeRegulation> { object.setRegulatedEntity(geteParser().parseObject(node)); } else if (node.getNodeName().equalsIgnoreCase("regulator")) { object.setRegulator(getDoParser().parseObject(node)); + } else if (node.getNodeName().equalsIgnoreCase("containedInPathway")) { + object.setRegulator(getpParser().parseObject(node)); } else { getParentParser().updateColumnFromNode(object, node); }