From 3a346de2daeb2d71db8977840620bb0f4dfc183b Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 30 Jun 2017 14:15:41 +0200
Subject: [PATCH] regulation contain information about containedInPathway
---
.../reactome/model/ReactomeRegulation.java | 40 ++++++++++++++++---
.../columnParser/RegulationColumnParser.java | 2 +
2 files changed, 36 insertions(+), 6 deletions(-)
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 ca1e444af2..220e738700 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 39f16dfb7c..08beeb87dd 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);
}
--
GitLab