diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeStableIdentifier.java b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeStableIdentifier.java index aca56837f9c49d4346aa7261a61f4fa347c01b15..99ac1b80b67f95f08bee8d629e8479c80df6b4d6 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeStableIdentifier.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeStableIdentifier.java @@ -9,17 +9,37 @@ package lcsb.mapviewer.reactome.model; * */ public class ReactomeStableIdentifier extends ReactomeDatabaseObject { + /** - * Identifier in reactome model. More information can be found <a - * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. + * Identifier in reactome model. More information can be found + * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. */ private String identifier; + /** - * Identifier version in reactome model. More information can be found <a - * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. + * Identifier version in reactome model. More information can be found + * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. */ private String identifierVersion; + /** + * Old identifier used in reactome model. More information can be found + * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. + */ + private String oldIdentifier; + + /** + * Old identifier version used in reactome model. More information can be + * found + * <a href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>. + */ + private String oldIdentifierVersion; + + /** + * Undocumented by reactome... + */ + private boolean released; + /** * @return the identifier * @see #identifier @@ -54,4 +74,55 @@ public class ReactomeStableIdentifier extends ReactomeDatabaseObject { this.identifierVersion = identifierVersion; } + /** + * @return the oldIdentifier + * @see #oldIdentifier + */ + public String getOldIdentifier() { + return oldIdentifier; + } + + /** + * @param oldIdentifier + * the oldIdentifier to set + * @see #oldIdentifier + */ + public void setOldIdentifier(String oldIdentifier) { + this.oldIdentifier = oldIdentifier; + } + + /** + * @return the oldIdentifierVersion + * @see #oldIdentifierVersion + */ + public String getOldIdentifierVersion() { + return oldIdentifierVersion; + } + + /** + * @param oldIdentifierVersion + * the oldIdentifierVersion to set + * @see #oldIdentifierVersion + */ + public void setOldIdentifierVersion(String oldIdentifierVersion) { + this.oldIdentifierVersion = oldIdentifierVersion; + } + + /** + * @return the released + * @see #released + */ + public boolean isReleased() { + return released; + } + + /** + * @param released + * the released to set + * @see #released + */ + public void setReleased(boolean released) { + this.released = released; + } + } diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/DatabaseObjectColumnParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/DatabaseObjectColumnParser.java index 448733a71f31f5dbd0ef7f10d311e4f3b4e06e94..b4f6aa1d20ff9d4f3c60ff4102e3b5acc66a0525 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/DatabaseObjectColumnParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/DatabaseObjectColumnParser.java @@ -47,8 +47,8 @@ public class DatabaseObjectColumnParser extends ColumnParser<ReactomeDatabaseObj } else if (node.getNodeName().equalsIgnoreCase("stableIdentifier")) { object.setStableIdentifier(getSiParser().parseSimplifiedObject(node)); } else { - throw new InvalidArgumentException("Unknown node type for ReactomeDatabaseObject: " + node.getNodeName() + ". Object: " + object.getClass() + " [" - + object.getDbId() + "]"); + throw new InvalidArgumentException( + "Unknown node type for ReactomeDatabaseObject: " + node.getNodeName() + ". Object: " + object.getClass() + " [" + object.getDbId() + "]"); } } } diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/StableIdentifierColumnParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/StableIdentifierColumnParser.java index 1beb753c1dd81626f61c0d231bb11f3384ffcbc3..90947ae36f8a7d761be2ab70c924fc75035570f1 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/StableIdentifierColumnParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/StableIdentifierColumnParser.java @@ -27,6 +27,12 @@ public class StableIdentifierColumnParser extends ColumnParser<ReactomeStableIde object.setIdentifier(node.getTextContent()); } else if (node.getNodeName().equalsIgnoreCase("identifierVersion")) { object.setIdentifierVersion(node.getTextContent()); + } else if (node.getNodeName().equalsIgnoreCase("oldIdentifier")) { + object.setOldIdentifier(node.getTextContent()); + } else if (node.getNodeName().equalsIgnoreCase("oldIdentifierVersion")) { + object.setOldIdentifierVersion(node.getTextContent()); + } else if (node.getNodeName().equalsIgnoreCase("released")) { + object.setReleased("true".equalsIgnoreCase(node.getTextContent())); } else { getParentParser().updateColumnFromNode(object, node); }