diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/package-info.java b/reactome/src/main/java/lcsb/mapviewer/reactome/package-info.java index 55b7a2fe06f2f0564d6f2b59e9bd6271165ecb58..98ccb86955ed0537fee9539fa979b9396d30af8e 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/package-info.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/package-info.java @@ -2,7 +2,7 @@ * This package provides interface to access data in <a * href="http://www.reactome.org/">Reactome</a> database. Information from this * database are retrieved using <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * > Reactome RESTful API</a>. Reactome model was implemented in * {@link lcsb.mapviewer.reactome.model model} subpackage. By design all * reactome objects inherit from diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java index 6f01e9d5a6d5ea1ed82c6ba4c681306731a7d0d6..3c0984bea4cf813955154b4c4f59fd1bb4e54f01 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java @@ -136,7 +136,7 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp /** * Url used for accessing Reactome RestFULL API. */ - private static final String REACTOME_URL = "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/RESTfulWS/"; + private static final String REACTOME_URL = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/"; @Override public List<ReactomePhysicalEntity> getEntitiesForName(String name) throws IOException { @@ -752,7 +752,7 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp @Override public ExternalServiceStatus getServiceStatus() { ExternalServiceStatus status = new ExternalServiceStatus( - "Reactome RESTful API", "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"); + "Reactome RESTful API", "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"); GeneralCacheInterface cacheCopy = getCache(); this.setCache(null); diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAbstractModifiedResidueParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAbstractModifiedResidueParser.java index 04bc387dcfc20d0eac749d979785291c1347bdff..11cc1de3dfcaa05956477f898f8d9803541658c2 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAbstractModifiedResidueParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAbstractModifiedResidueParser.java @@ -4,9 +4,9 @@ import lcsb.mapviewer.reactome.model.ReactomeAbstractModifiedResidue; import lcsb.mapviewer.reactome.xml.columnParser.AbstractModifiedResidueColumnParser; /** - * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" - * >Reactome API</a> for <a href= + * Parser for reactome xml retrieved from + * <a href= "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" > + * Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=AbstractModifiedResidue" * >AbstractModifiedResidue</a> object. * diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAffiliationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAffiliationParser.java index 51b689991c9563687c21d21bfb20f4cbc695d6c9..12568ee661428d8c22965b30b210b34a8f306a7d 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAffiliationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAffiliationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.AffiliationColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Affiliation" * >Affiliation</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParser.java index 150cbb219c65a56848c4d46807896a965c795824..4bef2d69d5f534c1b357cfd66142c0b4f0a1fc03 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.BlackBoxEventColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=BlackBoxEvent" * >BlackBoxEvent</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBookParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBookParser.java index 6b41e126183a049dd7eb57a43489bd3b8f04516d..55f97847d229e943f9259893af84e892a16f51a9 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBookParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBookParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.BookColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Book" * >Book</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParser.java index a1a5f5f09fe4d47207decd10fd0f820eea0c72a1..6502ddac4859d9cc2c247e98e1dd406a212652ae 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.CandidateSetColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=CandidateSet" * >CandidateSet</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParser.java index 42c5be11f7c15ce7d4ef6a0b5fdb721d65126fc6..c61305def042ad94b6e98342bb576047ab8a9b13 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.CatalystActivityColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=CatalystActivity" * >CatalystActivity</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCellTypeParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCellTypeParser.java index d6f94a33e01e1db95302b7eddddeb19859b7b912..80e2b07fdf614eefe1310ed845800bcdc40656b8 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCellTypeParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCellTypeParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.CellTypeColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=CellType" * >CellType</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCompartmentParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCompartmentParser.java index 6ce2f7f5c52fcb700fde248eb877269890eb8bee..4e404f94a2cf1a7203742a9e4ddc81b2f64e4139 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCompartmentParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCompartmentParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.CompartmentColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Compartment" * >Compartment</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeComplexParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeComplexParser.java index f266625a0c69421f5bc3aaf7ac3112564a542e16..686ff0b2636c9362b99023f3f94684b5928e648c 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeComplexParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeComplexParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ComplexColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Complex" * >Complex</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeConcurrentEventSetParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeConcurrentEventSetParser.java index 0334bc396a4d96c21cac5eea88fc79fa843e206f..3999fe8fb4fad4ab53293cf90353168600c627c6 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeConcurrentEventSetParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeConcurrentEventSetParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ConcurrentEventSetColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ConcurrentEventSet" * >ConcurrentEventSet</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseIdentifierParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseIdentifierParser.java index 8ca36d620d1eafbe421c5ba52e0b88fb5ce64430..267aa457f48d7cabd8ed14a930beffa547b6e953 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseIdentifierParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseIdentifierParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DatabaseIdentifierColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=DatabaseIdentifier" * >DatabaseIdentifier</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseObjectParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseObjectParser.java index 01040414ad5b64f466d8d548c7c98423a63d548f..b9aee00586c70f48b318c38c1f62591b2ad9951d 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseObjectParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseObjectParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DatabaseObjectColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=DatabaseObject" * >DatabaseObject</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParser.java index d757bfd846b65ebacd6165fbb875657f3e62f6aa..845e85453b058dad116931cf1691edbf7373bbcf 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DefinedSetColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=DefinedSet" * >DefinedSet</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDepolymerisationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDepolymerisationParser.java index a7696cfcf33280808ad73d55c8f7e1a647764640..62ce3555b2156fcbfeaad6e27ccd167ff08d3144 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDepolymerisationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDepolymerisationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DepolymerisationColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Depolymerisation" * >Depolymerisation</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDiseaseParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDiseaseParser.java index 9ce0a5a0a5504fee1ac96f58f147760d58af09ca..aa5fcbbb2ef5bd4564dbb2c54fc603c32ef4d17f 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDiseaseParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDiseaseParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DiseaseColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Disease" * >Disease</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityCompartmentParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityCompartmentParser.java index 8196e34b931032f41943b8d705fec4ad31214d0c..ddb0c348f38dc74e1e019594ec1eecde5fcce15e 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityCompartmentParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityCompartmentParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EntityCompartmentColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=EntityCompartment" * >EntityCompartment</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityFunctionalStatusParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityFunctionalStatusParser.java index 31f6c6ab1263c9e16cce38a3eac1351724f0aa0e..bb7e5b12e189f97e6a7acdce723d31f0819b889e 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityFunctionalStatusParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityFunctionalStatusParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EntityFunctionalStatusColumnPars /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=EntityFunctionalStatus" * >EntityFunctionalStatus</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntitySetParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntitySetParser.java index d1bd3026be81a36ae8ece809859b0e4cc0d7102f..f64466ea7de54ae0df68a2d51e78dd73b8eac121 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntitySetParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntitySetParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EntitySetColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=EntitySet" * >EntitySet</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityWithAccessionedSequenceParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityWithAccessionedSequenceParser.java index 8f263a65beedcd3b0e6d7cdf9866962ef118fd65..5bde95aff46b5ecb062c6c2d1a8026b34a6e4c88 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityWithAccessionedSequenceParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityWithAccessionedSequenceParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EntityWithAccessionedSequenceCol /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=EntityWithAccessionedSequence" * >EntityWithAccessionedSequence</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEventParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEventParser.java index 980f663d03b19a51a0fcfe959a301ed746f0d9c3..0f35448ec000e9060343cd52dbcdd6d89d21ab53 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEventParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEventParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EventColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Event" * >Event</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEvidenceTypeParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEvidenceTypeParser.java index bbb9389656af1c4cecb9cd06c76c35fcd3f60d52..005faa81b1090b5423c61581935a4c370774151d 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEvidenceTypeParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEvidenceTypeParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EvidenceTypeColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=EvidenceType" * >EvidenceType</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFigureParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFigureParser.java index 08bf87d4eccddb202a6224ea4c1b7a870114324d..193aae734d5d879f857085d0d74625199e61b2d8 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFigureParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFigureParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.FigureColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Figure" * >Figure</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentDeletionModificationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentDeletionModificationParser.java index 1de4d5e074f064d314a57014a818d7541ed63716..f80f2803cce169184b178ef715a09fa6da56447d 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentDeletionModificationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentDeletionModificationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.FragmentDeletionModificationColu /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=FragmentDeletionModification" * >FragmentDeletionModification</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentInsertionModificationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentInsertionModificationParser.java index b2ad033943c108fe8891979ce1379d86a26a0116..8df7feda7a42b0ee888711125749a5331ccabba1 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentInsertionModificationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentInsertionModificationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.FragmentInsertionModificationCol /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=FragmentInsertionModification" * >FragmentInsertionModification</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentReplacedModificationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentReplacedModificationParser.java index c7bbc93b57f87a36db79d9594a31f3cb8dc51ef8..831bcc67196d9e5cae59765d15880b06db2b1ab4 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentReplacedModificationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFragmentReplacedModificationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.FragmentReplacedModificationColu /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=FragmentReplacedModification" * >FragmentReplacedModification</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFrontPageParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFrontPageParser.java index 3c4e4b2723d77a49f0d1911fb52b9b53cc708253..0e5b363a766447ae3869a24a56dd3cbdc8fc5f35 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFrontPageParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFrontPageParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.FrontPageColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=FrontPage" * >FrontPage</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFunctionalStatusParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFunctionalStatusParser.java index 42fb376632aeff7172ec48f22fd8335de1130e1d..8c880c31986ef0d98d7e7d7cc17ad3032f302d8a 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFunctionalStatusParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFunctionalStatusParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.FunctionalStatusColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=FunctionalStatus" * >FunctionalStatus</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFunctionalStatusTypeParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFunctionalStatusTypeParser.java index dbbdc371511ee408d155d614dd6bb0bfc6fd7149..e99e063e83f78d809d5e3af171b185d3c5f1017b 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFunctionalStatusTypeParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeFunctionalStatusTypeParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.FunctionalStatusTypeColumnParser /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=FunctionalStatusType" * >FunctionalStatusType</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGenericDomainParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGenericDomainParser.java index f7d70c1090da9f1beecb359f162446f6aeb08250..32464b1f41de8b0b36bbd69ef1669994a32bea7f 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGenericDomainParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGenericDomainParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.GenericDomainColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=GenericDomain" * >GenericDomain</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoBiologicalProcessParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoBiologicalProcessParser.java index e1949ca49ca537a922cb7c6289bb00ffb8b770a4..df4bcc641f74395968bd4d9291f0821ba007c699 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoBiologicalProcessParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoBiologicalProcessParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.GoBiologicalProcessColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=GO_BiologicalProcess" * >GoBiologicalProcess</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoCellularComponentParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoCellularComponentParser.java index e3d6fe8599ecce7ce7a2f1bf5e835e1cc5d02562..b25db047e4006097ff465f89aecdd6a15f83efac 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoCellularComponentParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoCellularComponentParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.GoCellularComponentColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=GO_CellularComponent" * >GoCellularComponent</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoMolecularFunctionParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoMolecularFunctionParser.java index 044de56f2c6ec95eeaea7956082381f27d38e401..c7bc06099c269eed8966993d5bf701554e782799 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoMolecularFunctionParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGoMolecularFunctionParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.GoMolecularFunctionColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=GO_MolecularFunction" * >GoMolecularFunction</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGroupModifiedResidueParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGroupModifiedResidueParser.java index 8caa9c4de83cddb02bbcb0e21db635a00302614f..21346fbe01d3d09e244eeaa790837b6f6b32c79b 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGroupModifiedResidueParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeGroupModifiedResidueParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.GroupModifiedResidueColumnParser /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=GroupModifiedResidue" * >GroupModifiedResidue</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeInstanceEditParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeInstanceEditParser.java index 54ba2cc9797264821047459a4ea9be24c635787b..d44400f7607af68936efbbe594694cd06ad79cd0 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeInstanceEditParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeInstanceEditParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.InstanceEditColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=InstanceEdit" * >InstanceEdit</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeInterChainCrosslinkedResidueParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeInterChainCrosslinkedResidueParser.java index 8119ba657431cad6841c7d559fe09afff9017ba9..f409361c4623fb8afce61ff7e13305e1e81e8e97 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeInterChainCrosslinkedResidueParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeInterChainCrosslinkedResidueParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.InterChainCrosslinkedResidueColu /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=InterChainCrosslinkedResidue" * >InterChainCrosslinkedResidue</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeIntraChainCrosslinkedResidueParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeIntraChainCrosslinkedResidueParser.java index f4a12a706941346ab85c3def1b31ea478e29e87c..7917c35a89565f2f77d94101e754d100aa25b6ce 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeIntraChainCrosslinkedResidueParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeIntraChainCrosslinkedResidueParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.IntraChainCrosslinkedResidueColu /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=IntraChainCrosslinkedResidue" * >IntraChainCrosslinkedResidue</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeLiteratureReferenceParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeLiteratureReferenceParser.java index 8664b210c0a62b9907e6f01cc2456f49f7ea8df5..7eb163140d466b2edb5856220ca4f07429313a58 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeLiteratureReferenceParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeLiteratureReferenceParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.LiteratureReferenceColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=LiteratureReference" * >LiteratureReference</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeModifiedResidueParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeModifiedResidueParser.java index 4f0cc9235764d8a60c792a9ce2f75b17ab454c82..14e4e06949f0d8c31bece7de0a9294f30461bcd7 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeModifiedResidueParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeModifiedResidueParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ModifiedResidueColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=NegativeRegulation" * >NegativeRegulation</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeNegativeRegulationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeNegativeRegulationParser.java index 3b20ca7ec2cd78bb0f29536ff4f26f3b90359dd4..2fb0b89165d29e09de72ec94b8fbe059ca8f8e3b 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeNegativeRegulationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeNegativeRegulationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.NegativeRegulationColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=NegativeRegulation" * >NegativeRegulation</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeOpenSetParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeOpenSetParser.java index 558be583112c4aaa00b1674cc63e30ce88718477..c026b34eb3599121513da8ee2fb30d5a8744c3da 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeOpenSetParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeOpenSetParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.OpenSetColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=OpenSet" * >OpenSet</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeOtherEntityParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeOtherEntityParser.java index d5b971e0fe21f17e6c28af3f4d3cb55eb9a3dc0e..85546fd9dd67255ff6dc1433a78850bde0e8ef4c 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeOtherEntityParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeOtherEntityParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.OtherEntityColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=OtherEntity" * >OtherEntity</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayCoordinatesParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayCoordinatesParser.java index 5db28f0c5273f13506c5ebab43e7ea71e369a63e..f00c4344d5544cf34fec2bc9046e490d19ca77dc 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayCoordinatesParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayCoordinatesParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PathwayCoordinatesColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=PathwayCoordinates" * >PathwayCoordinates</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayDiagramParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayDiagramParser.java index 92d40a137fa57f390b7821841fe0c0c1c1840e04..b569cbacf2719d312ff7b36ca4bcb512b33ec096 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayDiagramParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayDiagramParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PathwayDiagramColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=PathwayDiagram" * >PathwayDiagram</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayParser.java index 225f5ffff8dbd75f0465198f72c897da68e871e6..9c25d551a31ac78b4d4688111dc064f63d2f7165 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PathwayColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Pathway" * >Pathway</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayVertexParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayVertexParser.java index 15406f18f1257b34b00240d18a1c53bcf3a4ec48..d44c862ecd8739a3e7bf3b6ec5a13cf4ee94c07e 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayVertexParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePathwayVertexParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PathwayVertexColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=PathwayVertex" * >PathwayVertex</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePersonParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePersonParser.java index a96e6d7f1792bbdf8b5d1193c8473f28817f795e..8d047fd29eb35993c168404e87c1d7f058951e4b 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePersonParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePersonParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PersonColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Person" * >Person</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePhysicalEntityParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePhysicalEntityParser.java index de892b7ed065145d84fa1a0e9430854295232d7e..e209e99f049bdd37137800f149d08f7b5792b5b7 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePhysicalEntityParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePhysicalEntityParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PhysicalEntityColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=PhysicalEntity" * >PhysicalEntity</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePolymerParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePolymerParser.java index daa573fde1c7f628a5fca8adabd42c2d6bf686e3..9684ddfc3432712e16ac05580f8c05587a5cef34 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePolymerParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePolymerParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PolymerColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Polymer" * >Polymer</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePolymerisationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePolymerisationParser.java index 10dec3ee76c5f48f966042eba84f62a43f6b61ac..7cad3eec462b6319d55eff85423ce9553358c153 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePolymerisationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePolymerisationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PolymerisationColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Polymerisation" * >Polymerisation</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePositiveRegulationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePositiveRegulationParser.java index fa740e6e49f1f19f186e7a41d6ed2008fa8ee8d5..e9af8e8d93e10ebfed6b6656da0f54008e172022 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePositiveRegulationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePositiveRegulationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PositiveRegulationColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=PositiveRegulation" * >PositiveRegulation</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePsiModParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePsiModParser.java index 80532b55f990dd1decb2ee24b451286ebd3bb090..42774459de2013eff325eefd240bed2ea979db9a 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePsiModParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePsiModParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PsiModColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=PsiMod" * >PsiMod</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePublicationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePublicationParser.java index a8b47f1222e88660882b6530e765f7f8b95a662d..23765fd91c2fd9e995ebffc9340e6f2e43eb79ce 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePublicationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomePublicationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.PublicationColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Publication" * >Publication</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionCoordinatesParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionCoordinatesParser.java index d8b968036c6eb0b7f197368ff067505482741423..c6082bbd1df4ab8969be746151b1f8b82d34ed4c 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionCoordinatesParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionCoordinatesParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReactionCoordinatesColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReactionCoordinates" * >ReactionCoordinates</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionParser.java index 6413b0d04779d925e683ab494b9acd58bb9cae92..85e790b7e7cf19c7d64eecaefdebffeaf276fed0 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReactionColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Reaction" * >Reaction</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionVertexParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionVertexParser.java index 6a7dfa9badfff718e1be41d76030e8455410fd5a..d3d9f54dcb69625d8d50416bbbb9c34a69369ad8 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionVertexParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionVertexParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReactionVertexColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReactionVertex" * >ReactionVertex</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionlikeEventParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionlikeEventParser.java index 59ffd855deb75f8f00688fcaa96addb7b33fbd40..387d4e0be258f4f3454833e130140d357c8bdfa2 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionlikeEventParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionlikeEventParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReactionlikeEventColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReactionlikeEvent" * >ReactionlikeEvent</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceDNASequenceParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceDNASequenceParser.java index 8fcbf4b96d5eeff8517b2a6c03f89e7d60670b1f..d71831964ff243793f2f42b915b2cc4b1093ce0c 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceDNASequenceParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceDNASequenceParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceDNASequenceColumnParser /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceDNASequence" * >ReferenceDNASequence</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceDatabaseParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceDatabaseParser.java index a5bef64b09ff159f9fd334e9fd258d56cc92c31f..2bcd564af537202d5fbbed28518131ad502600fd 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceDatabaseParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceDatabaseParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceDatabaseColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceDatabase" * >ReferenceDatabase</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceEntityParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceEntityParser.java index 20acd6bd8d22fedc3157e7736a4b45be309face7..1367865111a2008fba40cc945c873eea5fad6de6 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceEntityParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceEntityParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceEntityColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceEntity" * >ReferenceEntity</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParser.java index b60a6611c3b5817a50f3bbd2b3a6137ae6034038..7ef303753f328db5dc69a2aeb6f4423b8650fc8f 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParser.java @@ -6,7 +6,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceGeneProductColumnParser /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceGeneProduct" * >ReferenceGeneProduct</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGroupParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGroupParser.java index ee2676171c32bc0ba015b306f426c9d261d274ed..fa5f8a91a838187b82f65f3048f02b94b55cff22 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGroupParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGroupParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceGroupColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceGroup" * >ReferenceGroup</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParser.java index b3d5f78175f45c0c6a8de82a3efc51e4f939b166..598a9dd548e9a6a1d50a2ecff5059b2446dd6c13 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParser.java @@ -6,7 +6,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceIsoproductColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceIsoform" * >ReferenceIsoform</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceMoleculeParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceMoleculeParser.java index 5ab67784b313da4871047a8b042a5fa569dcaabb..99f6fb05cdd4ca4b42546a7f354e802ccc061de7 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceMoleculeParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceMoleculeParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceMoleculeColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceMolecule" * >ReferenceMolecule</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceRNASequenceParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceRNASequenceParser.java index 0f4e29ecf8d6b5ba27ad2799e3167b950d0349fd..cc014ab2edc7a613d84fd27b935b6fdd5670dd55 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceRNASequenceParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceRNASequenceParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceRNASequenceColumnParser /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceRNASequence" * >ReferenceRNASequence</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceSequenceParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceSequenceParser.java index 0e9d3281e7da2a37b3a52688df46fd9a9c3127f1..e555d8c7ece03d68928ebf12601ec6a8e99eb568 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceSequenceParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceSequenceParser.java @@ -6,7 +6,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReferenceSequenceColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReferenceSequence" * >ReferenceSequence</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeRegulationTypeParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeRegulationTypeParser.java index 6e36073ca90fb59f3f09f80603c7f463a88d1f99..446afe2e8911259d6795e826e224863a6d0f4126 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeRegulationTypeParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeRegulationTypeParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.RegulationTypeColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=RegulationType" * >RegulationType</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReplacedResidueParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReplacedResidueParser.java index e8b118a27230b2992f811f5743ff9c5924115474..4d7cfb7f469031ceffa7bd7577d49a43983a4d24 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReplacedResidueParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReplacedResidueParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ReplacedResidueColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReplacedResidue" * >ReplacedResidue</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeRequirementParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeRequirementParser.java index 3ecd3bbf2b6ddfc4f43412d1aa70f18f0ec25a8a..a1f9bc17c6279bdbcc3d60019dfbe70aa06017a9 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeRequirementParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeRequirementParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.RequirementColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Requirement" * >Requirement</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSequenceDomainParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSequenceDomainParser.java index 75494b542e4812573a6ae6165391480054e08e55..34deb0f2a9a541f94ec44893543be985928cbd46 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSequenceDomainParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSequenceDomainParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.SequenceDomainColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=SequenceDomain"> * SequenceDomain</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSequenceOntologyParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSequenceOntologyParser.java index 2d3661cc7b7b0e102eb9cb46d5783e474e3d8e25..06f2f7d02af5c798f5f5d7e15d7fbbeb7c3c7302 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSequenceOntologyParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSequenceOntologyParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.SequenceOntologyColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=SequenceOntology" * >SequenceOntology</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSimpleEntityParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSimpleEntityParser.java index b33c1547117e8dc6ea89ec8a92619daa33754be6..8e1e0094ee2ca64f23c624b487ed96f3db36c5d4 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSimpleEntityParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSimpleEntityParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.SimpleEntityColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=SimpleEntity" * >SimpleEntity</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSpeciesParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSpeciesParser.java index 03463613784e2765a758b54a881e7a8986e52906..f936a8d3d9165f804313d1568ddd87d11b5d4c4a 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSpeciesParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSpeciesParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.SpeciesColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Species" * >Species</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeStableIdentifierParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeStableIdentifierParser.java index ae43a4e509afe54255aacdc6949dddc49228885f..9fee035680731a11b110c7cdd3e09036bebd041d 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeStableIdentifierParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeStableIdentifierParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.StableIdentifierColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=StableIdentifier" * >StableIdentifier</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSummationParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSummationParser.java index 48d94528b11a3eb380905beff202a49c863295db..b1926e2b6a55fbd95c8e2f18601dbfc8c483e9d6 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSummationParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeSummationParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.SummationColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Summation" * >Summation</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeTaxonParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeTaxonParser.java index 9bcd3ed85aba70b76dcdcc745ceaea8fd4bb343f..3f4fca0c5e3ef93027bd14e4ae66145ffda6f883 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeTaxonParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeTaxonParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.TaxonColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Taxon" * >Taxon</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeURLParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeURLParser.java index b9cbae25ef628c35be3c52ca7f645f4d9843fd06..9aafded9645b004d7f573b6d16cda4e9cf8a1d40 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeURLParser.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeURLParser.java @@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.URLColumnParser; /** * Parser for reactome xml retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a> for <a href= * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=URL" * >URL</a> object. diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/package-info.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/package-info.java index f370b3576ceab7c93fe45783a73c943b15f6ee1f..9f8103390ac2ab12f66392fbb717ac96cc4c9e3b 100644 --- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/package-info.java +++ b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/package-info.java @@ -1,6 +1,6 @@ /** * Provides parsers for xml data retrieved from <a href= - * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" + * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" * >Reactome API</a>. */ package lcsb.mapviewer.reactome.xml; diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java index 1c8e5b6bfa7865b711c9456db1112283cd29c96a..65aed9ba0998833b2d56e8b96f926dc0ccf244f6 100644 --- a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java +++ b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java @@ -169,7 +169,7 @@ public class ReactomeConnectorTest extends ReactomeTestFunctions { @Test(timeout = 15000) public void testCachableInterfaceByParams() throws Exception { - String url = "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/RESTfulWS/listByQuery/DatabaseObjects"; + String url = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/listByQuery/DatabaseObjects"; String query = "identifier=2562550\n" + url; String newRes = "hello"; try {