From bd4bd354d62b1c3aba6c42574219856f56333f9d Mon Sep 17 00:00:00 2001 From: jprocter Date: Sun, 24 Feb 2008 20:08:56 +0000 Subject: [PATCH] sequenceId is a string, not an integer - allows generation of unlimited unique sequential sequence Ids --- src/castor.properties | 236 +++++++++++++++ .../version2/descriptors/JSeqDescriptor.java | 18 +- src/jalview/schemes/ResidueProperties.java | 49 ++++ src/uk/ac/ebi/picr/model/CrossReference.java | 302 ++++++++++++++++++++ .../ac/ebi/picr/model/CrossReference_Helper.java | 95 ++++++ src/uk/ac/ebi/picr/model/UPEntry.java | 251 ++++++++++++++++ src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 82 ++++++ .../AccessionMapperBindingStub.java | 254 ++++++++++++++++ .../AccessionMapperInterface.java | 14 + .../AccessionMapperService.java | 16 ++ .../AccessionMapperServiceLocator.java | 136 +++++++++ 11 files changed, 1442 insertions(+), 11 deletions(-) create mode 100644 src/castor.properties create mode 100644 src/uk/ac/ebi/picr/model/CrossReference.java create mode 100644 src/uk/ac/ebi/picr/model/CrossReference_Helper.java create mode 100644 src/uk/ac/ebi/picr/model/UPEntry.java create mode 100644 src/uk/ac/ebi/picr/model/UPEntry_Helper.java create mode 100644 src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java create mode 100644 src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java create mode 100644 src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java create mode 100644 src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java diff --git a/src/castor.properties b/src/castor.properties new file mode 100644 index 0000000..72f4ee6 --- /dev/null +++ b/src/castor.properties @@ -0,0 +1,236 @@ +# THE CASTOR PROPERTIES FILE +# This file specifies values for Castor run-time which may be configured +# by the user. +# $Id$ + +# This section defines Backwards compatibility switches. +# +# Hashtable/Map default mapping. +# For backward compatibility with 0.9.5.2 and earlier. +# +#org.exolab.castor.xml.saveMapKeys=false + +# Defines the default XML parser to be used by Castor. +# The parser must implement org.xml.sax.Parser. +# +org.exolab.castor.parser=org.apache.xerces.parsers.SAXParser + +# Defines the (default) XML serializer factory to use by Castor, which must +# implement org.exolab.castor.xml.SerializerFactory; default is +# org.exolab.castor.xml.XercesXMLSerializerFactory +# +# When using Castor XML with JDK 5.0, you may switch to the XercesJDK5XMLSerializerFactory +# which will use the Xerces instance as shipped with the JDK itself; this avoids +# having to download another Xerces instance and installing it. +org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesXMLSerializerFactory +#org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesJDK5XMLSerializerFactory + +# Defines the NodeType for use with Java primitive types (int, long, boolean, +# etc). This value is only used by the Introspector. Valid values are either +# "attribute" or "element". By default, all primitives are marshaled as +# attributes. Uncomment the following line to change the NodeType to element. +# +#org.exolab.castor.xml.introspector.primitive.nodetype=element + +# Defines the Naming "style" or conventions to use when creating XML names +# from Java class or field names. +# Valid values are as follows: +# ----------------------------------------------------------------- +# lower (default) | All names are lowercase with hyphens +# | separating words. +# | +# | Example: personInfo = person-info +# ----------------------------------------------------------------- +# mixed | All names are mixed case, with Uppercase +# | character as the first letter of a new word. +# | +# | Example: personInfo = personInfo +# | Example: FooBar = fooBar +# ----------------------------------------------------------------- +# {Any ClassName} | Any Class which implements +# | org.exolab.castor.xml.XMLNaming +# ----------------------------------------------------------------- +# +# By default, all names are treated as the "lower" option. To preserve the +# Java mixed-case conventions, uncomment the following line. +# +#org.exolab.castor.xml.naming=mixed + +############################### +# REGULAR EXPRESSION EVALUATORS +# +# Defines the Regular Expression Evaluator to be used by Castor. +# The evaluator must implement org.exolab.castor.util.RegExpEvaluator. +# +# Uncomment the following to basically suppress Regular expressions evaluation: +#org.exolab.castor.regexp=org.exolab.castor.xml.util.AlwaysTrueRegExpEvaluator +# +# An implementation which uses the Jakarta RegExp library: +#org.exolab.castor.regexp=org.exolab.castor.util.JakartaRegExpEvaluator +# +# An implementation which uses the Jakarta ORO library: +org.exolab.castor.regexp=org.exolab.castor.util.JakartaOroEvaluator + +# True if all documents should be indented on output by default. +# Defaults to false. +# +#org.exolab.castor.indent=true + +# True if xml documents should be validated by the SAX Parser +# Defaults to false. +# +org.exolab.castor.parser.validation=false + +# True for parser to support Namespaces. +# Defaults to false. +# +org.exolab.castor.parser.namespaces=false + +# True if all documents should be validated by the marshaling framework +# Defaults to true. +# +org.exolab.castor.marshalling.validation=true + +# Comma separated list of SAX 2 features that should be enabled for the +# default parser. +# +#org.exolab.castor.sax.features= + +# Comma separated list of SAX 2 features that should be disabled for the +# default parser. +# +#org.exolab.castor.sax.features-to-disable + +# True if debugging output should be generated. +# Defaults to false. +# +org.exolab.castor.debug=true + +# List of collection handlers for Java 1.1 and Java 1.2 run-times: +# +org.exolab.castor.mapping.collections=\ + org.exolab.castor.mapping.loader.J1CollectionHandlers,\ + org.exolab.castor.mapping.loader.J2CollectionHandlers + +# List of persistence factories for the supported database servers: +# +org.exolab.castor.jdo.engines=\ + org.exolab.castor.jdo.drivers.OracleFactory,\ + org.exolab.castor.jdo.drivers.PostgreSQLFactory,\ + org.exolab.castor.jdo.drivers.SybaseFactory,\ + org.exolab.castor.jdo.drivers.SQLServerFactory,\ + org.exolab.castor.jdo.drivers.DB2Factory,\ + org.exolab.castor.jdo.drivers.InformixFactory,\ + org.exolab.castor.jdo.drivers.HsqlFactory,\ + org.exolab.castor.jdo.drivers.InstantDBFactory,\ + org.exolab.castor.jdo.drivers.InterbaseFactory,\ + org.exolab.castor.jdo.drivers.MySQLFactory,\ + org.exolab.castor.jdo.drivers.SapDbFactory,\ + org.exolab.castor.jdo.drivers.GenericFactory,\ + org.exolab.castor.jdo.drivers.DerbyFactory,\ + org.castor.jdo.drivers.PointbaseFactory,\ + org.castor.jdo.drivers.ProgressFactory + +# List of key generator factories: +# +org.exolab.castor.jdo.keyGeneratorFactories=\ + org.exolab.castor.jdo.keygen.MaxKeyGeneratorFactory,\ + org.exolab.castor.jdo.keygen.HighLowKeyGeneratorFactory,\ + org.exolab.castor.jdo.keygen.IdentityKeyGeneratorFactory,\ + org.exolab.castor.jdo.keygen.SequenceKeyGeneratorFactory,\ + org.exolab.castor.jdo.keygen.UUIDKeyGeneratorFactory + +# Collection handlers for the source code generator: +# +org.exolab.castor.builder.type.j2=\ + org.exolab.castor.builder.FieldInfoFactoryJ2 +org.exolab.castor.builder.type.j1=\ + org.exolab.castor.builder.FieldInfoFactory +org.exolab.castor.builder.type.odmg=\ + org.exolab.castor.builder.FieldInfoFactoryODMG30 + +# Configures the default time zone to apply to dates/times fetched from +# database fields (if not already part of the data). Specify same format as +# in java.util.TimeZone.getTimeZone, or the empty string to use the computer's +# local time zone. Please see http://de.wikipedia.org/wiki/Zeitzone for +# detailed information about time zones. +# +org.exolab.castor.jdo.defaultTimeZone= +#org.exolab.castor.jdo.defaultTimeZone=GMT-8:00 + +# List of TxSynchronizeable implementations: +# +#org.exolab.castor.persist.TxSynchronizable= + +# Sets the buffer size in bytes for fetching LOBs (this is dependent upon +# the JDBC driver implementation). The value below == 5k. +# +org.exolab.castor.jdo.lobBufferSize=5120 + +# True if database configuration should be initalization +# when loading it (default: true). +# +#org.exolab.castor.jdo.DatabaseInitializeAtLoad=true + +# True if proxy classes should be used for JDBC connections and +# prepared statements. +# Defaults to true. +# +org.exolab.castor.persist.useProxies=false + +# MappingLoader implementations: +# +org.castor.mapping.loaderFactories=\ + org.castor.mapping.JDOMappingLoaderFactory,\ + org.castor.mapping.XMLMappingLoaderFactory + +# Cache implementations: +# +org.castor.cache.Factories=\ + org.castor.cache.simple.NoCacheFactory,\ + org.castor.cache.simple.TimeLimitedFactory,\ + org.castor.cache.simple.CountLimitedFactory,\ + org.castor.cache.simple.UnlimitedFactory,\ + org.castor.cache.distributed.FKCacheFactory,\ + org.castor.cache.distributed.JcsCacheFactory,\ + org.castor.cache.distributed.JCacheFactory,\ + org.castor.cache.distributed.CoherenceCacheFactory,\ + org.castor.cache.distributed.OsCacheFactory,\ + org.castor.cache.hashbelt.FIFOHashbeltFactory,\ + org.castor.cache.hashbelt.LRUHashbeltFactory,\ + org.castor.cache.distributed.EHCacheFactory,\ + org.castor.cache.distributed.GigaspacesCacheFactory + +# TransactionManagerFactory implementations: +# +org.castor.transactionmanager.Factories=\ + org.castor.transactionmanager.WebSphereTransactionManagerFactory,\ + org.castor.transactionmanager.WebSphere5TransactionManagerFactory,\ + org.castor.transactionmanager.WebSphere51TransactionManagerFactory,\ + org.castor.transactionmanager.LocalTransactionManagerFactory,\ + org.castor.transactionmanager.JNDIENCTransactionManagerFactory,\ + org.castor.transactionmanager.JOTMTransactionManagerFactory + +# Selects whether the TransactionManager should be initialized at registration, +# or lazily when requested for the first time. +# Defaults to false. +# +org.castor.transactionmanager.InitializeAtRegistration=false + +# Instructs Castor JDO to use the JDBC 3.0-specific features to obtain +# the generated value of an identity column. +# Defaults to false. +# +org.castor.jdo.use.jdbc30=false + +# Specifies whether to use ANSI-compliant SQL for MS SQL Server. +# Defaults to false. +# +org.exolab.castor.jdo.sqlserver.ansi-compliant=false + +# Specifyies whether the ClassDescriptorResolver should (automatically) search +# for and consult with package mapping files (.castor.xml) to retrieve class +# descriptor information; on by default. +# Defaults to true. +# +#org.exolab.castor.xml.loadPackageMappings=false diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java index 738d4fc..427702d 100644 --- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java @@ -193,24 +193,21 @@ public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto } desc.setValidator(fieldValidator); //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { JSeq target = (JSeq) object; - if (!target.hasId()) { return null; } - return new java.lang.Integer(target.getId()); + return target.getId(); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException { try { JSeq target = (JSeq) object; - // ignore null values for non optional primitives - if (value == null) { return; } - - target.setId( ((java.lang.Integer) value).intValue()); + target.setId( (java.lang.String) value); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); } @@ -228,11 +225,10 @@ public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto fieldValidator = new org.exolab.castor.xml.FieldValidator(); fieldValidator.setMinOccurs(1); { //-- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + typeValidator.setWhiteSpace("preserve"); } desc.setValidator(fieldValidator); //-- _hidden diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index e55ce18..98868d2 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1290,4 +1290,53 @@ public class ResidueProperties } return ss.toString(); } + // main method generates perl representation of residue property hash + /// cut here + public static void main(String[] args) + { + Hashtable aa = new Hashtable(); + System.out.println("my %aa = {"); + // invert property hashes + Enumeration prop = propHash.keys(); + while (prop.hasMoreElements()) + { + String pname = (String) prop.nextElement(); + Hashtable phash = (Hashtable) propHash.get(pname); + Enumeration res = phash.keys(); + while (res.hasMoreElements()) + { + String rname = (String) res.nextElement(); + Vector aprops = (Vector) aa.get(rname); + if (aprops==null) + { + aprops = new Vector(); + aa.put(rname, aprops); + } + Integer hasprop = (Integer) phash.get(rname); + if (hasprop.intValue()==1) + { + aprops.addElement(pname); + } + } + } + Enumeration res = aa.keys(); + while (res.hasMoreElements()) + { + String rname = (String) res.nextElement(); + + System.out.print("'"+rname+"' => ["); + Enumeration props = ((Vector) aa.get(rname)).elements(); + while (props.hasMoreElements()) + { + System.out.print("'"+(String)props.nextElement()+"'"); + if (props.hasMoreElements()) + { + System.out.println(", "); + } + } + System.out.println("]"+(res.hasMoreElements() ? "," : "")); + } + System.out.println("};"); + } + // to here } diff --git a/src/uk/ac/ebi/picr/model/CrossReference.java b/src/uk/ac/ebi/picr/model/CrossReference.java new file mode 100644 index 0000000..04b50bf --- /dev/null +++ b/src/uk/ac/ebi/picr/model/CrossReference.java @@ -0,0 +1,302 @@ +/** + * CrossReference.java + * + * This file was auto-generated from WSDL + * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. + */ + +package uk.ac.ebi.picr.model; + +public class CrossReference implements java.io.Serializable { + private java.lang.String accession; + private java.lang.String accessionVersion; + private java.lang.String databaseDescription; + private java.lang.String databaseName; + private java.util.Calendar dateAdded; + private java.util.Calendar dateDeleted; + private boolean deleted; + private java.lang.String gi; + private java.lang.String taxonId; + + public CrossReference() { + } + + public CrossReference( + java.lang.String accession, + java.lang.String accessionVersion, + java.lang.String databaseDescription, + java.lang.String databaseName, + java.util.Calendar dateAdded, + java.util.Calendar dateDeleted, + boolean deleted, + java.lang.String gi, + java.lang.String taxonId) { + this.accession = accession; + this.accessionVersion = accessionVersion; + this.databaseDescription = databaseDescription; + this.databaseName = databaseName; + this.dateAdded = dateAdded; + this.dateDeleted = dateDeleted; + this.deleted = deleted; + this.gi = gi; + this.taxonId = taxonId; + } + + + /** + * Gets the accession value for this CrossReference. + * + * @return accession + */ + public java.lang.String getAccession() { + return accession; + } + + + /** + * Sets the accession value for this CrossReference. + * + * @param accession + */ + public void setAccession(java.lang.String accession) { + this.accession = accession; + } + + + /** + * Gets the accessionVersion value for this CrossReference. + * + * @return accessionVersion + */ + public java.lang.String getAccessionVersion() { + return accessionVersion; + } + + + /** + * Sets the accessionVersion value for this CrossReference. + * + * @param accessionVersion + */ + public void setAccessionVersion(java.lang.String accessionVersion) { + this.accessionVersion = accessionVersion; + } + + + /** + * Gets the databaseDescription value for this CrossReference. + * + * @return databaseDescription + */ + public java.lang.String getDatabaseDescription() { + return databaseDescription; + } + + + /** + * Sets the databaseDescription value for this CrossReference. + * + * @param databaseDescription + */ + public void setDatabaseDescription(java.lang.String databaseDescription) { + this.databaseDescription = databaseDescription; + } + + + /** + * Gets the databaseName value for this CrossReference. + * + * @return databaseName + */ + public java.lang.String getDatabaseName() { + return databaseName; + } + + + /** + * Sets the databaseName value for this CrossReference. + * + * @param databaseName + */ + public void setDatabaseName(java.lang.String databaseName) { + this.databaseName = databaseName; + } + + + /** + * Gets the dateAdded value for this CrossReference. + * + * @return dateAdded + */ + public java.util.Calendar getDateAdded() { + return dateAdded; + } + + + /** + * Sets the dateAdded value for this CrossReference. + * + * @param dateAdded + */ + public void setDateAdded(java.util.Calendar dateAdded) { + this.dateAdded = dateAdded; + } + + + /** + * Gets the dateDeleted value for this CrossReference. + * + * @return dateDeleted + */ + public java.util.Calendar getDateDeleted() { + return dateDeleted; + } + + + /** + * Sets the dateDeleted value for this CrossReference. + * + * @param dateDeleted + */ + public void setDateDeleted(java.util.Calendar dateDeleted) { + this.dateDeleted = dateDeleted; + } + + + /** + * Gets the deleted value for this CrossReference. + * + * @return deleted + */ + public boolean isDeleted() { + return deleted; + } + + + /** + * Sets the deleted value for this CrossReference. + * + * @param deleted + */ + public void setDeleted(boolean deleted) { + this.deleted = deleted; + } + + + /** + * Gets the gi value for this CrossReference. + * + * @return gi + */ + public java.lang.String getGi() { + return gi; + } + + + /** + * Sets the gi value for this CrossReference. + * + * @param gi + */ + public void setGi(java.lang.String gi) { + this.gi = gi; + } + + + /** + * Gets the taxonId value for this CrossReference. + * + * @return taxonId + */ + public java.lang.String getTaxonId() { + return taxonId; + } + + + /** + * Sets the taxonId value for this CrossReference. + * + * @param taxonId + */ + public void setTaxonId(java.lang.String taxonId) { + this.taxonId = taxonId; + } + + private java.lang.Object __equalsCalc = null; + public synchronized boolean equals(java.lang.Object obj) { + if (!(obj instanceof CrossReference)) return false; + CrossReference other = (CrossReference) obj; + if (obj == null) return false; + if (this == obj) return true; + if (__equalsCalc != null) { + return (__equalsCalc == obj); + } + __equalsCalc = obj; + boolean _equals; + _equals = true && + ((this.accession==null && other.getAccession()==null) || + (this.accession!=null && + this.accession.equals(other.getAccession()))) && + ((this.accessionVersion==null && other.getAccessionVersion()==null) || + (this.accessionVersion!=null && + this.accessionVersion.equals(other.getAccessionVersion()))) && + ((this.databaseDescription==null && other.getDatabaseDescription()==null) || + (this.databaseDescription!=null && + this.databaseDescription.equals(other.getDatabaseDescription()))) && + ((this.databaseName==null && other.getDatabaseName()==null) || + (this.databaseName!=null && + this.databaseName.equals(other.getDatabaseName()))) && + ((this.dateAdded==null && other.getDateAdded()==null) || + (this.dateAdded!=null && + this.dateAdded.equals(other.getDateAdded()))) && + ((this.dateDeleted==null && other.getDateDeleted()==null) || + (this.dateDeleted!=null && + this.dateDeleted.equals(other.getDateDeleted()))) && + this.deleted == other.isDeleted() && + ((this.gi==null && other.getGi()==null) || + (this.gi!=null && + this.gi.equals(other.getGi()))) && + ((this.taxonId==null && other.getTaxonId()==null) || + (this.taxonId!=null && + this.taxonId.equals(other.getTaxonId()))); + __equalsCalc = null; + return _equals; + } + + private boolean __hashCodeCalc = false; + public synchronized int hashCode() { + if (__hashCodeCalc) { + return 0; + } + __hashCodeCalc = true; + int _hashCode = 1; + if (getAccession() != null) { + _hashCode += getAccession().hashCode(); + } + if (getAccessionVersion() != null) { + _hashCode += getAccessionVersion().hashCode(); + } + if (getDatabaseDescription() != null) { + _hashCode += getDatabaseDescription().hashCode(); + } + if (getDatabaseName() != null) { + _hashCode += getDatabaseName().hashCode(); + } + if (getDateAdded() != null) { + _hashCode += getDateAdded().hashCode(); + } + if (getDateDeleted() != null) { + _hashCode += getDateDeleted().hashCode(); + } + _hashCode += (isDeleted() ? Boolean.TRUE : Boolean.FALSE).hashCode(); + if (getGi() != null) { + _hashCode += getGi().hashCode(); + } + if (getTaxonId() != null) { + _hashCode += getTaxonId().hashCode(); + } + __hashCodeCalc = false; + return _hashCode; + } + +} diff --git a/src/uk/ac/ebi/picr/model/CrossReference_Helper.java b/src/uk/ac/ebi/picr/model/CrossReference_Helper.java new file mode 100644 index 0000000..0613a0c --- /dev/null +++ b/src/uk/ac/ebi/picr/model/CrossReference_Helper.java @@ -0,0 +1,95 @@ +/** + * CrossReference_Helper.java + * + * This file was auto-generated from WSDL + * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. + */ + +package uk.ac.ebi.picr.model; + +public class CrossReference_Helper { + // Type metadata + private static org.apache.axis.description.TypeDesc typeDesc = + new org.apache.axis.description.TypeDesc(CrossReference.class, true); + + static { + typeDesc.setXmlType(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "CrossReference")); + org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("accession"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "accession")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string")); + typeDesc.addFieldDesc(elemField); + elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("accessionVersion"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "accessionVersion")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string")); + typeDesc.addFieldDesc(elemField); + elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("databaseDescription"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "databaseDescription")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string")); + typeDesc.addFieldDesc(elemField); + elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("databaseName"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "databaseName")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string")); + typeDesc.addFieldDesc(elemField); + elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("dateAdded"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "dateAdded")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "dateTime")); + typeDesc.addFieldDesc(elemField); + elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("dateDeleted"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "dateDeleted")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "dateTime")); + typeDesc.addFieldDesc(elemField); + elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("deleted"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "deleted")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean")); + typeDesc.addFieldDesc(elemField); + elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("gi"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "gi")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string")); + typeDesc.addFieldDesc(elemField); + elemField = new org.apache.axis.description.ElementDesc(); + elemField.setFieldName("taxonId"); + elemField.setXmlName(new javax.xml.namespace.QName("http://model.picr.ebi.ac.uk", "taxonId")); + elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string")); + typeDesc.addFieldDesc(elemField); + } + + /** + * Return type metadata object + */ + public static org.apache.axis.description.TypeDesc getTypeDesc() { + return typeDesc; + } + + /** + * Get Custom Serializer + */ + public static org.apache.axis.encoding.Serializer getSerializer( + java.lang.String mechType, + java.lang.Class _javaType, + javax.xml.namespace.QName _xmlType) { + return + new org.apache.axis.encoding.ser.BeanSerializer( + _javaType, _xmlType, typeDesc); + } + + /** + * Get Custom Deserializer + */ + public static org.apache.axis.encoding.Deserializer getDeserializer( + java.lang.String mechType, + java.lang.Class _javaType, + javax.xml.namespace.QName _xmlType) { + return + new org.apache.axis.encoding.ser.BeanDeserializer( + _javaType, _xmlType, typeDesc); + } + +} diff --git a/src/uk/ac/ebi/picr/model/UPEntry.java b/src/uk/ac/ebi/picr/model/UPEntry.java new file mode 100644 index 0000000..2237ba8 --- /dev/null +++ b/src/uk/ac/ebi/picr/model/UPEntry.java @@ -0,0 +1,251 @@ +/** + * UPEntry.java + * + * This file was auto-generated from WSDL + * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. + */ + +package uk.ac.ebi.picr.model; + +public class UPEntry implements java.io.Serializable { + private java.lang.String CRC64; + private java.lang.String UPI; + private uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences; + private uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences; + private java.lang.String sequence; + private java.util.Calendar timestamp; + + public UPEntry() { + } + + public UPEntry( + java.lang.String CRC64, + java.lang.String UPI, + uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences, + uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences, + java.lang.String sequence, + java.util.Calendar timestamp) { + this.CRC64 = CRC64; + this.UPI = UPI; + this.identicalCrossReferences = identicalCrossReferences; + this.logicalCrossReferences = logicalCrossReferences; + this.sequence = sequence; + this.timestamp = timestamp; + } + + + /** + * Gets the CRC64 value for this UPEntry. + * + * @return CRC64 + */ + public java.lang.String getCRC64() { + return CRC64; + } + + + /** + * Sets the CRC64 value for this UPEntry. + * + * @param CRC64 + */ + public void setCRC64(java.lang.String CRC64) { + this.CRC64 = CRC64; + } + + + /** + * Gets the UPI value for this UPEntry. + * + * @return UPI + */ + public java.lang.String getUPI() { + return UPI; + } + + + /** + * Sets the UPI value for this UPEntry. + * + * @param UPI + */ + public void setUPI(java.lang.String UPI) { + this.UPI = UPI; + } + + + /** + * Gets the identicalCrossReferences value for this UPEntry. + * + * @return identicalCrossReferences + */ + public uk.ac.ebi.picr.model.CrossReference[] getIdenticalCrossReferences() { + return identicalCrossReferences; + } + + + /** + * Sets the identicalCrossReferences value for this UPEntry. + * + * @param identicalCrossReferences + */ + public void setIdenticalCrossReferences(uk.ac.ebi.picr.model.CrossReference[] identicalCrossReferences) { + this.identicalCrossReferences = identicalCrossReferences; + } + + public uk.ac.ebi.picr.model.CrossReference getIdenticalCrossReferences(int i) { + return this.identicalCrossReferences[i]; + } + + public void setIdenticalCrossReferences(int i, uk.ac.ebi.picr.model.CrossReference _value) { + this.identicalCrossReferences[i] = _value; + } + + + /** + * Gets the logicalCrossReferences value for this UPEntry. + * + * @return logicalCrossReferences + */ + public uk.ac.ebi.picr.model.CrossReference[] getLogicalCrossReferences() { + return logicalCrossReferences; + } + + + /** + * Sets the logicalCrossReferences value for this UPEntry. + * + * @param logicalCrossReferences + */ + public void setLogicalCrossReferences(uk.ac.ebi.picr.model.CrossReference[] logicalCrossReferences) { + this.logicalCrossReferences = logicalCrossReferences; + } + + public uk.ac.ebi.picr.model.CrossReference getLogicalCrossReferences(int i) { + return this.logicalCrossReferences[i]; + } + + public void setLogicalCrossReferences(int i, uk.ac.ebi.picr.model.CrossReference _value) { + this.logicalCrossReferences[i] = _value; + } + + + /** + * Gets the sequence value for this UPEntry. + * + * @return sequence + */ + public java.lang.String getSequence() { + return sequence; + } + + + /** + * Sets the sequence value for this UPEntry. + * + * @param sequence + */ + public void setSequence(java.lang.String sequence) { + this.sequence = sequence; + } + + + /** + * Gets the timestamp value for this UPEntry. + * + * @return timestamp + */ + public java.util.Calendar getTimestamp() { + return timestamp; + } + + + /** + * Sets the timestamp value for this UPEntry. + * + * @param timestamp + */ + public void setTimestamp(java.util.Calendar timestamp) { + this.timestamp = timestamp; + } + + private java.lang.Object __equalsCalc = null; + public synchronized boolean equals(java.lang.Object obj) { + if (!(obj instanceof UPEntry)) return false; + UPEntry other = (UPEntry) obj; + if (obj == null) return false; + if (this == obj) return true; + if (__equalsCalc != null) { + return (__equalsCalc == obj); + } + __equalsCalc = obj; + boolean _equals; + _equals = true && + ((this.CRC64==null && other.getCRC64()==null) || + (this.CRC64!=null && + this.CRC64.equals(other.getCRC64()))) && + ((this.UPI==null && other.getUPI()==null) || + (this.UPI!=null && + this.UPI.equals(other.getUPI()))) && + ((this.identicalCrossReferences==null && other.getIdenticalCrossReferences()==null) || + (this.identicalCrossReferences!=null && + java.util.Arrays.equals(this.identicalCrossReferences, other.getIdenticalCrossReferences()))) && + ((this.logicalCrossReferences==null && other.getLogicalCrossReferences()==null) || + (this.logicalCrossReferences!=null && + java.util.Arrays.equals(this.logicalCrossReferences, other.getLogicalCrossReferences()))) && + ((this.sequence==null && other.getSequence()==null) || + (this.sequence!=null && + this.sequence.equals(other.getSequence()))) && + ((this.timestamp==null && other.getTimestamp()==null) || + (this.timestamp!=null && + this.timestamp.equals(other.getTimestamp()))); + __equalsCalc = null; + return _equals; + } + + private boolean __hashCodeCalc = false; + public synchronized int hashCode() { + if (__hashCodeCalc) { + return 0; + } + __hashCodeCalc = true; + int _hashCode = 1; + if (getCRC64() != null) { + _hashCode += getCRC64().hashCode(); + } + if (getUPI() != null) { + _hashCode += getUPI().hashCode(); + } + if (getIdenticalCrossReferences() != null) { + for (int i=0; + i