############################################################################### # Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) # Copyright (C) $$Year-Rel$$ The Jalview Authors # # This file is part of Jalview. # # Jalview is free software: you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. # # Jalview is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty # of MERCHANTABILITY or FITNESS FOR A PARTICULAR # PURPOSE. See the GNU General Public License for more details. # # You should have received a copy of the GNU General Public License along with Jalview. If not, see . # The Jalview Authors are detailed in the 'AUTHORS' file. ############################################################################### # 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=false # 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