###############################################################################
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
# The Jalview Authors are detailed in the 'AUTHORS' file.
###############################################################################
- # THE CASTOR PROPERTIES FILE\r
- # This file specifies values for Castor run-time which may be configured\r
- # by the user.\r
- # $Id$\r
- \r
- # This section defines Backwards compatibility switches.\r
- #\r
- # Hashtable/Map default mapping.\r
- # For backward compatibility with 0.9.5.2 and earlier.\r
- #\r
- #org.exolab.castor.xml.saveMapKeys=false\r
- \r
- # Defines the default XML parser to be used by Castor.\r
- # The parser must implement org.xml.sax.Parser.\r
- #\r
- org.exolab.castor.parser=org.apache.xerces.parsers.SAXParser\r
- \r
- # Defines the (default) XML serializer factory to use by Castor, which must\r
- # implement org.exolab.castor.xml.SerializerFactory; default is \r
- # org.exolab.castor.xml.XercesXMLSerializerFactory\r
- # \r
- # When using Castor XML with JDK 5.0, you may switch to the XercesJDK5XMLSerializerFactory\r
- # which will use the Xerces instance as shipped with the JDK itself; this avoids\r
- # having to download another Xerces instance and installing it. \r
- org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesXMLSerializerFactory\r
- #org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesJDK5XMLSerializerFactory\r
- \r
- # Defines the NodeType for use with Java primitive types (int, long, boolean,\r
- # etc). This value is only used by the Introspector. Valid values are either\r
- # "attribute" or "element". By default, all primitives are marshaled as\r
- # attributes. Uncomment the following line to change the NodeType to element.\r
- #\r
- #org.exolab.castor.xml.introspector.primitive.nodetype=element\r
- \r
- # Defines the Naming "style" or conventions to use when creating XML names\r
- # from Java class or field names.\r
- # Valid values are as follows:\r
- # -----------------------------------------------------------------\r
- # lower (default) | All names are lowercase with hyphens\r
- # | separating words.\r
- # |\r
- # | Example: personInfo = person-info\r
- # -----------------------------------------------------------------\r
- # mixed | All names are mixed case, with Uppercase\r
- # | character as the first letter of a new word.\r
- # |\r
- # | Example: personInfo = personInfo\r
- # | Example: FooBar = fooBar\r
- # -----------------------------------------------------------------\r
- # {Any ClassName} | Any Class which implements\r
- # | org.exolab.castor.xml.XMLNaming\r
- # -----------------------------------------------------------------\r
- #\r
- # By default, all names are treated as the "lower" option. To preserve the\r
- # Java mixed-case conventions, uncomment the following line.\r
- #\r
- #org.exolab.castor.xml.naming=mixed\r
- \r
- ###############################\r
- # REGULAR EXPRESSION EVALUATORS\r
- #\r
- # Defines the Regular Expression Evaluator to be used by Castor.\r
- # The evaluator must implement org.exolab.castor.util.RegExpEvaluator.\r
- #\r
- # Uncomment the following to basically suppress Regular expressions evaluation:\r
- #org.exolab.castor.regexp=org.exolab.castor.xml.util.AlwaysTrueRegExpEvaluator\r
- #\r
- # An implementation which uses the Jakarta RegExp library:\r
- #org.exolab.castor.regexp=org.exolab.castor.util.JakartaRegExpEvaluator\r
- #\r
- # An implementation which uses the Jakarta ORO library:\r
- org.exolab.castor.regexp=org.exolab.castor.util.JakartaOroEvaluator\r
- \r
- # True if all documents should be indented on output by default.\r
- # Defaults to false.\r
- #\r
- #org.exolab.castor.indent=true\r
- \r
- # True if xml documents should be validated by the SAX Parser\r
- # Defaults to false.\r
- #\r
- org.exolab.castor.parser.validation=false\r
- \r
- # True for parser to support Namespaces.\r
- # Defaults to false.\r
- #\r
- org.exolab.castor.parser.namespaces=false\r
- \r
- # True if all documents should be validated by the marshaling framework\r
- # Defaults to true.\r
- #\r
- org.exolab.castor.marshalling.validation=true\r
- \r
- # Comma separated list of SAX 2 features that should be enabled for the\r
- # default parser.\r
- #\r
- #org.exolab.castor.sax.features=\r
- \r
- # Comma separated list of SAX 2 features that should be disabled for the\r
- # default parser.\r
- #\r
- #org.exolab.castor.sax.features-to-disable\r
- \r
- # True if debugging output should be generated.\r
- # Defaults to false.\r
- #\r
- org.exolab.castor.debug=false\r
- \r
- # List of collection handlers for Java 1.1 and Java 1.2 run-times:\r
- #\r
- org.exolab.castor.mapping.collections=\\r
- org.exolab.castor.mapping.loader.J1CollectionHandlers,\\r
- org.exolab.castor.mapping.loader.J2CollectionHandlers\r
- \r
- # List of persistence factories for the supported database servers:\r
- #\r
- org.exolab.castor.jdo.engines=\\r
- org.exolab.castor.jdo.drivers.OracleFactory,\\r
- org.exolab.castor.jdo.drivers.PostgreSQLFactory,\\r
- org.exolab.castor.jdo.drivers.SybaseFactory,\\r
- org.exolab.castor.jdo.drivers.SQLServerFactory,\\r
- org.exolab.castor.jdo.drivers.DB2Factory,\\r
- org.exolab.castor.jdo.drivers.InformixFactory,\\r
- org.exolab.castor.jdo.drivers.HsqlFactory,\\r
- org.exolab.castor.jdo.drivers.InstantDBFactory,\\r
- org.exolab.castor.jdo.drivers.InterbaseFactory,\\r
- org.exolab.castor.jdo.drivers.MySQLFactory,\\r
- org.exolab.castor.jdo.drivers.SapDbFactory,\\r
- org.exolab.castor.jdo.drivers.GenericFactory,\\r
- org.exolab.castor.jdo.drivers.DerbyFactory,\\r
- org.castor.jdo.drivers.PointbaseFactory,\\r
- org.castor.jdo.drivers.ProgressFactory\r
- \r
- # List of key generator factories:\r
- #\r
- org.exolab.castor.jdo.keyGeneratorFactories=\\r
- org.exolab.castor.jdo.keygen.MaxKeyGeneratorFactory,\\r
- org.exolab.castor.jdo.keygen.HighLowKeyGeneratorFactory,\\r
- org.exolab.castor.jdo.keygen.IdentityKeyGeneratorFactory,\\r
- org.exolab.castor.jdo.keygen.SequenceKeyGeneratorFactory,\\r
- org.exolab.castor.jdo.keygen.UUIDKeyGeneratorFactory\r
- \r
- # Collection handlers for the source code generator:\r
- #\r
- org.exolab.castor.builder.type.j2=\\r
- org.exolab.castor.builder.FieldInfoFactoryJ2\r
- org.exolab.castor.builder.type.j1=\\r
- org.exolab.castor.builder.FieldInfoFactory\r
- org.exolab.castor.builder.type.odmg=\\r
- org.exolab.castor.builder.FieldInfoFactoryODMG30\r
- \r
- # Configures the default time zone to apply to dates/times fetched from\r
- # database fields (if not already part of the data). Specify same format as\r
- # in java.util.TimeZone.getTimeZone, or the empty string to use the computer's\r
- # local time zone. Please see http://de.wikipedia.org/wiki/Zeitzone for\r
- # detailed information about time zones.\r
- #\r
- org.exolab.castor.jdo.defaultTimeZone=\r
- #org.exolab.castor.jdo.defaultTimeZone=GMT-8:00\r
- \r
- # List of TxSynchronizeable implementations:\r
- #\r
- #org.exolab.castor.persist.TxSynchronizable=\r
- \r
- # Sets the buffer size in bytes for fetching LOBs (this is dependent upon\r
- # the JDBC driver implementation). The value below == 5k.\r
- #\r
- org.exolab.castor.jdo.lobBufferSize=5120\r
- \r
- # True if database configuration should be initalization\r
- # when loading it (default: true).\r
- #\r
- #org.exolab.castor.jdo.DatabaseInitializeAtLoad=true\r
- \r
- # True if proxy classes should be used for JDBC connections and\r
- # prepared statements.\r
- # Defaults to true.\r
- #\r
- org.exolab.castor.persist.useProxies=false\r
- \r
- # MappingLoader implementations:\r
- #\r
- org.castor.mapping.loaderFactories=\\r
- org.castor.mapping.JDOMappingLoaderFactory,\\r
- org.castor.mapping.XMLMappingLoaderFactory\r
- \r
- # Cache implementations:\r
- #\r
- org.castor.cache.Factories=\\r
- org.castor.cache.simple.NoCacheFactory,\\r
- org.castor.cache.simple.TimeLimitedFactory,\\r
- org.castor.cache.simple.CountLimitedFactory,\\r
- org.castor.cache.simple.UnlimitedFactory,\\r
- org.castor.cache.distributed.FKCacheFactory,\\r
- org.castor.cache.distributed.JcsCacheFactory,\\r
- org.castor.cache.distributed.JCacheFactory,\\r
- org.castor.cache.distributed.CoherenceCacheFactory,\\r
- org.castor.cache.distributed.OsCacheFactory,\\r
- org.castor.cache.hashbelt.FIFOHashbeltFactory,\\r
- org.castor.cache.hashbelt.LRUHashbeltFactory,\\r
- org.castor.cache.distributed.EHCacheFactory,\\r
- org.castor.cache.distributed.GigaspacesCacheFactory\r
- \r
- # TransactionManagerFactory implementations:\r
- #\r
- org.castor.transactionmanager.Factories=\\r
- org.castor.transactionmanager.WebSphereTransactionManagerFactory,\\r
- org.castor.transactionmanager.WebSphere5TransactionManagerFactory,\\r
- org.castor.transactionmanager.WebSphere51TransactionManagerFactory,\\r
- org.castor.transactionmanager.LocalTransactionManagerFactory,\\r
- org.castor.transactionmanager.JNDIENCTransactionManagerFactory,\\r
- org.castor.transactionmanager.JOTMTransactionManagerFactory\r
- \r
- # Selects whether the TransactionManager should be initialized at registration,\r
- # or lazily when requested for the first time.\r
- # Defaults to false.\r
- #\r
- org.castor.transactionmanager.InitializeAtRegistration=false\r
- \r
- # Instructs Castor JDO to use the JDBC 3.0-specific features to obtain\r
- # the generated value of an identity column.\r
- # Defaults to false.\r
- #\r
- org.castor.jdo.use.jdbc30=false\r
- \r
- # Specifies whether to use ANSI-compliant SQL for MS SQL Server.\r
- # Defaults to false.\r
- #\r
- org.exolab.castor.jdo.sqlserver.ansi-compliant=false\r
- \r
- # Specifyies whether the ClassDescriptorResolver should (automatically) search\r
- # for and consult with package mapping files (.castor.xml) to retrieve class\r
- # descriptor information; on by default.\r
- # Defaults to true.\r
- #\r
- #org.exolab.castor.xml.loadPackageMappings=false\r
+ # 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
git://source.jalview.org / jalview.git / commitdiff