From: gmungoc Date: Mon, 3 Dec 2018 15:03:53 +0000 (+0000) Subject: JAL-3063 Castor removed from codebase X-Git-Tag: Release_2_11_0~17^2~97^2~29^2~1^2~2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8669979d57e2019889afaefafe65b945ae7c172d;p=jalview.git JAL-3063 Castor removed from codebase --- diff --git a/.ant-targets-build.xml b/.ant-targets-build.xml index 15432a1..6edefcd 100644 --- a/.ant-targets-build.xml +++ b/.ant-targets-build.xml @@ -3,7 +3,6 @@ buildPropertiesFile buildTests buildextclients buildindices -castorbinding clean compileApplet distclean diff --git a/.classpath b/.classpath index 0da91bb..cacda5a 100644 --- a/.classpath +++ b/.classpath @@ -13,7 +13,6 @@ - diff --git a/build.xml b/build.xml index 5ca105a..0415735 100755 --- a/build.xml +++ b/build.xml @@ -699,30 +699,6 @@ - - - - - - - - - - - - - - - - - - - - - - diff --git a/lib/castor-1.1-cycle-xml.jar b/lib/castor-1.1-cycle-xml.jar deleted file mode 100644 index 5070435..0000000 Binary files a/lib/castor-1.1-cycle-xml.jar and /dev/null differ diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml deleted file mode 100644 index 3b80821..0000000 --- a/resources/embl_mapping.xml +++ /dev/null @@ -1,139 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/schemas/castor-mapping.xsd b/schemas/castor-mapping.xsd deleted file mode 100644 index c33b8a4..0000000 --- a/schemas/castor-mapping.xsd +++ /dev/null @@ -1,315 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The 'bind-xml' element is used for specifying XML specific databinding - properties and behavior for a specific field. 'bind-xml' may only appear - as a child of a 'field' element. - - - - - - - - - - - - - - An optional attribute used for specifying the XML name for the - field associated with the 'bind-xml' element. - - - - - - - - - - - Allows specifying how Castor should automatically determines - the XML name of this field when no name has been specified. - In most cases the XML name is determined by using the field name, - but in some cases the user may want to use the Class name of - the field type. This attribute allows choosing between the - two approaches. If this attribute is not specified, the field - name is used as the XML name. - - - - - - - - - - - - - - - Allows specifying a nested location path for this field, - the value should just be a simplified XPath like value - where names are separated by "/". - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/castor.properties b/src/castor.properties deleted file mode 100644 index 5b17458..0000000 --- a/src/castor.properties +++ /dev/null @@ -1,254 +0,0 @@ -############################################################################### -# 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 diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java deleted file mode 100644 index 0116b44..0000000 --- a/src/jalview/binding/Alignment.java +++ /dev/null @@ -1,180 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Alignment. - * - * @version $Revision$ $Date$ - */ -public class Alignment implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _annotation. - */ - private jalview.binding.Annotation _annotation; - - /** - * Field _sequenceSet. - */ - private jalview.binding.SequenceSet _sequenceSet; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Alignment() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'annotation'. - * - * @return the value of field 'Annotation'. - */ - public jalview.binding.Annotation getAnnotation() - { - return this._annotation; - } - - /** - * Returns the value of field 'sequenceSet'. - * - * @return the value of field 'SequenceSet'. - */ - public jalview.binding.SequenceSet getSequenceSet() - { - return this._sequenceSet; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'annotation'. - * - * @param annotation - * the value of field 'annotation'. - */ - public void setAnnotation(final jalview.binding.Annotation annotation) - { - this._annotation = annotation; - } - - /** - * Sets the value of field 'sequenceSet'. - * - * @param sequenceSet - * the value of field 'sequenceSet'. - */ - public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet) - { - this._sequenceSet = sequenceSet; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Alignment - */ - public static jalview.binding.Alignment unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Alignment) Unmarshaller - .unmarshal(jalview.binding.Alignment.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java deleted file mode 100644 index 2c9414b..0000000 --- a/src/jalview/binding/Annotation.java +++ /dev/null @@ -1,459 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Annotation. - * - * @version $Revision$ $Date$ - */ -public class Annotation implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _graph. - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _graphType. - */ - private int _graphType; - - /** - * keeps track of state for field: _graphType - */ - private boolean _has_graphType; - - /** - * Field _annotationElementList. - */ - private java.util.Vector _annotationElementList; - - /** - * Field _label. - */ - private java.lang.String _label; - - /** - * Field _description. - */ - private java.lang.String _description; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Annotation() - { - super(); - this._annotationElementList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotationElement( - final jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - this._annotationElementList.addElement(vAnnotationElement); - } - - /** - * - * - * @param index - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotationElement(final int index, - final jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - this._annotationElementList.add(index, vAnnotationElement); - } - - /** - */ - public void deleteGraph() - { - this._has_graph = false; - } - - /** - */ - public void deleteGraphType() - { - this._has_graphType = false; - } - - /** - * Method enumerateAnnotationElement. - * - * @return an Enumeration over all jalview.binding.AnnotationElement elements - */ - public java.util.Enumeration enumerateAnnotationElement() - { - return this._annotationElementList.elements(); - } - - /** - * Method getAnnotationElement. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.AnnotationElement at the given - * index - */ - public jalview.binding.AnnotationElement getAnnotationElement( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationElementList.size()) - { - throw new IndexOutOfBoundsException( - "getAnnotationElement: Index value '" + index - + "' not in range [0.." - + (this._annotationElementList.size() - 1) + "]"); - } - - return (jalview.binding.AnnotationElement) _annotationElementList - .get(index); - } - - /** - * Method getAnnotationElement.Returns the contents of the collection in an - * Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.AnnotationElement[] getAnnotationElement() - { - jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0]; - return (jalview.binding.AnnotationElement[]) this._annotationElementList - .toArray(array); - } - - /** - * Method getAnnotationElementCount. - * - * @return the size of this collection - */ - public int getAnnotationElementCount() - { - return this._annotationElementList.size(); - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean getGraph() - { - return this._graph; - } - - /** - * Returns the value of field 'graphType'. - * - * @return the value of field 'GraphType'. - */ - public int getGraphType() - { - return this._graphType; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel() - { - return this._label; - } - - /** - * Method hasGraph. - * - * @return true if at least one Graph has been added - */ - public boolean hasGraph() - { - return this._has_graph; - } - - /** - * Method hasGraphType. - * - * @return true if at least one GraphType has been added - */ - public boolean hasGraphType() - { - return this._has_graphType; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean isGraph() - { - return this._graph; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAnnotationElement() - { - this._annotationElementList.clear(); - } - - /** - * Method removeAnnotationElement. - * - * @param vAnnotationElement - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotationElement( - final jalview.binding.AnnotationElement vAnnotationElement) - { - boolean removed = _annotationElementList.remove(vAnnotationElement); - return removed; - } - - /** - * Method removeAnnotationElementAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.AnnotationElement removeAnnotationElementAt( - final int index) - { - java.lang.Object obj = this._annotationElementList.remove(index); - return (jalview.binding.AnnotationElement) obj; - } - - /** - * - * - * @param index - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAnnotationElement(final int index, - final jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationElementList.size()) - { - throw new IndexOutOfBoundsException( - "setAnnotationElement: Index value '" + index - + "' not in range [0.." - + (this._annotationElementList.size() - 1) + "]"); - } - - this._annotationElementList.set(index, vAnnotationElement); - } - - /** - * - * - * @param vAnnotationElementArray - */ - public void setAnnotationElement( - final jalview.binding.AnnotationElement[] vAnnotationElementArray) - { - // -- copy array - _annotationElementList.clear(); - - for (int i = 0; i < vAnnotationElementArray.length; i++) - { - this._annotationElementList.add(vAnnotationElementArray[i]); - } - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'graph'. - * - * @param graph - * the value of field 'graph'. - */ - public void setGraph(final boolean graph) - { - this._graph = graph; - this._has_graph = true; - } - - /** - * Sets the value of field 'graphType'. - * - * @param graphType - * the value of field 'graphType'. - */ - public void setGraphType(final int graphType) - { - this._graphType = graphType; - this._has_graphType = true; - } - - /** - * Sets the value of field 'label'. - * - * @param label - * the value of field 'label'. - */ - public void setLabel(final java.lang.String label) - { - this._label = label; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Annotation - */ - public static jalview.binding.Annotation unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Annotation) Unmarshaller - .unmarshal(jalview.binding.Annotation.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java deleted file mode 100644 index 505d91e..0000000 --- a/src/jalview/binding/AnnotationElement.java +++ /dev/null @@ -1,305 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class AnnotationElement. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElement implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _position. - */ - private int _position; - - /** - * keeps track of state for field: _position - */ - private boolean _has_position; - - /** - * Field _displayCharacter. - */ - private java.lang.String _displayCharacter; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _secondaryStructure. - */ - private java.lang.String _secondaryStructure; - - /** - * Field _value. - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationElement() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deletePosition() - { - this._has_position = false; - } - - /** - */ - public void deleteValue() - { - this._has_value = false; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'displayCharacter'. - * - * @return the value of field 'DisplayCharacter'. - */ - public java.lang.String getDisplayCharacter() - { - return this._displayCharacter; - } - - /** - * Returns the value of field 'position'. - * - * @return the value of field 'Position'. - */ - public int getPosition() - { - return this._position; - } - - /** - * Returns the value of field 'secondaryStructure'. - * - * @return the value of field 'SecondaryStructure'. - */ - public java.lang.String getSecondaryStructure() - { - return this._secondaryStructure; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public float getValue() - { - return this._value; - } - - /** - * Method hasPosition. - * - * @return true if at least one Position has been added - */ - public boolean hasPosition() - { - return this._has_position; - } - - /** - * Method hasValue. - * - * @return true if at least one Value has been added - */ - public boolean hasValue() - { - return this._has_value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'displayCharacter'. - * - * @param displayCharacter - * the value of field 'displayCharacter' - */ - public void setDisplayCharacter(final java.lang.String displayCharacter) - { - this._displayCharacter = displayCharacter; - } - - /** - * Sets the value of field 'position'. - * - * @param position - * the value of field 'position'. - */ - public void setPosition(final int position) - { - this._position = position; - this._has_position = true; - } - - /** - * Sets the value of field 'secondaryStructure'. - * - * @param secondaryStructure - * the value of field 'secondaryStructure'. - */ - public void setSecondaryStructure( - final java.lang.String secondaryStructure) - { - this._secondaryStructure = secondaryStructure; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final float value) - { - this._value = value; - this._has_value = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.AnnotationElement - */ - public static jalview.binding.AnnotationElement unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.AnnotationElement) Unmarshaller - .unmarshal(jalview.binding.AnnotationElement.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java deleted file mode 100644 index f51e9af..0000000 --- a/src/jalview/binding/Colour.java +++ /dev/null @@ -1,707 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Colour. - * - * @version $Revision$ $Date$ - */ -public class Colour implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Single letter residue code for an alignment colour scheme, or feature type - * for a feature colour scheme - */ - private java.lang.String _name; - - /** - * Field _RGB. - */ - private java.lang.String _RGB; - - /** - * Field _minRGB. - */ - private java.lang.String _minRGB; - - /** - * Field _noValueColour. - */ - private jalview.binding.types.NoValueColour _noValueColour = jalview.binding.types.NoValueColour - .valueOf("Min"); - - /** - * Field _threshType. - */ - private jalview.binding.types.ColourThreshTypeType _threshType; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - /** - * name of feature attribute to colour by, or attribute and sub-attribute - */ - private java.util.Vector _attributeNameList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Colour() - { - super(); - setNoValueColour(jalview.binding.types.NoValueColour.valueOf("Min")); - this._attributeNameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.addElement(vAttributeName); - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.add(index, vAttributeName); - } - - /** - */ - public void deleteAutoScale() - { - this._has_autoScale = false; - } - - /** - */ - public void deleteColourByLabel() - { - this._has_colourByLabel = false; - } - - /** - */ - public void deleteMax() - { - this._has_max = false; - } - - /** - */ - public void deleteMin() - { - this._has_min = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - * Method enumerateAttributeName. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateAttributeName() - { - return this._attributeNameList.elements(); - } - - /** - * Method getAttributeName. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getAttributeName(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("getAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - return (java.lang.String) _attributeNameList.get(index); - } - - /** - * Method getAttributeName.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getAttributeName() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._attributeNameList.toArray(array); - } - - /** - * Method getAttributeNameCount. - * - * @return the size of this collection - */ - public int getAttributeNameCount() - { - return this._attributeNameList.size(); - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel() - { - return this._colourByLabel; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax() - { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin() - { - return this._min; - } - - /** - * Returns the value of field 'minRGB'. - * - * @return the value of field 'MinRGB'. - */ - public java.lang.String getMinRGB() - { - return this._minRGB; - } - - /** - * Returns the value of field 'name'. The field 'name' has the following - * description: Single letter residue code for an alignment colour scheme, or - * feature type for a feature colour scheme - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'noValueColour'. - * - * @return the value of field 'NoValueColour'. - */ - public jalview.binding.types.NoValueColour getNoValueColour() - { - return this._noValueColour; - } - - /** - * Returns the value of field 'RGB'. - * - * @return the value of field 'RGB'. - */ - public java.lang.String getRGB() - { - return this._RGB; - } - - /** - * Returns the value of field 'threshType'. - * - * @return the value of field 'ThreshType'. - */ - public jalview.binding.types.ColourThreshTypeType getThreshType() - { - return this._threshType; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale() - { - return this._has_autoScale; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel() - { - return this._has_colourByLabel; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax() - { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin() - { - return this._has_min; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel() - { - return this._colourByLabel; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAttributeName() - { - this._attributeNameList.clear(); - } - - /** - * Method removeAttributeName. - * - * @param vAttributeName - * @return true if the object was removed from the collection. - */ - public boolean removeAttributeName(final java.lang.String vAttributeName) - { - boolean removed = _attributeNameList.remove(vAttributeName); - return removed; - } - - /** - * Method removeAttributeNameAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeAttributeNameAt(final int index) - { - java.lang.Object obj = this._attributeNameList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("setAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - this._attributeNameList.set(index, vAttributeName); - } - - /** - * - * - * @param vAttributeNameArray - */ - public void setAttributeName(final java.lang.String[] vAttributeNameArray) - { - // -- copy array - _attributeNameList.clear(); - - for (int i = 0; i < vAttributeNameArray.length; i++) - { - this._attributeNameList.add(vAttributeNameArray[i]); - } - } - - /** - * Sets the value of field 'autoScale'. - * - * @param autoScale - * the value of field 'autoScale'. - */ - public void setAutoScale(final boolean autoScale) - { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * Sets the value of field 'colourByLabel'. - * - * @param colourByLabel - * the value of field 'colourByLabel'. - */ - public void setColourByLabel(final boolean colourByLabel) - { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = true; - } - - /** - * Sets the value of field 'max'. - * - * @param max - * the value of field 'max'. - */ - public void setMax(final float max) - { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min - * the value of field 'min'. - */ - public void setMin(final float min) - { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'minRGB'. - * - * @param minRGB - * the value of field 'minRGB'. - */ - public void setMinRGB(final java.lang.String minRGB) - { - this._minRGB = minRGB; - } - - /** - * Sets the value of field 'name'. The field 'name' has the following - * description: Single letter residue code for an alignment colour scheme, or - * feature type for a feature colour scheme - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'noValueColour'. - * - * @param noValueColour - * the value of field 'noValueColour'. - */ - public void setNoValueColour( - final jalview.binding.types.NoValueColour noValueColour) - { - this._noValueColour = noValueColour; - } - - /** - * Sets the value of field 'RGB'. - * - * @param RGB - * the value of field 'RGB'. - */ - public void setRGB(final java.lang.String RGB) - { - this._RGB = RGB; - } - - /** - * Sets the value of field 'threshType'. - * - * @param threshType - * the value of field 'threshType'. - */ - public void setThreshType( - final jalview.binding.types.ColourThreshTypeType threshType) - { - this._threshType = threshType; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold - * the value of field 'threshold'. - */ - public void setThreshold(final float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Colour - */ - public static jalview.binding.Colour unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Colour) Unmarshaller - .unmarshal(jalview.binding.Colour.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/CompoundMatcher.java b/src/jalview/binding/CompoundMatcher.java deleted file mode 100644 index a2d1048..0000000 --- a/src/jalview/binding/CompoundMatcher.java +++ /dev/null @@ -1,368 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class CompoundMatcher. - * - * @version $Revision$ $Date$ - */ -public class CompoundMatcher implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * If true, matchers are AND-ed, if false they are OR-ed - */ - private boolean _and; - - /** - * keeps track of state for field: _and - */ - private boolean _has_and; - - /** - * Field _matcherSetList. - */ - private java.util.Vector _matcherSetList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public CompoundMatcher() - { - super(); - this._matcherSetList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMatcherSet(final jalview.binding.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._matcherSetList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addMatcherSet has a maximum of 2"); - } - - this._matcherSetList.addElement(vMatcherSet); - } - - /** - * - * - * @param index - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMatcherSet(final int index, - final jalview.binding.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._matcherSetList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addMatcherSet has a maximum of 2"); - } - - this._matcherSetList.add(index, vMatcherSet); - } - - /** - */ - public void deleteAnd() - { - this._has_and = false; - } - - /** - * Method enumerateMatcherSet. - * - * @return an Enumeration over all jalview.binding.MatcherSet elements - */ - public java.util.Enumeration enumerateMatcherSet() - { - return this._matcherSetList.elements(); - } - - /** - * Returns the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @return the value of field 'And'. - */ - public boolean getAnd() - { - return this._and; - } - - /** - * Method getMatcherSet. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.MatcherSet at the given index - */ - public jalview.binding.MatcherSet getMatcherSet(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._matcherSetList.size()) - { - throw new IndexOutOfBoundsException( - "getMatcherSet: Index value '" + index + "' not in range [0.." - + (this._matcherSetList.size() - 1) + "]"); - } - - return (jalview.binding.MatcherSet) _matcherSetList.get(index); - } - - /** - * Method getMatcherSet.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.MatcherSet[] getMatcherSet() - { - jalview.binding.MatcherSet[] array = new jalview.binding.MatcherSet[0]; - return (jalview.binding.MatcherSet[]) this._matcherSetList - .toArray(array); - } - - /** - * Method getMatcherSetCount. - * - * @return the size of this collection - */ - public int getMatcherSetCount() - { - return this._matcherSetList.size(); - } - - /** - * Method hasAnd. - * - * @return true if at least one And has been added - */ - public boolean hasAnd() - { - return this._has_and; - } - - /** - * Returns the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @return the value of field 'And'. - */ - public boolean isAnd() - { - return this._and; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllMatcherSet() - { - this._matcherSetList.clear(); - } - - /** - * Method removeMatcherSet. - * - * @param vMatcherSet - * @return true if the object was removed from the collection. - */ - public boolean removeMatcherSet( - final jalview.binding.MatcherSet vMatcherSet) - { - boolean removed = _matcherSetList.remove(vMatcherSet); - return removed; - } - - /** - * Method removeMatcherSetAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.MatcherSet removeMatcherSetAt(final int index) - { - java.lang.Object obj = this._matcherSetList.remove(index); - return (jalview.binding.MatcherSet) obj; - } - - /** - * Sets the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @param and - * the value of field 'and'. - */ - public void setAnd(final boolean and) - { - this._and = and; - this._has_and = true; - } - - /** - * - * - * @param index - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setMatcherSet(final int index, - final jalview.binding.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._matcherSetList.size()) - { - throw new IndexOutOfBoundsException( - "setMatcherSet: Index value '" + index + "' not in range [0.." - + (this._matcherSetList.size() - 1) + "]"); - } - - this._matcherSetList.set(index, vMatcherSet); - } - - /** - * - * - * @param vMatcherSetArray - */ - public void setMatcherSet( - final jalview.binding.MatcherSet[] vMatcherSetArray) - { - // -- copy array - _matcherSetList.clear(); - - for (int i = 0; i < vMatcherSetArray.length; i++) - { - this._matcherSetList.add(vMatcherSetArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.CompoundMatcher - */ - public static jalview.binding.CompoundMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.CompoundMatcher) Unmarshaller - .unmarshal(jalview.binding.CompoundMatcher.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java deleted file mode 100644 index d72b29c..0000000 --- a/src/jalview/binding/Feature.java +++ /dev/null @@ -1,304 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Feature. - * - * @version $Revision$ $Date$ - */ -public class Feature implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _begin. - */ - private int _begin; - - /** - * keeps track of state for field: _begin - */ - private boolean _has_begin; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _status. - */ - private java.lang.String _status; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Feature() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteBegin() - { - this._has_begin = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - * Returns the value of field 'begin'. - * - * @return the value of field 'Begin'. - */ - public int getBegin() - { - return this._begin; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'status'. - * - * @return the value of field 'Status'. - */ - public java.lang.String getStatus() - { - return this._status; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method hasBegin. - * - * @return true if at least one Begin has been added - */ - public boolean hasBegin() - { - return this._has_begin; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'begin'. - * - * @param begin - * the value of field 'begin'. - */ - public void setBegin(final int begin) - { - this._begin = begin; - this._has_begin = true; - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'status'. - * - * @param status - * the value of field 'status'. - */ - public void setStatus(final java.lang.String status) - { - this._status = status; - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Feature - */ - public static jalview.binding.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Feature) Unmarshaller - .unmarshal(jalview.binding.Feature.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/FeatureMatcher.java b/src/jalview/binding/FeatureMatcher.java deleted file mode 100644 index e4e52fb..0000000 --- a/src/jalview/binding/FeatureMatcher.java +++ /dev/null @@ -1,381 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class FeatureMatcher. - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcher implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _by. - */ - private jalview.binding.types.FeatureMatcherByType _by; - - /** - * name of feature attribute to filter on, or attribute and sub-attribute - */ - private java.util.Vector _attributeNameList; - - /** - * Field _condition. - */ - private java.lang.String _condition; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureMatcher() - { - super(); - this._attributeNameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.addElement(vAttributeName); - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.add(index, vAttributeName); - } - - /** - * Method enumerateAttributeName. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateAttributeName() - { - return this._attributeNameList.elements(); - } - - /** - * Method getAttributeName. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getAttributeName(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("getAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - return (java.lang.String) _attributeNameList.get(index); - } - - /** - * Method getAttributeName.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getAttributeName() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._attributeNameList.toArray(array); - } - - /** - * Method getAttributeNameCount. - * - * @return the size of this collection - */ - public int getAttributeNameCount() - { - return this._attributeNameList.size(); - } - - /** - * Returns the value of field 'by'. - * - * @return the value of field 'By'. - */ - public jalview.binding.types.FeatureMatcherByType getBy() - { - return this._by; - } - - /** - * Returns the value of field 'condition'. - * - * @return the value of field 'Condition'. - */ - public java.lang.String getCondition() - { - return this._condition; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue() - { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAttributeName() - { - this._attributeNameList.clear(); - } - - /** - * Method removeAttributeName. - * - * @param vAttributeName - * @return true if the object was removed from the collection. - */ - public boolean removeAttributeName(final java.lang.String vAttributeName) - { - boolean removed = _attributeNameList.remove(vAttributeName); - return removed; - } - - /** - * Method removeAttributeNameAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeAttributeNameAt(final int index) - { - java.lang.Object obj = this._attributeNameList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("setAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - this._attributeNameList.set(index, vAttributeName); - } - - /** - * - * - * @param vAttributeNameArray - */ - public void setAttributeName(final java.lang.String[] vAttributeNameArray) - { - // -- copy array - _attributeNameList.clear(); - - for (int i = 0; i < vAttributeNameArray.length; i++) - { - this._attributeNameList.add(vAttributeNameArray[i]); - } - } - - /** - * Sets the value of field 'by'. - * - * @param by - * the value of field 'by'. - */ - public void setBy(final jalview.binding.types.FeatureMatcherByType by) - { - this._by = by; - } - - /** - * Sets the value of field 'condition'. - * - * @param condition - * the value of field 'condition'. - */ - public void setCondition(final java.lang.String condition) - { - this._condition = condition; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final java.lang.String value) - { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureMatcher - */ - public static jalview.binding.FeatureMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureMatcher) Unmarshaller - .unmarshal(jalview.binding.FeatureMatcher.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/FeatureMatcherSet.java b/src/jalview/binding/FeatureMatcherSet.java deleted file mode 100644 index 7ba5f0e..0000000 --- a/src/jalview/binding/FeatureMatcherSet.java +++ /dev/null @@ -1,200 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * A feature match condition, which may be simple or compound - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcherSet implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * Field _matchCondition. - */ - private jalview.binding.MatchCondition _matchCondition; - - /** - * Field _compoundMatcher. - */ - private jalview.binding.CompoundMatcher _compoundMatcher; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureMatcherSet() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'choiceValue'. The field 'choiceValue' has the - * following description: Internal choice value storage - * - * @return the value of field 'ChoiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } - - /** - * Returns the value of field 'compoundMatcher'. - * - * @return the value of field 'CompoundMatcher'. - */ - public jalview.binding.CompoundMatcher getCompoundMatcher() - { - return this._compoundMatcher; - } - - /** - * Returns the value of field 'matchCondition'. - * - * @return the value of field 'MatchCondition'. - */ - public jalview.binding.MatchCondition getMatchCondition() - { - return this._matchCondition; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'compoundMatcher'. - * - * @param compoundMatcher - * the value of field 'compoundMatcher'. - */ - public void setCompoundMatcher( - final jalview.binding.CompoundMatcher compoundMatcher) - { - this._compoundMatcher = compoundMatcher; - this._choiceValue = compoundMatcher; - } - - /** - * Sets the value of field 'matchCondition'. - * - * @param matchCondition - * the value of field 'matchCondition'. - */ - public void setMatchCondition( - final jalview.binding.MatchCondition matchCondition) - { - this._matchCondition = matchCondition; - this._choiceValue = matchCondition; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureMatcherSet - */ - public static jalview.binding.FeatureMatcherSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureMatcherSet) Unmarshaller - .unmarshal(jalview.binding.FeatureMatcherSet.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java deleted file mode 100644 index 321536d..0000000 --- a/src/jalview/binding/FeatureSettings.java +++ /dev/null @@ -1,289 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class FeatureSettings. - * - * @version $Revision$ $Date$ - */ -public class FeatureSettings implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _settingList. - */ - private java.util.Vector _settingList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureSettings() - { - super(); - this._settingList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSetting(final jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - this._settingList.addElement(vSetting); - } - - /** - * - * - * @param index - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSetting(final int index, - final jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - this._settingList.add(index, vSetting); - } - - /** - * Method enumerateSetting. - * - * @return an Enumeration over all jalview.binding.Setting elements - */ - public java.util.Enumeration enumerateSetting() - { - return this._settingList.elements(); - } - - /** - * Method getSetting. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Setting at the given index - */ - public jalview.binding.Setting getSetting(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._settingList.size()) - { - throw new IndexOutOfBoundsException( - "getSetting: Index value '" + index + "' not in range [0.." - + (this._settingList.size() - 1) + "]"); - } - - return (jalview.binding.Setting) _settingList.get(index); - } - - /** - * Method getSetting.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Setting[] getSetting() - { - jalview.binding.Setting[] array = new jalview.binding.Setting[0]; - return (jalview.binding.Setting[]) this._settingList.toArray(array); - } - - /** - * Method getSettingCount. - * - * @return the size of this collection - */ - public int getSettingCount() - { - return this._settingList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSetting() - { - this._settingList.clear(); - } - - /** - * Method removeSetting. - * - * @param vSetting - * @return true if the object was removed from the collection. - */ - public boolean removeSetting(final jalview.binding.Setting vSetting) - { - boolean removed = _settingList.remove(vSetting); - return removed; - } - - /** - * Method removeSettingAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Setting removeSettingAt(final int index) - { - java.lang.Object obj = this._settingList.remove(index); - return (jalview.binding.Setting) obj; - } - - /** - * - * - * @param index - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSetting(final int index, - final jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._settingList.size()) - { - throw new IndexOutOfBoundsException( - "setSetting: Index value '" + index + "' not in range [0.." - + (this._settingList.size() - 1) + "]"); - } - - this._settingList.set(index, vSetting); - } - - /** - * - * - * @param vSettingArray - */ - public void setSetting(final jalview.binding.Setting[] vSettingArray) - { - // -- copy array - _settingList.clear(); - - for (int i = 0; i < vSettingArray.length; i++) - { - this._settingList.add(vSettingArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureSettings - */ - public static jalview.binding.FeatureSettings unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureSettings) Unmarshaller - .unmarshal(jalview.binding.FeatureSettings.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java deleted file mode 100644 index bf283df..0000000 --- a/src/jalview/binding/Features.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Features. - * - * @version $Revision$ $Date$ - */ -public class Features extends Feature implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Features() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Feature - */ - public static jalview.binding.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Feature) Unmarshaller - .unmarshal(jalview.binding.Features.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Filter.java b/src/jalview/binding/Filter.java deleted file mode 100644 index 687ae91..0000000 --- a/src/jalview/binding/Filter.java +++ /dev/null @@ -1,180 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Filter. - * - * @version $Revision$ $Date$ - */ -public class Filter implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _featureType. - */ - private java.lang.String _featureType; - - /** - * Field _matcherSet. - */ - private jalview.binding.MatcherSet _matcherSet; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Filter() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'featureType'. - * - * @return the value of field 'FeatureType'. - */ - public java.lang.String getFeatureType() - { - return this._featureType; - } - - /** - * Returns the value of field 'matcherSet'. - * - * @return the value of field 'MatcherSet'. - */ - public jalview.binding.MatcherSet getMatcherSet() - { - return this._matcherSet; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'featureType'. - * - * @param featureType - * the value of field 'featureType'. - */ - public void setFeatureType(final java.lang.String featureType) - { - this._featureType = featureType; - } - - /** - * Sets the value of field 'matcherSet'. - * - * @param matcherSet - * the value of field 'matcherSet'. - */ - public void setMatcherSet(final jalview.binding.MatcherSet matcherSet) - { - this._matcherSet = matcherSet; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Filter - */ - public static jalview.binding.Filter unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Filter) Unmarshaller - .unmarshal(jalview.binding.Filter.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java deleted file mode 100644 index 555c2fd..0000000 --- a/src/jalview/binding/JGroup.java +++ /dev/null @@ -1,761 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JGroup. - * - * @version $Revision$ $Date$ - */ -public class JGroup implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _colour. - */ - private java.lang.String _colour; - - /** - * Field _consThreshold. - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold. - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _outlineColour. - */ - private int _outlineColour; - - /** - * keeps track of state for field: _outlineColour - */ - private boolean _has_outlineColour; - - /** - * Field _displayBoxes. - */ - private boolean _displayBoxes; - - /** - * keeps track of state for field: _displayBoxes - */ - private boolean _has_displayBoxes; - - /** - * Field _displayText. - */ - private boolean _displayText; - - /** - * keeps track of state for field: _displayText - */ - private boolean _has_displayText; - - /** - * Field _colourText. - */ - private boolean _colourText; - - /** - * keeps track of state for field: _colourText - */ - private boolean _has_colourText; - - /** - * Field _seqList. - */ - private java.util.Vector _seqList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JGroup() - { - super(); - this._seqList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSeq(final int vSeq) - throws java.lang.IndexOutOfBoundsException - { - this._seqList.addElement(new java.lang.Integer(vSeq)); - } - - /** - * - * - * @param index - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSeq(final int index, final int vSeq) - throws java.lang.IndexOutOfBoundsException - { - this._seqList.add(index, new java.lang.Integer(vSeq)); - } - - /** - */ - public void deleteColourText() - { - this._has_colourText = false; - } - - /** - */ - public void deleteConsThreshold() - { - this._has_consThreshold = false; - } - - /** - */ - public void deleteDisplayBoxes() - { - this._has_displayBoxes = false; - } - - /** - */ - public void deleteDisplayText() - { - this._has_displayText = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteOutlineColour() - { - this._has_outlineColour = false; - } - - /** - */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Method enumerateSeq. - * - * @return an Enumeration over all int elements - */ - public java.util.Enumeration enumerateSeq() - { - return this._seqList.elements(); - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public java.lang.String getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'colourText'. - * - * @return the value of field 'ColourText'. - */ - public boolean getColourText() - { - return this._colourText; - } - - /** - * Returns the value of field 'consThreshold'. - * - * @return the value of field 'ConsThreshold'. - */ - public int getConsThreshold() - { - return this._consThreshold; - } - - /** - * Returns the value of field 'displayBoxes'. - * - * @return the value of field 'DisplayBoxes'. - */ - public boolean getDisplayBoxes() - { - return this._displayBoxes; - } - - /** - * Returns the value of field 'displayText'. - * - * @return the value of field 'DisplayText'. - */ - public boolean getDisplayText() - { - return this._displayText; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'outlineColour'. - * - * @return the value of field 'OutlineColour'. - */ - public int getOutlineColour() - { - return this._outlineColour; - } - - /** - * Returns the value of field 'pidThreshold'. - * - * @return the value of field 'PidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } - - /** - * Method getSeq. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the int at the given index - */ - public int getSeq(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._seqList.size()) - { - throw new IndexOutOfBoundsException("getSeq: Index value '" + index - + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - return ((java.lang.Integer) _seqList.get(index)).intValue(); - } - - /** - * Method getSeq.Returns the contents of the collection in an Array. - * - * @return this collection as an Array - */ - public int[] getSeq() - { - int size = this._seqList.size(); - int[] array = new int[size]; - java.util.Iterator iter = _seqList.iterator(); - for (int index = 0; index < size; index++) - { - array[index] = ((java.lang.Integer) iter.next()).intValue(); - } - return array; - } - - /** - * Method getSeqCount. - * - * @return the size of this collection - */ - public int getSeqCount() - { - return this._seqList.size(); - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasColourText. - * - * @return true if at least one ColourText has been added - */ - public boolean hasColourText() - { - return this._has_colourText; - } - - /** - * Method hasConsThreshold. - * - * @return true if at least one ConsThreshold has been added - */ - public boolean hasConsThreshold() - { - return this._has_consThreshold; - } - - /** - * Method hasDisplayBoxes. - * - * @return true if at least one DisplayBoxes has been added - */ - public boolean hasDisplayBoxes() - { - return this._has_displayBoxes; - } - - /** - * Method hasDisplayText. - * - * @return true if at least one DisplayText has been added - */ - public boolean hasDisplayText() - { - return this._has_displayText; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasOutlineColour. - * - * @return true if at least one OutlineColour has been added - */ - public boolean hasOutlineColour() - { - return this._has_outlineColour; - } - - /** - * Method hasPidThreshold. - * - * @return true if at least one PidThreshold has been added - */ - public boolean hasPidThreshold() - { - return this._has_pidThreshold; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Returns the value of field 'colourText'. - * - * @return the value of field 'ColourText'. - */ - public boolean isColourText() - { - return this._colourText; - } - - /** - * Returns the value of field 'displayBoxes'. - * - * @return the value of field 'DisplayBoxes'. - */ - public boolean isDisplayBoxes() - { - return this._displayBoxes; - } - - /** - * Returns the value of field 'displayText'. - * - * @return the value of field 'DisplayText'. - */ - public boolean isDisplayText() - { - return this._displayText; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSeq() - { - this._seqList.clear(); - } - - /** - * Method removeSeq. - * - * @param vSeq - * @return true if the object was removed from the collection. - */ - public boolean removeSeq(final int vSeq) - { - boolean removed = _seqList.remove(new java.lang.Integer(vSeq)); - return removed; - } - - /** - * Method removeSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public int removeSeqAt(final int index) - { - java.lang.Object obj = this._seqList.remove(index); - return ((java.lang.Integer) obj).intValue(); - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final java.lang.String colour) - { - this._colour = colour; - } - - /** - * Sets the value of field 'colourText'. - * - * @param colourText - * the value of field 'colourText'. - */ - public void setColourText(final boolean colourText) - { - this._colourText = colourText; - this._has_colourText = true; - } - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold - * the value of field 'consThreshold'. - */ - public void setConsThreshold(final int consThreshold) - { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } - - /** - * Sets the value of field 'displayBoxes'. - * - * @param displayBoxes - * the value of field 'displayBoxes'. - */ - public void setDisplayBoxes(final boolean displayBoxes) - { - this._displayBoxes = displayBoxes; - this._has_displayBoxes = true; - } - - /** - * Sets the value of field 'displayText'. - * - * @param displayText - * the value of field 'displayText'. - */ - public void setDisplayText(final boolean displayText) - { - this._displayText = displayText; - this._has_displayText = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'outlineColour'. - * - * @param outlineColour - * the value of field 'outlineColour'. - */ - public void setOutlineColour(final int outlineColour) - { - this._outlineColour = outlineColour; - this._has_outlineColour = true; - } - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold - * the value of field 'pidThreshold'. - */ - public void setPidThreshold(final int pidThreshold) - { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } - - /** - * - * - * @param index - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSeq(final int index, final int vSeq) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._seqList.size()) - { - throw new IndexOutOfBoundsException("setSeq: Index value '" + index - + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - this._seqList.set(index, new java.lang.Integer(vSeq)); - } - - /** - * - * - * @param vSeqArray - */ - public void setSeq(final int[] vSeqArray) - { - // -- copy array - _seqList.clear(); - - for (int i = 0; i < vSeqArray.length; i++) - { - this._seqList.add(new java.lang.Integer(vSeqArray[i])); - } - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JGroup - */ - public static jalview.binding.JGroup unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JGroup) Unmarshaller - .unmarshal(jalview.binding.JGroup.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java deleted file mode 100644 index 49334e1..0000000 --- a/src/jalview/binding/JSeq.java +++ /dev/null @@ -1,645 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JSeq. - * - * @version $Revision$ $Date$ - */ -public class JSeq implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _id. - */ - private int _id; - - /** - * keeps track of state for field: _id - */ - private boolean _has_id; - - /** - * Field _featuresList. - */ - private java.util.Vector _featuresList; - - /** - * Field _pdbidsList. - */ - private java.util.Vector _pdbidsList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JSeq() - { - super(); - this._featuresList = new java.util.Vector(); - this._pdbidsList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFeatures(final jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.addElement(vFeatures); - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFeatures(final int index, - final jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.add(index, vFeatures); - } - - /** - * - * - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - this._pdbidsList.addElement(vPdbids); - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final int index, - final jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - this._pdbidsList.add(index, vPdbids); - } - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteId() - { - this._has_id = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Method enumerateFeatures. - * - * @return an Enumeration over all jalview.binding.Features elements - */ - public java.util.Enumeration enumerateFeatures() - { - return this._featuresList.elements(); - } - - /** - * Method enumeratePdbids. - * - * @return an Enumeration over all jalview.binding.Pdbids elements - */ - public java.util.Enumeration enumeratePdbids() - { - return this._pdbidsList.elements(); - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Method getFeatures. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Features at the given index - */ - public jalview.binding.Features getFeatures(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) - { - throw new IndexOutOfBoundsException( - "getFeatures: Index value '" + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); - } - - return (jalview.binding.Features) _featuresList.get(index); - } - - /** - * Method getFeatures.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Features[] getFeatures() - { - jalview.binding.Features[] array = new jalview.binding.Features[0]; - return (jalview.binding.Features[]) this._featuresList.toArray(array); - } - - /** - * Method getFeaturesCount. - * - * @return the size of this collection - */ - public int getFeaturesCount() - { - return this._featuresList.size(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public int getId() - { - return this._id; - } - - /** - * Method getPdbids. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Pdbids at the given index - */ - public jalview.binding.Pdbids getPdbids(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) - { - throw new IndexOutOfBoundsException( - "getPdbids: Index value '" + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); - } - - return (jalview.binding.Pdbids) _pdbidsList.get(index); - } - - /** - * Method getPdbids.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Pdbids[] getPdbids() - { - jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0]; - return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array); - } - - /** - * Method getPdbidsCount. - * - * @return the size of this collection - */ - public int getPdbidsCount() - { - return this._pdbidsList.size(); - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasId. - * - * @return true if at least one Id has been added - */ - public boolean hasId() - { - return this._has_id; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllFeatures() - { - this._featuresList.clear(); - } - - /** - */ - public void removeAllPdbids() - { - this._pdbidsList.clear(); - } - - /** - * Method removeFeatures. - * - * @param vFeatures - * @return true if the object was removed from the collection. - */ - public boolean removeFeatures(final jalview.binding.Features vFeatures) - { - boolean removed = _featuresList.remove(vFeatures); - return removed; - } - - /** - * Method removeFeaturesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Features removeFeaturesAt(final int index) - { - java.lang.Object obj = this._featuresList.remove(index); - return (jalview.binding.Features) obj; - } - - /** - * Method removePdbids. - * - * @param vPdbids - * @return true if the object was removed from the collection. - */ - public boolean removePdbids(final jalview.binding.Pdbids vPdbids) - { - boolean removed = _pdbidsList.remove(vPdbids); - return removed; - } - - /** - * Method removePdbidsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Pdbids removePdbidsAt(final int index) - { - java.lang.Object obj = this._pdbidsList.remove(index); - return (jalview.binding.Pdbids) obj; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setFeatures(final int index, - final jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) - { - throw new IndexOutOfBoundsException( - "setFeatures: Index value '" + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); - } - - this._featuresList.set(index, vFeatures); - } - - /** - * - * - * @param vFeaturesArray - */ - public void setFeatures(final jalview.binding.Features[] vFeaturesArray) - { - // -- copy array - _featuresList.clear(); - - for (int i = 0; i < vFeaturesArray.length; i++) - { - this._featuresList.add(vFeaturesArray[i]); - } - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final int id) - { - this._id = id; - this._has_id = true; - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbids(final int index, - final jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) - { - throw new IndexOutOfBoundsException( - "setPdbids: Index value '" + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); - } - - this._pdbidsList.set(index, vPdbids); - } - - /** - * - * - * @param vPdbidsArray - */ - public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray) - { - // -- copy array - _pdbidsList.clear(); - - for (int i = 0; i < vPdbidsArray.length; i++) - { - this._pdbidsList.add(vPdbidsArray[i]); - } - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JSeq - */ - public static jalview.binding.JSeq unmarshal(final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JSeq) Unmarshaller - .unmarshal(jalview.binding.JSeq.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java deleted file mode 100644 index 28645e0..0000000 --- a/src/jalview/binding/JalviewModel.java +++ /dev/null @@ -1,233 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewModel. - * - * @version $Revision$ $Date$ - */ -public class JalviewModel implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _creationDate. - */ - private java.util.Date _creationDate; - - /** - * Field _version. - */ - private java.lang.String _version; - - /** - * Field _vamsasModel. - */ - private jalview.binding.VamsasModel _vamsasModel; - - /** - * Field _jalviewModelSequence. - */ - private jalview.binding.JalviewModelSequence _jalviewModelSequence; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModel() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'creationDate'. - * - * @return the value of field 'CreationDate'. - */ - public java.util.Date getCreationDate() - { - return this._creationDate; - } - - /** - * Returns the value of field 'jalviewModelSequence'. - * - * @return the value of field 'JalviewModelSequence'. - */ - public jalview.binding.JalviewModelSequence getJalviewModelSequence() - { - return this._jalviewModelSequence; - } - - /** - * Returns the value of field 'vamsasModel'. - * - * @return the value of field 'VamsasModel'. - */ - public jalview.binding.VamsasModel getVamsasModel() - { - return this._vamsasModel; - } - - /** - * Returns the value of field 'version'. - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion() - { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'creationDate'. - * - * @param creationDate - * the value of field 'creationDate'. - */ - public void setCreationDate(final java.util.Date creationDate) - { - this._creationDate = creationDate; - } - - /** - * Sets the value of field 'jalviewModelSequence'. - * - * @param jalviewModelSequence - * the value of field 'jalviewModelSequence'. - */ - public void setJalviewModelSequence( - final jalview.binding.JalviewModelSequence jalviewModelSequence) - { - this._jalviewModelSequence = jalviewModelSequence; - } - - /** - * Sets the value of field 'vamsasModel'. - * - * @param vamsasModel - * the value of field 'vamsasModel'. - */ - public void setVamsasModel(final jalview.binding.VamsasModel vamsasModel) - { - this._vamsasModel = vamsasModel; - } - - /** - * Sets the value of field 'version'. - * - * @param version - * the value of field 'version'. - */ - public void setVersion(final java.lang.String version) - { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JalviewModel - */ - public static jalview.binding.JalviewModel unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewModel) Unmarshaller - .unmarshal(jalview.binding.JalviewModel.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java deleted file mode 100644 index 9020ce2..0000000 --- a/src/jalview/binding/JalviewModelSequence.java +++ /dev/null @@ -1,955 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewModelSequence. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelSequence implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _JSeqList. - */ - private java.util.Vector _JSeqList; - - /** - * Field _JGroupList. - */ - private java.util.Vector _JGroupList; - - /** - * Field _viewportList. - */ - private java.util.Vector _viewportList; - - /** - * Field _userColoursList. - */ - private java.util.Vector _userColoursList; - - /** - * Field _treeList. - */ - private java.util.Vector _treeList; - - /** - * Field _featureSettings. - */ - private jalview.binding.FeatureSettings _featureSettings; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModelSequence() - { - super(); - this._JSeqList = new java.util.Vector(); - this._JGroupList = new java.util.Vector(); - this._viewportList = new java.util.Vector(); - this._userColoursList = new java.util.Vector(); - this._treeList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJGroup(final jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - this._JGroupList.addElement(vJGroup); - } - - /** - * - * - * @param index - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJGroup(final int index, - final jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - this._JGroupList.add(index, vJGroup); - } - - /** - * - * - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJSeq(final jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - this._JSeqList.addElement(vJSeq); - } - - /** - * - * - * @param index - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJSeq(final int index, final jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - this._JSeqList.add(index, vJSeq); - } - - /** - * - * - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.addElement(vTree); - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final int index, final jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.add(index, vTree); - } - - /** - * - * - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addUserColours(final jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - this._userColoursList.addElement(vUserColours); - } - - /** - * - * - * @param index - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addUserColours(final int index, - final jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - this._userColoursList.add(index, vUserColours); - } - - /** - * - * - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addViewport(final jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - this._viewportList.addElement(vViewport); - } - - /** - * - * - * @param index - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addViewport(final int index, - final jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - this._viewportList.add(index, vViewport); - } - - /** - * Method enumerateJGroup. - * - * @return an Enumeration over all jalview.binding.JGroup elements - */ - public java.util.Enumeration enumerateJGroup() - { - return this._JGroupList.elements(); - } - - /** - * Method enumerateJSeq. - * - * @return an Enumeration over all jalview.binding.JSeq elements - */ - public java.util.Enumeration enumerateJSeq() - { - return this._JSeqList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all jalview.binding.Tree elements - */ - public java.util.Enumeration enumerateTree() - { - return this._treeList.elements(); - } - - /** - * Method enumerateUserColours. - * - * @return an Enumeration over all jalview.binding.UserColours elements - */ - public java.util.Enumeration enumerateUserColours() - { - return this._userColoursList.elements(); - } - - /** - * Method enumerateViewport. - * - * @return an Enumeration over all jalview.binding.Viewport elements - */ - public java.util.Enumeration enumerateViewport() - { - return this._viewportList.elements(); - } - - /** - * Returns the value of field 'featureSettings'. - * - * @return the value of field 'FeatureSettings'. - */ - public jalview.binding.FeatureSettings getFeatureSettings() - { - return this._featureSettings; - } - - /** - * Method getJGroup. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.JGroup at the given index - */ - public jalview.binding.JGroup getJGroup(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JGroupList.size()) - { - throw new IndexOutOfBoundsException( - "getJGroup: Index value '" + index + "' not in range [0.." - + (this._JGroupList.size() - 1) + "]"); - } - - return (jalview.binding.JGroup) _JGroupList.get(index); - } - - /** - * Method getJGroup.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.JGroup[] getJGroup() - { - jalview.binding.JGroup[] array = new jalview.binding.JGroup[0]; - return (jalview.binding.JGroup[]) this._JGroupList.toArray(array); - } - - /** - * Method getJGroupCount. - * - * @return the size of this collection - */ - public int getJGroupCount() - { - return this._JGroupList.size(); - } - - /** - * Method getJSeq. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.JSeq at the given index - */ - public jalview.binding.JSeq getJSeq(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JSeqList.size()) - { - throw new IndexOutOfBoundsException("getJSeq: Index value '" + index - + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); - } - - return (jalview.binding.JSeq) _JSeqList.get(index); - } - - /** - * Method getJSeq.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.JSeq[] getJSeq() - { - jalview.binding.JSeq[] array = new jalview.binding.JSeq[0]; - return (jalview.binding.JSeq[]) this._JSeqList.toArray(array); - } - - /** - * Method getJSeqCount. - * - * @return the size of this collection - */ - public int getJSeqCount() - { - return this._JSeqList.size(); - } - - /** - * Method getTree. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Tree at the given index - */ - public jalview.binding.Tree getTree(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("getTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - return (jalview.binding.Tree) _treeList.get(index); - } - - /** - * Method getTree.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Tree[] getTree() - { - jalview.binding.Tree[] array = new jalview.binding.Tree[0]; - return (jalview.binding.Tree[]) this._treeList.toArray(array); - } - - /** - * Method getTreeCount. - * - * @return the size of this collection - */ - public int getTreeCount() - { - return this._treeList.size(); - } - - /** - * Method getUserColours. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.UserColours at the given index - */ - public jalview.binding.UserColours getUserColours(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._userColoursList.size()) - { - throw new IndexOutOfBoundsException("getUserColours: Index value '" - + index + "' not in range [0.." - + (this._userColoursList.size() - 1) + "]"); - } - - return (jalview.binding.UserColours) _userColoursList.get(index); - } - - /** - * Method getUserColours.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.UserColours[] getUserColours() - { - jalview.binding.UserColours[] array = new jalview.binding.UserColours[0]; - return (jalview.binding.UserColours[]) this._userColoursList - .toArray(array); - } - - /** - * Method getUserColoursCount. - * - * @return the size of this collection - */ - public int getUserColoursCount() - { - return this._userColoursList.size(); - } - - /** - * Method getViewport. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Viewport at the given index - */ - public jalview.binding.Viewport getViewport(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._viewportList.size()) - { - throw new IndexOutOfBoundsException( - "getViewport: Index value '" + index + "' not in range [0.." - + (this._viewportList.size() - 1) + "]"); - } - - return (jalview.binding.Viewport) _viewportList.get(index); - } - - /** - * Method getViewport.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Viewport[] getViewport() - { - jalview.binding.Viewport[] array = new jalview.binding.Viewport[0]; - return (jalview.binding.Viewport[]) this._viewportList.toArray(array); - } - - /** - * Method getViewportCount. - * - * @return the size of this collection - */ - public int getViewportCount() - { - return this._viewportList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllJGroup() - { - this._JGroupList.clear(); - } - - /** - */ - public void removeAllJSeq() - { - this._JSeqList.clear(); - } - - /** - */ - public void removeAllTree() - { - this._treeList.clear(); - } - - /** - */ - public void removeAllUserColours() - { - this._userColoursList.clear(); - } - - /** - */ - public void removeAllViewport() - { - this._viewportList.clear(); - } - - /** - * Method removeJGroup. - * - * @param vJGroup - * @return true if the object was removed from the collection. - */ - public boolean removeJGroup(final jalview.binding.JGroup vJGroup) - { - boolean removed = _JGroupList.remove(vJGroup); - return removed; - } - - /** - * Method removeJGroupAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.JGroup removeJGroupAt(final int index) - { - java.lang.Object obj = this._JGroupList.remove(index); - return (jalview.binding.JGroup) obj; - } - - /** - * Method removeJSeq. - * - * @param vJSeq - * @return true if the object was removed from the collection. - */ - public boolean removeJSeq(final jalview.binding.JSeq vJSeq) - { - boolean removed = _JSeqList.remove(vJSeq); - return removed; - } - - /** - * Method removeJSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.JSeq removeJSeqAt(final int index) - { - java.lang.Object obj = this._JSeqList.remove(index); - return (jalview.binding.JSeq) obj; - } - - /** - * Method removeTree. - * - * @param vTree - * @return true if the object was removed from the collection. - */ - public boolean removeTree(final jalview.binding.Tree vTree) - { - boolean removed = _treeList.remove(vTree); - return removed; - } - - /** - * Method removeTreeAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Tree removeTreeAt(final int index) - { - java.lang.Object obj = this._treeList.remove(index); - return (jalview.binding.Tree) obj; - } - - /** - * Method removeUserColours. - * - * @param vUserColours - * @return true if the object was removed from the collection. - */ - public boolean removeUserColours( - final jalview.binding.UserColours vUserColours) - { - boolean removed = _userColoursList.remove(vUserColours); - return removed; - } - - /** - * Method removeUserColoursAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.UserColours removeUserColoursAt(final int index) - { - java.lang.Object obj = this._userColoursList.remove(index); - return (jalview.binding.UserColours) obj; - } - - /** - * Method removeViewport. - * - * @param vViewport - * @return true if the object was removed from the collection. - */ - public boolean removeViewport(final jalview.binding.Viewport vViewport) - { - boolean removed = _viewportList.remove(vViewport); - return removed; - } - - /** - * Method removeViewportAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Viewport removeViewportAt(final int index) - { - java.lang.Object obj = this._viewportList.remove(index); - return (jalview.binding.Viewport) obj; - } - - /** - * Sets the value of field 'featureSettings'. - * - * @param featureSettings - * the value of field 'featureSettings'. - */ - public void setFeatureSettings( - final jalview.binding.FeatureSettings featureSettings) - { - this._featureSettings = featureSettings; - } - - /** - * - * - * @param index - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setJGroup(final int index, - final jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JGroupList.size()) - { - throw new IndexOutOfBoundsException( - "setJGroup: Index value '" + index + "' not in range [0.." - + (this._JGroupList.size() - 1) + "]"); - } - - this._JGroupList.set(index, vJGroup); - } - - /** - * - * - * @param vJGroupArray - */ - public void setJGroup(final jalview.binding.JGroup[] vJGroupArray) - { - // -- copy array - _JGroupList.clear(); - - for (int i = 0; i < vJGroupArray.length; i++) - { - this._JGroupList.add(vJGroupArray[i]); - } - } - - /** - * - * - * @param index - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setJSeq(final int index, final jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JSeqList.size()) - { - throw new IndexOutOfBoundsException("setJSeq: Index value '" + index - + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); - } - - this._JSeqList.set(index, vJSeq); - } - - /** - * - * - * @param vJSeqArray - */ - public void setJSeq(final jalview.binding.JSeq[] vJSeqArray) - { - // -- copy array - _JSeqList.clear(); - - for (int i = 0; i < vJSeqArray.length; i++) - { - this._JSeqList.add(vJSeqArray[i]); - } - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setTree(final int index, final jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("setTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - this._treeList.set(index, vTree); - } - - /** - * - * - * @param vTreeArray - */ - public void setTree(final jalview.binding.Tree[] vTreeArray) - { - // -- copy array - _treeList.clear(); - - for (int i = 0; i < vTreeArray.length; i++) - { - this._treeList.add(vTreeArray[i]); - } - } - - /** - * - * - * @param index - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setUserColours(final int index, - final jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._userColoursList.size()) - { - throw new IndexOutOfBoundsException("setUserColours: Index value '" - + index + "' not in range [0.." - + (this._userColoursList.size() - 1) + "]"); - } - - this._userColoursList.set(index, vUserColours); - } - - /** - * - * - * @param vUserColoursArray - */ - public void setUserColours( - final jalview.binding.UserColours[] vUserColoursArray) - { - // -- copy array - _userColoursList.clear(); - - for (int i = 0; i < vUserColoursArray.length; i++) - { - this._userColoursList.add(vUserColoursArray[i]); - } - } - - /** - * - * - * @param index - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setViewport(final int index, - final jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._viewportList.size()) - { - throw new IndexOutOfBoundsException( - "setViewport: Index value '" + index + "' not in range [0.." - + (this._viewportList.size() - 1) + "]"); - } - - this._viewportList.set(index, vViewport); - } - - /** - * - * - * @param vViewportArray - */ - public void setViewport(final jalview.binding.Viewport[] vViewportArray) - { - // -- copy array - _viewportList.clear(); - - for (int i = 0; i < vViewportArray.length; i++) - { - this._viewportList.add(vViewportArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JalviewModelSequence - */ - public static jalview.binding.JalviewModelSequence unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewModelSequence) Unmarshaller - .unmarshal(jalview.binding.JalviewModelSequence.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java deleted file mode 100644 index 67ee5a2..0000000 --- a/src/jalview/binding/JalviewUserColours.java +++ /dev/null @@ -1,503 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewUserColours. - * - * @version $Revision$ $Date$ - */ -public class JalviewUserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _schemeName. - */ - private java.lang.String _schemeName; - - /** - * Jalview colour scheme document version. - * - */ - private java.lang.String _version; - - /** - * Field _colourList. - */ - private java.util.Vector _colourList; - - /** - * Field _filterList. - */ - private java.util.Vector _filterList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewUserColours() - { - super(); - this._colourList = new java.util.Vector(); - this._filterList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addColour(final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - this._colourList.addElement(vColour); - } - - /** - * - * - * @param index - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addColour(final int index, final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - this._colourList.add(index, vColour); - } - - /** - * - * - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFilter(final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - this._filterList.addElement(vFilter); - } - - /** - * - * - * @param index - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFilter(final int index, final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - this._filterList.add(index, vFilter); - } - - /** - * Method enumerateColour. - * - * @return an Enumeration over all Colour elements - */ - public java.util.Enumeration enumerateColour() - { - return this._colourList.elements(); - } - - /** - * Method enumerateFilter. - * - * @return an Enumeration over all Filter elements - */ - public java.util.Enumeration enumerateFilter() - { - return this._filterList.elements(); - } - - /** - * Method getColour. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the Colour at the given index - */ - public Colour getColour(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._colourList.size()) - { - throw new IndexOutOfBoundsException( - "getColour: Index value '" + index + "' not in range [0.." - + (this._colourList.size() - 1) + "]"); - } - - return (Colour) _colourList.get(index); - } - - /** - * Method getColour.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Colour[] getColour() - { - Colour[] array = new Colour[0]; - return (Colour[]) this._colourList.toArray(array); - } - - /** - * Method getColourCount. - * - * @return the size of this collection - */ - public int getColourCount() - { - return this._colourList.size(); - } - - /** - * Method getFilter. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the Filter at the given index - */ - public Filter getFilter(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._filterList.size()) - { - throw new IndexOutOfBoundsException( - "getFilter: Index value '" + index + "' not in range [0.." - + (this._filterList.size() - 1) + "]"); - } - - return (Filter) _filterList.get(index); - } - - /** - * Method getFilter.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Filter[] getFilter() - { - Filter[] array = new Filter[0]; - return (Filter[]) this._filterList.toArray(array); - } - - /** - * Method getFilterCount. - * - * @return the size of this collection - */ - public int getFilterCount() - { - return this._filterList.size(); - } - - /** - * Returns the value of field 'schemeName'. - * - * @return the value of field 'SchemeName'. - */ - public java.lang.String getSchemeName() - { - return this._schemeName; - } - - /** - * Returns the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document version. - * - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion() - { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllColour() - { - this._colourList.clear(); - } - - /** - */ - public void removeAllFilter() - { - this._filterList.clear(); - } - - /** - * Method removeColour. - * - * @param vColour - * @return true if the object was removed from the collection. - */ - public boolean removeColour(final Colour vColour) - { - boolean removed = _colourList.remove(vColour); - return removed; - } - - /** - * Method removeColourAt. - * - * @param index - * @return the element removed from the collection - */ - public Colour removeColourAt(final int index) - { - java.lang.Object obj = this._colourList.remove(index); - return (Colour) obj; - } - - /** - * Method removeFilter. - * - * @param vFilter - * @return true if the object was removed from the collection. - */ - public boolean removeFilter(final Filter vFilter) - { - boolean removed = _filterList.remove(vFilter); - return removed; - } - - /** - * Method removeFilterAt. - * - * @param index - * @return the element removed from the collection - */ - public Filter removeFilterAt(final int index) - { - java.lang.Object obj = this._filterList.remove(index); - return (Filter) obj; - } - - /** - * - * - * @param index - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setColour(final int index, final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._colourList.size()) - { - throw new IndexOutOfBoundsException( - "setColour: Index value '" + index + "' not in range [0.." - + (this._colourList.size() - 1) + "]"); - } - - this._colourList.set(index, vColour); - } - - /** - * - * - * @param vColourArray - */ - public void setColour(final Colour[] vColourArray) - { - // -- copy array - _colourList.clear(); - - for (int i = 0; i < vColourArray.length; i++) - { - this._colourList.add(vColourArray[i]); - } - } - - /** - * - * - * @param index - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setFilter(final int index, final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._filterList.size()) - { - throw new IndexOutOfBoundsException( - "setFilter: Index value '" + index + "' not in range [0.." - + (this._filterList.size() - 1) + "]"); - } - - this._filterList.set(index, vFilter); - } - - /** - * - * - * @param vFilterArray - */ - public void setFilter(final Filter[] vFilterArray) - { - // -- copy array - _filterList.clear(); - - for (int i = 0; i < vFilterArray.length; i++) - { - this._filterList.add(vFilterArray[i]); - } - } - - /** - * Sets the value of field 'schemeName'. - * - * @param schemeName - * the value of field 'schemeName'. - */ - public void setSchemeName(final java.lang.String schemeName) - { - this._schemeName = schemeName; - } - - /** - * Sets the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document version. - * - * - * @param version - * the value of field 'version'. - */ - public void setVersion(final java.lang.String version) - { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JalviewUserColours - */ - public static jalview.binding.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewUserColours) Unmarshaller - .unmarshal(jalview.binding.JalviewUserColours.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/MatchCondition.java b/src/jalview/binding/MatchCondition.java deleted file mode 100644 index 44a3d3e..0000000 --- a/src/jalview/binding/MatchCondition.java +++ /dev/null @@ -1,125 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class MatchCondition. - * - * @version $Revision$ $Date$ - */ -public class MatchCondition extends FeatureMatcher - implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MatchCondition() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureMatcher - */ - public static jalview.binding.FeatureMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureMatcher) Unmarshaller - .unmarshal(jalview.binding.MatchCondition.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/MatcherSet.java b/src/jalview/binding/MatcherSet.java deleted file mode 100644 index 756d93a..0000000 --- a/src/jalview/binding/MatcherSet.java +++ /dev/null @@ -1,125 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class MatcherSet. - * - * @version $Revision$ $Date$ - */ -public class MatcherSet extends FeatureMatcherSet - implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MatcherSet() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureMatcherSet - */ - public static jalview.binding.FeatureMatcherSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureMatcherSet) Unmarshaller - .unmarshal(jalview.binding.MatcherSet.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java deleted file mode 100644 index 77bb446..0000000 --- a/src/jalview/binding/Pdbentry.java +++ /dev/null @@ -1,344 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Pdbentry. - * - * @version $Revision$ $Date$ - */ -public class Pdbentry implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _items. - */ - private java.util.Vector _items; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Pdbentry() - { - super(); - this._items = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbentryItem( - final jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.addElement(vPdbentryItem); - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbentryItem(final int index, - final jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.add(index, vPdbentryItem); - } - - /** - * Method enumeratePdbentryItem. - * - * @return an Enumeration over all jalview.binding.PdbentryItem elements - */ - public java.util.Enumeration enumeratePdbentryItem() - { - return this._items.elements(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Method getPdbentryItem. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.PdbentryItem at the given index - */ - public jalview.binding.PdbentryItem getPdbentryItem(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._items.size()) - { - throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" - + index + "' not in range [0.." + (this._items.size() - 1) - + "]"); - } - - return (jalview.binding.PdbentryItem) _items.get(index); - } - - /** - * Method getPdbentryItem.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.PdbentryItem[] getPdbentryItem() - { - jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0]; - return (jalview.binding.PdbentryItem[]) this._items.toArray(array); - } - - /** - * Method getPdbentryItemCount. - * - * @return the size of this collection - */ - public int getPdbentryItemCount() - { - return this._items.size(); - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllPdbentryItem() - { - this._items.clear(); - } - - /** - * Method removePdbentryItem. - * - * @param vPdbentryItem - * @return true if the object was removed from the collection. - */ - public boolean removePdbentryItem( - final jalview.binding.PdbentryItem vPdbentryItem) - { - boolean removed = _items.remove(vPdbentryItem); - return removed; - } - - /** - * Method removePdbentryItemAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.PdbentryItem removePdbentryItemAt(final int index) - { - java.lang.Object obj = this._items.remove(index); - return (jalview.binding.PdbentryItem) obj; - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbentryItem(final int index, - final jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._items.size()) - { - throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" - + index + "' not in range [0.." + (this._items.size() - 1) - + "]"); - } - - this._items.set(index, vPdbentryItem); - } - - /** - * - * - * @param vPdbentryItemArray - */ - public void setPdbentryItem( - final jalview.binding.PdbentryItem[] vPdbentryItemArray) - { - // -- copy array - _items.clear(); - - for (int i = 0; i < vPdbentryItemArray.length; i++) - { - this._items.add(vPdbentryItemArray[i]); - } - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Pdbentry - */ - public static jalview.binding.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Pdbentry) Unmarshaller - .unmarshal(jalview.binding.Pdbentry.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java deleted file mode 100644 index 30a0512..0000000 --- a/src/jalview/binding/PdbentryItem.java +++ /dev/null @@ -1,196 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -/** - * Class PdbentryItem. - * - * @version $Revision$ $Date$ - */ -public class PdbentryItem implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _propertyList. - */ - private java.util.Vector _propertyList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbentryItem() - { - super(); - this._propertyList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addProperty(final jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.addElement(vProperty); - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addProperty(final int index, - final jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.add(index, vProperty); - } - - /** - * Method enumerateProperty. - * - * @return an Enumeration over all jalview.binding.Property elements - */ - public java.util.Enumeration enumerateProperty() - { - return this._propertyList.elements(); - } - - /** - * Method getProperty. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Property at the given index - */ - public jalview.binding.Property getProperty(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException( - "getProperty: Index value '" + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - return (jalview.binding.Property) _propertyList.get(index); - } - - /** - * Method getProperty.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Property[] getProperty() - { - jalview.binding.Property[] array = new jalview.binding.Property[0]; - return (jalview.binding.Property[]) this._propertyList.toArray(array); - } - - /** - * Method getPropertyCount. - * - * @return the size of this collection - */ - public int getPropertyCount() - { - return this._propertyList.size(); - } - - /** - */ - public void removeAllProperty() - { - this._propertyList.clear(); - } - - /** - * Method removeProperty. - * - * @param vProperty - * @return true if the object was removed from the collection. - */ - public boolean removeProperty(final jalview.binding.Property vProperty) - { - boolean removed = _propertyList.remove(vProperty); - return removed; - } - - /** - * Method removePropertyAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Property removePropertyAt(final int index) - { - java.lang.Object obj = this._propertyList.remove(index); - return (jalview.binding.Property) obj; - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setProperty(final int index, - final jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException( - "setProperty: Index value '" + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - this._propertyList.set(index, vProperty); - } - - /** - * - * - * @param vPropertyArray - */ - public void setProperty(final jalview.binding.Property[] vPropertyArray) - { - // -- copy array - _propertyList.clear(); - - for (int i = 0; i < vPropertyArray.length; i++) - { - this._propertyList.add(vPropertyArray[i]); - } - } - -} diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java deleted file mode 100644 index 79cae6c..0000000 --- a/src/jalview/binding/Pdbids.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Pdbids. - * - * @version $Revision$ $Date$ - */ -public class Pdbids extends Pdbentry implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Pdbids() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Pdbentry - */ - public static jalview.binding.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Pdbentry) Unmarshaller - .unmarshal(jalview.binding.Pdbids.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java deleted file mode 100644 index 5823fed..0000000 --- a/src/jalview/binding/Property.java +++ /dev/null @@ -1,180 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Property. - * - * @version $Revision$ $Date$ - */ -public class Property implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Property() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue() - { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final java.lang.String value) - { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Property - */ - public static jalview.binding.Property unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Property) Unmarshaller - .unmarshal(jalview.binding.Property.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java deleted file mode 100644 index 845f224..0000000 --- a/src/jalview/binding/Sequence.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends SequenceType implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Sequence() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.SequenceType - */ - public static jalview.binding.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.SequenceType) Unmarshaller - .unmarshal(jalview.binding.Sequence.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java deleted file mode 100644 index 3d81bae..0000000 --- a/src/jalview/binding/SequenceSet.java +++ /dev/null @@ -1,538 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class SequenceSet. - * - * @version $Revision$ $Date$ - */ -public class SequenceSet implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _gapChar. - */ - private java.lang.String _gapChar; - - /** - * Field _aligned. - */ - private boolean _aligned; - - /** - * keeps track of state for field: _aligned - */ - private boolean _has_aligned; - - /** - * Field _sequenceList. - */ - private java.util.Vector _sequenceList; - - /** - * Field _annotationList. - */ - private java.util.Vector _annotationList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSet() - { - super(); - this._sequenceList = new java.util.Vector(); - this._annotationList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotation(final jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - this._annotationList.addElement(vAnnotation); - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotation(final int index, - final jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - this._annotationList.add(index, vAnnotation); - } - - /** - * - * - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequence(final jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceList.addElement(vSequence); - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequence(final int index, - final jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceList.add(index, vSequence); - } - - /** - */ - public void deleteAligned() - { - this._has_aligned = false; - } - - /** - * Method enumerateAnnotation. - * - * @return an Enumeration over all jalview.binding.Annotation elements - */ - public java.util.Enumeration enumerateAnnotation() - { - return this._annotationList.elements(); - } - - /** - * Method enumerateSequence. - * - * @return an Enumeration over all jalview.binding.Sequence elements - */ - public java.util.Enumeration enumerateSequence() - { - return this._sequenceList.elements(); - } - - /** - * Returns the value of field 'aligned'. - * - * @return the value of field 'Aligned'. - */ - public boolean getAligned() - { - return this._aligned; - } - - /** - * Method getAnnotation. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Annotation at the given index - */ - public jalview.binding.Annotation getAnnotation(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) - { - throw new IndexOutOfBoundsException( - "getAnnotation: Index value '" + index + "' not in range [0.." - + (this._annotationList.size() - 1) + "]"); - } - - return (jalview.binding.Annotation) _annotationList.get(index); - } - - /** - * Method getAnnotation.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Annotation[] getAnnotation() - { - jalview.binding.Annotation[] array = new jalview.binding.Annotation[0]; - return (jalview.binding.Annotation[]) this._annotationList - .toArray(array); - } - - /** - * Method getAnnotationCount. - * - * @return the size of this collection - */ - public int getAnnotationCount() - { - return this._annotationList.size(); - } - - /** - * Returns the value of field 'gapChar'. - * - * @return the value of field 'GapChar'. - */ - public java.lang.String getGapChar() - { - return this._gapChar; - } - - /** - * Method getSequence. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Sequence at the given index - */ - public jalview.binding.Sequence getSequence(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) - { - throw new IndexOutOfBoundsException( - "getSequence: Index value '" + index + "' not in range [0.." - + (this._sequenceList.size() - 1) + "]"); - } - - return (jalview.binding.Sequence) _sequenceList.get(index); - } - - /** - * Method getSequence.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Sequence[] getSequence() - { - jalview.binding.Sequence[] array = new jalview.binding.Sequence[0]; - return (jalview.binding.Sequence[]) this._sequenceList.toArray(array); - } - - /** - * Method getSequenceCount. - * - * @return the size of this collection - */ - public int getSequenceCount() - { - return this._sequenceList.size(); - } - - /** - * Method hasAligned. - * - * @return true if at least one Aligned has been added - */ - public boolean hasAligned() - { - return this._has_aligned; - } - - /** - * Returns the value of field 'aligned'. - * - * @return the value of field 'Aligned'. - */ - public boolean isAligned() - { - return this._aligned; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAnnotation() - { - this._annotationList.clear(); - } - - /** - */ - public void removeAllSequence() - { - this._sequenceList.clear(); - } - - /** - * Method removeAnnotation. - * - * @param vAnnotation - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotation( - final jalview.binding.Annotation vAnnotation) - { - boolean removed = _annotationList.remove(vAnnotation); - return removed; - } - - /** - * Method removeAnnotationAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Annotation removeAnnotationAt(final int index) - { - java.lang.Object obj = this._annotationList.remove(index); - return (jalview.binding.Annotation) obj; - } - - /** - * Method removeSequence. - * - * @param vSequence - * @return true if the object was removed from the collection. - */ - public boolean removeSequence(final jalview.binding.Sequence vSequence) - { - boolean removed = _sequenceList.remove(vSequence); - return removed; - } - - /** - * Method removeSequenceAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Sequence removeSequenceAt(final int index) - { - java.lang.Object obj = this._sequenceList.remove(index); - return (jalview.binding.Sequence) obj; - } - - /** - * Sets the value of field 'aligned'. - * - * @param aligned - * the value of field 'aligned'. - */ - public void setAligned(final boolean aligned) - { - this._aligned = aligned; - this._has_aligned = true; - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAnnotation(final int index, - final jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) - { - throw new IndexOutOfBoundsException( - "setAnnotation: Index value '" + index + "' not in range [0.." - + (this._annotationList.size() - 1) + "]"); - } - - this._annotationList.set(index, vAnnotation); - } - - /** - * - * - * @param vAnnotationArray - */ - public void setAnnotation( - final jalview.binding.Annotation[] vAnnotationArray) - { - // -- copy array - _annotationList.clear(); - - for (int i = 0; i < vAnnotationArray.length; i++) - { - this._annotationList.add(vAnnotationArray[i]); - } - } - - /** - * Sets the value of field 'gapChar'. - * - * @param gapChar - * the value of field 'gapChar'. - */ - public void setGapChar(final java.lang.String gapChar) - { - this._gapChar = gapChar; - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSequence(final int index, - final jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) - { - throw new IndexOutOfBoundsException( - "setSequence: Index value '" + index + "' not in range [0.." - + (this._sequenceList.size() - 1) + "]"); - } - - this._sequenceList.set(index, vSequence); - } - - /** - * - * - * @param vSequenceArray - */ - public void setSequence(final jalview.binding.Sequence[] vSequenceArray) - { - // -- copy array - _sequenceList.clear(); - - for (int i = 0; i < vSequenceArray.length; i++) - { - this._sequenceList.add(vSequenceArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.SequenceSet - */ - public static jalview.binding.SequenceSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.SequenceSet) Unmarshaller - .unmarshal(jalview.binding.SequenceSet.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java deleted file mode 100644 index 7f10bca..0000000 --- a/src/jalview/binding/SequenceType.java +++ /dev/null @@ -1,206 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class SequenceType. - * - * @version $Revision$ $Date$ - */ -public class SequenceType implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _sequence. - */ - private java.lang.String _sequence; - - /** - * Field _name. - */ - private java.lang.String _name; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceType() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'sequence'. - * - * @return the value of field 'Sequence'. - */ - public java.lang.String getSequence() - { - return this._sequence; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'sequence'. - * - * @param sequence - * the value of field 'sequence'. - */ - public void setSequence(final java.lang.String sequence) - { - this._sequence = sequence; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.SequenceType - */ - public static jalview.binding.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.SequenceType) Unmarshaller - .unmarshal(jalview.binding.SequenceType.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java deleted file mode 100644 index d098303..0000000 --- a/src/jalview/binding/Setting.java +++ /dev/null @@ -1,262 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Setting. - * - * @version $Revision$ $Date$ - */ -public class Setting implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _display. - */ - private boolean _display; - - /** - * keeps track of state for field: _display - */ - private boolean _has_display; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Setting() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteDisplay() - { - this._has_display = false; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean getDisplay() - { - return this._display; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasDisplay. - * - * @return true if at least one Display has been added - */ - public boolean hasDisplay() - { - return this._has_display; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean isDisplay() - { - return this._display; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'display'. - * - * @param display - * the value of field 'display'. - */ - public void setDisplay(final boolean display) - { - this._display = display; - this._has_display = true; - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Setting - */ - public static jalview.binding.Setting unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Setting) Unmarshaller - .unmarshal(jalview.binding.Setting.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java deleted file mode 100644 index 7005c93..0000000 --- a/src/jalview/binding/Tree.java +++ /dev/null @@ -1,843 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Tree. - * - * @version $Revision$ $Date$ - */ -public class Tree implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _width. - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height. - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _xpos. - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos. - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _fontName. - */ - private java.lang.String _fontName; - - /** - * Field _fontSize. - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle. - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _showBootstrap. - */ - private boolean _showBootstrap; - - /** - * keeps track of state for field: _showBootstrap - */ - private boolean _has_showBootstrap; - - /** - * Field _showDistances. - */ - private boolean _showDistances; - - /** - * keeps track of state for field: _showDistances - */ - private boolean _has_showDistances; - - /** - * Field _markUnlinked. - */ - private boolean _markUnlinked; - - /** - * keeps track of state for field: _markUnlinked - */ - private boolean _has_markUnlinked; - - /** - * Field _fitToWindow. - */ - private boolean _fitToWindow; - - /** - * keeps track of state for field: _fitToWindow - */ - private boolean _has_fitToWindow; - - /** - * Field _currentTree. - */ - private boolean _currentTree; - - /** - * keeps track of state for field: _currentTree - */ - private boolean _has_currentTree; - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * Field _newick. - */ - private java.lang.String _newick; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Tree() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteCurrentTree() - { - this._has_currentTree = false; - } - - /** - */ - public void deleteFitToWindow() - { - this._has_fitToWindow = false; - } - - /** - */ - public void deleteFontSize() - { - this._has_fontSize = false; - } - - /** - */ - public void deleteFontStyle() - { - this._has_fontStyle = false; - } - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deleteMarkUnlinked() - { - this._has_markUnlinked = false; - } - - /** - */ - public void deleteShowBootstrap() - { - this._has_showBootstrap = false; - } - - /** - */ - public void deleteShowDistances() - { - this._has_showDistances = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - */ - public void deleteWidth() - { - this._has_width = false; - } - - /** - */ - public void deleteXpos() - { - this._has_xpos = false; - } - - /** - */ - public void deleteYpos() - { - this._has_ypos = false; - } - - /** - * Returns the value of field 'currentTree'. - * - * @return the value of field 'CurrentTree'. - */ - public boolean getCurrentTree() - { - return this._currentTree; - } - - /** - * Returns the value of field 'fitToWindow'. - * - * @return the value of field 'FitToWindow'. - */ - public boolean getFitToWindow() - { - return this._fitToWindow; - } - - /** - * Returns the value of field 'fontName'. - * - * @return the value of field 'FontName'. - */ - public java.lang.String getFontName() - { - return this._fontName; - } - - /** - * Returns the value of field 'fontSize'. - * - * @return the value of field 'FontSize'. - */ - public int getFontSize() - { - return this._fontSize; - } - - /** - * Returns the value of field 'fontStyle'. - * - * @return the value of field 'FontStyle'. - */ - public int getFontStyle() - { - return this._fontStyle; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Returns the value of field 'markUnlinked'. - * - * @return the value of field 'MarkUnlinked'. - */ - public boolean getMarkUnlinked() - { - return this._markUnlinked; - } - - /** - * Returns the value of field 'newick'. - * - * @return the value of field 'Newick'. - */ - public java.lang.String getNewick() - { - return this._newick; - } - - /** - * Returns the value of field 'showBootstrap'. - * - * @return the value of field 'ShowBootstrap'. - */ - public boolean getShowBootstrap() - { - return this._showBootstrap; - } - - /** - * Returns the value of field 'showDistances'. - * - * @return the value of field 'ShowDistances'. - */ - public boolean getShowDistances() - { - return this._showDistances; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle() - { - return this._title; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth() - { - return this._width; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos() - { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos() - { - return this._ypos; - } - - /** - * Method hasCurrentTree. - * - * @return true if at least one CurrentTree has been added - */ - public boolean hasCurrentTree() - { - return this._has_currentTree; - } - - /** - * Method hasFitToWindow. - * - * @return true if at least one FitToWindow has been added - */ - public boolean hasFitToWindow() - { - return this._has_fitToWindow; - } - - /** - * Method hasFontSize. - * - * @return true if at least one FontSize has been added - */ - public boolean hasFontSize() - { - return this._has_fontSize; - } - - /** - * Method hasFontStyle. - * - * @return true if at least one FontStyle has been added - */ - public boolean hasFontStyle() - { - return this._has_fontStyle; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasMarkUnlinked. - * - * @return true if at least one MarkUnlinked has been added - */ - public boolean hasMarkUnlinked() - { - return this._has_markUnlinked; - } - - /** - * Method hasShowBootstrap. - * - * @return true if at least one ShowBootstrap has been added - */ - public boolean hasShowBootstrap() - { - return this._has_showBootstrap; - } - - /** - * Method hasShowDistances. - * - * @return true if at least one ShowDistances has been added - */ - public boolean hasShowDistances() - { - return this._has_showDistances; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth() - { - return this._has_width; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos() - { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos() - { - return this._has_ypos; - } - - /** - * Returns the value of field 'currentTree'. - * - * @return the value of field 'CurrentTree'. - */ - public boolean isCurrentTree() - { - return this._currentTree; - } - - /** - * Returns the value of field 'fitToWindow'. - * - * @return the value of field 'FitToWindow'. - */ - public boolean isFitToWindow() - { - return this._fitToWindow; - } - - /** - * Returns the value of field 'markUnlinked'. - * - * @return the value of field 'MarkUnlinked'. - */ - public boolean isMarkUnlinked() - { - return this._markUnlinked; - } - - /** - * Returns the value of field 'showBootstrap'. - * - * @return the value of field 'ShowBootstrap'. - */ - public boolean isShowBootstrap() - { - return this._showBootstrap; - } - - /** - * Returns the value of field 'showDistances'. - * - * @return the value of field 'ShowDistances'. - */ - public boolean isShowDistances() - { - return this._showDistances; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'currentTree'. - * - * @param currentTree - * the value of field 'currentTree'. - */ - public void setCurrentTree(final boolean currentTree) - { - this._currentTree = currentTree; - this._has_currentTree = true; - } - - /** - * Sets the value of field 'fitToWindow'. - * - * @param fitToWindow - * the value of field 'fitToWindow'. - */ - public void setFitToWindow(final boolean fitToWindow) - { - this._fitToWindow = fitToWindow; - this._has_fitToWindow = true; - } - - /** - * Sets the value of field 'fontName'. - * - * @param fontName - * the value of field 'fontName'. - */ - public void setFontName(final java.lang.String fontName) - { - this._fontName = fontName; - } - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize - * the value of field 'fontSize'. - */ - public void setFontSize(final int fontSize) - { - this._fontSize = fontSize; - this._has_fontSize = true; - } - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle - * the value of field 'fontStyle'. - */ - public void setFontStyle(final int fontStyle) - { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } - - /** - * Sets the value of field 'height'. - * - * @param height - * the value of field 'height'. - */ - public void setHeight(final int height) - { - this._height = height; - this._has_height = true; - } - - /** - * Sets the value of field 'markUnlinked'. - * - * @param markUnlinked - * the value of field 'markUnlinked'. - */ - public void setMarkUnlinked(final boolean markUnlinked) - { - this._markUnlinked = markUnlinked; - this._has_markUnlinked = true; - } - - /** - * Sets the value of field 'newick'. - * - * @param newick - * the value of field 'newick'. - */ - public void setNewick(final java.lang.String newick) - { - this._newick = newick; - } - - /** - * Sets the value of field 'showBootstrap'. - * - * @param showBootstrap - * the value of field 'showBootstrap'. - */ - public void setShowBootstrap(final boolean showBootstrap) - { - this._showBootstrap = showBootstrap; - this._has_showBootstrap = true; - } - - /** - * Sets the value of field 'showDistances'. - * - * @param showDistances - * the value of field 'showDistances'. - */ - public void setShowDistances(final boolean showDistances) - { - this._showDistances = showDistances; - this._has_showDistances = true; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold - * the value of field 'threshold'. - */ - public void setThreshold(final float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title - * the value of field 'title'. - */ - public void setTitle(final java.lang.String title) - { - this._title = title; - } - - /** - * Sets the value of field 'width'. - * - * @param width - * the value of field 'width'. - */ - public void setWidth(final int width) - { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos - * the value of field 'xpos'. - */ - public void setXpos(final int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos - * the value of field 'ypos'. - */ - public void setYpos(final int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Tree - */ - public static jalview.binding.Tree unmarshal(final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Tree) Unmarshaller - .unmarshal(jalview.binding.Tree.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java deleted file mode 100644 index e1a1a2f..0000000 --- a/src/jalview/binding/UserColourScheme.java +++ /dev/null @@ -1,125 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class UserColourScheme. - * - * @version $Revision$ $Date$ - */ -public class UserColourScheme extends JalviewUserColours - implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColourScheme() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JalviewUserColours - */ - public static jalview.binding.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewUserColours) Unmarshaller - .unmarshal(jalview.binding.UserColourScheme.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java deleted file mode 100644 index 9dbcc9e..0000000 --- a/src/jalview/binding/UserColours.java +++ /dev/null @@ -1,181 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class UserColours. - * - * @version $Revision$ $Date$ - */ -public class UserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _userColourScheme. - */ - private jalview.binding.UserColourScheme _userColourScheme; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColours() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'userColourScheme'. - * - * @return the value of field 'UserColourScheme'. - */ - public jalview.binding.UserColourScheme getUserColourScheme() - { - return this._userColourScheme; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'userColourScheme'. - * - * @param userColourScheme - * the value of field 'userColourScheme' - */ - public void setUserColourScheme( - final jalview.binding.UserColourScheme userColourScheme) - { - this._userColourScheme = userColourScheme; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.UserColours - */ - public static jalview.binding.UserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.UserColours) Unmarshaller - .unmarshal(jalview.binding.UserColours.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java deleted file mode 100644 index b5a32da..0000000 --- a/src/jalview/binding/VAMSAS.java +++ /dev/null @@ -1,605 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class VAMSAS. - * - * @version $Revision$ $Date$ - */ -public class VAMSAS implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _alignmentList. - */ - private java.util.Vector _alignmentList; - - /** - * Field _treeList. - */ - private java.util.Vector _treeList; - - /** - * Field _sequenceSetList. - */ - private java.util.Vector _sequenceSetList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VAMSAS() - { - super(); - this._alignmentList = new java.util.Vector(); - this._treeList = new java.util.Vector(); - this._sequenceSetList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAlignment - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlignment(final Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - this._alignmentList.addElement(vAlignment); - } - - /** - * - * - * @param index - * @param vAlignment - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlignment(final int index, final Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - this._alignmentList.add(index, vAlignment); - } - - /** - * - * - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSet(final SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetList.addElement(vSequenceSet); - } - - /** - * - * - * @param index - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSet(final int index, - final SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetList.add(index, vSequenceSet); - } - - /** - * - * - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.addElement(vTree); - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final int index, final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.add(index, vTree); - } - - /** - * Method enumerateAlignment. - * - * @return an Enumeration over all Alignment elements - */ - public java.util.Enumeration enumerateAlignment() - { - return this._alignmentList.elements(); - } - - /** - * Method enumerateSequenceSet. - * - * @return an Enumeration over all SequenceSet elements - */ - public java.util.Enumeration enumerateSequenceSet() - { - return this._sequenceSetList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateTree() - { - return this._treeList.elements(); - } - - /** - * Method getAlignment. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the Alignment at the given index - */ - public Alignment getAlignment(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alignmentList.size()) - { - throw new IndexOutOfBoundsException( - "getAlignment: Index value '" + index + "' not in range [0.." - + (this._alignmentList.size() - 1) + "]"); - } - - return (Alignment) _alignmentList.get(index); - } - - /** - * Method getAlignment.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Alignment[] getAlignment() - { - Alignment[] array = new Alignment[0]; - return (Alignment[]) this._alignmentList.toArray(array); - } - - /** - * Method getAlignmentCount. - * - * @return the size of this collection - */ - public int getAlignmentCount() - { - return this._alignmentList.size(); - } - - /** - * Method getSequenceSet. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the SequenceSet at the given index - */ - public SequenceSet getSequenceSet(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetList.size()) - { - throw new IndexOutOfBoundsException("getSequenceSet: Index value '" - + index + "' not in range [0.." - + (this._sequenceSetList.size() - 1) + "]"); - } - - return (SequenceSet) _sequenceSetList.get(index); - } - - /** - * Method getSequenceSet.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public SequenceSet[] getSequenceSet() - { - SequenceSet[] array = new SequenceSet[0]; - return (SequenceSet[]) this._sequenceSetList.toArray(array); - } - - /** - * Method getSequenceSetCount. - * - * @return the size of this collection - */ - public int getSequenceSetCount() - { - return this._sequenceSetList.size(); - } - - /** - * Method getTree. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getTree(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("getTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - return (java.lang.String) _treeList.get(index); - } - - /** - * Method getTree.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getTree() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._treeList.toArray(array); - } - - /** - * Method getTreeCount. - * - * @return the size of this collection - */ - public int getTreeCount() - { - return this._treeList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method removeAlignment. - * - * @param vAlignment - * @return true if the object was removed from the collection. - */ - public boolean removeAlignment(final Alignment vAlignment) - { - boolean removed = _alignmentList.remove(vAlignment); - return removed; - } - - /** - * Method removeAlignmentAt. - * - * @param index - * @return the element removed from the collection - */ - public Alignment removeAlignmentAt(final int index) - { - java.lang.Object obj = this._alignmentList.remove(index); - return (Alignment) obj; - } - - /** - */ - public void removeAllAlignment() - { - this._alignmentList.clear(); - } - - /** - */ - public void removeAllSequenceSet() - { - this._sequenceSetList.clear(); - } - - /** - */ - public void removeAllTree() - { - this._treeList.clear(); - } - - /** - * Method removeSequenceSet. - * - * @param vSequenceSet - * @return true if the object was removed from the collection. - */ - public boolean removeSequenceSet(final SequenceSet vSequenceSet) - { - boolean removed = _sequenceSetList.remove(vSequenceSet); - return removed; - } - - /** - * Method removeSequenceSetAt. - * - * @param index - * @return the element removed from the collection - */ - public SequenceSet removeSequenceSetAt(final int index) - { - java.lang.Object obj = this._sequenceSetList.remove(index); - return (SequenceSet) obj; - } - - /** - * Method removeTree. - * - * @param vTree - * @return true if the object was removed from the collection. - */ - public boolean removeTree(final java.lang.String vTree) - { - boolean removed = _treeList.remove(vTree); - return removed; - } - - /** - * Method removeTreeAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeTreeAt(final int index) - { - java.lang.Object obj = this._treeList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vAlignment - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlignment(final int index, final Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alignmentList.size()) - { - throw new IndexOutOfBoundsException( - "setAlignment: Index value '" + index + "' not in range [0.." - + (this._alignmentList.size() - 1) + "]"); - } - - this._alignmentList.set(index, vAlignment); - } - - /** - * - * - * @param vAlignmentArray - */ - public void setAlignment(final Alignment[] vAlignmentArray) - { - // -- copy array - _alignmentList.clear(); - - for (int i = 0; i < vAlignmentArray.length; i++) - { - this._alignmentList.add(vAlignmentArray[i]); - } - } - - /** - * - * - * @param index - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSequenceSet(final int index, - final SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetList.size()) - { - throw new IndexOutOfBoundsException("setSequenceSet: Index value '" - + index + "' not in range [0.." - + (this._sequenceSetList.size() - 1) + "]"); - } - - this._sequenceSetList.set(index, vSequenceSet); - } - - /** - * - * - * @param vSequenceSetArray - */ - public void setSequenceSet(final SequenceSet[] vSequenceSetArray) - { - // -- copy array - _sequenceSetList.clear(); - - for (int i = 0; i < vSequenceSetArray.length; i++) - { - this._sequenceSetList.add(vSequenceSetArray[i]); - } - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setTree(final int index, final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("setTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - this._treeList.set(index, vTree); - } - - /** - * - * - * @param vTreeArray - */ - public void setTree(final java.lang.String[] vTreeArray) - { - // -- copy array - _treeList.clear(); - - for (int i = 0; i < vTreeArray.length; i++) - { - this._treeList.add(vTreeArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.VAMSAS - */ - public static jalview.binding.VAMSAS unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.VAMSAS) Unmarshaller - .unmarshal(jalview.binding.VAMSAS.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java deleted file mode 100644 index d3c90cf..0000000 --- a/src/jalview/binding/VamsasModel.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class VamsasModel. - * - * @version $Revision$ $Date$ - */ -public class VamsasModel extends VAMSAS implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VamsasModel() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.VAMSAS - */ - public static jalview.binding.VAMSAS unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.VAMSAS) Unmarshaller - .unmarshal(jalview.binding.VamsasModel.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java deleted file mode 100644 index 183e048..0000000 --- a/src/jalview/binding/Viewport.java +++ /dev/null @@ -1,1463 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Viewport. - * - * @version $Revision$ $Date$ - */ -public class Viewport implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _conservationSelected. - */ - private boolean _conservationSelected; - - /** - * keeps track of state for field: _conservationSelected - */ - private boolean _has_conservationSelected; - - /** - * Field _pidSelected. - */ - private boolean _pidSelected; - - /** - * keeps track of state for field: _pidSelected - */ - private boolean _has_pidSelected; - - /** - * Field _bgColour. - */ - private java.lang.String _bgColour; - - /** - * Field _consThreshold. - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold. - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * Field _showFullId. - */ - private boolean _showFullId; - - /** - * keeps track of state for field: _showFullId - */ - private boolean _has_showFullId; - - /** - * Field _showText. - */ - private boolean _showText; - - /** - * keeps track of state for field: _showText - */ - private boolean _has_showText; - - /** - * Field _showColourText. - */ - private boolean _showColourText; - - /** - * keeps track of state for field: _showColourText - */ - private boolean _has_showColourText; - - /** - * Field _showBoxes. - */ - private boolean _showBoxes; - - /** - * keeps track of state for field: _showBoxes - */ - private boolean _has_showBoxes; - - /** - * Field _wrapAlignment. - */ - private boolean _wrapAlignment; - - /** - * keeps track of state for field: _wrapAlignment - */ - private boolean _has_wrapAlignment; - - /** - * Field _renderGaps. - */ - private boolean _renderGaps; - - /** - * keeps track of state for field: _renderGaps - */ - private boolean _has_renderGaps; - - /** - * Field _showSequenceFeatures. - */ - private boolean _showSequenceFeatures; - - /** - * keeps track of state for field: _showSequenceFeatures - */ - private boolean _has_showSequenceFeatures; - - /** - * Field _showAnnotation. - */ - private boolean _showAnnotation; - - /** - * keeps track of state for field: _showAnnotation - */ - private boolean _has_showAnnotation; - - /** - * Field _showConservation. - */ - private boolean _showConservation; - - /** - * keeps track of state for field: _showConservation - */ - private boolean _has_showConservation; - - /** - * Field _showQuality. - */ - private boolean _showQuality; - - /** - * keeps track of state for field: _showQuality - */ - private boolean _has_showQuality; - - /** - * Field _showIdentity. - */ - private boolean _showIdentity; - - /** - * keeps track of state for field: _showIdentity - */ - private boolean _has_showIdentity; - - /** - * Field _xpos. - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos. - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _width. - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height. - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _startRes. - */ - private int _startRes; - - /** - * keeps track of state for field: _startRes - */ - private boolean _has_startRes; - - /** - * Field _startSeq. - */ - private int _startSeq; - - /** - * keeps track of state for field: _startSeq - */ - private boolean _has_startSeq; - - /** - * Field _fontName. - */ - private java.lang.String _fontName; - - /** - * Field _fontSize. - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle. - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Viewport() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteConsThreshold() - { - this._has_consThreshold = false; - } - - /** - */ - public void deleteConservationSelected() - { - this._has_conservationSelected = false; - } - - /** - */ - public void deleteFontSize() - { - this._has_fontSize = false; - } - - /** - */ - public void deleteFontStyle() - { - this._has_fontStyle = false; - } - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deletePidSelected() - { - this._has_pidSelected = false; - } - - /** - */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } - - /** - */ - public void deleteRenderGaps() - { - this._has_renderGaps = false; - } - - /** - */ - public void deleteShowAnnotation() - { - this._has_showAnnotation = false; - } - - /** - */ - public void deleteShowBoxes() - { - this._has_showBoxes = false; - } - - /** - */ - public void deleteShowColourText() - { - this._has_showColourText = false; - } - - /** - */ - public void deleteShowConservation() - { - this._has_showConservation = false; - } - - /** - */ - public void deleteShowFullId() - { - this._has_showFullId = false; - } - - /** - */ - public void deleteShowIdentity() - { - this._has_showIdentity = false; - } - - /** - */ - public void deleteShowQuality() - { - this._has_showQuality = false; - } - - /** - */ - public void deleteShowSequenceFeatures() - { - this._has_showSequenceFeatures = false; - } - - /** - */ - public void deleteShowText() - { - this._has_showText = false; - } - - /** - */ - public void deleteStartRes() - { - this._has_startRes = false; - } - - /** - */ - public void deleteStartSeq() - { - this._has_startSeq = false; - } - - /** - */ - public void deleteWidth() - { - this._has_width = false; - } - - /** - */ - public void deleteWrapAlignment() - { - this._has_wrapAlignment = false; - } - - /** - */ - public void deleteXpos() - { - this._has_xpos = false; - } - - /** - */ - public void deleteYpos() - { - this._has_ypos = false; - } - - /** - * Returns the value of field 'bgColour'. - * - * @return the value of field 'BgColour'. - */ - public java.lang.String getBgColour() - { - return this._bgColour; - } - - /** - * Returns the value of field 'consThreshold'. - * - * @return the value of field 'ConsThreshold'. - */ - public int getConsThreshold() - { - return this._consThreshold; - } - - /** - * Returns the value of field 'conservationSelected'. - * - * @return the value of field 'ConservationSelected'. - */ - public boolean getConservationSelected() - { - return this._conservationSelected; - } - - /** - * Returns the value of field 'fontName'. - * - * @return the value of field 'FontName'. - */ - public java.lang.String getFontName() - { - return this._fontName; - } - - /** - * Returns the value of field 'fontSize'. - * - * @return the value of field 'FontSize'. - */ - public int getFontSize() - { - return this._fontSize; - } - - /** - * Returns the value of field 'fontStyle'. - * - * @return the value of field 'FontStyle'. - */ - public int getFontStyle() - { - return this._fontStyle; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Returns the value of field 'pidSelected'. - * - * @return the value of field 'PidSelected'. - */ - public boolean getPidSelected() - { - return this._pidSelected; - } - - /** - * Returns the value of field 'pidThreshold'. - * - * @return the value of field 'PidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } - - /** - * Returns the value of field 'renderGaps'. - * - * @return the value of field 'RenderGaps'. - */ - public boolean getRenderGaps() - { - return this._renderGaps; - } - - /** - * Returns the value of field 'showAnnotation'. - * - * @return the value of field 'ShowAnnotation'. - */ - public boolean getShowAnnotation() - { - return this._showAnnotation; - } - - /** - * Returns the value of field 'showBoxes'. - * - * @return the value of field 'ShowBoxes'. - */ - public boolean getShowBoxes() - { - return this._showBoxes; - } - - /** - * Returns the value of field 'showColourText'. - * - * @return the value of field 'ShowColourText'. - */ - public boolean getShowColourText() - { - return this._showColourText; - } - - /** - * Returns the value of field 'showConservation'. - * - * @return the value of field 'ShowConservation'. - */ - public boolean getShowConservation() - { - return this._showConservation; - } - - /** - * Returns the value of field 'showFullId'. - * - * @return the value of field 'ShowFullId'. - */ - public boolean getShowFullId() - { - return this._showFullId; - } - - /** - * Returns the value of field 'showIdentity'. - * - * @return the value of field 'ShowIdentity'. - */ - public boolean getShowIdentity() - { - return this._showIdentity; - } - - /** - * Returns the value of field 'showQuality'. - * - * @return the value of field 'ShowQuality'. - */ - public boolean getShowQuality() - { - return this._showQuality; - } - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return the value of field 'ShowSequenceFeatures'. - */ - public boolean getShowSequenceFeatures() - { - return this._showSequenceFeatures; - } - - /** - * Returns the value of field 'showText'. - * - * @return the value of field 'ShowText'. - */ - public boolean getShowText() - { - return this._showText; - } - - /** - * Returns the value of field 'startRes'. - * - * @return the value of field 'StartRes'. - */ - public int getStartRes() - { - return this._startRes; - } - - /** - * Returns the value of field 'startSeq'. - * - * @return the value of field 'StartSeq'. - */ - public int getStartSeq() - { - return this._startSeq; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle() - { - return this._title; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth() - { - return this._width; - } - - /** - * Returns the value of field 'wrapAlignment'. - * - * @return the value of field 'WrapAlignment'. - */ - public boolean getWrapAlignment() - { - return this._wrapAlignment; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos() - { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos() - { - return this._ypos; - } - - /** - * Method hasConsThreshold. - * - * @return true if at least one ConsThreshold has been added - */ - public boolean hasConsThreshold() - { - return this._has_consThreshold; - } - - /** - * Method hasConservationSelected. - * - * @return true if at least one ConservationSelected has been added - */ - public boolean hasConservationSelected() - { - return this._has_conservationSelected; - } - - /** - * Method hasFontSize. - * - * @return true if at least one FontSize has been added - */ - public boolean hasFontSize() - { - return this._has_fontSize; - } - - /** - * Method hasFontStyle. - * - * @return true if at least one FontStyle has been added - */ - public boolean hasFontStyle() - { - return this._has_fontStyle; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasPidSelected. - * - * @return true if at least one PidSelected has been added - */ - public boolean hasPidSelected() - { - return this._has_pidSelected; - } - - /** - * Method hasPidThreshold. - * - * @return true if at least one PidThreshold has been added - */ - public boolean hasPidThreshold() - { - return this._has_pidThreshold; - } - - /** - * Method hasRenderGaps. - * - * @return true if at least one RenderGaps has been added - */ - public boolean hasRenderGaps() - { - return this._has_renderGaps; - } - - /** - * Method hasShowAnnotation. - * - * @return true if at least one ShowAnnotation has been added - */ - public boolean hasShowAnnotation() - { - return this._has_showAnnotation; - } - - /** - * Method hasShowBoxes. - * - * @return true if at least one ShowBoxes has been added - */ - public boolean hasShowBoxes() - { - return this._has_showBoxes; - } - - /** - * Method hasShowColourText. - * - * @return true if at least one ShowColourText has been added - */ - public boolean hasShowColourText() - { - return this._has_showColourText; - } - - /** - * Method hasShowConservation. - * - * @return true if at least one ShowConservation has been added - */ - public boolean hasShowConservation() - { - return this._has_showConservation; - } - - /** - * Method hasShowFullId. - * - * @return true if at least one ShowFullId has been added - */ - public boolean hasShowFullId() - { - return this._has_showFullId; - } - - /** - * Method hasShowIdentity. - * - * @return true if at least one ShowIdentity has been added - */ - public boolean hasShowIdentity() - { - return this._has_showIdentity; - } - - /** - * Method hasShowQuality. - * - * @return true if at least one ShowQuality has been added - */ - public boolean hasShowQuality() - { - return this._has_showQuality; - } - - /** - * Method hasShowSequenceFeatures. - * - * @return true if at least one ShowSequenceFeatures has been added - */ - public boolean hasShowSequenceFeatures() - { - return this._has_showSequenceFeatures; - } - - /** - * Method hasShowText. - * - * @return true if at least one ShowText has been added - */ - public boolean hasShowText() - { - return this._has_showText; - } - - /** - * Method hasStartRes. - * - * @return true if at least one StartRes has been added - */ - public boolean hasStartRes() - { - return this._has_startRes; - } - - /** - * Method hasStartSeq. - * - * @return true if at least one StartSeq has been added - */ - public boolean hasStartSeq() - { - return this._has_startSeq; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth() - { - return this._has_width; - } - - /** - * Method hasWrapAlignment. - * - * @return true if at least one WrapAlignment has been added - */ - public boolean hasWrapAlignment() - { - return this._has_wrapAlignment; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos() - { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos() - { - return this._has_ypos; - } - - /** - * Returns the value of field 'conservationSelected'. - * - * @return the value of field 'ConservationSelected'. - */ - public boolean isConservationSelected() - { - return this._conservationSelected; - } - - /** - * Returns the value of field 'pidSelected'. - * - * @return the value of field 'PidSelected'. - */ - public boolean isPidSelected() - { - return this._pidSelected; - } - - /** - * Returns the value of field 'renderGaps'. - * - * @return the value of field 'RenderGaps'. - */ - public boolean isRenderGaps() - { - return this._renderGaps; - } - - /** - * Returns the value of field 'showAnnotation'. - * - * @return the value of field 'ShowAnnotation'. - */ - public boolean isShowAnnotation() - { - return this._showAnnotation; - } - - /** - * Returns the value of field 'showBoxes'. - * - * @return the value of field 'ShowBoxes'. - */ - public boolean isShowBoxes() - { - return this._showBoxes; - } - - /** - * Returns the value of field 'showColourText'. - * - * @return the value of field 'ShowColourText'. - */ - public boolean isShowColourText() - { - return this._showColourText; - } - - /** - * Returns the value of field 'showConservation'. - * - * @return the value of field 'ShowConservation'. - */ - public boolean isShowConservation() - { - return this._showConservation; - } - - /** - * Returns the value of field 'showFullId'. - * - * @return the value of field 'ShowFullId'. - */ - public boolean isShowFullId() - { - return this._showFullId; - } - - /** - * Returns the value of field 'showIdentity'. - * - * @return the value of field 'ShowIdentity'. - */ - public boolean isShowIdentity() - { - return this._showIdentity; - } - - /** - * Returns the value of field 'showQuality'. - * - * @return the value of field 'ShowQuality'. - */ - public boolean isShowQuality() - { - return this._showQuality; - } - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return the value of field 'ShowSequenceFeatures'. - */ - public boolean isShowSequenceFeatures() - { - return this._showSequenceFeatures; - } - - /** - * Returns the value of field 'showText'. - * - * @return the value of field 'ShowText'. - */ - public boolean isShowText() - { - return this._showText; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * Returns the value of field 'wrapAlignment'. - * - * @return the value of field 'WrapAlignment'. - */ - public boolean isWrapAlignment() - { - return this._wrapAlignment; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'bgColour'. - * - * @param bgColour - * the value of field 'bgColour'. - */ - public void setBgColour(final java.lang.String bgColour) - { - this._bgColour = bgColour; - } - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold - * the value of field 'consThreshold'. - */ - public void setConsThreshold(final int consThreshold) - { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } - - /** - * Sets the value of field 'conservationSelected'. - * - * @param conservationSelected - * the value of field 'conservationSelected'. - */ - public void setConservationSelected(final boolean conservationSelected) - { - this._conservationSelected = conservationSelected; - this._has_conservationSelected = true; - } - - /** - * Sets the value of field 'fontName'. - * - * @param fontName - * the value of field 'fontName'. - */ - public void setFontName(final java.lang.String fontName) - { - this._fontName = fontName; - } - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize - * the value of field 'fontSize'. - */ - public void setFontSize(final int fontSize) - { - this._fontSize = fontSize; - this._has_fontSize = true; - } - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle - * the value of field 'fontStyle'. - */ - public void setFontStyle(final int fontStyle) - { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } - - /** - * Sets the value of field 'height'. - * - * @param height - * the value of field 'height'. - */ - public void setHeight(final int height) - { - this._height = height; - this._has_height = true; - } - - /** - * Sets the value of field 'pidSelected'. - * - * @param pidSelected - * the value of field 'pidSelected'. - */ - public void setPidSelected(final boolean pidSelected) - { - this._pidSelected = pidSelected; - this._has_pidSelected = true; - } - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold - * the value of field 'pidThreshold'. - */ - public void setPidThreshold(final int pidThreshold) - { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } - - /** - * Sets the value of field 'renderGaps'. - * - * @param renderGaps - * the value of field 'renderGaps'. - */ - public void setRenderGaps(final boolean renderGaps) - { - this._renderGaps = renderGaps; - this._has_renderGaps = true; - } - - /** - * Sets the value of field 'showAnnotation'. - * - * @param showAnnotation - * the value of field 'showAnnotation'. - */ - public void setShowAnnotation(final boolean showAnnotation) - { - this._showAnnotation = showAnnotation; - this._has_showAnnotation = true; - } - - /** - * Sets the value of field 'showBoxes'. - * - * @param showBoxes - * the value of field 'showBoxes'. - */ - public void setShowBoxes(final boolean showBoxes) - { - this._showBoxes = showBoxes; - this._has_showBoxes = true; - } - - /** - * Sets the value of field 'showColourText'. - * - * @param showColourText - * the value of field 'showColourText'. - */ - public void setShowColourText(final boolean showColourText) - { - this._showColourText = showColourText; - this._has_showColourText = true; - } - - /** - * Sets the value of field 'showConservation'. - * - * @param showConservation - * the value of field 'showConservation' - */ - public void setShowConservation(final boolean showConservation) - { - this._showConservation = showConservation; - this._has_showConservation = true; - } - - /** - * Sets the value of field 'showFullId'. - * - * @param showFullId - * the value of field 'showFullId'. - */ - public void setShowFullId(final boolean showFullId) - { - this._showFullId = showFullId; - this._has_showFullId = true; - } - - /** - * Sets the value of field 'showIdentity'. - * - * @param showIdentity - * the value of field 'showIdentity'. - */ - public void setShowIdentity(final boolean showIdentity) - { - this._showIdentity = showIdentity; - this._has_showIdentity = true; - } - - /** - * Sets the value of field 'showQuality'. - * - * @param showQuality - * the value of field 'showQuality'. - */ - public void setShowQuality(final boolean showQuality) - { - this._showQuality = showQuality; - this._has_showQuality = true; - } - - /** - * Sets the value of field 'showSequenceFeatures'. - * - * @param showSequenceFeatures - * the value of field 'showSequenceFeatures'. - */ - public void setShowSequenceFeatures(final boolean showSequenceFeatures) - { - this._showSequenceFeatures = showSequenceFeatures; - this._has_showSequenceFeatures = true; - } - - /** - * Sets the value of field 'showText'. - * - * @param showText - * the value of field 'showText'. - */ - public void setShowText(final boolean showText) - { - this._showText = showText; - this._has_showText = true; - } - - /** - * Sets the value of field 'startRes'. - * - * @param startRes - * the value of field 'startRes'. - */ - public void setStartRes(final int startRes) - { - this._startRes = startRes; - this._has_startRes = true; - } - - /** - * Sets the value of field 'startSeq'. - * - * @param startSeq - * the value of field 'startSeq'. - */ - public void setStartSeq(final int startSeq) - { - this._startSeq = startSeq; - this._has_startSeq = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title - * the value of field 'title'. - */ - public void setTitle(final java.lang.String title) - { - this._title = title; - } - - /** - * Sets the value of field 'width'. - * - * @param width - * the value of field 'width'. - */ - public void setWidth(final int width) - { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'wrapAlignment'. - * - * @param wrapAlignment - * the value of field 'wrapAlignment'. - */ - public void setWrapAlignment(final boolean wrapAlignment) - { - this._wrapAlignment = wrapAlignment; - this._has_wrapAlignment = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos - * the value of field 'xpos'. - */ - public void setXpos(final int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos - * the value of field 'ypos'. - */ - public void setYpos(final int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Viewport - */ - public static jalview.binding.Viewport unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Viewport) Unmarshaller - .unmarshal(jalview.binding.Viewport.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/types/ColourThreshTypeType.java b/src/jalview/binding/types/ColourThreshTypeType.java deleted file mode 100644 index 024f2c0..0000000 --- a/src/jalview/binding/types/ColourThreshTypeType.java +++ /dev/null @@ -1,168 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding.types; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.util.Hashtable; - -/** - * Class ColourThreshTypeType. - * - * @version $Revision$ $Date$ - */ -public class ColourThreshTypeType implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * The NONE type - */ - public static final int NONE_TYPE = 0; - - /** - * The instance of the NONE type - */ - public static final ColourThreshTypeType NONE = new ColourThreshTypeType(NONE_TYPE, "NONE"); - - /** - * The ABOVE type - */ - public static final int ABOVE_TYPE = 1; - - /** - * The instance of the ABOVE type - */ - public static final ColourThreshTypeType ABOVE = new ColourThreshTypeType(ABOVE_TYPE, "ABOVE"); - - /** - * The BELOW type - */ - public static final int BELOW_TYPE = 2; - - /** - * The instance of the BELOW type - */ - public static final ColourThreshTypeType BELOW = new ColourThreshTypeType(BELOW_TYPE, "BELOW"); - - /** - * Field _memberTable. - */ - private static java.util.Hashtable _memberTable = init(); - - /** - * Field type. - */ - private int type = -1; - - /** - * Field stringValue. - */ - private java.lang.String stringValue = null; - - - //----------------/ - //- Constructors -/ - //----------------/ - - private ColourThreshTypeType(final int type, final java.lang.String value) { - super(); - this.type = type; - this.stringValue = value; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method enumerate.Returns an enumeration of all possible - * instances of ColourThreshTypeType - * - * @return an Enumeration over all possible instances of - * ColourThreshTypeType - */ - public static java.util.Enumeration enumerate( - ) { - return _memberTable.elements(); - } - - /** - * Method getType.Returns the type of this ColourThreshTypeType - * - * @return the type of this ColourThreshTypeType - */ - public int getType( - ) { - return this.type; - } - - /** - * Method init. - * - * @return the initialized Hashtable for the member table - */ - private static java.util.Hashtable init( - ) { - Hashtable members = new Hashtable(); - members.put("NONE", NONE); - members.put("ABOVE", ABOVE); - members.put("BELOW", BELOW); - return members; - } - - /** - * Method readResolve. will be called during deserialization to - * replace the deserialized object with the correct constant - * instance. - * - * @return this deserialized object - */ - private java.lang.Object readResolve( - ) { - return valueOf(this.stringValue); - } - - /** - * Method toString.Returns the String representation of this - * ColourThreshTypeType - * - * @return the String representation of this ColourThreshTypeTyp - */ - public java.lang.String toString( - ) { - return this.stringValue; - } - - /** - * Method valueOf.Returns a new ColourThreshTypeType based on - * the given String value. - * - * @param string - * @return the ColourThreshTypeType value of parameter 'string' - */ - public static jalview.binding.types.ColourThreshTypeType valueOf( - final java.lang.String string) { - java.lang.Object obj = null; - if (string != null) { - obj = _memberTable.get(string); - } - if (obj == null) { - String err = "" + string + " is not a valid ColourThreshTypeType"; - throw new IllegalArgumentException(err); - } - return (ColourThreshTypeType) obj; - } - -} diff --git a/src/jalview/binding/types/FeatureMatcherByType.java b/src/jalview/binding/types/FeatureMatcherByType.java deleted file mode 100644 index 2185bba..0000000 --- a/src/jalview/binding/types/FeatureMatcherByType.java +++ /dev/null @@ -1,168 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding.types; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.util.Hashtable; - -/** - * Class FeatureMatcherByType. - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcherByType implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * The byLabel type - */ - public static final int BYLABEL_TYPE = 0; - - /** - * The instance of the byLabel type - */ - public static final FeatureMatcherByType BYLABEL = new FeatureMatcherByType(BYLABEL_TYPE, "byLabel"); - - /** - * The byScore type - */ - public static final int BYSCORE_TYPE = 1; - - /** - * The instance of the byScore type - */ - public static final FeatureMatcherByType BYSCORE = new FeatureMatcherByType(BYSCORE_TYPE, "byScore"); - - /** - * The byAttribute type - */ - public static final int BYATTRIBUTE_TYPE = 2; - - /** - * The instance of the byAttribute type - */ - public static final FeatureMatcherByType BYATTRIBUTE = new FeatureMatcherByType(BYATTRIBUTE_TYPE, "byAttribute"); - - /** - * Field _memberTable. - */ - private static java.util.Hashtable _memberTable = init(); - - /** - * Field type. - */ - private int type = -1; - - /** - * Field stringValue. - */ - private java.lang.String stringValue = null; - - - //----------------/ - //- Constructors -/ - //----------------/ - - private FeatureMatcherByType(final int type, final java.lang.String value) { - super(); - this.type = type; - this.stringValue = value; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method enumerate.Returns an enumeration of all possible - * instances of FeatureMatcherByType - * - * @return an Enumeration over all possible instances of - * FeatureMatcherByType - */ - public static java.util.Enumeration enumerate( - ) { - return _memberTable.elements(); - } - - /** - * Method getType.Returns the type of this FeatureMatcherByType - * - * @return the type of this FeatureMatcherByType - */ - public int getType( - ) { - return this.type; - } - - /** - * Method init. - * - * @return the initialized Hashtable for the member table - */ - private static java.util.Hashtable init( - ) { - Hashtable members = new Hashtable(); - members.put("byLabel", BYLABEL); - members.put("byScore", BYSCORE); - members.put("byAttribute", BYATTRIBUTE); - return members; - } - - /** - * Method readResolve. will be called during deserialization to - * replace the deserialized object with the correct constant - * instance. - * - * @return this deserialized object - */ - private java.lang.Object readResolve( - ) { - return valueOf(this.stringValue); - } - - /** - * Method toString.Returns the String representation of this - * FeatureMatcherByType - * - * @return the String representation of this FeatureMatcherByTyp - */ - public java.lang.String toString( - ) { - return this.stringValue; - } - - /** - * Method valueOf.Returns a new FeatureMatcherByType based on - * the given String value. - * - * @param string - * @return the FeatureMatcherByType value of parameter 'string' - */ - public static jalview.binding.types.FeatureMatcherByType valueOf( - final java.lang.String string) { - java.lang.Object obj = null; - if (string != null) { - obj = _memberTable.get(string); - } - if (obj == null) { - String err = "" + string + " is not a valid FeatureMatcherByType"; - throw new IllegalArgumentException(err); - } - return (FeatureMatcherByType) obj; - } - -} diff --git a/src/jalview/binding/types/NoValueColour.java b/src/jalview/binding/types/NoValueColour.java deleted file mode 100644 index c1540f6..0000000 --- a/src/jalview/binding/types/NoValueColour.java +++ /dev/null @@ -1,169 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding.types; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import java.util.Hashtable; - -/** - * Graduated feature colour if no score (or attribute) value - * - * @version $Revision$ $Date$ - */ -public class NoValueColour implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * The None type - */ - public static final int NONE_TYPE = 0; - - /** - * The instance of the None type - */ - public static final NoValueColour NONE = new NoValueColour(NONE_TYPE, - "None"); - - /** - * The Min type - */ - public static final int MIN_TYPE = 1; - - /** - * The instance of the Min type - */ - public static final NoValueColour MIN = new NoValueColour(MIN_TYPE, - "Min"); - - /** - * The Max type - */ - public static final int MAX_TYPE = 2; - - /** - * The instance of the Max type - */ - public static final NoValueColour MAX = new NoValueColour(MAX_TYPE, - "Max"); - - /** - * Field _memberTable. - */ - private static java.util.Hashtable _memberTable = init(); - - /** - * Field type. - */ - private int type = -1; - - /** - * Field stringValue. - */ - private java.lang.String stringValue = null; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - private NoValueColour(final int type, final java.lang.String value) - { - super(); - this.type = type; - this.stringValue = value; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method enumerate.Returns an enumeration of all possible instances of - * NoValueColour - * - * @return an Enumeration over all possible instances of NoValueColour - */ - public static java.util.Enumeration enumerate() - { - return _memberTable.elements(); - } - - /** - * Method getType.Returns the type of this NoValueColour - * - * @return the type of this NoValueColour - */ - public int getType() - { - return this.type; - } - - /** - * Method init. - * - * @return the initialized Hashtable for the member table - */ - private static java.util.Hashtable init() - { - Hashtable members = new Hashtable(); - members.put("None", NONE); - members.put("Min", MIN); - members.put("Max", MAX); - return members; - } - - /** - * Method readResolve. will be called during deserialization to replace the - * deserialized object with the correct constant instance. - * - * @return this deserialized object - */ - private java.lang.Object readResolve() - { - return valueOf(this.stringValue); - } - - /** - * Method toString.Returns the String representation of this NoValueColour - * - * @return the String representation of this NoValueColour - */ - public java.lang.String toString() - { - return this.stringValue; - } - - /** - * Method valueOf.Returns a new NoValueColour based on the given String value. - * - * @param string - * @return the NoValueColour value of parameter 'string' - */ - public static jalview.binding.types.NoValueColour valueOf( - final java.lang.String string) - { - java.lang.Object obj = null; - if (string != null) - { - obj = _memberTable.get(string); - } - if (obj == null) - { - String err = "" + string + " is not a valid NoValueColour"; - throw new IllegalArgumentException(err); - } - return (NoValueColour) obj; - } - -} diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index bbdddbb..b4a38a9 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -38,6 +38,7 @@ import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; +import jalview.project.Jalview2XML; import jalview.structure.StructureSelectionManager; import jalview.urls.IdOrgSettings; import jalview.util.ImageMaker; @@ -1599,16 +1600,13 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a file chooser dialog and writes out the current session as a Jalview + * project file */ @Override - public void saveState_actionPerformed(boolean asCastor) + public void saveState_actionPerformed() { - JalviewFileChooser chooser = new JalviewFileChooser( - asCastor ? "jvp" : "jvx", + JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project"); chooser.setFileView(new JalviewFileView()); @@ -1637,14 +1635,7 @@ public class Desktop extends jalview.jbgui.GDesktop // TODO prevent user from messing with the Desktop whilst we're saving try { - if (asCastor) - { - new Jalview2XML().saveState(choice); - } - else - { - new jalview.project.Jalview2XML().saveState(choice); - } + new Jalview2XML().saveState(choice); } catch (OutOfMemoryError oom) { new OOMWarning( @@ -1680,22 +1671,15 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a file chooser dialog and tries to read in the selected file as a + * Jalview project */ @Override - public void loadState_actionPerformed(boolean asCastor) - { - final String[] suffix = asCastor ? new String[] { "jvp", "jar" } - : new String[] - { "jvx" }; - final String[] desc = asCastor - ? new String[] - { "Jalview Project", "Jalview Project (old)" } - : new String[] - { "Jalview Project" }; + public void loadState_actionPerformed() + { + final String[] suffix = new String[] { "jvp", "jar" }; + final String[] desc = new String[] { "Jalview Project", + "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY"), suffix, desc, @@ -1721,14 +1705,7 @@ public class Desktop extends jalview.jbgui.GDesktop { choice }), choice.hashCode()); try { - if (asCastor) - { - new Jalview2XML().loadJalviewAlign(choice); - } - else - { - new jalview.project.Jalview2XML().loadJalviewAlign(choice); - } + new Jalview2XML().loadJalviewAlign(choice); } catch (OutOfMemoryError oom) { new OOMWarning("Whilst loading project from " + choice, oom); diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java deleted file mode 100644 index 87b8d87..0000000 --- a/src/jalview/gui/Jalview2XML.java +++ /dev/null @@ -1,5999 +0,0 @@ -/* - * 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. - */ -package jalview.gui; - -import jalview.analysis.Conservation; -import jalview.api.FeatureColourI; -import jalview.api.ViewStyleI; -import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; -import jalview.datamodel.AlignedCodonFrame; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.GraphLine; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.RnaViewerModel; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.datamodel.StructureViewerModel; -import jalview.datamodel.StructureViewerModel.StructureData; -import jalview.datamodel.features.FeatureMatcher; -import jalview.datamodel.features.FeatureMatcherI; -import jalview.datamodel.features.FeatureMatcherSet; -import jalview.datamodel.features.FeatureMatcherSetI; -import jalview.ext.varna.RnaModel; -import jalview.gui.StructureViewer.ViewerType; -import jalview.io.DataSourceType; -import jalview.io.FileFormat; -import jalview.renderer.ResidueShaderI; -import jalview.schemabinding.version2.AlcodMap; -import jalview.schemabinding.version2.AlcodonFrame; -import jalview.schemabinding.version2.Annotation; -import jalview.schemabinding.version2.AnnotationColours; -import jalview.schemabinding.version2.AnnotationElement; -import jalview.schemabinding.version2.CalcIdParam; -import jalview.schemabinding.version2.Colour; -import jalview.schemabinding.version2.CompoundMatcher; -import jalview.schemabinding.version2.DBRef; -import jalview.schemabinding.version2.Features; -import jalview.schemabinding.version2.Group; -import jalview.schemabinding.version2.HiddenColumns; -import jalview.schemabinding.version2.JGroup; -import jalview.schemabinding.version2.JSeq; -import jalview.schemabinding.version2.JalviewModel; -import jalview.schemabinding.version2.JalviewModelSequence; -import jalview.schemabinding.version2.MapListFrom; -import jalview.schemabinding.version2.MapListTo; -import jalview.schemabinding.version2.Mapping; -import jalview.schemabinding.version2.MappingChoice; -import jalview.schemabinding.version2.MatchCondition; -import jalview.schemabinding.version2.MatcherSet; -import jalview.schemabinding.version2.OtherData; -import jalview.schemabinding.version2.PdbentryItem; -import jalview.schemabinding.version2.Pdbids; -import jalview.schemabinding.version2.Property; -import jalview.schemabinding.version2.RnaViewer; -import jalview.schemabinding.version2.SecondaryStructure; -import jalview.schemabinding.version2.Sequence; -import jalview.schemabinding.version2.SequenceSet; -import jalview.schemabinding.version2.SequenceSetProperties; -import jalview.schemabinding.version2.Setting; -import jalview.schemabinding.version2.StructureState; -import jalview.schemabinding.version2.ThresholdLine; -import jalview.schemabinding.version2.Tree; -import jalview.schemabinding.version2.UserColours; -import jalview.schemabinding.version2.Viewport; -import jalview.schemabinding.version2.types.ColourThreshTypeType; -import jalview.schemabinding.version2.types.FeatureMatcherByType; -import jalview.schemabinding.version2.types.NoValueColour; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.FeatureColour; -import jalview.schemes.ResidueProperties; -import jalview.schemes.UserColourScheme; -import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.Format; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.util.StringUtils; -import jalview.util.jarInputStreamProvider; -import jalview.util.matcher.Condition; -import jalview.viewmodel.AlignmentViewport; -import jalview.viewmodel.ViewportRanges; -import jalview.viewmodel.seqfeatures.FeatureRendererSettings; -import jalview.viewmodel.seqfeatures.FeaturesDisplayed; -import jalview.ws.jws2.Jws2Discoverer; -import jalview.ws.jws2.dm.AAConSettings; -import jalview.ws.jws2.jabaws2.Jws2Instance; -import jalview.ws.params.ArgumentI; -import jalview.ws.params.AutoCalcSetting; -import jalview.ws.params.WsParamSetI; - -import java.awt.Color; -import java.awt.Rectangle; -import java.io.BufferedReader; -import java.io.DataInputStream; -import java.io.DataOutputStream; -import java.io.File; -import java.io.FileInputStream; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.OutputStreamWriter; -import java.io.PrintWriter; -import java.lang.reflect.InvocationTargetException; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.Enumeration; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Hashtable; -import java.util.IdentityHashMap; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.Map.Entry; -import java.util.Set; -import java.util.Vector; -import java.util.jar.JarEntry; -import java.util.jar.JarInputStream; -import java.util.jar.JarOutputStream; - -import javax.swing.JInternalFrame; -import javax.swing.SwingUtilities; - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Write out the current jalview desktop state as a Jalview XML stream. - * - * Note: the vamsas objects referred to here are primitive versions of the - * VAMSAS project schema elements - they are not the same and most likely never - * will be :) - * - * @author $author$ - * @version $Revision: 1.134 $ - */ -public class Jalview2XML -{ - private static final String VIEWER_PREFIX = "viewer_"; - - private static final String RNA_PREFIX = "rna_"; - - private static final String UTF_8 = "UTF-8"; - - // use this with nextCounter() to make unique names for entities - private int counter = 0; - - /* - * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps - * of sequence objects are created. - */ - IdentityHashMap seqsToIds = null; - - /** - * jalview XML Sequence ID to jalview sequence object reference (both dataset - * and alignment sequences. Populated as XML reps of sequence objects are - * created.) - */ - Map seqRefIds = null; - - Map incompleteSeqs = null; - - List frefedSequence = null; - - boolean raiseGUI = true; // whether errors are raised in dialog boxes or not - - /* - * Map of reconstructed AlignFrame objects that appear to have come from - * SplitFrame objects (have a dna/protein complement view). - */ - private Map splitFrameCandidates = new HashMap<>(); - - /* - * Map from displayed rna structure models to their saved session state jar - * entry names - */ - private Map rnaSessions = new HashMap<>(); - - /** - * create/return unique hash string for sq - * - * @param sq - * @return new or existing unique string for sq - */ - String seqHash(SequenceI sq) - { - if (seqsToIds == null) - { - initSeqRefs(); - } - if (seqsToIds.containsKey(sq)) - { - return seqsToIds.get(sq); - } - else - { - // create sequential key - String key = "sq" + (seqsToIds.size() + 1); - key = makeHashCode(sq, key); // check we don't have an external reference - // for it already. - seqsToIds.put(sq, key); - return key; - } - } - - void initSeqRefs() - { - if (seqsToIds == null) - { - seqsToIds = new IdentityHashMap<>(); - } - if (seqRefIds == null) - { - seqRefIds = new HashMap<>(); - } - if (incompleteSeqs == null) - { - incompleteSeqs = new HashMap<>(); - } - if (frefedSequence == null) - { - frefedSequence = new ArrayList<>(); - } - } - - public Jalview2XML() - { - } - - public Jalview2XML(boolean raiseGUI) - { - this.raiseGUI = raiseGUI; - } - - /** - * base class for resolving forward references to sequences by their ID - * - * @author jprocter - * - */ - abstract class SeqFref - { - String sref; - - String type; - - public SeqFref(String _sref, String type) - { - sref = _sref; - this.type = type; - } - - public String getSref() - { - return sref; - } - - public SequenceI getSrefSeq() - { - return seqRefIds.get(sref); - } - - public boolean isResolvable() - { - return seqRefIds.get(sref) != null; - } - - public SequenceI getSrefDatasetSeq() - { - SequenceI sq = seqRefIds.get(sref); - if (sq != null) - { - while (sq.getDatasetSequence() != null) - { - sq = sq.getDatasetSequence(); - } - } - return sq; - } - - /** - * @return true if the forward reference was fully resolved - */ - abstract boolean resolve(); - - @Override - public String toString() - { - return type + " reference to " + sref; - } - } - - /** - * create forward reference for a mapping - * - * @param sref - * @param _jmap - * @return - */ - public SeqFref newMappingRef(final String sref, - final jalview.datamodel.Mapping _jmap) - { - SeqFref fref = new SeqFref(sref, "Mapping") - { - public jalview.datamodel.Mapping jmap = _jmap; - - @Override - boolean resolve() - { - SequenceI seq = getSrefDatasetSeq(); - if (seq == null) - { - return false; - } - jmap.setTo(seq); - return true; - } - }; - return fref; - } - - public SeqFref newAlcodMapRef(final String sref, - final AlignedCodonFrame _cf, - final jalview.datamodel.Mapping _jmap) - { - - SeqFref fref = new SeqFref(sref, "Codon Frame") - { - AlignedCodonFrame cf = _cf; - - public jalview.datamodel.Mapping mp = _jmap; - - @Override - public boolean isResolvable() - { - return super.isResolvable() && mp.getTo() != null; - }; - - @Override - boolean resolve() - { - SequenceI seq = getSrefDatasetSeq(); - if (seq == null) - { - return false; - } - cf.addMap(seq, mp.getTo(), mp.getMap()); - return true; - } - }; - return fref; - } - - public void resolveFrefedSequences() - { - Iterator nextFref = frefedSequence.iterator(); - int toresolve = frefedSequence.size(); - int unresolved = 0, failedtoresolve = 0; - while (nextFref.hasNext()) - { - SeqFref ref = nextFref.next(); - if (ref.isResolvable()) - { - try - { - if (ref.resolve()) - { - nextFref.remove(); - } - else - { - failedtoresolve++; - } - } catch (Exception x) - { - System.err.println( - "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence " - + ref.getSref()); - x.printStackTrace(); - failedtoresolve++; - } - } - else - { - unresolved++; - } - } - if (unresolved > 0) - { - System.err.println("Jalview Project Import: There were " + unresolved - + " forward references left unresolved on the stack."); - } - if (failedtoresolve > 0) - { - System.err.println("SERIOUS! " + failedtoresolve - + " resolvable forward references failed to resolve."); - } - if (incompleteSeqs != null && incompleteSeqs.size() > 0) - { - System.err.println( - "Jalview Project Import: There are " + incompleteSeqs.size() - + " sequences which may have incomplete metadata."); - if (incompleteSeqs.size() < 10) - { - for (SequenceI s : incompleteSeqs.values()) - { - System.err.println(s.toString()); - } - } - else - { - System.err.println( - "Too many to report. Skipping output of incomplete sequences."); - } - } - } - - /** - * This maintains a map of viewports, the key being the seqSetId. Important to - * set historyItem and redoList for multiple views - */ - Map viewportsAdded = new HashMap<>(); - - Map annotationIds = new HashMap<>(); - - String uniqueSetSuffix = ""; - - /** - * List of pdbfiles added to Jar - */ - List pdbfiles = null; - - // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE - public void saveState(File statefile) - { - FileOutputStream fos = null; - try - { - fos = new FileOutputStream(statefile); - JarOutputStream jout = new JarOutputStream(fos); - saveState(jout); - - } catch (Exception e) - { - // TODO: inform user of the problem - they need to know if their data was - // not saved ! - if (errorMessage == null) - { - errorMessage = "Couldn't write Jalview Archive to output file '" - + statefile + "' - See console error log for details"; - } - else - { - errorMessage += "(output file was '" + statefile + "')"; - } - e.printStackTrace(); - } finally - { - if (fos != null) - { - try - { - fos.close(); - } catch (IOException e) - { - // ignore - } - } - } - reportErrors(); - } - - /** - * Writes a jalview project archive to the given Jar output stream. - * - * @param jout - */ - public void saveState(JarOutputStream jout) - { - AlignFrame[] frames = Desktop.getAlignFrames(); - - if (frames == null) - { - return; - } - saveAllFrames(Arrays.asList(frames), jout); - } - - /** - * core method for storing state for a set of AlignFrames. - * - * @param frames - * - frames involving all data to be exported (including containing - * splitframes) - * @param jout - * - project output stream - */ - private void saveAllFrames(List frames, JarOutputStream jout) - { - Hashtable dsses = new Hashtable<>(); - - /* - * ensure cached data is clear before starting - */ - // todo tidy up seqRefIds, seqsToIds initialisation / reset - rnaSessions.clear(); - splitFrameCandidates.clear(); - - try - { - - // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - // ////////////////////////////////////////////////// - - List shortNames = new ArrayList<>(); - List viewIds = new ArrayList<>(); - - // REVERSE ORDER - for (int i = frames.size() - 1; i > -1; i--) - { - AlignFrame af = frames.get(i); - // skip ? - if (skipList != null && skipList - .containsKey(af.getViewport().getSequenceSetId())) - { - continue; - } - - String shortName = makeFilename(af, shortNames); - - int ap, apSize = af.alignPanels.size(); - - for (ap = 0; ap < apSize; ap++) - { - AlignmentPanel apanel = af.alignPanels.get(ap); - String fileName = apSize == 1 ? shortName : ap + shortName; - if (!fileName.endsWith(".xml")) - { - fileName = fileName + ".xml"; - } - - saveState(apanel, fileName, jout, viewIds); - - String dssid = getDatasetIdRef( - af.getViewport().getAlignment().getDataset()); - if (!dsses.containsKey(dssid)) - { - dsses.put(dssid, af); - } - } - } - - writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix, - jout); - - try - { - jout.flush(); - } catch (Exception foo) - { - } - ; - jout.close(); - } catch (Exception ex) - { - // TODO: inform user of the problem - they need to know if their data was - // not saved ! - if (errorMessage == null) - { - errorMessage = "Couldn't write Jalview Archive - see error output for details"; - } - ex.printStackTrace(); - } - } - - /** - * Generates a distinct file name, based on the title of the AlignFrame, by - * appending _n for increasing n until an unused name is generated. The new - * name (without its extension) is added to the list. - * - * @param af - * @param namesUsed - * @return the generated name, with .xml extension - */ - protected String makeFilename(AlignFrame af, List namesUsed) - { - String shortName = af.getTitle(); - - if (shortName.indexOf(File.separatorChar) > -1) - { - shortName = shortName - .substring(shortName.lastIndexOf(File.separatorChar) + 1); - } - - int count = 1; - - while (namesUsed.contains(shortName)) - { - if (shortName.endsWith("_" + (count - 1))) - { - shortName = shortName.substring(0, shortName.lastIndexOf("_")); - } - - shortName = shortName.concat("_" + count); - count++; - } - - namesUsed.add(shortName); - - if (!shortName.endsWith(".xml")) - { - shortName = shortName + ".xml"; - } - return shortName; - } - - // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW - public boolean saveAlignment(AlignFrame af, String jarFile, - String fileName) - { - try - { - FileOutputStream fos = new FileOutputStream(jarFile); - JarOutputStream jout = new JarOutputStream(fos); - List frames = new ArrayList<>(); - - // resolve splitframes - if (af.getViewport().getCodingComplement() != null) - { - frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames(); - } - else - { - frames.add(af); - } - saveAllFrames(frames, jout); - try - { - jout.flush(); - } catch (Exception foo) - { - } - ; - jout.close(); - return true; - } catch (Exception ex) - { - errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details"; - ex.printStackTrace(); - return false; - } - } - - private void writeDatasetFor(Hashtable dsses, - String fileName, JarOutputStream jout) - { - - for (String dssids : dsses.keySet()) - { - AlignFrame _af = dsses.get(dssids); - String jfileName = fileName + " Dataset for " + _af.getTitle(); - if (!jfileName.endsWith(".xml")) - { - jfileName = jfileName + ".xml"; - } - saveState(_af.alignPanel, jfileName, true, jout, null); - } - } - - /** - * create a JalviewModel from an alignment view and marshall it to a - * JarOutputStream - * - * @param ap - * panel to create jalview model for - * @param fileName - * name of alignment panel written to output stream - * @param jout - * jar output stream - * @param viewIds - * @param out - * jar entry name - */ - public JalviewModel saveState(AlignmentPanel ap, String fileName, - JarOutputStream jout, List viewIds) - { - return saveState(ap, fileName, false, jout, viewIds); - } - - /** - * create a JalviewModel from an alignment view and marshall it to a - * JarOutputStream - * - * @param ap - * panel to create jalview model for - * @param fileName - * name of alignment panel written to output stream - * @param storeDS - * when true, only write the dataset for the alignment, not the data - * associated with the view. - * @param jout - * jar output stream - * @param out - * jar entry name - */ - public JalviewModel saveState(AlignmentPanel ap, String fileName, - boolean storeDS, JarOutputStream jout, List viewIds) - { - if (viewIds == null) - { - viewIds = new ArrayList<>(); - } - - initSeqRefs(); - - List userColours = new ArrayList<>(); - - AlignViewport av = ap.av; - ViewportRanges vpRanges = av.getRanges(); - - JalviewModel object = new JalviewModel(); - object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); - - object.setCreationDate(new java.util.Date(System.currentTimeMillis())); - object.setVersion( - jalview.bin.Cache.getDefault("VERSION", "Development Build")); - - /** - * rjal is full height alignment, jal is actual alignment with full metadata - * but excludes hidden sequences. - */ - jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal; - - if (av.hasHiddenRows()) - { - rjal = jal.getHiddenSequences().getFullAlignment(); - } - - SequenceSet vamsasSet = new SequenceSet(); - Sequence vamsasSeq; - JalviewModelSequence jms = new JalviewModelSequence(); - - vamsasSet.setGapChar(jal.getGapCharacter() + ""); - - if (jal.getDataset() != null) - { - // dataset id is the dataset's hashcode - vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset())); - if (storeDS) - { - // switch jal and the dataset - jal = jal.getDataset(); - rjal = jal; - } - } - if (jal.getProperties() != null) - { - Enumeration en = jal.getProperties().keys(); - while (en.hasMoreElements()) - { - String key = en.nextElement().toString(); - SequenceSetProperties ssp = new SequenceSetProperties(); - ssp.setKey(key); - ssp.setValue(jal.getProperties().get(key).toString()); - vamsasSet.addSequenceSetProperties(ssp); - } - } - - JSeq jseq; - Set calcIdSet = new HashSet<>(); - // record the set of vamsas sequence XML POJO we create. - HashMap vamsasSetIds = new HashMap<>(); - // SAVE SEQUENCES - for (final SequenceI jds : rjal.getSequences()) - { - final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds - : jds.getDatasetSequence(); - String id = seqHash(jds); - if (vamsasSetIds.get(id) == null) - { - if (seqRefIds.get(id) != null && !storeDS) - { - // This happens for two reasons: 1. multiple views are being - // serialised. - // 2. the hashCode has collided with another sequence's code. This - // DOES - // HAPPEN! (PF00072.15.stk does this) - // JBPNote: Uncomment to debug writing out of files that do not read - // back in due to ArrayOutOfBoundExceptions. - // System.err.println("vamsasSeq backref: "+id+""); - // System.err.println(jds.getName()+" - // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString()); - // System.err.println("Hashcode: "+seqHash(jds)); - // SequenceI rsq = (SequenceI) seqRefIds.get(id + ""); - // System.err.println(rsq.getName()+" - // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString()); - // System.err.println("Hashcode: "+seqHash(rsq)); - } - else - { - vamsasSeq = createVamsasSequence(id, jds); - vamsasSet.addSequence(vamsasSeq); - vamsasSetIds.put(id, vamsasSeq); - seqRefIds.put(id, jds); - } - } - jseq = new JSeq(); - jseq.setStart(jds.getStart()); - jseq.setEnd(jds.getEnd()); - jseq.setColour(av.getSequenceColour(jds).getRGB()); - - jseq.setId(id); // jseq id should be a string not a number - if (!storeDS) - { - // Store any sequences this sequence represents - if (av.hasHiddenRows()) - { - // use rjal, contains the full height alignment - jseq.setHidden( - av.getAlignment().getHiddenSequences().isHidden(jds)); - - if (av.isHiddenRepSequence(jds)) - { - jalview.datamodel.SequenceI[] reps = av - .getRepresentedSequences(jds).getSequencesInOrder(rjal); - - for (int h = 0; h < reps.length; h++) - { - if (reps[h] != jds) - { - jseq.addHiddenSequences(rjal.findIndex(reps[h])); - } - } - } - } - // mark sequence as reference - if it is the reference for this view - if (jal.hasSeqrep()) - { - jseq.setViewreference(jds == jal.getSeqrep()); - } - } - - // TODO: omit sequence features from each alignment view's XML dump if we - // are storing dataset - List sfs = jds - .getSequenceFeatures(); - for (SequenceFeature sf : sfs) - { - Features features = new Features(); - - features.setBegin(sf.getBegin()); - features.setEnd(sf.getEnd()); - features.setDescription(sf.getDescription()); - features.setType(sf.getType()); - features.setFeatureGroup(sf.getFeatureGroup()); - features.setScore(sf.getScore()); - if (sf.links != null) - { - for (int l = 0; l < sf.links.size(); l++) - { - OtherData keyValue = new OtherData(); - keyValue.setKey("LINK_" + l); - keyValue.setValue(sf.links.elementAt(l).toString()); - features.addOtherData(keyValue); - } - } - if (sf.otherDetails != null) - { - /* - * save feature attributes, which may be simple strings or - * map valued (have sub-attributes) - */ - for (Entry entry : sf.otherDetails.entrySet()) - { - String key = entry.getKey(); - Object value = entry.getValue(); - if (value instanceof Map) - { - for (Entry subAttribute : ((Map) value) - .entrySet()) - { - OtherData otherData = new OtherData(); - otherData.setKey(key); - otherData.setKey2(subAttribute.getKey()); - otherData.setValue(subAttribute.getValue().toString()); - features.addOtherData(otherData); - } - } - else - { - OtherData otherData = new OtherData(); - otherData.setKey(key); - otherData.setValue(value.toString()); - features.addOtherData(otherData); - } - } - } - - jseq.addFeatures(features); - } - - if (jdatasq.getAllPDBEntries() != null) - { - Enumeration en = jdatasq.getAllPDBEntries().elements(); - while (en.hasMoreElements()) - { - Pdbids pdb = new Pdbids(); - jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en - .nextElement(); - - String pdbId = entry.getId(); - pdb.setId(pdbId); - pdb.setType(entry.getType()); - - /* - * Store any structure views associated with this sequence. This - * section copes with duplicate entries in the project, so a dataset - * only view *should* be coped with sensibly. - */ - // This must have been loaded, is it still visible? - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - String matchedFile = null; - for (int f = frames.length - 1; f > -1; f--) - { - if (frames[f] instanceof StructureViewerBase) - { - StructureViewerBase viewFrame = (StructureViewerBase) frames[f]; - matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds, - matchedFile, viewFrame); - /* - * Only store each structure viewer's state once in the project - * jar. First time through only (storeDS==false) - */ - String viewId = viewFrame.getViewId(); - if (!storeDS && !viewIds.contains(viewId)) - { - viewIds.add(viewId); - try - { - String viewerState = viewFrame.getStateInfo(); - writeJarEntry(jout, getViewerJarEntryName(viewId), - viewerState.getBytes()); - } catch (IOException e) - { - System.err.println( - "Error saving viewer state: " + e.getMessage()); - } - } - } - } - - if (matchedFile != null || entry.getFile() != null) - { - if (entry.getFile() != null) - { - // use entry's file - matchedFile = entry.getFile(); - } - pdb.setFile(matchedFile); // entry.getFile()); - if (pdbfiles == null) - { - pdbfiles = new ArrayList<>(); - } - - if (!pdbfiles.contains(pdbId)) - { - pdbfiles.add(pdbId); - copyFileToJar(jout, matchedFile, pdbId); - } - } - - Enumeration props = entry.getProperties(); - if (props.hasMoreElements()) - { - PdbentryItem item = new PdbentryItem(); - while (props.hasMoreElements()) - { - Property prop = new Property(); - String key = props.nextElement(); - prop.setName(key); - prop.setValue(entry.getProperty(key).toString()); - item.addProperty(prop); - } - pdb.addPdbentryItem(item); - } - - jseq.addPdbids(pdb); - } - } - - saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS); - - jms.addJSeq(jseq); - } - - if (!storeDS && av.hasHiddenRows()) - { - jal = av.getAlignment(); - } - // SAVE MAPPINGS - // FOR DATASET - if (storeDS && jal.getCodonFrames() != null) - { - List jac = jal.getCodonFrames(); - for (AlignedCodonFrame acf : jac) - { - AlcodonFrame alc = new AlcodonFrame(); - if (acf.getProtMappings() != null - && acf.getProtMappings().length > 0) - { - boolean hasMap = false; - SequenceI[] dnas = acf.getdnaSeqs(); - jalview.datamodel.Mapping[] pmaps = acf.getProtMappings(); - for (int m = 0; m < pmaps.length; m++) - { - AlcodMap alcmap = new AlcodMap(); - alcmap.setDnasq(seqHash(dnas[m])); - alcmap.setMapping( - createVamsasMapping(pmaps[m], dnas[m], null, false)); - alc.addAlcodMap(alcmap); - hasMap = true; - } - if (hasMap) - { - vamsasSet.addAlcodonFrame(alc); - } - } - // TODO: delete this ? dead code from 2.8.3->2.9 ? - // { - // AlcodonFrame alc = new AlcodonFrame(); - // vamsasSet.addAlcodonFrame(alc); - // for (int p = 0; p < acf.aaWidth; p++) - // { - // Alcodon cmap = new Alcodon(); - // if (acf.codons[p] != null) - // { - // // Null codons indicate a gapped column in the translated peptide - // // alignment. - // cmap.setPos1(acf.codons[p][0]); - // cmap.setPos2(acf.codons[p][1]); - // cmap.setPos3(acf.codons[p][2]); - // } - // alc.addAlcodon(cmap); - // } - // if (acf.getProtMappings() != null - // && acf.getProtMappings().length > 0) - // { - // SequenceI[] dnas = acf.getdnaSeqs(); - // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings(); - // for (int m = 0; m < pmaps.length; m++) - // { - // AlcodMap alcmap = new AlcodMap(); - // alcmap.setDnasq(seqHash(dnas[m])); - // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, - // false)); - // alc.addAlcodMap(alcmap); - // } - // } - } - } - - // SAVE TREES - // ///////////////////////////////// - if (!storeDS && av.getCurrentTree() != null) - { - // FIND ANY ASSOCIATED TREES - // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT - if (Desktop.desktop != null) - { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - - for (int t = 0; t < frames.length; t++) - { - if (frames[t] instanceof TreePanel) - { - TreePanel tp = (TreePanel) frames[t]; - - if (tp.getTreeCanvas().getViewport().getAlignment() == jal) - { - Tree tree = new Tree(); - tree.setTitle(tp.getTitle()); - tree.setCurrentTree((av.getCurrentTree() == tp.getTree())); - tree.setNewick(tp.getTree().print()); - tree.setThreshold(tp.getTreeCanvas().getThreshold()); - - tree.setFitToWindow(tp.fitToWindow.getState()); - tree.setFontName(tp.getTreeFont().getName()); - tree.setFontSize(tp.getTreeFont().getSize()); - tree.setFontStyle(tp.getTreeFont().getStyle()); - tree.setMarkUnlinked(tp.placeholdersMenu.getState()); - - tree.setShowBootstrap(tp.bootstrapMenu.getState()); - tree.setShowDistances(tp.distanceMenu.getState()); - - tree.setHeight(tp.getHeight()); - tree.setWidth(tp.getWidth()); - tree.setXpos(tp.getX()); - tree.setYpos(tp.getY()); - tree.setId(makeHashCode(tp, null)); - jms.addTree(tree); - } - } - } - } - } - - // SAVE ANNOTATIONS - /** - * store forward refs from an annotationRow to any groups - */ - IdentityHashMap groupRefs = new IdentityHashMap<>(); - if (storeDS) - { - for (SequenceI sq : jal.getSequences()) - { - // Store annotation on dataset sequences only - AlignmentAnnotation[] aa = sq.getAnnotation(); - if (aa != null && aa.length > 0) - { - storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS, - vamsasSet); - } - } - } - else - { - if (jal.getAlignmentAnnotation() != null) - { - // Store the annotation shown on the alignment. - AlignmentAnnotation[] aa = jal.getAlignmentAnnotation(); - storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS, - vamsasSet); - } - } - // SAVE GROUPS - if (jal.getGroups() != null) - { - JGroup[] groups = new JGroup[jal.getGroups().size()]; - int i = -1; - for (jalview.datamodel.SequenceGroup sg : jal.getGroups()) - { - JGroup jGroup = new JGroup(); - groups[++i] = jGroup; - - jGroup.setStart(sg.getStartRes()); - jGroup.setEnd(sg.getEndRes()); - jGroup.setName(sg.getName()); - if (groupRefs.containsKey(sg)) - { - // group has references so set its ID field - jGroup.setId(groupRefs.get(sg)); - } - ColourSchemeI colourScheme = sg.getColourScheme(); - if (colourScheme != null) - { - ResidueShaderI groupColourScheme = sg.getGroupColourScheme(); - if (groupColourScheme.conservationApplied()) - { - jGroup.setConsThreshold(groupColourScheme.getConservationInc()); - - if (colourScheme instanceof jalview.schemes.UserColourScheme) - { - jGroup.setColour( - setUserColourScheme(colourScheme, userColours, jms)); - } - else - { - jGroup.setColour(colourScheme.getSchemeName()); - } - } - else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient) - { - jGroup.setColour("AnnotationColourGradient"); - jGroup.setAnnotationColours(constructAnnotationColours( - (jalview.schemes.AnnotationColourGradient) colourScheme, - userColours, jms)); - } - else if (colourScheme instanceof jalview.schemes.UserColourScheme) - { - jGroup.setColour( - setUserColourScheme(colourScheme, userColours, jms)); - } - else - { - jGroup.setColour(colourScheme.getSchemeName()); - } - - jGroup.setPidThreshold(groupColourScheme.getThreshold()); - } - - jGroup.setOutlineColour(sg.getOutlineColour().getRGB()); - jGroup.setDisplayBoxes(sg.getDisplayBoxes()); - jGroup.setDisplayText(sg.getDisplayText()); - jGroup.setColourText(sg.getColourText()); - jGroup.setTextCol1(sg.textColour.getRGB()); - jGroup.setTextCol2(sg.textColour2.getRGB()); - jGroup.setTextColThreshold(sg.thresholdTextColour); - jGroup.setShowUnconserved(sg.getShowNonconserved()); - jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); - jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram()); - jGroup.setShowSequenceLogo(sg.isShowSequenceLogo()); - jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo()); - for (SequenceI seq : sg.getSequences()) - { - jGroup.addSeq(seqHash(seq)); - } - } - - jms.setJGroup(groups); - } - if (!storeDS) - { - // /////////SAVE VIEWPORT - Viewport view = new Viewport(); - view.setTitle(ap.alignFrame.getTitle()); - view.setSequenceSetId( - makeHashCode(av.getSequenceSetId(), av.getSequenceSetId())); - view.setId(av.getViewId()); - if (av.getCodingComplement() != null) - { - view.setComplementId(av.getCodingComplement().getViewId()); - } - view.setViewName(av.getViewName()); - view.setGatheredViews(av.isGatherViewsHere()); - - Rectangle size = ap.av.getExplodedGeometry(); - Rectangle position = size; - if (size == null) - { - size = ap.alignFrame.getBounds(); - if (av.getCodingComplement() != null) - { - position = ((SplitFrame) ap.alignFrame.getSplitViewContainer()) - .getBounds(); - } - else - { - position = size; - } - } - view.setXpos(position.x); - view.setYpos(position.y); - - view.setWidth(size.width); - view.setHeight(size.height); - - view.setStartRes(vpRanges.getStartRes()); - view.setStartSeq(vpRanges.getStartSeq()); - - if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) - { - view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(), - userColours, jms)); - } - else if (av - .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) - { - AnnotationColours ac = constructAnnotationColours( - (jalview.schemes.AnnotationColourGradient) av - .getGlobalColourScheme(), - userColours, jms); - - view.setAnnotationColours(ac); - view.setBgColour("AnnotationColourGradient"); - } - else - { - view.setBgColour(ColourSchemeProperty - .getColourName(av.getGlobalColourScheme())); - } - - ResidueShaderI vcs = av.getResidueShading(); - ColourSchemeI cs = av.getGlobalColourScheme(); - - if (cs != null) - { - if (vcs.conservationApplied()) - { - view.setConsThreshold(vcs.getConservationInc()); - if (cs instanceof jalview.schemes.UserColourScheme) - { - view.setBgColour(setUserColourScheme(cs, userColours, jms)); - } - } - view.setPidThreshold(vcs.getThreshold()); - } - - view.setConservationSelected(av.getConservationSelected()); - view.setPidSelected(av.getAbovePIDThreshold()); - view.setFontName(av.font.getName()); - view.setFontSize(av.font.getSize()); - view.setFontStyle(av.font.getStyle()); - view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna()); - view.setRenderGaps(av.isRenderGaps()); - view.setShowAnnotation(av.isShowAnnotation()); - view.setShowBoxes(av.getShowBoxes()); - view.setShowColourText(av.getColourText()); - view.setShowFullId(av.getShowJVSuffix()); - view.setRightAlignIds(av.isRightAlignIds()); - view.setShowSequenceFeatures(av.isShowSequenceFeatures()); - view.setShowText(av.getShowText()); - view.setShowUnconserved(av.getShowUnconserved()); - view.setWrapAlignment(av.getWrapAlignment()); - view.setTextCol1(av.getTextColour().getRGB()); - view.setTextCol2(av.getTextColour2().getRGB()); - view.setTextColThreshold(av.getThresholdTextColour()); - view.setShowConsensusHistogram(av.isShowConsensusHistogram()); - view.setShowSequenceLogo(av.isShowSequenceLogo()); - view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo()); - view.setShowGroupConsensus(av.isShowGroupConsensus()); - view.setShowGroupConservation(av.isShowGroupConservation()); - view.setShowNPfeatureTooltip(av.isShowNPFeats()); - view.setShowDbRefTooltip(av.isShowDBRefs()); - view.setFollowHighlight(av.isFollowHighlight()); - view.setFollowSelection(av.followSelection); - view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus()); - if (av.getFeaturesDisplayed() != null) - { - jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); - - FeatureRenderer fr = ap.getSeqPanel().seqCanvas - .getFeatureRenderer(); - String[] renderOrder = fr.getRenderOrder().toArray(new String[0]); - - Vector settingsAdded = new Vector<>(); - if (renderOrder != null) - { - for (String featureType : renderOrder) - { - Setting setting = new Setting(); - setting.setType(featureType); - - /* - * save any filter for the feature type - */ - FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); - if (filter != null) { - Iterator filters = filter.getMatchers().iterator(); - FeatureMatcherI firstFilter = filters.next(); - setting.setMatcherSet(Jalview2XML.marshalFilter( - firstFilter, filters, filter.isAnded())); - } - - /* - * save colour scheme for the feature type - */ - FeatureColourI fcol = fr.getFeatureStyle(featureType); - if (!fcol.isSimpleColour()) - { - setting.setColour(fcol.getMaxColour().getRGB()); - setting.setMincolour(fcol.getMinColour().getRGB()); - setting.setMin(fcol.getMin()); - setting.setMax(fcol.getMax()); - setting.setColourByLabel(fcol.isColourByLabel()); - if (fcol.isColourByAttribute()) - { - setting.setAttributeName(fcol.getAttributeName()); - } - setting.setAutoScale(fcol.isAutoScaled()); - setting.setThreshold(fcol.getThreshold()); - Color noColour = fcol.getNoColour(); - if (noColour == null) - { - setting.setNoValueColour(NoValueColour.NONE); - } - else if (noColour.equals(fcol.getMaxColour())) - { - setting.setNoValueColour(NoValueColour.MAX); - } - else - { - setting.setNoValueColour(NoValueColour.MIN); - } - // -1 = No threshold, 0 = Below, 1 = Above - setting.setThreshstate(fcol.isAboveThreshold() ? 1 - : (fcol.isBelowThreshold() ? 0 : -1)); - } - else - { - setting.setColour(fcol.getColour().getRGB()); - } - - setting.setDisplay( - av.getFeaturesDisplayed().isVisible(featureType)); - float rorder = fr - .getOrder(featureType); - if (rorder > -1) - { - setting.setOrder(rorder); - } - fs.addSetting(setting); - settingsAdded.addElement(featureType); - } - } - - // is groups actually supposed to be a map here ? - Iterator en = fr.getFeatureGroups().iterator(); - Vector groupsAdded = new Vector<>(); - while (en.hasNext()) - { - String grp = en.next(); - if (groupsAdded.contains(grp)) - { - continue; - } - Group g = new Group(); - g.setName(grp); - g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false)) - .booleanValue()); - fs.addGroup(g); - groupsAdded.addElement(grp); - } - jms.setFeatureSettings(fs); - } - - if (av.hasHiddenColumns()) - { - jalview.datamodel.HiddenColumns hidden = av.getAlignment() - .getHiddenColumns(); - if (hidden == null) - { - warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this."); - } - else - { - Iterator hiddenRegions = hidden.iterator(); - while (hiddenRegions.hasNext()) - { - int[] region = hiddenRegions.next(); - HiddenColumns hc = new HiddenColumns(); - hc.setStart(region[0]); - hc.setEnd(region[1]); - view.addHiddenColumns(hc); - } - } - } - if (calcIdSet.size() > 0) - { - for (String calcId : calcIdSet) - { - if (calcId.trim().length() > 0) - { - CalcIdParam cidp = createCalcIdParam(calcId, av); - // Some calcIds have no parameters. - if (cidp != null) - { - view.addCalcIdParam(cidp); - } - } - } - } - - jms.addViewport(view); - } - object.setJalviewModelSequence(jms); - object.getVamsasModel().addSequenceSet(vamsasSet); - - if (jout != null && fileName != null) - { - // We may not want to write the object to disk, - // eg we can copy the alignViewport to a new view object - // using save and then load - try - { - System.out.println("Writing jar entry " + fileName); - JarEntry entry = new JarEntry(fileName); - jout.putNextEntry(entry); - PrintWriter pout = new PrintWriter( - new OutputStreamWriter(jout, UTF_8)); - Marshaller marshaller = new Marshaller(pout); - marshaller.marshal(object); - pout.flush(); - jout.closeEntry(); - } catch (Exception ex) - { - // TODO: raise error in GUI if marshalling failed. - ex.printStackTrace(); - } - } - return object; - } - - /** - * Save any Varna viewers linked to this sequence. Writes an rnaViewer element - * for each viewer, with - *

    - *
  • viewer geometry (position, size, split pane divider location)
    • - *
  • index of the selected structure in the viewer (currently shows gapped - * or ungapped)
    • - *
  • the id of the annotation holding RNA secondary structure
    • - *
  • (currently only one SS is shown per viewer, may be more in future)
    • - *
- * Varna viewer state is also written out (in native Varna XML) to separate - * project jar entries. A separate entry is written for each RNA structure - * displayed, with the naming convention - *
    - *
  • rna_viewId_sequenceId_annotationId_[gapped|trimmed]
    • - *
- * - * @param jout - * @param jseq - * @param jds - * @param viewIds - * @param ap - * @param storeDataset - */ - protected void saveRnaViewers(JarOutputStream jout, JSeq jseq, - final SequenceI jds, List viewIds, AlignmentPanel ap, - boolean storeDataset) - { - if (Desktop.desktop == null) - { - return; - } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - for (int f = frames.length - 1; f > -1; f--) - { - if (frames[f] instanceof AppVarna) - { - AppVarna varna = (AppVarna) frames[f]; - /* - * link the sequence to every viewer that is showing it and is linked to - * its alignment panel - */ - if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel()) - { - String viewId = varna.getViewId(); - RnaViewer rna = new RnaViewer(); - rna.setViewId(viewId); - rna.setTitle(varna.getTitle()); - rna.setXpos(varna.getX()); - rna.setYpos(varna.getY()); - rna.setWidth(varna.getWidth()); - rna.setHeight(varna.getHeight()); - rna.setDividerLocation(varna.getDividerLocation()); - rna.setSelectedRna(varna.getSelectedIndex()); - jseq.addRnaViewer(rna); - - /* - * Store each Varna panel's state once in the project per sequence. - * First time through only (storeDataset==false) - */ - // boolean storeSessions = false; - // String sequenceViewId = viewId + seqsToIds.get(jds); - // if (!storeDataset && !viewIds.contains(sequenceViewId)) - // { - // viewIds.add(sequenceViewId); - // storeSessions = true; - // } - for (RnaModel model : varna.getModels()) - { - if (model.seq == jds) - { - /* - * VARNA saves each view (sequence or alignment secondary - * structure, gapped or trimmed) as a separate XML file - */ - String jarEntryName = rnaSessions.get(model); - if (jarEntryName == null) - { - - String varnaStateFile = varna.getStateInfo(model.rna); - jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter(); - copyFileToJar(jout, varnaStateFile, jarEntryName); - rnaSessions.put(model, jarEntryName); - } - SecondaryStructure ss = new SecondaryStructure(); - String annotationId = varna.getAnnotation(jds).annotationId; - ss.setAnnotationId(annotationId); - ss.setViewerState(jarEntryName); - ss.setGapped(model.gapped); - ss.setTitle(model.title); - rna.addSecondaryStructure(ss); - } - } - } - } - } - } - - /** - * Copy the contents of a file to a new entry added to the output jar - * - * @param jout - * @param infilePath - * @param jarEntryName - */ - protected void copyFileToJar(JarOutputStream jout, String infilePath, - String jarEntryName) - { - DataInputStream dis = null; - try - { - File file = new File(infilePath); - if (file.exists() && jout != null) - { - dis = new DataInputStream(new FileInputStream(file)); - byte[] data = new byte[(int) file.length()]; - dis.readFully(data); - writeJarEntry(jout, jarEntryName, data); - } - } catch (Exception ex) - { - ex.printStackTrace(); - } finally - { - if (dis != null) - { - try - { - dis.close(); - } catch (IOException e) - { - // ignore - } - } - } - } - - /** - * Write the data to a new entry of given name in the output jar file - * - * @param jout - * @param jarEntryName - * @param data - * @throws IOException - */ - protected void writeJarEntry(JarOutputStream jout, String jarEntryName, - byte[] data) throws IOException - { - if (jout != null) - { - System.out.println("Writing jar entry " + jarEntryName); - jout.putNextEntry(new JarEntry(jarEntryName)); - DataOutputStream dout = new DataOutputStream(jout); - dout.write(data, 0, data.length); - dout.flush(); - jout.closeEntry(); - } - } - - /** - * Save the state of a structure viewer - * - * @param ap - * @param jds - * @param pdb - * the archive XML element under which to save the state - * @param entry - * @param viewIds - * @param matchedFile - * @param viewFrame - * @return - */ - protected String saveStructureState(AlignmentPanel ap, SequenceI jds, - Pdbids pdb, PDBEntry entry, List viewIds, - String matchedFile, StructureViewerBase viewFrame) - { - final AAStructureBindingModel bindingModel = viewFrame.getBinding(); - - /* - * Look for any bindings for this viewer to the PDB file of interest - * (including part matches excluding chain id) - */ - for (int peid = 0; peid < bindingModel.getPdbCount(); peid++) - { - final PDBEntry pdbentry = bindingModel.getPdbEntry(peid); - final String pdbId = pdbentry.getId(); - if (!pdbId.equals(entry.getId()) - && !(entry.getId().length() > 4 && entry.getId().toLowerCase() - .startsWith(pdbId.toLowerCase()))) - { - /* - * not interested in a binding to a different PDB entry here - */ - continue; - } - if (matchedFile == null) - { - matchedFile = pdbentry.getFile(); - } - else if (!matchedFile.equals(pdbentry.getFile())) - { - Cache.log.warn( - "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): " - + pdbentry.getFile()); - } - // record the - // file so we - // can get at it if the ID - // match is ambiguous (e.g. - // 1QIP==1qipA) - - for (int smap = 0; smap < viewFrame.getBinding() - .getSequence()[peid].length; smap++) - { - // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1) - if (jds == viewFrame.getBinding().getSequence()[peid][smap]) - { - StructureState state = new StructureState(); - state.setVisible(true); - state.setXpos(viewFrame.getX()); - state.setYpos(viewFrame.getY()); - state.setWidth(viewFrame.getWidth()); - state.setHeight(viewFrame.getHeight()); - final String viewId = viewFrame.getViewId(); - state.setViewId(viewId); - state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap)); - state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap)); - state.setColourByJmol(viewFrame.isColouredByViewer()); - state.setType(viewFrame.getViewerType().toString()); - pdb.addStructureState(state); - } - } - } - return matchedFile; - } - - /** - * Populates the AnnotationColours xml for save. This captures the settings of - * the options in the 'Colour by Annotation' dialog. - * - * @param acg - * @param userColours - * @param jms - * @return - */ - private AnnotationColours constructAnnotationColours( - AnnotationColourGradient acg, List userColours, - JalviewModelSequence jms) - { - AnnotationColours ac = new AnnotationColours(); - ac.setAboveThreshold(acg.getAboveThreshold()); - ac.setThreshold(acg.getAnnotationThreshold()); - // 2.10.2 save annotationId (unique) not annotation label - ac.setAnnotation(acg.getAnnotation().annotationId); - if (acg.getBaseColour() instanceof UserColourScheme) - { - ac.setColourScheme( - setUserColourScheme(acg.getBaseColour(), userColours, jms)); - } - else - { - ac.setColourScheme( - ColourSchemeProperty.getColourName(acg.getBaseColour())); - } - - ac.setMaxColour(acg.getMaxColour().getRGB()); - ac.setMinColour(acg.getMinColour().getRGB()); - ac.setPerSequence(acg.isSeqAssociated()); - ac.setPredefinedColours(acg.isPredefinedColours()); - return ac; - } - - private void storeAlignmentAnnotation(AlignmentAnnotation[] aa, - IdentityHashMap groupRefs, - AlignmentViewport av, Set calcIdSet, boolean storeDS, - SequenceSet vamsasSet) - { - - for (int i = 0; i < aa.length; i++) - { - Annotation an = new Annotation(); - - AlignmentAnnotation annotation = aa[i]; - if (annotation.annotationId != null) - { - annotationIds.put(annotation.annotationId, annotation); - } - - an.setId(annotation.annotationId); - - an.setVisible(annotation.visible); - - an.setDescription(annotation.description); - - if (annotation.sequenceRef != null) - { - // 2.9 JAL-1781 xref on sequence id rather than name - an.setSequenceRef(seqsToIds.get(annotation.sequenceRef)); - } - if (annotation.groupRef != null) - { - String groupIdr = groupRefs.get(annotation.groupRef); - if (groupIdr == null) - { - // make a locally unique String - groupRefs.put(annotation.groupRef, - groupIdr = ("" + System.currentTimeMillis() - + annotation.groupRef.getName() - + groupRefs.size())); - } - an.setGroupRef(groupIdr.toString()); - } - - // store all visualization attributes for annotation - an.setGraphHeight(annotation.graphHeight); - an.setCentreColLabels(annotation.centreColLabels); - an.setScaleColLabels(annotation.scaleColLabel); - an.setShowAllColLabels(annotation.showAllColLabels); - an.setBelowAlignment(annotation.belowAlignment); - - if (annotation.graph > 0) - { - an.setGraph(true); - an.setGraphType(annotation.graph); - an.setGraphGroup(annotation.graphGroup); - if (annotation.getThreshold() != null) - { - ThresholdLine line = new ThresholdLine(); - line.setLabel(annotation.getThreshold().label); - line.setValue(annotation.getThreshold().value); - line.setColour(annotation.getThreshold().colour.getRGB()); - an.setThresholdLine(line); - } - } - else - { - an.setGraph(false); - } - - an.setLabel(annotation.label); - - if (annotation == av.getAlignmentQualityAnnot() - || annotation == av.getAlignmentConservationAnnotation() - || annotation == av.getAlignmentConsensusAnnotation() - || annotation.autoCalculated) - { - // new way of indicating autocalculated annotation - - an.setAutoCalculated(annotation.autoCalculated); - } - if (annotation.hasScore()) - { - an.setScore(annotation.getScore()); - } - - if (annotation.getCalcId() != null) - { - calcIdSet.add(annotation.getCalcId()); - an.setCalcId(annotation.getCalcId()); - } - if (annotation.hasProperties()) - { - for (String pr : annotation.getProperties()) - { - Property prop = new Property(); - prop.setName(pr); - prop.setValue(annotation.getProperty(pr)); - an.addProperty(prop); - } - } - - AnnotationElement ae; - if (annotation.annotations != null) - { - an.setScoreOnly(false); - for (int a = 0; a < annotation.annotations.length; a++) - { - if ((annotation == null) || (annotation.annotations[a] == null)) - { - continue; - } - - ae = new AnnotationElement(); - if (annotation.annotations[a].description != null) - { - ae.setDescription(annotation.annotations[a].description); - } - if (annotation.annotations[a].displayCharacter != null) - { - ae.setDisplayCharacter( - annotation.annotations[a].displayCharacter); - } - - if (!Float.isNaN(annotation.annotations[a].value)) - { - ae.setValue(annotation.annotations[a].value); - } - - ae.setPosition(a); - if (annotation.annotations[a].secondaryStructure > ' ') - { - ae.setSecondaryStructure( - annotation.annotations[a].secondaryStructure + ""); - } - - if (annotation.annotations[a].colour != null - && annotation.annotations[a].colour != java.awt.Color.black) - { - ae.setColour(annotation.annotations[a].colour.getRGB()); - } - - an.addAnnotationElement(ae); - if (annotation.autoCalculated) - { - // only write one non-null entry into the annotation row - - // sufficient to get the visualization attributes necessary to - // display data - continue; - } - } - } - else - { - an.setScoreOnly(true); - } - if (!storeDS || (storeDS && !annotation.autoCalculated)) - { - // skip autocalculated annotation - these are only provided for - // alignments - vamsasSet.addAnnotation(an); - } - } - - } - - private CalcIdParam createCalcIdParam(String calcId, AlignViewport av) - { - AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId); - if (settings != null) - { - CalcIdParam vCalcIdParam = new CalcIdParam(); - vCalcIdParam.setCalcId(calcId); - vCalcIdParam.addServiceURL(settings.getServiceURI()); - // generic URI allowing a third party to resolve another instance of the - // service used for this calculation - for (String urls : settings.getServiceURLs()) - { - vCalcIdParam.addServiceURL(urls); - } - vCalcIdParam.setVersion("1.0"); - if (settings.getPreset() != null) - { - WsParamSetI setting = settings.getPreset(); - vCalcIdParam.setName(setting.getName()); - vCalcIdParam.setDescription(setting.getDescription()); - } - else - { - vCalcIdParam.setName(""); - vCalcIdParam.setDescription("Last used parameters"); - } - // need to be able to recover 1) settings 2) user-defined presets or - // recreate settings from preset 3) predefined settings provided by - // service - or settings that can be transferred (or discarded) - vCalcIdParam.setParameters( - settings.getWsParamFile().replace("\n", "|\\n|")); - vCalcIdParam.setAutoUpdate(settings.isAutoUpdate()); - // todo - decide if updateImmediately is needed for any projects. - - return vCalcIdParam; - } - return null; - } - - private boolean recoverCalcIdParam(CalcIdParam calcIdParam, - AlignViewport av) - { - if (calcIdParam.getVersion().equals("1.0")) - { - Jws2Instance service = Jws2Discoverer.getDiscoverer() - .getPreferredServiceFor(calcIdParam.getServiceURL()); - if (service != null) - { - WsParamSetI parmSet = null; - try - { - parmSet = service.getParamStore().parseServiceParameterFile( - calcIdParam.getName(), calcIdParam.getDescription(), - calcIdParam.getServiceURL(), - calcIdParam.getParameters().replace("|\\n|", "\n")); - } catch (IOException x) - { - warn("Couldn't parse parameter data for " - + calcIdParam.getCalcId(), x); - return false; - } - List argList = null; - if (calcIdParam.getName().length() > 0) - { - parmSet = service.getParamStore() - .getPreset(calcIdParam.getName()); - if (parmSet != null) - { - // TODO : check we have a good match with settings in AACon - - // otherwise we'll need to create a new preset - } - } - else - { - argList = parmSet.getArguments(); - parmSet = null; - } - AAConSettings settings = new AAConSettings( - calcIdParam.isAutoUpdate(), service, parmSet, argList); - av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings, - calcIdParam.isNeedsUpdate()); - return true; - } - else - { - warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server."); - return false; - } - } - throw new Error(MessageManager.formatMessage( - "error.unsupported_version_calcIdparam", new Object[] - { calcIdParam.toString() })); - } - - /** - * External mapping between jalview objects and objects yielding a valid and - * unique object ID string. This is null for normal Jalview project IO, but - * non-null when a jalview project is being read or written as part of a - * vamsas session. - */ - IdentityHashMap jv2vobj = null; - - /** - * Construct a unique ID for jvobj using either existing bindings or if none - * exist, the result of the hashcode call for the object. - * - * @param jvobj - * jalview data object - * @return unique ID for referring to jvobj - */ - private String makeHashCode(Object jvobj, String altCode) - { - if (jv2vobj != null) - { - Object id = jv2vobj.get(jvobj); - if (id != null) - { - return id.toString(); - } - // check string ID mappings - if (jvids2vobj != null && jvobj instanceof String) - { - id = jvids2vobj.get(jvobj); - } - if (id != null) - { - return id.toString(); - } - // give up and warn that something has gone wrong - warn("Cannot find ID for object in external mapping : " + jvobj); - } - return altCode; - } - - /** - * return local jalview object mapped to ID, if it exists - * - * @param idcode - * (may be null) - * @return null or object bound to idcode - */ - private Object retrieveExistingObj(String idcode) - { - if (idcode != null && vobj2jv != null) - { - return vobj2jv.get(idcode); - } - return null; - } - - /** - * binding from ID strings from external mapping table to jalview data model - * objects. - */ - private Hashtable vobj2jv; - - private Sequence createVamsasSequence(String id, SequenceI jds) - { - return createVamsasSequence(true, id, jds, null); - } - - private Sequence createVamsasSequence(boolean recurse, String id, - SequenceI jds, SequenceI parentseq) - { - Sequence vamsasSeq = new Sequence(); - vamsasSeq.setId(id); - vamsasSeq.setName(jds.getName()); - vamsasSeq.setSequence(jds.getSequenceAsString()); - vamsasSeq.setDescription(jds.getDescription()); - jalview.datamodel.DBRefEntry[] dbrefs = null; - if (jds.getDatasetSequence() != null) - { - vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); - } - else - { - // seqId==dsseqid so we can tell which sequences really are - // dataset sequences only - vamsasSeq.setDsseqid(id); - dbrefs = jds.getDBRefs(); - if (parentseq == null) - { - parentseq = jds; - } - } - if (dbrefs != null) - { - for (int d = 0; d < dbrefs.length; d++) - { - DBRef dbref = new DBRef(); - dbref.setSource(dbrefs[d].getSource()); - dbref.setVersion(dbrefs[d].getVersion()); - dbref.setAccessionId(dbrefs[d].getAccessionId()); - if (dbrefs[d].hasMap()) - { - Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, - jds, recurse); - dbref.setMapping(mp); - } - vamsasSeq.addDBRef(dbref); - } - } - return vamsasSeq; - } - - private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp, - SequenceI parentseq, SequenceI jds, boolean recurse) - { - Mapping mp = null; - if (jmp.getMap() != null) - { - mp = new Mapping(); - - jalview.util.MapList mlst = jmp.getMap(); - List r = mlst.getFromRanges(); - for (int[] range : r) - { - MapListFrom mfrom = new MapListFrom(); - mfrom.setStart(range[0]); - mfrom.setEnd(range[1]); - mp.addMapListFrom(mfrom); - } - r = mlst.getToRanges(); - for (int[] range : r) - { - MapListTo mto = new MapListTo(); - mto.setStart(range[0]); - mto.setEnd(range[1]); - mp.addMapListTo(mto); - } - mp.setMapFromUnit(mlst.getFromRatio()); - mp.setMapToUnit(mlst.getToRatio()); - if (jmp.getTo() != null) - { - MappingChoice mpc = new MappingChoice(); - - // check/create ID for the sequence referenced by getTo() - - String jmpid = ""; - SequenceI ps = null; - if (parentseq != jmp.getTo() - && parentseq.getDatasetSequence() != jmp.getTo()) - { - // chaining dbref rather than a handshaking one - jmpid = seqHash(ps = jmp.getTo()); - } - else - { - jmpid = seqHash(ps = parentseq); - } - mpc.setDseqFor(jmpid); - if (!seqRefIds.containsKey(mpc.getDseqFor())) - { - jalview.bin.Cache.log.debug("creatign new DseqFor ID"); - seqRefIds.put(mpc.getDseqFor(), ps); - } - else - { - jalview.bin.Cache.log.debug("reusing DseqFor ID"); - } - - mp.setMappingChoice(mpc); - } - } - return mp; - } - - String setUserColourScheme(jalview.schemes.ColourSchemeI cs, - List userColours, JalviewModelSequence jms) - { - String id = null; - jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; - boolean newucs = false; - if (!userColours.contains(ucs)) - { - userColours.add(ucs); - newucs = true; - } - id = "ucs" + userColours.indexOf(ucs); - if (newucs) - { - // actually create the scheme's entry in the XML model - java.awt.Color[] colours = ucs.getColours(); - jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours(); - jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme(); - - for (int i = 0; i < colours.length; i++) - { - jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); - col.setName(ResidueProperties.aa[i]); - col.setRGB(jalview.util.Format.getHexString(colours[i])); - jbucs.addColour(col); - } - if (ucs.getLowerCaseColours() != null) - { - colours = ucs.getLowerCaseColours(); - for (int i = 0; i < colours.length; i++) - { - jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); - col.setName(ResidueProperties.aa[i].toLowerCase()); - col.setRGB(jalview.util.Format.getHexString(colours[i])); - jbucs.addColour(col); - } - } - - uc.setId(id); - uc.setUserColourScheme(jbucs); - jms.addUserColours(uc); - } - - return id; - } - - jalview.schemes.UserColourScheme getUserColourScheme( - JalviewModelSequence jms, String id) - { - UserColours[] uc = jms.getUserColours(); - UserColours colours = null; - - for (int i = 0; i < uc.length; i++) - { - if (uc[i].getId().equals(id)) - { - colours = uc[i]; - - break; - } - } - - java.awt.Color[] newColours = new java.awt.Color[24]; - - for (int i = 0; i < 24; i++) - { - newColours[i] = new java.awt.Color(Integer.parseInt( - colours.getUserColourScheme().getColour(i).getRGB(), 16)); - } - - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - newColours); - - if (colours.getUserColourScheme().getColourCount() > 24) - { - newColours = new java.awt.Color[23]; - for (int i = 0; i < 23; i++) - { - newColours[i] = new java.awt.Color(Integer.parseInt( - colours.getUserColourScheme().getColour(i + 24).getRGB(), - 16)); - } - ucs.setLowerCaseColours(newColours); - } - - return ucs; - } - - /** - * contains last error message (if any) encountered by XML loader. - */ - String errorMessage = null; - - /** - * flag to control whether the Jalview2XML_V1 parser should be deferred to if - * exceptions are raised during project XML parsing - */ - public boolean attemptversion1parse = true; - - /** - * Load a jalview project archive from a jar file - * - * @param file - * - HTTP URL or filename - */ - public AlignFrame loadJalviewAlign(final String file) - { - - jalview.gui.AlignFrame af = null; - - try - { - // create list to store references for any new Jmol viewers created - newStructureViewers = new Vector<>(); - // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING - // Workaround is to make sure caller implements the JarInputStreamProvider - // interface - // so we can re-open the jar input stream for each entry. - - jarInputStreamProvider jprovider = createjarInputStreamProvider(file); - af = loadJalviewAlign(jprovider); - af.setMenusForViewport(); - - } catch (MalformedURLException e) - { - errorMessage = "Invalid URL format for '" + file + "'"; - reportErrors(); - } finally - { - try - { - SwingUtilities.invokeAndWait(new Runnable() - { - @Override - public void run() - { - setLoadingFinishedForNewStructureViewers(); - }; - }); - } catch (Exception x) - { - System.err.println("Error loading alignment: " + x.getMessage()); - } - } - return af; - } - - private jarInputStreamProvider createjarInputStreamProvider( - final String file) throws MalformedURLException - { - URL url = null; - errorMessage = null; - uniqueSetSuffix = null; - seqRefIds = null; - viewportsAdded.clear(); - frefedSequence = null; - - if (file.startsWith("http://")) - { - url = new URL(file); - } - final URL _url = url; - return new jarInputStreamProvider() - { - - @Override - public JarInputStream getJarInputStream() throws IOException - { - if (_url != null) - { - return new JarInputStream(_url.openStream()); - } - else - { - return new JarInputStream(new FileInputStream(file)); - } - } - - @Override - public String getFilename() - { - return file; - } - }; - } - - /** - * Recover jalview session from a jalview project archive. Caller may - * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence - * themselves. Any null fields will be initialised with default values, - * non-null fields are left alone. - * - * @param jprovider - * @return - */ - public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider) - { - errorMessage = null; - if (uniqueSetSuffix == null) - { - uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; - } - if (seqRefIds == null) - { - initSeqRefs(); - } - AlignFrame af = null, _af = null; - IdentityHashMap importedDatasets = new IdentityHashMap<>(); - Map gatherToThisFrame = new HashMap<>(); - final String file = jprovider.getFilename(); - try - { - JarInputStream jin = null; - JarEntry jarentry = null; - int entryCount = 1; - - do - { - jin = jprovider.getJarInputStream(); - for (int i = 0; i < entryCount; i++) - { - jarentry = jin.getNextJarEntry(); - } - - if (jarentry != null && jarentry.getName().endsWith(".xml")) - { - InputStreamReader in = new InputStreamReader(jin, UTF_8); - JalviewModel object = new JalviewModel(); - - Unmarshaller unmar = new Unmarshaller(object); - unmar.setValidation(false); - object = (JalviewModel) unmar.unmarshal(in); - if (true) // !skipViewport(object)) - { - _af = loadFromObject(object, file, true, jprovider); - if (_af != null && object.getJalviewModelSequence() - .getViewportCount() > 0) - { - if (af == null) - { - // store a reference to the first view - af = _af; - } - if (_af.viewport.isGatherViewsHere()) - { - // if this is a gathered view, keep its reference since - // after gathering views, only this frame will remain - af = _af; - gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af); - } - // Save dataset to register mappings once all resolved - importedDatasets.put(af.viewport.getAlignment().getDataset(), - af.viewport.getAlignment().getDataset()); - } - } - entryCount++; - } - else if (jarentry != null) - { - // Some other file here. - entryCount++; - } - } while (jarentry != null); - resolveFrefedSequences(); - } catch (IOException ex) - { - ex.printStackTrace(); - errorMessage = "Couldn't locate Jalview XML file : " + file; - System.err.println( - "Exception whilst loading jalview XML file : " + ex + "\n"); - } catch (Exception ex) - { - System.err.println("Parsing as Jalview Version 2 file failed."); - ex.printStackTrace(System.err); - if (attemptversion1parse) - { - // Is Version 1 Jar file? - try - { - af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider); - } catch (Exception ex2) - { - System.err.println("Exception whilst loading as jalviewXMLV1:"); - ex2.printStackTrace(); - af = null; - } - } - if (Desktop.instance != null) - { - Desktop.instance.stopLoading(); - } - if (af != null) - { - System.out.println("Successfully loaded archive file"); - return af; - } - ex.printStackTrace(); - - System.err.println( - "Exception whilst loading jalview XML file : " + ex + "\n"); - } catch (OutOfMemoryError e) - { - // Don't use the OOM Window here - errorMessage = "Out of memory loading jalview XML file"; - System.err.println("Out of memory whilst loading jalview XML file"); - e.printStackTrace(); - } - - /* - * Regather multiple views (with the same sequence set id) to the frame (if - * any) that is flagged as the one to gather to, i.e. convert them to tabbed - * views instead of separate frames. Note this doesn't restore a state where - * some expanded views in turn have tabbed views - the last "first tab" read - * in will play the role of gatherer for all. - */ - for (AlignFrame fr : gatherToThisFrame.values()) - { - Desktop.instance.gatherViews(fr); - } - - restoreSplitFrames(); - for (AlignmentI ds : importedDatasets.keySet()) - { - if (ds.getCodonFrames() != null) - { - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) - .registerMappings(ds.getCodonFrames()); - } - } - if (errorMessage != null) - { - reportErrors(); - } - - if (Desktop.instance != null) - { - Desktop.instance.stopLoading(); - } - - return af; - } - - /** - * Try to reconstruct and display SplitFrame windows, where each contains - * complementary dna and protein alignments. Done by pairing up AlignFrame - * objects (created earlier) which have complementary viewport ids associated. - */ - protected void restoreSplitFrames() - { - List gatherTo = new ArrayList<>(); - List addedToSplitFrames = new ArrayList<>(); - Map dna = new HashMap<>(); - - /* - * Identify the DNA alignments - */ - for (Entry candidate : splitFrameCandidates - .entrySet()) - { - AlignFrame af = candidate.getValue(); - if (af.getViewport().getAlignment().isNucleotide()) - { - dna.put(candidate.getKey().getId(), af); - } - } - - /* - * Try to match up the protein complements - */ - for (Entry candidate : splitFrameCandidates - .entrySet()) - { - AlignFrame af = candidate.getValue(); - if (!af.getViewport().getAlignment().isNucleotide()) - { - String complementId = candidate.getKey().getComplementId(); - // only non-null complements should be in the Map - if (complementId != null && dna.containsKey(complementId)) - { - final AlignFrame dnaFrame = dna.get(complementId); - SplitFrame sf = createSplitFrame(dnaFrame, af); - addedToSplitFrames.add(dnaFrame); - addedToSplitFrames.add(af); - dnaFrame.setMenusForViewport(); - af.setMenusForViewport(); - if (af.viewport.isGatherViewsHere()) - { - gatherTo.add(sf); - } - } - } - } - - /* - * Open any that we failed to pair up (which shouldn't happen!) as - * standalone AlignFrame's. - */ - for (Entry candidate : splitFrameCandidates - .entrySet()) - { - AlignFrame af = candidate.getValue(); - if (!addedToSplitFrames.contains(af)) - { - Viewport view = candidate.getKey(); - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), - view.getHeight()); - af.setMenusForViewport(); - System.err.println("Failed to restore view " + view.getTitle() - + " to split frame"); - } - } - - /* - * Gather back into tabbed views as flagged. - */ - for (SplitFrame sf : gatherTo) - { - Desktop.instance.gatherViews(sf); - } - - splitFrameCandidates.clear(); - } - - /** - * Construct and display one SplitFrame holding DNA and protein alignments. - * - * @param dnaFrame - * @param proteinFrame - * @return - */ - protected SplitFrame createSplitFrame(AlignFrame dnaFrame, - AlignFrame proteinFrame) - { - SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame); - String title = MessageManager.getString("label.linked_view_title"); - int width = (int) dnaFrame.getBounds().getWidth(); - int height = (int) (dnaFrame.getBounds().getHeight() - + proteinFrame.getBounds().getHeight() + 50); - - /* - * SplitFrame location is saved to both enclosed frames - */ - splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY()); - Desktop.addInternalFrame(splitFrame, title, width, height); - - /* - * And compute cDNA consensus (couldn't do earlier with consensus as - * mappings were not yet present) - */ - proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel); - - return splitFrame; - } - - /** - * check errorMessage for a valid error message and raise an error box in the - * GUI or write the current errorMessage to stderr and then clear the error - * state. - */ - protected void reportErrors() - { - reportErrors(false); - } - - protected void reportErrors(final boolean saving) - { - if (errorMessage != null) - { - final String finalErrorMessage = errorMessage; - if (raiseGUI) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - finalErrorMessage, - "Error " + (saving ? "saving" : "loading") - + " Jalview file", - JvOptionPane.WARNING_MESSAGE); - } - }); - } - else - { - System.err.println("Problem loading Jalview file: " + errorMessage); - } - } - errorMessage = null; - } - - Map alreadyLoadedPDB = new HashMap<>(); - - /** - * when set, local views will be updated from view stored in JalviewXML - * Currently (28th Sep 2008) things will go horribly wrong in vamsas document - * sync if this is set to true. - */ - private final boolean updateLocalViews = false; - - /** - * Returns the path to a temporary file holding the PDB file for the given PDB - * id. The first time of asking, searches for a file of that name in the - * Jalview project jar, and copies it to a new temporary file. Any repeat - * requests just return the path to the file previously created. - * - * @param jprovider - * @param pdbId - * @return - */ - String loadPDBFile(jarInputStreamProvider jprovider, String pdbId, - String origFile) - { - if (alreadyLoadedPDB.containsKey(pdbId)) - { - return alreadyLoadedPDB.get(pdbId).toString(); - } - - String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb", - origFile); - if (tempFile != null) - { - alreadyLoadedPDB.put(pdbId, tempFile); - } - return tempFile; - } - - /** - * Copies the jar entry of given name to a new temporary file and returns the - * path to the file, or null if the entry is not found. - * - * @param jprovider - * @param jarEntryName - * @param prefix - * a prefix for the temporary file name, must be at least three - * characters long - * @param origFile - * null or original file - so new file can be given the same suffix - * as the old one - * @return - */ - protected String copyJarEntry(jarInputStreamProvider jprovider, - String jarEntryName, String prefix, String origFile) - { - BufferedReader in = null; - PrintWriter out = null; - String suffix = ".tmp"; - if (origFile == null) - { - origFile = jarEntryName; - } - int sfpos = origFile.lastIndexOf("."); - if (sfpos > -1 && sfpos < (origFile.length() - 3)) - { - suffix = "." + origFile.substring(sfpos + 1); - } - try - { - JarInputStream jin = jprovider.getJarInputStream(); - /* - * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new - * URL(jprovider).openStream()); } else { jin = new JarInputStream(new - * FileInputStream(jprovider)); } - */ - - JarEntry entry = null; - do - { - entry = jin.getNextJarEntry(); - } while (entry != null && !entry.getName().equals(jarEntryName)); - if (entry != null) - { - in = new BufferedReader(new InputStreamReader(jin, UTF_8)); - File outFile = File.createTempFile(prefix, suffix); - outFile.deleteOnExit(); - out = new PrintWriter(new FileOutputStream(outFile)); - String data; - - while ((data = in.readLine()) != null) - { - out.println(data); - } - out.flush(); - String t = outFile.getAbsolutePath(); - return t; - } - else - { - warn("Couldn't find entry in Jalview Jar for " + jarEntryName); - } - } catch (Exception ex) - { - ex.printStackTrace(); - } finally - { - if (in != null) - { - try - { - in.close(); - } catch (IOException e) - { - // ignore - } - } - if (out != null) - { - out.close(); - } - } - - return null; - } - - private class JvAnnotRow - { - public JvAnnotRow(int i, AlignmentAnnotation jaa) - { - order = i; - template = jaa; - } - - /** - * persisted version of annotation row from which to take vis properties - */ - public jalview.datamodel.AlignmentAnnotation template; - - /** - * original position of the annotation row in the alignment - */ - public int order; - } - - /** - * Load alignment frame from jalview XML DOM object - * - * @param object - * DOM - * @param file - * filename source string - * @param loadTreesAndStructures - * when false only create Viewport - * @param jprovider - * data source provider - * @return alignment frame created from view stored in DOM - */ - AlignFrame loadFromObject(JalviewModel object, String file, - boolean loadTreesAndStructures, jarInputStreamProvider jprovider) - { - SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); - Sequence[] vamsasSeq = vamsasSet.getSequence(); - - JalviewModelSequence jms = object.getJalviewModelSequence(); - - Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0) - : null; - - // //////////////////////////////// - // LOAD SEQUENCES - - List hiddenSeqs = null; - - List tmpseqs = new ArrayList<>(); - - boolean multipleView = false; - SequenceI referenceseqForView = null; - JSeq[] jseqs = object.getJalviewModelSequence().getJSeq(); - int vi = 0; // counter in vamsasSeq array - for (int i = 0; i < jseqs.length; i++) - { - String seqId = jseqs[i].getId(); - - SequenceI tmpSeq = seqRefIds.get(seqId); - if (tmpSeq != null) - { - if (!incompleteSeqs.containsKey(seqId)) - { - // may not need this check, but keep it for at least 2.9,1 release - if (tmpSeq.getStart() != jseqs[i].getStart() - || tmpSeq.getEnd() != jseqs[i].getEnd()) - { - System.err.println( - "Warning JAL-2154 regression: updating start/end for sequence " - + tmpSeq.toString() + " to " + jseqs[i]); - } - } - else - { - incompleteSeqs.remove(seqId); - } - if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId)) - { - // most likely we are reading a dataset XML document so - // update from vamsasSeq section of XML for this sequence - tmpSeq.setName(vamsasSeq[vi].getName()); - tmpSeq.setDescription(vamsasSeq[vi].getDescription()); - tmpSeq.setSequence(vamsasSeq[vi].getSequence()); - vi++; - } - else - { - // reading multiple views, so vamsasSeq set is a subset of JSeq - multipleView = true; - } - tmpSeq.setStart(jseqs[i].getStart()); - tmpSeq.setEnd(jseqs[i].getEnd()); - tmpseqs.add(tmpSeq); - } - else - { - tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(), - vamsasSeq[vi].getSequence()); - tmpSeq.setDescription(vamsasSeq[vi].getDescription()); - tmpSeq.setStart(jseqs[i].getStart()); - tmpSeq.setEnd(jseqs[i].getEnd()); - tmpSeq.setVamsasId(uniqueSetSuffix + seqId); - seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq); - tmpseqs.add(tmpSeq); - vi++; - } - - if (jseqs[i].hasViewreference() && jseqs[i].getViewreference()) - { - referenceseqForView = tmpseqs.get(tmpseqs.size() - 1); - } - - if (jseqs[i].getHidden()) - { - if (hiddenSeqs == null) - { - hiddenSeqs = new ArrayList<>(); - } - - hiddenSeqs.add(tmpSeq); - } - } - - // / - // Create the alignment object from the sequence set - // /////////////////////////////// - SequenceI[] orderedSeqs = tmpseqs - .toArray(new SequenceI[tmpseqs.size()]); - - AlignmentI al = null; - // so we must create or recover the dataset alignment before going further - // /////////////////////////////// - if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "") - { - // older jalview projects do not have a dataset - so creat alignment and - // dataset - al = new Alignment(orderedSeqs); - al.setDataset(null); - } - else - { - boolean isdsal = object.getJalviewModelSequence() - .getViewportCount() == 0; - if (isdsal) - { - // we are importing a dataset record, so - // recover reference to an alignment already materialsed as dataset - al = getDatasetFor(vamsasSet.getDatasetId()); - } - if (al == null) - { - // materialse the alignment - al = new Alignment(orderedSeqs); - } - if (isdsal) - { - addDatasetRef(vamsasSet.getDatasetId(), al); - } - - // finally, verify all data in vamsasSet is actually present in al - // passing on flag indicating if it is actually a stored dataset - recoverDatasetFor(vamsasSet, al, isdsal); - } - - if (referenceseqForView != null) - { - al.setSeqrep(referenceseqForView); - } - // / Add the alignment properties - for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) - { - SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i); - al.setProperty(ssp.getKey(), ssp.getValue()); - } - - // /////////////////////////////// - - Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this?? - if (!multipleView) - { - // load sequence features, database references and any associated PDB - // structures for the alignment - // - // prior to 2.10, this part would only be executed the first time a - // sequence was encountered, but not afterwards. - // now, for 2.10 projects, this is also done if the xml doc includes - // dataset sequences not actually present in any particular view. - // - for (int i = 0; i < vamsasSeq.length; i++) - { - if (jseqs[i].getFeaturesCount() > 0) - { - Features[] features = jseqs[i].getFeatures(); - for (int f = 0; f < features.length; f++) - { - SequenceFeature sf = new SequenceFeature(features[f].getType(), - features[f].getDescription(), features[f].getBegin(), - features[f].getEnd(), features[f].getScore(), - features[f].getFeatureGroup()); - sf.setStatus(features[f].getStatus()); - - /* - * load any feature attributes - include map-valued attributes - */ - Map> mapAttributes = new HashMap<>(); - for (int od = 0; od < features[f].getOtherDataCount(); od++) - { - OtherData keyValue = features[f].getOtherData(od); - String attributeName = keyValue.getKey(); - String attributeValue = keyValue.getValue(); - if (attributeName.startsWith("LINK")) - { - sf.addLink(attributeValue); - } - else - { - String subAttribute = keyValue.getKey2(); - if (subAttribute == null) - { - // simple string-valued attribute - sf.setValue(attributeName, attributeValue); - } - else - { - // attribute 'key' has sub-attribute 'key2' - if (!mapAttributes.containsKey(attributeName)) - { - mapAttributes.put(attributeName, new HashMap<>()); - } - mapAttributes.get(attributeName).put(subAttribute, - attributeValue); - } - } - } - for (Entry> mapAttribute : mapAttributes - .entrySet()) - { - sf.setValue(mapAttribute.getKey(), mapAttribute.getValue()); - } - - // adds feature to datasequence's feature set (since Jalview 2.10) - al.getSequenceAt(i).addSequenceFeature(sf); - } - } - if (vamsasSeq[i].getDBRefCount() > 0) - { - // adds dbrefs to datasequence's set (since Jalview 2.10) - addDBRefs( - al.getSequenceAt(i).getDatasetSequence() == null - ? al.getSequenceAt(i) - : al.getSequenceAt(i).getDatasetSequence(), - vamsasSeq[i]); - } - if (jseqs[i].getPdbidsCount() > 0) - { - Pdbids[] ids = jseqs[i].getPdbids(); - for (int p = 0; p < ids.length; p++) - { - jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); - entry.setId(ids[p].getId()); - if (ids[p].getType() != null) - { - if (PDBEntry.Type.getType(ids[p].getType()) != null) - { - entry.setType(PDBEntry.Type.getType(ids[p].getType())); - } - else - { - entry.setType(PDBEntry.Type.FILE); - } - } - // jprovider is null when executing 'New View' - if (ids[p].getFile() != null && jprovider != null) - { - if (!pdbloaded.containsKey(ids[p].getFile())) - { - entry.setFile(loadPDBFile(jprovider, ids[p].getId(), - ids[p].getFile())); - } - else - { - entry.setFile(pdbloaded.get(ids[p].getId()).toString()); - } - } - if (ids[p].getPdbentryItem() != null) - { - for (PdbentryItem item : ids[p].getPdbentryItem()) - { - for (Property pr : item.getProperty()) - { - entry.setProperty(pr.getName(), pr.getValue()); - } - } - } - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) - .registerPDBEntry(entry); - // adds PDBEntry to datasequence's set (since Jalview 2.10) - if (al.getSequenceAt(i).getDatasetSequence() != null) - { - al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); - } - else - { - al.getSequenceAt(i).addPDBId(entry); - } - } - } - } - } // end !multipleview - - // /////////////////////////////// - // LOAD SEQUENCE MAPPINGS - - if (vamsasSet.getAlcodonFrameCount() > 0) - { - // TODO Potentially this should only be done once for all views of an - // alignment - AlcodonFrame[] alc = vamsasSet.getAlcodonFrame(); - for (int i = 0; i < alc.length; i++) - { - AlignedCodonFrame cf = new AlignedCodonFrame(); - if (alc[i].getAlcodMapCount() > 0) - { - AlcodMap[] maps = alc[i].getAlcodMap(); - for (int m = 0; m < maps.length; m++) - { - SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq()); - // Load Mapping - jalview.datamodel.Mapping mapping = null; - // attach to dna sequence reference. - if (maps[m].getMapping() != null) - { - mapping = addMapping(maps[m].getMapping()); - if (dnaseq != null && mapping.getTo() != null) - { - cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); - } - else - { - // defer to later - frefedSequence.add( - newAlcodMapRef(maps[m].getDnasq(), cf, mapping)); - } - } - } - al.addCodonFrame(cf); - } - } - } - - // //////////////////////////////// - // LOAD ANNOTATIONS - List autoAlan = new ArrayList<>(); - - /* - * store any annotations which forward reference a group's ID - */ - Map> groupAnnotRefs = new Hashtable<>(); - - if (vamsasSet.getAnnotationCount() > 0) - { - Annotation[] an = vamsasSet.getAnnotation(); - - for (int i = 0; i < an.length; i++) - { - Annotation annotation = an[i]; - - /** - * test if annotation is automatically calculated for this view only - */ - boolean autoForView = false; - if (annotation.getLabel().equals("Quality") - || annotation.getLabel().equals("Conservation") - || annotation.getLabel().equals("Consensus")) - { - // Kludge for pre 2.5 projects which lacked the autocalculated flag - autoForView = true; - if (!annotation.hasAutoCalculated()) - { - annotation.setAutoCalculated(true); - } - } - if (autoForView || (annotation.hasAutoCalculated() - && annotation.isAutoCalculated())) - { - // remove ID - we don't recover annotation from other views for - // view-specific annotation - annotation.setId(null); - } - - // set visiblity for other annotation in this view - String annotationId = annotation.getId(); - if (annotationId != null && annotationIds.containsKey(annotationId)) - { - AlignmentAnnotation jda = annotationIds.get(annotationId); - // in principle Visible should always be true for annotation displayed - // in multiple views - if (annotation.hasVisible()) - { - jda.visible = annotation.getVisible(); - } - - al.addAnnotation(jda); - - continue; - } - // Construct new annotation from model. - AnnotationElement[] ae = annotation.getAnnotationElement(); - jalview.datamodel.Annotation[] anot = null; - java.awt.Color firstColour = null; - int anpos; - if (!annotation.getScoreOnly()) - { - anot = new jalview.datamodel.Annotation[al.getWidth()]; - for (int aa = 0; aa < ae.length && aa < anot.length; aa++) - { - anpos = ae[aa].getPosition(); - - if (anpos >= anot.length) - { - continue; - } - - anot[anpos] = new jalview.datamodel.Annotation( - - ae[aa].getDisplayCharacter(), ae[aa].getDescription(), - (ae[aa].getSecondaryStructure() == null - || ae[aa].getSecondaryStructure().length() == 0) - ? ' ' - : ae[aa].getSecondaryStructure() - .charAt(0), - ae[aa].getValue() - - ); - // JBPNote: Consider verifying dataflow for IO of secondary - // structure annotation read from Stockholm files - // this was added to try to ensure that - // if (anot[ae[aa].getPosition()].secondaryStructure>' ') - // { - // anot[ae[aa].getPosition()].displayCharacter = ""; - // } - anot[anpos].colour = new java.awt.Color(ae[aa].getColour()); - if (firstColour == null) - { - firstColour = anot[anpos].colour; - } - } - } - jalview.datamodel.AlignmentAnnotation jaa = null; - - if (annotation.getGraph()) - { - float llim = 0, hlim = 0; - // if (autoForView || an[i].isAutoCalculated()) { - // hlim=11f; - // } - jaa = new jalview.datamodel.AlignmentAnnotation( - annotation.getLabel(), annotation.getDescription(), anot, - llim, hlim, annotation.getGraphType()); - - jaa.graphGroup = annotation.getGraphGroup(); - jaa._linecolour = firstColour; - if (annotation.getThresholdLine() != null) - { - jaa.setThreshold(new jalview.datamodel.GraphLine( - annotation.getThresholdLine().getValue(), - annotation.getThresholdLine().getLabel(), - new java.awt.Color( - annotation.getThresholdLine().getColour()))); - - } - if (autoForView || annotation.isAutoCalculated()) - { - // Hardwire the symbol display line to ensure that labels for - // histograms are displayed - jaa.hasText = true; - } - } - else - { - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot); - jaa._linecolour = firstColour; - } - // register new annotation - if (an[i].getId() != null) - { - annotationIds.put(an[i].getId(), jaa); - jaa.annotationId = an[i].getId(); - } - // recover sequence association - String sequenceRef = an[i].getSequenceRef(); - if (sequenceRef != null) - { - // from 2.9 sequenceRef is to sequence id (JAL-1781) - SequenceI sequence = seqRefIds.get(sequenceRef); - if (sequence == null) - { - // in pre-2.9 projects sequence ref is to sequence name - sequence = al.findName(sequenceRef); - } - if (sequence != null) - { - jaa.createSequenceMapping(sequence, 1, true); - sequence.addAlignmentAnnotation(jaa); - } - } - // and make a note of any group association - if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0) - { - List aal = groupAnnotRefs - .get(an[i].getGroupRef()); - if (aal == null) - { - aal = new ArrayList<>(); - groupAnnotRefs.put(an[i].getGroupRef(), aal); - } - aal.add(jaa); - } - - if (an[i].hasScore()) - { - jaa.setScore(an[i].getScore()); - } - if (an[i].hasVisible()) - { - jaa.visible = an[i].getVisible(); - } - - if (an[i].hasCentreColLabels()) - { - jaa.centreColLabels = an[i].getCentreColLabels(); - } - - if (an[i].hasScaleColLabels()) - { - jaa.scaleColLabel = an[i].getScaleColLabels(); - } - if (an[i].hasAutoCalculated() && an[i].isAutoCalculated()) - { - // newer files have an 'autoCalculated' flag and store calculation - // state in viewport properties - jaa.autoCalculated = true; // means annotation will be marked for - // update at end of load. - } - if (an[i].hasGraphHeight()) - { - jaa.graphHeight = an[i].getGraphHeight(); - } - if (an[i].hasBelowAlignment()) - { - jaa.belowAlignment = an[i].isBelowAlignment(); - } - jaa.setCalcId(an[i].getCalcId()); - if (an[i].getPropertyCount() > 0) - { - for (jalview.schemabinding.version2.Property prop : an[i] - .getProperty()) - { - jaa.setProperty(prop.getName(), prop.getValue()); - } - } - if (jaa.autoCalculated) - { - autoAlan.add(new JvAnnotRow(i, jaa)); - } - else - // if (!autoForView) - { - // add autocalculated group annotation and any user created annotation - // for the view - al.addAnnotation(jaa); - } - } - } - // /////////////////////// - // LOAD GROUPS - // Create alignment markup and styles for this view - if (jms.getJGroupCount() > 0) - { - JGroup[] groups = jms.getJGroup(); - boolean addAnnotSchemeGroup = false; - for (int i = 0; i < groups.length; i++) - { - JGroup jGroup = groups[i]; - ColourSchemeI cs = null; - if (jGroup.getColour() != null) - { - if (jGroup.getColour().startsWith("ucs")) - { - cs = getUserColourScheme(jms, jGroup.getColour()); - } - else if (jGroup.getColour().equals("AnnotationColourGradient") - && jGroup.getAnnotationColours() != null) - { - addAnnotSchemeGroup = true; - } - else - { - cs = ColourSchemeProperty.getColourScheme(al, - jGroup.getColour()); - } - } - int pidThreshold = jGroup.getPidThreshold(); - - Vector seqs = new Vector<>(); - - for (int s = 0; s < jGroup.getSeqCount(); s++) - { - String seqId = jGroup.getSeq(s) + ""; - SequenceI ts = seqRefIds.get(seqId); - - if (ts != null) - { - seqs.addElement(ts); - } - } - - if (seqs.size() < 1) - { - continue; - } - - SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs, - jGroup.getDisplayBoxes(), jGroup.getDisplayText(), - jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd()); - sg.getGroupColourScheme().setThreshold(pidThreshold, true); - sg.getGroupColourScheme() - .setConservationInc(jGroup.getConsThreshold()); - sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour())); - - sg.textColour = new java.awt.Color(jGroup.getTextCol1()); - sg.textColour2 = new java.awt.Color(jGroup.getTextCol2()); - sg.setShowNonconserved( - jGroup.hasShowUnconserved() ? jGroup.isShowUnconserved() - : false); - sg.thresholdTextColour = jGroup.getTextColThreshold(); - if (jGroup.hasShowConsensusHistogram()) - { - sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); - } - ; - if (jGroup.hasShowSequenceLogo()) - { - sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); - } - if (jGroup.hasNormaliseSequenceLogo()) - { - sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); - } - if (jGroup.hasIgnoreGapsinConsensus()) - { - sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus()); - } - if (jGroup.getConsThreshold() != 0) - { - Conservation c = new Conservation("All", sg.getSequences(null), 0, - sg.getWidth() - 1); - c.calculate(); - c.verdict(false, 25); - sg.cs.setConservation(c); - } - - if (jGroup.getId() != null && groupAnnotRefs.size() > 0) - { - // re-instate unique group/annotation row reference - List jaal = groupAnnotRefs - .get(jGroup.getId()); - if (jaal != null) - { - for (AlignmentAnnotation jaa : jaal) - { - jaa.groupRef = sg; - if (jaa.autoCalculated) - { - // match up and try to set group autocalc alignment row for this - // annotation - if (jaa.label.startsWith("Consensus for ")) - { - sg.setConsensus(jaa); - } - // match up and try to set group autocalc alignment row for this - // annotation - if (jaa.label.startsWith("Conservation for ")) - { - sg.setConservationRow(jaa); - } - } - } - } - } - al.addGroup(sg); - if (addAnnotSchemeGroup) - { - // reconstruct the annotation colourscheme - sg.setColourScheme(constructAnnotationColour( - jGroup.getAnnotationColours(), null, al, jms, false)); - } - } - } - if (view == null) - { - // only dataset in this model, so just return. - return null; - } - // /////////////////////////////// - // LOAD VIEWPORT - - // If we just load in the same jar file again, the sequenceSetId - // will be the same, and we end up with multiple references - // to the same sequenceSet. We must modify this id on load - // so that each load of the file gives a unique id - String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; - String viewId = (view.getId() == null ? null - : view.getId() + uniqueSetSuffix); - AlignFrame af = null; - AlignViewport av = null; - // now check to see if we really need to create a new viewport. - if (multipleView && viewportsAdded.size() == 0) - { - // We recovered an alignment for which a viewport already exists. - // TODO: fix up any settings necessary for overlaying stored state onto - // state recovered from another document. (may not be necessary). - // we may need a binding from a viewport in memory to one recovered from - // XML. - // and then recover its containing af to allow the settings to be applied. - // TODO: fix for vamsas demo - System.err.println( - "About to recover a viewport for existing alignment: Sequence set ID is " - + uniqueSeqSetId); - Object seqsetobj = retrieveExistingObj(uniqueSeqSetId); - if (seqsetobj != null) - { - if (seqsetobj instanceof String) - { - uniqueSeqSetId = (String) seqsetobj; - System.err.println( - "Recovered extant sequence set ID mapping for ID : New Sequence set ID is " - + uniqueSeqSetId); - } - else - { - System.err.println( - "Warning : Collision between sequence set ID string and existing jalview object mapping."); - } - - } - } - /** - * indicate that annotation colours are applied across all groups (pre - * Jalview 2.8.1 behaviour) - */ - boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1", - object.getVersion()); - - AlignmentPanel ap = null; - boolean isnewview = true; - if (viewId != null) - { - // Check to see if this alignment already has a view id == viewId - jalview.gui.AlignmentPanel views[] = Desktop - .getAlignmentPanels(uniqueSeqSetId); - if (views != null && views.length > 0) - { - for (int v = 0; v < views.length; v++) - { - if (views[v].av.getViewId().equalsIgnoreCase(viewId)) - { - // recover the existing alignpanel, alignframe, viewport - af = views[v].alignFrame; - av = views[v].av; - ap = views[v]; - // TODO: could even skip resetting view settings if we don't want to - // change the local settings from other jalview processes - isnewview = false; - } - } - } - } - - if (isnewview) - { - af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view, - uniqueSeqSetId, viewId, autoAlan); - av = af.viewport; - ap = af.alignPanel; - } - - /* - * Load any trees, PDB structures and viewers - * - * Not done if flag is false (when this method is used for New View) - */ - if (loadTreesAndStructures) - { - loadTrees(jms, view, af, av, ap); - loadPDBStructures(jprovider, jseqs, af, ap); - loadRnaViewers(jprovider, jseqs, ap); - } - // and finally return. - return af; - } - - /** - * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna - * panel is restored from separate jar entries, two (gapped and trimmed) per - * sequence and secondary structure. - * - * Currently each viewer shows just one sequence and structure (gapped and - * trimmed), however this method is designed to support multiple sequences or - * structures in viewers if wanted in future. - * - * @param jprovider - * @param jseqs - * @param ap - */ - private void loadRnaViewers(jarInputStreamProvider jprovider, - JSeq[] jseqs, AlignmentPanel ap) - { - /* - * scan the sequences for references to viewers; create each one the first - * time it is referenced, add Rna models to existing viewers - */ - for (JSeq jseq : jseqs) - { - for (int i = 0; i < jseq.getRnaViewerCount(); i++) - { - RnaViewer viewer = jseq.getRnaViewer(i); - AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix, - ap); - - for (int j = 0; j < viewer.getSecondaryStructureCount(); j++) - { - SecondaryStructure ss = viewer.getSecondaryStructure(j); - SequenceI seq = seqRefIds.get(jseq.getId()); - AlignmentAnnotation ann = this.annotationIds - .get(ss.getAnnotationId()); - - /* - * add the structure to the Varna display (with session state copied - * from the jar to a temporary file) - */ - boolean gapped = ss.isGapped(); - String rnaTitle = ss.getTitle(); - String sessionState = ss.getViewerState(); - String tempStateFile = copyJarEntry(jprovider, sessionState, - "varna", null); - RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); - appVarna.addModelSession(rna, rnaTitle, tempStateFile); - } - appVarna.setInitialSelection(viewer.getSelectedRna()); - } - } - } - - /** - * Locate and return an already instantiated matching AppVarna, or create one - * if not found - * - * @param viewer - * @param viewIdSuffix - * @param ap - * @return - */ - protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer, - String viewIdSuffix, AlignmentPanel ap) - { - /* - * on each load a suffix is appended to the saved viewId, to avoid conflicts - * if load is repeated - */ - String postLoadId = viewer.getViewId() + viewIdSuffix; - for (JInternalFrame frame : getAllFrames()) - { - if (frame instanceof AppVarna) - { - AppVarna varna = (AppVarna) frame; - if (postLoadId.equals(varna.getViewId())) - { - // this viewer is already instantiated - // could in future here add ap as another 'parent' of the - // AppVarna window; currently just 1-to-many - return varna; - } - } - } - - /* - * viewer not found - make it - */ - RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(), - viewer.getXpos(), viewer.getYpos(), viewer.getWidth(), - viewer.getHeight(), viewer.getDividerLocation()); - AppVarna varna = new AppVarna(model, ap); - - return varna; - } - - /** - * Load any saved trees - * - * @param jms - * @param view - * @param af - * @param av - * @param ap - */ - protected void loadTrees(JalviewModelSequence jms, Viewport view, - AlignFrame af, AlignViewport av, AlignmentPanel ap) - { - // TODO result of automated refactoring - are all these parameters needed? - try - { - for (int t = 0; t < jms.getTreeCount(); t++) - { - - Tree tree = jms.getTree(t); - - TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); - if (tp == null) - { - tp = af.showNewickTree( - new jalview.io.NewickFile(tree.getNewick()), - tree.getTitle(), tree.getWidth(), tree.getHeight(), - tree.getXpos(), tree.getYpos()); - if (tree.getId() != null) - { - // perhaps bind the tree id to something ? - } - } - else - { - // update local tree attributes ? - // TODO: should check if tp has been manipulated by user - if so its - // settings shouldn't be modified - tp.setTitle(tree.getTitle()); - tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), - tree.getWidth(), tree.getHeight())); - tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all - // views' - // works still - tp.getTreeCanvas().setViewport(av); // af.viewport; - tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel; - - } - if (tp == null) - { - warn("There was a problem recovering stored Newick tree: \n" - + tree.getNewick()); - continue; - } - - tp.fitToWindow.setState(tree.getFitToWindow()); - tp.fitToWindow_actionPerformed(null); - - if (tree.getFontName() != null) - { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), - tree.getFontStyle(), tree.getFontSize())); - } - else - { - tp.setTreeFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), tree.getFontSize())); - } - - tp.showPlaceholders(tree.getMarkUnlinked()); - tp.showBootstrap(tree.getShowBootstrap()); - tp.showDistances(tree.getShowDistances()); - - tp.getTreeCanvas().setThreshold(tree.getThreshold()); - - if (tree.getCurrentTree()) - { - af.viewport.setCurrentTree(tp.getTree()); - } - } - - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - /** - * Load and link any saved structure viewers. - * - * @param jprovider - * @param jseqs - * @param af - * @param ap - */ - protected void loadPDBStructures(jarInputStreamProvider jprovider, - JSeq[] jseqs, AlignFrame af, AlignmentPanel ap) - { - /* - * Run through all PDB ids on the alignment, and collect mappings between - * distinct view ids and all sequences referring to that view. - */ - Map structureViewers = new LinkedHashMap<>(); - - for (int i = 0; i < jseqs.length; i++) - { - if (jseqs[i].getPdbidsCount() > 0) - { - Pdbids[] ids = jseqs[i].getPdbids(); - for (int p = 0; p < ids.length; p++) - { - final int structureStateCount = ids[p].getStructureStateCount(); - for (int s = 0; s < structureStateCount; s++) - { - // check to see if we haven't already created this structure view - final StructureState structureState = ids[p] - .getStructureState(s); - String sviewid = (structureState.getViewId() == null) ? null - : structureState.getViewId() + uniqueSetSuffix; - jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); - // Originally : ids[p].getFile() - // : TODO: verify external PDB file recovery still works in normal - // jalview project load - jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(), - ids[p].getFile())); - jpdb.setId(ids[p].getId()); - - int x = structureState.getXpos(); - int y = structureState.getYpos(); - int width = structureState.getWidth(); - int height = structureState.getHeight(); - - // Probably don't need to do this anymore... - // Desktop.desktop.getComponentAt(x, y); - // TODO: NOW: check that this recovers the PDB file correctly. - String pdbFile = loadPDBFile(jprovider, ids[p].getId(), - ids[p].getFile()); - jalview.datamodel.SequenceI seq = seqRefIds - .get(jseqs[i].getId() + ""); - if (sviewid == null) - { - sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + "," - + height; - } - if (!structureViewers.containsKey(sviewid)) - { - structureViewers.put(sviewid, - new StructureViewerModel(x, y, width, height, false, - false, true, structureState.getViewId(), - structureState.getType())); - // Legacy pre-2.7 conversion JAL-823 : - // do not assume any view has to be linked for colour by - // sequence - } - - // assemble String[] { pdb files }, String[] { id for each - // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { - // seqs_file 2}, boolean[] { - // linkAlignPanel,superposeWithAlignpanel}} from hash - StructureViewerModel jmoldat = structureViewers.get(sviewid); - jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel() - | (structureState.hasAlignwithAlignPanel() - ? structureState.getAlignwithAlignPanel() - : false)); - - /* - * Default colour by linked panel to false if not specified (e.g. - * for pre-2.7 projects) - */ - boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel(); - colourWithAlignPanel |= (structureState - .hasColourwithAlignPanel() - ? structureState.getColourwithAlignPanel() - : false); - jmoldat.setColourWithAlignPanel(colourWithAlignPanel); - - /* - * Default colour by viewer to true if not specified (e.g. for - * pre-2.7 projects) - */ - boolean colourByViewer = jmoldat.isColourByViewer(); - colourByViewer &= structureState.hasColourByJmol() - ? structureState.getColourByJmol() - : true; - jmoldat.setColourByViewer(colourByViewer); - - if (jmoldat.getStateData().length() < structureState - .getContent().length()) - { - { - jmoldat.setStateData(structureState.getContent()); - } - } - if (ids[p].getFile() != null) - { - File mapkey = new File(ids[p].getFile()); - StructureData seqstrmaps = jmoldat.getFileData().get(mapkey); - if (seqstrmaps == null) - { - jmoldat.getFileData().put(mapkey, - seqstrmaps = jmoldat.new StructureData(pdbFile, - ids[p].getId())); - } - if (!seqstrmaps.getSeqList().contains(seq)) - { - seqstrmaps.getSeqList().add(seq); - // TODO and chains? - } - } - else - { - errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747"); - warn(errorMessage); - } - } - } - } - } - // Instantiate the associated structure views - for (Entry entry : structureViewers - .entrySet()) - { - try - { - createOrLinkStructureViewer(entry, af, ap, jprovider); - } catch (Exception e) - { - System.err.println( - "Error loading structure viewer: " + e.getMessage()); - // failed - try the next one - } - } - } - - /** - * - * @param viewerData - * @param af - * @param ap - * @param jprovider - */ - protected void createOrLinkStructureViewer( - Entry viewerData, AlignFrame af, - AlignmentPanel ap, jarInputStreamProvider jprovider) - { - final StructureViewerModel stateData = viewerData.getValue(); - - /* - * Search for any viewer windows already open from other alignment views - * that exactly match the stored structure state - */ - StructureViewerBase comp = findMatchingViewer(viewerData); - - if (comp != null) - { - linkStructureViewer(ap, comp, stateData); - return; - } - - /* - * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry - * "viewer_"+stateData.viewId - */ - if (ViewerType.CHIMERA.toString().equals(stateData.getType())) - { - createChimeraViewer(viewerData, af, jprovider); - } - else - { - /* - * else Jmol (if pre-2.9, stateData contains JMOL state string) - */ - createJmolViewer(viewerData, af, jprovider); - } - } - - /** - * Create a new Chimera viewer. - * - * @param data - * @param af - * @param jprovider - */ - protected void createChimeraViewer( - Entry viewerData, AlignFrame af, - jarInputStreamProvider jprovider) - { - StructureViewerModel data = viewerData.getValue(); - String chimeraSessionFile = data.getStateData(); - - /* - * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file - * - * NB this is the 'saved' viewId as in the project file XML, _not_ the - * 'uniquified' sviewid used to reconstruct the viewer here - */ - String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); - chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName, - "chimera", null); - - Set> fileData = data.getFileData() - .entrySet(); - List pdbs = new ArrayList<>(); - List allseqs = new ArrayList<>(); - for (Entry pdb : fileData) - { - String filePath = pdb.getValue().getFilePath(); - String pdbId = pdb.getValue().getPdbId(); - // pdbs.add(new PDBEntry(filePath, pdbId)); - pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath)); - final List seqList = pdb.getValue().getSeqList(); - SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]); - allseqs.add(seqs); - } - - boolean colourByChimera = data.isColourByViewer(); - boolean colourBySequence = data.isColourWithAlignPanel(); - - // TODO use StructureViewer as a factory here, see JAL-1761 - final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]); - final SequenceI[][] seqsArray = allseqs - .toArray(new SequenceI[allseqs.size()][]); - String newViewId = viewerData.getKey(); - - ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile, - af.alignPanel, pdbArray, seqsArray, colourByChimera, - colourBySequence, newViewId); - cvf.setSize(data.getWidth(), data.getHeight()); - cvf.setLocation(data.getX(), data.getY()); - } - - /** - * Create a new Jmol window. First parse the Jmol state to translate filenames - * loaded into the view, and record the order in which files are shown in the - * Jmol view, so we can add the sequence mappings in same order. - * - * @param viewerData - * @param af - * @param jprovider - */ - protected void createJmolViewer( - final Entry viewerData, - AlignFrame af, jarInputStreamProvider jprovider) - { - final StructureViewerModel svattrib = viewerData.getValue(); - String state = svattrib.getStateData(); - - /* - * Pre-2.9: state element value is the Jmol state string - * - * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_" - * + viewId - */ - if (ViewerType.JMOL.toString().equals(svattrib.getType())) - { - state = readJarEntry(jprovider, - getViewerJarEntryName(svattrib.getViewId())); - } - - List pdbfilenames = new ArrayList<>(); - List seqmaps = new ArrayList<>(); - List pdbids = new ArrayList<>(); - StringBuilder newFileLoc = new StringBuilder(64); - int cp = 0, ncp, ecp; - Map oldFiles = svattrib.getFileData(); - while ((ncp = state.indexOf("load ", cp)) > -1) - { - do - { - // look for next filename in load statement - newFileLoc.append(state.substring(cp, - ncp = (state.indexOf("\"", ncp + 1) + 1))); - String oldfilenam = state.substring(ncp, - ecp = state.indexOf("\"", ncp)); - // recover the new mapping data for this old filename - // have to normalize filename - since Jmol and jalview do - // filename - // translation differently. - StructureData filedat = oldFiles.get(new File(oldfilenam)); - if (filedat == null) - { - String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\"); - filedat = oldFiles.get(new File(reformatedOldFilename)); - } - newFileLoc.append(Platform.escapeString(filedat.getFilePath())); - pdbfilenames.add(filedat.getFilePath()); - pdbids.add(filedat.getPdbId()); - seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0])); - newFileLoc.append("\""); - cp = ecp + 1; // advance beyond last \" and set cursor so we can - // look for next file statement. - } while ((ncp = state.indexOf("/*file*/", cp)) > -1); - } - if (cp > 0) - { - // just append rest of state - newFileLoc.append(state.substring(cp)); - } - else - { - System.err.print("Ignoring incomplete Jmol state for PDB ids: "); - newFileLoc = new StringBuilder(state); - newFileLoc.append("; load append "); - for (File id : oldFiles.keySet()) - { - // add this and any other pdb files that should be present in - // the viewer - StructureData filedat = oldFiles.get(id); - newFileLoc.append(filedat.getFilePath()); - pdbfilenames.add(filedat.getFilePath()); - pdbids.add(filedat.getPdbId()); - seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0])); - newFileLoc.append(" \""); - newFileLoc.append(filedat.getFilePath()); - newFileLoc.append("\""); - - } - newFileLoc.append(";"); - } - - if (newFileLoc.length() == 0) - { - return; - } - int histbug = newFileLoc.indexOf("history = "); - if (histbug > -1) - { - /* - * change "history = [true|false];" to "history = [1|0];" - */ - histbug += 10; - int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug); - String val = (diff == -1) ? null - : newFileLoc.substring(histbug, diff); - if (val != null && val.length() >= 4) - { - if (val.contains("e")) // eh? what can it be? - { - if (val.trim().equals("true")) - { - val = "1"; - } - else - { - val = "0"; - } - newFileLoc.replace(histbug, diff, val); - } - } - } - - final String[] pdbf = pdbfilenames - .toArray(new String[pdbfilenames.size()]); - final String[] id = pdbids.toArray(new String[pdbids.size()]); - final SequenceI[][] sq = seqmaps - .toArray(new SequenceI[seqmaps.size()][]); - final String fileloc = newFileLoc.toString(); - final String sviewid = viewerData.getKey(); - final AlignFrame alf = af; - final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(), - svattrib.getWidth(), svattrib.getHeight()); - try - { - javax.swing.SwingUtilities.invokeAndWait(new Runnable() - { - @Override - public void run() - { - JalviewStructureDisplayI sview = null; - try - { - sview = new StructureViewer( - alf.alignPanel.getStructureSelectionManager()) - .createView(StructureViewer.ViewerType.JMOL, - pdbf, id, sq, alf.alignPanel, svattrib, - fileloc, rect, sviewid); - addNewStructureViewer(sview); - } catch (OutOfMemoryError ex) - { - new OOMWarning("restoring structure view for PDB id " + id, - (OutOfMemoryError) ex.getCause()); - if (sview != null && sview.isVisible()) - { - sview.closeViewer(false); - sview.setVisible(false); - sview.dispose(); - } - } - } - }); - } catch (InvocationTargetException ex) - { - warn("Unexpected error when opening Jmol view.", ex); - - } catch (InterruptedException e) - { - // e.printStackTrace(); - } - - } - - /** - * Generates a name for the entry in the project jar file to hold state - * information for a structure viewer - * - * @param viewId - * @return - */ - protected String getViewerJarEntryName(String viewId) - { - return VIEWER_PREFIX + viewId; - } - - /** - * Returns any open frame that matches given structure viewer data. The match - * is based on the unique viewId, or (for older project versions) the frame's - * geometry. - * - * @param viewerData - * @return - */ - protected StructureViewerBase findMatchingViewer( - Entry viewerData) - { - final String sviewid = viewerData.getKey(); - final StructureViewerModel svattrib = viewerData.getValue(); - StructureViewerBase comp = null; - JInternalFrame[] frames = getAllFrames(); - for (JInternalFrame frame : frames) - { - if (frame instanceof StructureViewerBase) - { - /* - * Post jalview 2.4 schema includes structure view id - */ - if (sviewid != null && ((StructureViewerBase) frame).getViewId() - .equals(sviewid)) - { - comp = (StructureViewerBase) frame; - break; // break added in 2.9 - } - /* - * Otherwise test for matching position and size of viewer frame - */ - else if (frame.getX() == svattrib.getX() - && frame.getY() == svattrib.getY() - && frame.getHeight() == svattrib.getHeight() - && frame.getWidth() == svattrib.getWidth()) - { - comp = (StructureViewerBase) frame; - // no break in faint hope of an exact match on viewId - } - } - } - return comp; - } - - /** - * Link an AlignmentPanel to an existing structure viewer. - * - * @param ap - * @param viewer - * @param oldFiles - * @param useinViewerSuperpos - * @param usetoColourbyseq - * @param viewerColouring - */ - protected void linkStructureViewer(AlignmentPanel ap, - StructureViewerBase viewer, StructureViewerModel stateData) - { - // NOTE: if the jalview project is part of a shared session then - // view synchronization should/could be done here. - - final boolean useinViewerSuperpos = stateData.isAlignWithPanel(); - final boolean usetoColourbyseq = stateData.isColourWithAlignPanel(); - final boolean viewerColouring = stateData.isColourByViewer(); - Map oldFiles = stateData.getFileData(); - - /* - * Add mapping for sequences in this view to an already open viewer - */ - final AAStructureBindingModel binding = viewer.getBinding(); - for (File id : oldFiles.keySet()) - { - // add this and any other pdb files that should be present in the - // viewer - StructureData filedat = oldFiles.get(id); - String pdbFile = filedat.getFilePath(); - SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]); - binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE, - null); - binding.addSequenceForStructFile(pdbFile, seq); - } - // and add the AlignmentPanel's reference to the view panel - viewer.addAlignmentPanel(ap); - if (useinViewerSuperpos) - { - viewer.useAlignmentPanelForSuperposition(ap); - } - else - { - viewer.excludeAlignmentPanelForSuperposition(ap); - } - if (usetoColourbyseq) - { - viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring); - } - else - { - viewer.excludeAlignmentPanelForColourbyseq(ap); - } - } - - /** - * Get all frames within the Desktop. - * - * @return - */ - protected JInternalFrame[] getAllFrames() - { - JInternalFrame[] frames = null; - // TODO is this necessary - is it safe - risk of hanging? - do - { - try - { - frames = Desktop.desktop.getAllFrames(); - } catch (ArrayIndexOutOfBoundsException e) - { - // occasional No such child exceptions are thrown here... - try - { - Thread.sleep(10); - } catch (InterruptedException f) - { - } - } - } while (frames == null); - return frames; - } - - /** - * Answers true if 'version' is equal to or later than 'supported', where each - * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix - * changes. Development and test values for 'version' are leniently treated - * i.e. answer true. - * - * @param supported - * - minimum version we are comparing against - * @param version - * - version of data being processsed - * @return - */ - public static boolean isVersionStringLaterThan(String supported, - String version) - { - if (supported == null || version == null - || version.equalsIgnoreCase("DEVELOPMENT BUILD") - || version.equalsIgnoreCase("Test") - || version.equalsIgnoreCase("AUTOMATED BUILD")) - { - System.err.println("Assuming project file with " - + (version == null ? "null" : version) - + " is compatible with Jalview version " + supported); - return true; - } - else - { - return StringUtils.compareVersions(version, supported, "b") >= 0; - } - } - - Vector newStructureViewers = null; - - protected void addNewStructureViewer(JalviewStructureDisplayI sview) - { - if (newStructureViewers != null) - { - sview.getBinding().setFinishedLoadingFromArchive(false); - newStructureViewers.add(sview); - } - } - - protected void setLoadingFinishedForNewStructureViewers() - { - if (newStructureViewers != null) - { - for (JalviewStructureDisplayI sview : newStructureViewers) - { - sview.getBinding().setFinishedLoadingFromArchive(true); - } - newStructureViewers.clear(); - newStructureViewers = null; - } - } - - AlignFrame loadViewport(String file, JSeq[] JSEQ, - List hiddenSeqs, AlignmentI al, - JalviewModelSequence jms, Viewport view, String uniqueSeqSetId, - String viewId, List autoAlan) - { - AlignFrame af = null; - af = new AlignFrame(al, view.getWidth(), view.getHeight(), - uniqueSeqSetId, viewId); - - af.setFileName(file, FileFormat.Jalview); - - for (int i = 0; i < JSEQ.length; i++) - { - af.viewport.setSequenceColour( - af.viewport.getAlignment().getSequenceAt(i), - new java.awt.Color(JSEQ[i].getColour())); - } - - if (al.hasSeqrep()) - { - af.getViewport().setColourByReferenceSeq(true); - af.getViewport().setDisplayReferenceSeq(true); - } - - af.viewport.setGatherViewsHere(view.getGatheredViews()); - - if (view.getSequenceSetId() != null) - { - AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId); - - af.viewport.setSequenceSetId(uniqueSeqSetId); - if (av != null) - { - // propagate shared settings to this new view - af.viewport.setHistoryList(av.getHistoryList()); - af.viewport.setRedoList(av.getRedoList()); - } - else - { - viewportsAdded.put(uniqueSeqSetId, af.viewport); - } - // TODO: check if this method can be called repeatedly without - // side-effects if alignpanel already registered. - PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); - } - // apply Hidden regions to view. - if (hiddenSeqs != null) - { - for (int s = 0; s < JSEQ.length; s++) - { - SequenceGroup hidden = new SequenceGroup(); - boolean isRepresentative = false; - for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) - { - isRepresentative = true; - SequenceI sequenceToHide = al - .getSequenceAt(JSEQ[s].getHiddenSequences(r)); - hidden.addSequence(sequenceToHide, false); - // remove from hiddenSeqs list so we don't try to hide it twice - hiddenSeqs.remove(sequenceToHide); - } - if (isRepresentative) - { - SequenceI representativeSequence = al.getSequenceAt(s); - hidden.addSequence(representativeSequence, false); - af.viewport.hideRepSequences(representativeSequence, hidden); - } - } - - SequenceI[] hseqs = hiddenSeqs - .toArray(new SequenceI[hiddenSeqs.size()]); - af.viewport.hideSequence(hseqs); - - } - // recover view properties and display parameters - - af.viewport.setShowAnnotation(view.getShowAnnotation()); - af.viewport.setAbovePIDThreshold(view.getPidSelected()); - af.viewport.setThreshold(view.getPidThreshold()); - - af.viewport.setColourText(view.getShowColourText()); - - af.viewport.setConservationSelected(view.getConservationSelected()); - af.viewport.setIncrement(view.getConsThreshold()); - af.viewport.setShowJVSuffix(view.getShowFullId()); - af.viewport.setRightAlignIds(view.getRightAlignIds()); - af.viewport.setFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), view.getFontSize()), true); - ViewStyleI vs = af.viewport.getViewStyle(); - vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna()); - af.viewport.setViewStyle(vs); - // TODO: allow custom charWidth/Heights to be restored by updating them - // after setting font - which means set above to false - af.viewport.setRenderGaps(view.getRenderGaps()); - af.viewport.setWrapAlignment(view.getWrapAlignment()); - af.viewport.setShowAnnotation(view.getShowAnnotation()); - - af.viewport.setShowBoxes(view.getShowBoxes()); - - af.viewport.setShowText(view.getShowText()); - - af.viewport.setTextColour(new java.awt.Color(view.getTextCol1())); - af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2())); - af.viewport.setThresholdTextColour(view.getTextColThreshold()); - af.viewport.setShowUnconserved( - view.hasShowUnconserved() ? view.isShowUnconserved() : false); - af.viewport.getRanges().setStartRes(view.getStartRes()); - - if (view.getViewName() != null) - { - af.viewport.setViewName(view.getViewName()); - af.setInitialTabVisible(); - } - af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), - view.getHeight()); - // startSeq set in af.alignPanel.updateLayout below - af.alignPanel.updateLayout(); - ColourSchemeI cs = null; - // apply colourschemes - if (view.getBgColour() != null) - { - if (view.getBgColour().startsWith("ucs")) - { - cs = getUserColourScheme(jms, view.getBgColour()); - } - else if (view.getBgColour().startsWith("Annotation")) - { - AnnotationColours viewAnnColour = view.getAnnotationColours(); - cs = constructAnnotationColour(viewAnnColour, af, al, jms, true); - - // annpos - - } - else - { - cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour()); - } - } - - af.viewport.setGlobalColourScheme(cs); - af.viewport.getResidueShading().setThreshold(view.getPidThreshold(), - view.getIgnoreGapsinConsensus()); - af.viewport.getResidueShading() - .setConsensus(af.viewport.getSequenceConsensusHash()); - af.viewport.setColourAppliesToAllGroups(false); - - if (view.getConservationSelected() && cs != null) - { - af.viewport.getResidueShading() - .setConservationInc(view.getConsThreshold()); - } - - af.changeColour(cs); - - af.viewport.setColourAppliesToAllGroups(true); - - af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures()); - - if (view.hasCentreColumnLabels()) - { - af.viewport.setCentreColumnLabels(view.getCentreColumnLabels()); - } - if (view.hasIgnoreGapsinConsensus()) - { - af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(), - null); - } - if (view.hasFollowHighlight()) - { - af.viewport.setFollowHighlight(view.getFollowHighlight()); - } - if (view.hasFollowSelection()) - { - af.viewport.followSelection = view.getFollowSelection(); - } - if (view.hasShowConsensusHistogram()) - { - af.viewport - .setShowConsensusHistogram(view.getShowConsensusHistogram()); - } - else - { - af.viewport.setShowConsensusHistogram(true); - } - if (view.hasShowSequenceLogo()) - { - af.viewport.setShowSequenceLogo(view.getShowSequenceLogo()); - } - else - { - af.viewport.setShowSequenceLogo(false); - } - if (view.hasNormaliseSequenceLogo()) - { - af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo()); - } - if (view.hasShowDbRefTooltip()) - { - af.viewport.setShowDBRefs(view.getShowDbRefTooltip()); - } - if (view.hasShowNPfeatureTooltip()) - { - af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip()); - } - if (view.hasShowGroupConsensus()) - { - af.viewport.setShowGroupConsensus(view.getShowGroupConsensus()); - } - else - { - af.viewport.setShowGroupConsensus(false); - } - if (view.hasShowGroupConservation()) - { - af.viewport.setShowGroupConservation(view.getShowGroupConservation()); - } - else - { - af.viewport.setShowGroupConservation(false); - } - - // recover feature settings - if (jms.getFeatureSettings() != null) - { - FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas - .getFeatureRenderer(); - FeaturesDisplayed fdi; - af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); - String[] renderOrder = new String[jms.getFeatureSettings() - .getSettingCount()]; - Map featureColours = new Hashtable<>(); - Map featureOrder = new Hashtable<>(); - - for (int fs = 0; fs < jms.getFeatureSettings() - .getSettingCount(); fs++) - { - Setting setting = jms.getFeatureSettings().getSetting(fs); - String featureType = setting.getType(); - - /* - * restore feature filters (if any) - */ - MatcherSet filters = setting.getMatcherSet(); - if (filters != null) - { - FeatureMatcherSetI filter = Jalview2XML - .unmarshalFilter(featureType, filters); - if (!filter.isEmpty()) - { - fr.setFeatureFilter(featureType, filter); - } - } - - /* - * restore feature colour scheme - */ - Color maxColour = new Color(setting.getColour()); - if (setting.hasMincolour()) - { - /* - * minColour is always set unless a simple colour - * (including for colour by label though it doesn't use it) - */ - Color minColour = new Color(setting.getMincolour()); - Color noValueColour = minColour; - NoValueColour noColour = setting.getNoValueColour(); - if (noColour == NoValueColour.NONE) - { - noValueColour = null; - } - else if (noColour == NoValueColour.MAX) - { - noValueColour = maxColour; - } - float min = setting.hasMin() ? setting.getMin() : 0f; - float max = setting.hasMin() ? setting.getMax() : 1f; - FeatureColourI gc = new FeatureColour(minColour, maxColour, - noValueColour, min, max); - if (setting.getAttributeNameCount() > 0) - { - gc.setAttributeName(setting.getAttributeName()); - } - if (setting.hasThreshold()) - { - gc.setThreshold(setting.getThreshold()); - int threshstate = setting.getThreshstate(); - // -1 = None, 0 = Below, 1 = Above threshold - if (threshstate == 0) - { - gc.setBelowThreshold(true); - } - else if (threshstate == 1) - { - gc.setAboveThreshold(true); - } - } - gc.setAutoScaled(true); // default - if (setting.hasAutoScale()) - { - gc.setAutoScaled(setting.getAutoScale()); - } - if (setting.hasColourByLabel()) - { - gc.setColourByLabel(setting.getColourByLabel()); - } - // and put in the feature colour table. - featureColours.put(featureType, gc); - } - else - { - featureColours.put(featureType, - new FeatureColour(maxColour)); - } - renderOrder[fs] = featureType; - if (setting.hasOrder()) - { - featureOrder.put(featureType, setting.getOrder()); - } - else - { - featureOrder.put(featureType, new Float( - fs / jms.getFeatureSettings().getSettingCount())); - } - if (setting.getDisplay()) - { - fdi.setVisible(featureType); - } - } - Map fgtable = new Hashtable<>(); - for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) - { - Group grp = jms.getFeatureSettings().getGroup(gs); - fgtable.put(grp.getName(), new Boolean(grp.getDisplay())); - } - // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, - // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ? - // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder); - FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, - fgtable, featureColours, 1.0f, featureOrder); - fr.transferSettings(frs); - } - - if (view.getHiddenColumnsCount() > 0) - { - for (int c = 0; c < view.getHiddenColumnsCount(); c++) - { - af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), - view.getHiddenColumns(c).getEnd() // +1 - ); - } - } - if (view.getCalcIdParam() != null) - { - for (CalcIdParam calcIdParam : view.getCalcIdParam()) - { - if (calcIdParam != null) - { - if (recoverCalcIdParam(calcIdParam, af.viewport)) - { - } - else - { - warn("Couldn't recover parameters for " - + calcIdParam.getCalcId()); - } - } - } - } - af.setMenusFromViewport(af.viewport); - af.setTitle(view.getTitle()); - // TODO: we don't need to do this if the viewport is aready visible. - /* - * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it - * has a 'cdna/protein complement' view, in which case save it in order to - * populate a SplitFrame once all views have been read in. - */ - String complementaryViewId = view.getComplementId(); - if (complementaryViewId == null) - { - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), - view.getHeight()); - // recompute any autoannotation - af.alignPanel.updateAnnotation(false, true); - reorderAutoannotation(af, al, autoAlan); - af.alignPanel.alignmentChanged(); - } - else - { - splitFrameCandidates.put(view, af); - } - return af; - } - - /** - * Reads saved data to restore Colour by Annotation settings - * - * @param viewAnnColour - * @param af - * @param al - * @param jms - * @param checkGroupAnnColour - * @return - */ - private ColourSchemeI constructAnnotationColour( - AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al, - JalviewModelSequence jms, boolean checkGroupAnnColour) - { - boolean propagateAnnColour = false; - AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al; - if (checkGroupAnnColour && al.getGroups() != null - && al.getGroups().size() > 0) - { - // pre 2.8.1 behaviour - // check to see if we should transfer annotation colours - propagateAnnColour = true; - for (SequenceGroup sg : al.getGroups()) - { - if (sg.getColourScheme() instanceof AnnotationColourGradient) - { - propagateAnnColour = false; - } - } - } - - /* - * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId - */ - String annotationId = viewAnnColour.getAnnotation(); - AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId); - - /* - * pre 2.10.2: saved annotationId is AlignmentAnnotation.label - */ - if (matchedAnnotation == null - && annAlignment.getAlignmentAnnotation() != null) - { - for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++) - { - if (annotationId - .equals(annAlignment.getAlignmentAnnotation()[i].label)) - { - matchedAnnotation = annAlignment.getAlignmentAnnotation()[i]; - break; - } - } - } - if (matchedAnnotation == null) - { - System.err.println("Failed to match annotation colour scheme for " - + annotationId); - return null; - } - if (matchedAnnotation.getThreshold() == null) - { - matchedAnnotation.setThreshold(new GraphLine( - viewAnnColour.getThreshold(), "Threshold", Color.black)); - } - - AnnotationColourGradient cs = null; - if (viewAnnColour.getColourScheme().equals("None")) - { - cs = new AnnotationColourGradient(matchedAnnotation, - new Color(viewAnnColour.getMinColour()), - new Color(viewAnnColour.getMaxColour()), - viewAnnColour.getAboveThreshold()); - } - else if (viewAnnColour.getColourScheme().startsWith("ucs")) - { - cs = new AnnotationColourGradient(matchedAnnotation, - getUserColourScheme(jms, viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); - } - else - { - cs = new AnnotationColourGradient(matchedAnnotation, - ColourSchemeProperty.getColourScheme(al, - viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); - } - - boolean perSequenceOnly = viewAnnColour.isPerSequence(); - boolean useOriginalColours = viewAnnColour.isPredefinedColours(); - cs.setSeqAssociated(perSequenceOnly); - cs.setPredefinedColours(useOriginalColours); - - if (propagateAnnColour && al.getGroups() != null) - { - // Also use these settings for all the groups - for (int g = 0; g < al.getGroups().size(); g++) - { - SequenceGroup sg = al.getGroups().get(g); - if (sg.getGroupColourScheme() == null) - { - continue; - } - - AnnotationColourGradient groupScheme = new AnnotationColourGradient( - matchedAnnotation, sg.getColourScheme(), - viewAnnColour.getAboveThreshold()); - sg.setColourScheme(groupScheme); - groupScheme.setSeqAssociated(perSequenceOnly); - groupScheme.setPredefinedColours(useOriginalColours); - } - } - return cs; - } - - private void reorderAutoannotation(AlignFrame af, AlignmentI al, - List autoAlan) - { - // copy over visualization settings for autocalculated annotation in the - // view - if (al.getAlignmentAnnotation() != null) - { - /** - * Kludge for magic autoannotation names (see JAL-811) - */ - String[] magicNames = new String[] { "Consensus", "Quality", - "Conservation" }; - JvAnnotRow nullAnnot = new JvAnnotRow(-1, null); - Hashtable visan = new Hashtable<>(); - for (String nm : magicNames) - { - visan.put(nm, nullAnnot); - } - for (JvAnnotRow auan : autoAlan) - { - visan.put(auan.template.label - + (auan.template.getCalcId() == null ? "" - : "\t" + auan.template.getCalcId()), - auan); - } - int hSize = al.getAlignmentAnnotation().length; - List reorder = new ArrayList<>(); - // work through any autoCalculated annotation already on the view - // removing it if it should be placed in a different location on the - // annotation panel. - List remains = new ArrayList<>(visan.keySet()); - for (int h = 0; h < hSize; h++) - { - jalview.datamodel.AlignmentAnnotation jalan = al - .getAlignmentAnnotation()[h]; - if (jalan.autoCalculated) - { - String k; - JvAnnotRow valan = visan.get(k = jalan.label); - if (jalan.getCalcId() != null) - { - valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId()); - } - - if (valan != null) - { - // delete the auto calculated row from the alignment - al.deleteAnnotation(jalan, false); - remains.remove(k); - hSize--; - h--; - if (valan != nullAnnot) - { - if (jalan != valan.template) - { - // newly created autoannotation row instance - // so keep a reference to the visible annotation row - // and copy over all relevant attributes - if (valan.template.graphHeight >= 0) - - { - jalan.graphHeight = valan.template.graphHeight; - } - jalan.visible = valan.template.visible; - } - reorder.add(new JvAnnotRow(valan.order, jalan)); - } - } - } - } - // Add any (possibly stale) autocalculated rows that were not appended to - // the view during construction - for (String other : remains) - { - JvAnnotRow othera = visan.get(other); - if (othera != nullAnnot && othera.template.getCalcId() != null - && othera.template.getCalcId().length() > 0) - { - reorder.add(othera); - } - } - // now put the automatic annotation in its correct place - int s = 0, srt[] = new int[reorder.size()]; - JvAnnotRow[] rws = new JvAnnotRow[reorder.size()]; - for (JvAnnotRow jvar : reorder) - { - rws[s] = jvar; - srt[s++] = jvar.order; - } - reorder.clear(); - jalview.util.QuickSort.sort(srt, rws); - // and re-insert the annotation at its correct position - for (JvAnnotRow jvar : rws) - { - al.addAnnotation(jvar.template, jvar.order); - } - af.alignPanel.adjustAnnotationHeight(); - } - } - - Hashtable skipList = null; - - /** - * TODO remove this method - * - * @param view - * @return AlignFrame bound to sequenceSetId from view, if one exists. private - * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) { - * throw new Error("Implementation Error. No skipList defined for this - * Jalview2XML instance."); } return (AlignFrame) - * skipList.get(view.getSequenceSetId()); } - */ - - /** - * Check if the Jalview view contained in object should be skipped or not. - * - * @param object - * @return true if view's sequenceSetId is a key in skipList - */ - private boolean skipViewport(JalviewModel object) - { - if (skipList == null) - { - return false; - } - String id; - if (skipList.containsKey( - id = object.getJalviewModelSequence().getViewport()[0] - .getSequenceSetId())) - { - if (Cache.log != null && Cache.log.isDebugEnabled()) - { - Cache.log.debug("Skipping seuqence set id " + id); - } - return true; - } - return false; - } - - public void addToSkipList(AlignFrame af) - { - if (skipList == null) - { - skipList = new Hashtable(); - } - skipList.put(af.getViewport().getSequenceSetId(), af); - } - - public void clearSkipList() - { - if (skipList != null) - { - skipList.clear(); - skipList = null; - } - } - - private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al, - boolean ignoreUnrefed) - { - jalview.datamodel.AlignmentI ds = getDatasetFor( - vamsasSet.getDatasetId()); - Vector dseqs = null; - if (ds == null) - { - // create a list of new dataset sequences - dseqs = new Vector(); - } - for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++) - { - Sequence vamsasSeq = vamsasSet.getSequence(i); - ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i); - } - // create a new dataset - if (ds == null) - { - SequenceI[] dsseqs = new SequenceI[dseqs.size()]; - dseqs.copyInto(dsseqs); - ds = new jalview.datamodel.Alignment(dsseqs); - debug("Created new dataset " + vamsasSet.getDatasetId() - + " for alignment " + System.identityHashCode(al)); - addDatasetRef(vamsasSet.getDatasetId(), ds); - } - // set the dataset for the newly imported alignment. - if (al.getDataset() == null && !ignoreUnrefed) - { - al.setDataset(ds); - } - } - - /** - * - * @param vamsasSeq - * sequence definition to create/merge dataset sequence for - * @param ds - * dataset alignment - * @param dseqs - * vector to add new dataset sequence to - * @param ignoreUnrefed - * - when true, don't create new sequences from vamsasSeq if it's id - * doesn't already have an asssociated Jalview sequence. - * @param vseqpos - * - used to reorder the sequence in the alignment according to the - * vamsasSeq array ordering, to preserve ordering of dataset - */ - private void ensureJalviewDatasetSequence(Sequence vamsasSeq, - AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos) - { - // JBP TODO: Check this is called for AlCodonFrames to support recovery of - // xRef Codon Maps - SequenceI sq = seqRefIds.get(vamsasSeq.getId()); - boolean reorder = false; - SequenceI dsq = null; - if (sq != null && sq.getDatasetSequence() != null) - { - dsq = sq.getDatasetSequence(); - } - else - { - reorder = true; - } - if (sq == null && ignoreUnrefed) - { - return; - } - String sqid = vamsasSeq.getDsseqid(); - if (dsq == null) - { - // need to create or add a new dataset sequence reference to this sequence - if (sqid != null) - { - dsq = seqRefIds.get(sqid); - } - // check again - if (dsq == null) - { - // make a new dataset sequence - dsq = sq.createDatasetSequence(); - if (sqid == null) - { - // make up a new dataset reference for this sequence - sqid = seqHash(dsq); - } - dsq.setVamsasId(uniqueSetSuffix + sqid); - seqRefIds.put(sqid, dsq); - if (ds == null) - { - if (dseqs != null) - { - dseqs.addElement(dsq); - } - } - else - { - ds.addSequence(dsq); - } - } - else - { - if (sq != dsq) - { // make this dataset sequence sq's dataset sequence - sq.setDatasetSequence(dsq); - // and update the current dataset alignment - if (ds == null) - { - if (dseqs != null) - { - if (!dseqs.contains(dsq)) - { - dseqs.add(dsq); - } - } - else - { - if (ds.findIndex(dsq) < 0) - { - ds.addSequence(dsq); - } - } - } - } - } - } - // TODO: refactor this as a merge dataset sequence function - // now check that sq (the dataset sequence) sequence really is the union of - // all references to it - // boolean pre = sq.getStart() < dsq.getStart(); - // boolean post = sq.getEnd() > dsq.getEnd(); - // if (pre || post) - if (sq != dsq) - { - // StringBuffer sb = new StringBuffer(); - String newres = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, sq.getSequenceAsString()); - if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) - && newres.length() > dsq.getLength()) - { - // Update with the longer sequence. - synchronized (dsq) - { - /* - * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() - - * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) { - * sb.append(newres.substring(newres.length() - sq.getEnd() - - * dsq.getEnd())); dsq.setEnd(sq.getEnd()); } - */ - dsq.setSequence(newres); - } - // TODO: merges will never happen if we 'know' we have the real dataset - // sequence - this should be detected when id==dssid - System.err.println( - "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // (" - // + (pre ? "prepended" : "") + " " - // + (post ? "appended" : "")); - } - } - else - { - // sequence refs are identical. We may need to update the existing dataset - // alignment with this one, though. - if (ds != null && dseqs == null) - { - int opos = ds.findIndex(dsq); - SequenceI tseq = null; - if (opos != -1 && vseqpos != opos) - { - // remove from old position - ds.deleteSequence(dsq); - } - if (vseqpos < ds.getHeight()) - { - if (vseqpos != opos) - { - // save sequence at destination position - tseq = ds.getSequenceAt(vseqpos); - ds.replaceSequenceAt(vseqpos, dsq); - ds.addSequence(tseq); - } - } - else - { - ds.addSequence(dsq); - } - } - } - } - - /* - * TODO use AlignmentI here and in related methods - needs - * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment - */ - Hashtable datasetIds = null; - - IdentityHashMap dataset2Ids = null; - - private AlignmentI getDatasetFor(String datasetId) - { - if (datasetIds == null) - { - datasetIds = new Hashtable<>(); - return null; - } - if (datasetIds.containsKey(datasetId)) - { - return datasetIds.get(datasetId); - } - return null; - } - - private void addDatasetRef(String datasetId, AlignmentI dataset) - { - if (datasetIds == null) - { - datasetIds = new Hashtable<>(); - } - datasetIds.put(datasetId, dataset); - } - - /** - * make a new dataset ID for this jalview dataset alignment - * - * @param dataset - * @return - */ - private String getDatasetIdRef(AlignmentI dataset) - { - if (dataset.getDataset() != null) - { - warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment..."); - } - String datasetId = makeHashCode(dataset, null); - if (datasetId == null) - { - // make a new datasetId and record it - if (dataset2Ids == null) - { - dataset2Ids = new IdentityHashMap<>(); - } - else - { - datasetId = dataset2Ids.get(dataset); - } - if (datasetId == null) - { - datasetId = "ds" + dataset2Ids.size() + 1; - dataset2Ids.put(dataset, datasetId); - } - } - return datasetId; - } - - private void addDBRefs(SequenceI datasetSequence, Sequence sequence) - { - for (int d = 0; d < sequence.getDBRefCount(); d++) - { - DBRef dr = sequence.getDBRef(d); - jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry( - sequence.getDBRef(d).getSource(), - sequence.getDBRef(d).getVersion(), - sequence.getDBRef(d).getAccessionId()); - if (dr.getMapping() != null) - { - entry.setMap(addMapping(dr.getMapping())); - } - datasetSequence.addDBRef(entry); - } - } - - private jalview.datamodel.Mapping addMapping(Mapping m) - { - SequenceI dsto = null; - // Mapping m = dr.getMapping(); - int fr[] = new int[m.getMapListFromCount() * 2]; - Enumeration f = m.enumerateMapListFrom(); - for (int _i = 0; f.hasMoreElements(); _i += 2) - { - MapListFrom mf = (MapListFrom) f.nextElement(); - fr[_i] = mf.getStart(); - fr[_i + 1] = mf.getEnd(); - } - int fto[] = new int[m.getMapListToCount() * 2]; - f = m.enumerateMapListTo(); - for (int _i = 0; f.hasMoreElements(); _i += 2) - { - MapListTo mf = (MapListTo) f.nextElement(); - fto[_i] = mf.getStart(); - fto[_i + 1] = mf.getEnd(); - } - jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr, - fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit()); - if (m.getMappingChoice() != null) - { - MappingChoice mc = m.getMappingChoice(); - if (mc.getDseqFor() != null) - { - String dsfor = "" + mc.getDseqFor(); - if (seqRefIds.containsKey(dsfor)) - { - /** - * recover from hash - */ - jmap.setTo(seqRefIds.get(dsfor)); - } - else - { - frefedSequence.add(newMappingRef(dsfor, jmap)); - } - } - else - { - /** - * local sequence definition - */ - Sequence ms = mc.getSequence(); - SequenceI djs = null; - String sqid = ms.getDsseqid(); - if (sqid != null && sqid.length() > 0) - { - /* - * recover dataset sequence - */ - djs = seqRefIds.get(sqid); - } - else - { - System.err.println( - "Warning - making up dataset sequence id for DbRef sequence map reference"); - sqid = ((Object) ms).toString(); // make up a new hascode for - // undefined dataset sequence hash - // (unlikely to happen) - } - - if (djs == null) - { - /** - * make a new dataset sequence and add it to refIds hash - */ - djs = new jalview.datamodel.Sequence(ms.getName(), - ms.getSequence()); - djs.setStart(jmap.getMap().getToLowest()); - djs.setEnd(jmap.getMap().getToHighest()); - djs.setVamsasId(uniqueSetSuffix + sqid); - jmap.setTo(djs); - incompleteSeqs.put(sqid, djs); - seqRefIds.put(sqid, djs); - - } - jalview.bin.Cache.log.debug("about to recurse on addDBRefs."); - addDBRefs(djs, ms); - - } - } - return (jmap); - - } - - /** - * Provides a 'copy' of an alignment view (on action New View) by 'saving' the - * view as XML (but not to file), and then reloading it - * - * @param ap - * @return - */ - public AlignmentPanel copyAlignPanel(AlignmentPanel ap) - { - initSeqRefs(); - JalviewModel jm = saveState(ap, null, null, null); - - uniqueSetSuffix = ""; - jm.getJalviewModelSequence().getViewport(0).setId(null); - // we don't overwrite the view we just copied - - if (this.frefedSequence == null) - { - frefedSequence = new Vector<>(); - } - - viewportsAdded.clear(); - - AlignFrame af = loadFromObject(jm, null, false, null); - af.alignPanels.clear(); - af.closeMenuItem_actionPerformed(true); - - /* - * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0; - * i(); - } - if (seqsToIds == null) - { - seqsToIds = new IdentityHashMap<>(); - } - seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj); - seqsToIds.put((SequenceI) jvobj, id); - } - else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation) - { - String anid; - AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj; - annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann); - if (jvann.annotationId == null) - { - jvann.annotationId = anid; - } - if (!jvann.annotationId.equals(anid)) - { - // TODO verify that this is the correct behaviour - this.warn("Overriding Annotation ID for " + anid - + " from different id : " + jvann.annotationId); - jvann.annotationId = anid; - } - } - else if (jvobj instanceof String) - { - if (jvids2vobj == null) - { - jvids2vobj = new Hashtable(); - jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString()); - } - } - else - { - Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id); - } - } - } - - /** - * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview - * objects created from the project archive. If string is null (default for - * construction) then suffix will be set automatically. - * - * @param string - */ - public void setUniqueSetSuffix(String string) - { - uniqueSetSuffix = string; - - } - - /** - * uses skipList2 as the skipList for skipping views on sequence sets - * associated with keys in the skipList - * - * @param skipList2 - */ - public void setSkipList(Hashtable skipList2) - { - skipList = skipList2; - } - - /** - * Reads the jar entry of given name and returns its contents, or null if the - * entry is not found. - * - * @param jprovider - * @param jarEntryName - * @return - */ - protected String readJarEntry(jarInputStreamProvider jprovider, - String jarEntryName) - { - String result = null; - BufferedReader in = null; - - try - { - /* - * Reopen the jar input stream and traverse its entries to find a matching - * name - */ - JarInputStream jin = jprovider.getJarInputStream(); - JarEntry entry = null; - do - { - entry = jin.getNextJarEntry(); - } while (entry != null && !entry.getName().equals(jarEntryName)); - - if (entry != null) - { - StringBuilder out = new StringBuilder(256); - in = new BufferedReader(new InputStreamReader(jin, UTF_8)); - String data; - - while ((data = in.readLine()) != null) - { - out.append(data); - } - result = out.toString(); - } - else - { - warn("Couldn't find entry in Jalview Jar for " + jarEntryName); - } - } catch (Exception ex) - { - ex.printStackTrace(); - } finally - { - if (in != null) - { - try - { - in.close(); - } catch (IOException e) - { - // ignore - } - } - } - - return result; - } - - /** - * Returns an incrementing counter (0, 1, 2...) - * - * @return - */ - private synchronized int nextCounter() - { - return counter++; - } - - /** - * Populates an XML model of the feature colour scheme for one feature type - * - * @param featureType - * @param fcol - * @return - */ - protected static jalview.schemabinding.version2.Colour marshalColour( - String featureType, FeatureColourI fcol) - { - jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); - if (fcol.isSimpleColour()) - { - col.setRGB(Format.getHexString(fcol.getColour())); - } - else - { - col.setRGB(Format.getHexString(fcol.getMaxColour())); - col.setMin(fcol.getMin()); - col.setMax(fcol.getMax()); - col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour())); - col.setAutoScale(fcol.isAutoScaled()); - col.setThreshold(fcol.getThreshold()); - col.setColourByLabel(fcol.isColourByLabel()); - col.setThreshType(fcol.isAboveThreshold() ? ColourThreshTypeType.ABOVE - : (fcol.isBelowThreshold() ? ColourThreshTypeType.BELOW - : ColourThreshTypeType.NONE)); - if (fcol.isColourByAttribute()) - { - col.setAttributeName(fcol.getAttributeName()); - } - Color noColour = fcol.getNoColour(); - if (noColour == null) - { - col.setNoValueColour(NoValueColour.NONE); - } - else if (noColour == fcol.getMaxColour()) - { - col.setNoValueColour(NoValueColour.MAX); - } - else - { - col.setNoValueColour(NoValueColour.MIN); - } - } - col.setName(featureType); - return col; - } - - /** - * Populates an XML model of the feature filter(s) for one feature type - * - * @param firstMatcher - * the first (or only) match condition) - * @param filter - * remaining match conditions (if any) - * @param and - * if true, conditions are and-ed, else or-ed - */ - protected static MatcherSet marshalFilter(FeatureMatcherI firstMatcher, - Iterator filters, boolean and) - { - MatcherSet result = new MatcherSet(); - - if (filters.hasNext()) - { - /* - * compound matcher - */ - CompoundMatcher compound = new CompoundMatcher(); - compound.setAnd(and); - MatcherSet matcher1 = marshalFilter(firstMatcher, - Collections.emptyIterator(), and); - compound.addMatcherSet(matcher1); - FeatureMatcherI nextMatcher = filters.next(); - MatcherSet matcher2 = marshalFilter(nextMatcher, filters, and); - compound.addMatcherSet(matcher2); - result.setCompoundMatcher(compound); - } - else - { - /* - * single condition matcher - */ - MatchCondition matcherModel = new MatchCondition(); - matcherModel.setCondition( - firstMatcher.getMatcher().getCondition().getStableName()); - matcherModel.setValue(firstMatcher.getMatcher().getPattern()); - if (firstMatcher.isByAttribute()) - { - matcherModel.setBy(FeatureMatcherByType.BYATTRIBUTE); - matcherModel.setAttributeName(firstMatcher.getAttribute()); - } - else if (firstMatcher.isByLabel()) - { - matcherModel.setBy(FeatureMatcherByType.BYLABEL); - } - else if (firstMatcher.isByScore()) - { - matcherModel.setBy(FeatureMatcherByType.BYSCORE); - } - result.setMatchCondition(matcherModel); - } - - return result; - } - - /** - * Loads one XML model of a feature filter to a Jalview object - * - * @param featureType - * @param matcherSetModel - * @return - */ - protected static FeatureMatcherSetI unmarshalFilter( - String featureType, MatcherSet matcherSetModel) - { - FeatureMatcherSetI result = new FeatureMatcherSet(); - try - { - unmarshalFilterConditions(result, matcherSetModel, true); - } catch (IllegalStateException e) - { - // mixing AND and OR conditions perhaps - System.err.println( - String.format("Error reading filter conditions for '%s': %s", - featureType, e.getMessage())); - // return as much as was parsed up to the error - } - - return result; - } - - /** - * Adds feature match conditions to matcherSet as unmarshalled from XML - * (possibly recursively for compound conditions) - * - * @param matcherSet - * @param matcherSetModel - * @param and - * if true, multiple conditions are AND-ed, else they are OR-ed - * @throws IllegalStateException - * if AND and OR conditions are mixed - */ - protected static void unmarshalFilterConditions( - FeatureMatcherSetI matcherSet, MatcherSet matcherSetModel, - boolean and) - { - MatchCondition mc = matcherSetModel.getMatchCondition(); - if (mc != null) - { - /* - * single condition - */ - FeatureMatcherByType filterBy = mc.getBy(); - Condition cond = Condition.fromString(mc.getCondition()); - String pattern = mc.getValue(); - FeatureMatcherI matchCondition = null; - if (filterBy == FeatureMatcherByType.BYLABEL) - { - matchCondition = FeatureMatcher.byLabel(cond, pattern); - } - else if (filterBy == FeatureMatcherByType.BYSCORE) - { - matchCondition = FeatureMatcher.byScore(cond, pattern); - - } - else if (filterBy == FeatureMatcherByType.BYATTRIBUTE) - { - String[] attNames = mc.getAttributeName(); - matchCondition = FeatureMatcher.byAttribute(cond, pattern, - attNames); - } - - /* - * note this throws IllegalStateException if AND-ing to a - * previously OR-ed compound condition, or vice versa - */ - if (and) - { - matcherSet.and(matchCondition); - } - else - { - matcherSet.or(matchCondition); - } - } - else - { - /* - * compound condition - */ - MatcherSet[] matchers = matcherSetModel.getCompoundMatcher() - .getMatcherSet(); - boolean anded = matcherSetModel.getCompoundMatcher().getAnd(); - if (matchers.length == 2) - { - unmarshalFilterConditions(matcherSet, matchers[0], anded); - unmarshalFilterConditions(matcherSet, matchers[1], anded); - } - else - { - System.err.println("Malformed compound filter condition"); - } - } - } - - /** - * Loads one XML model of a feature colour to a Jalview object - * - * @param colourModel - * @return - */ - protected static FeatureColourI unmarshalColour( - jalview.schemabinding.version2.Colour colourModel) - { - FeatureColourI colour = null; - - if (colourModel.hasMax()) - { - Color mincol = null; - Color maxcol = null; - Color noValueColour = null; - - try - { - mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16)); - maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16)); - } catch (Exception e) - { - Cache.log.warn("Couldn't parse out graduated feature color.", e); - } - - NoValueColour noCol = colourModel.getNoValueColour(); - if (noCol == NoValueColour.MIN) - { - noValueColour = mincol; - } - else if (noCol == NoValueColour.MAX) - { - noValueColour = maxcol; - } - - colour = new FeatureColour(mincol, maxcol, noValueColour, - colourModel.getMin(), - colourModel.getMax()); - String[] attributes = colourModel.getAttributeName(); - if (attributes != null && attributes.length > 0) - { - colour.setAttributeName(attributes); - } - if (colourModel.hasAutoScale()) - { - colour.setAutoScaled(colourModel.getAutoScale()); - } - if (colourModel.hasColourByLabel()) - { - colour.setColourByLabel(colourModel.getColourByLabel()); - } - if (colourModel.hasThreshold()) - { - colour.setThreshold(colourModel.getThreshold()); - } - ColourThreshTypeType ttyp = colourModel.getThreshType(); - if (ttyp != null) - { - if (ttyp == ColourThreshTypeType.ABOVE) - { - colour.setAboveThreshold(true); - } - else if (ttyp == ColourThreshTypeType.BELOW) - { - colour.setBelowThreshold(true); - } - } - } - else - { - Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16)); - colour = new FeatureColour(color); - } - - return colour; - } -} diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java deleted file mode 100755 index 9548839..0000000 --- a/src/jalview/gui/Jalview2XML_V1.java +++ /dev/null @@ -1,513 +0,0 @@ -/* - * 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. - */ -package jalview.gui; - -import jalview.analysis.Conservation; -import jalview.binding.Annotation; -import jalview.binding.AnnotationElement; -import jalview.binding.Features; -import jalview.binding.JGroup; -import jalview.binding.JSeq; -import jalview.binding.JalviewModel; -import jalview.binding.JalviewModelSequence; -import jalview.binding.Pdbids; -import jalview.binding.Sequence; -import jalview.binding.SequenceSet; -import jalview.binding.Setting; -import jalview.binding.Tree; -import jalview.binding.UserColours; -import jalview.binding.Viewport; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceFeature; -import jalview.io.FileFormat; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeProperty; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; -import jalview.util.jarInputStreamProvider; -import jalview.viewmodel.seqfeatures.FeatureRendererSettings; - -import java.io.InputStreamReader; -import java.io.Reader; -import java.net.UnknownHostException; -import java.util.Hashtable; -import java.util.Vector; -import java.util.jar.JarEntry; -import java.util.jar.JarInputStream; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class Jalview2XML_V1 -{ - boolean raiseGUI = true; - - public Jalview2XML_V1() - { - - }; - - public Jalview2XML_V1(boolean raiseGUI) - { - this.raiseGUI = raiseGUI; - }; - - jalview.schemes.UserColourScheme GetUserColourScheme( - JalviewModelSequence jms, String id) - { - UserColours[] uc = jms.getUserColours(); - UserColours colours = null; - - for (int i = 0; i < uc.length; i++) - { - if (uc[i].getId().equals(id)) - { - colours = uc[i]; - - break; - } - } - - int csize = colours.getUserColourScheme().getColourCount(); - java.awt.Color[] newColours = new java.awt.Color[csize]; - - for (int i = 0; i < csize; i++) - { - newColours[i] = new java.awt.Color(Integer.parseInt( - colours.getUserColourScheme().getColour(i).getRGB(), 16)); - } - - return new jalview.schemes.UserColourScheme(newColours); - } - - /** - * DOCUMENT ME! - * - * @param file - * DOCUMENT ME! - */ - public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider) - { - final String file = jprovider.getFilename(); - jalview.gui.AlignFrame af = null; - - try - { - JarInputStream jin = null; - JarEntry jarentry = null; - int entryCount = 1; - - do - { - jin = jprovider.getJarInputStream(); - - for (int i = 0; i < entryCount; i++) - { - jarentry = jin.getNextJarEntry(); - } - - if (jarentry != null) - { - entryCount++; - if (jarentry.getName().endsWith(".xml")) - { - Reader in = new InputStreamReader(jin, "UTF-8"); - JalviewModel object = new JalviewModel(); - - object = object.unmarshal(in); - - af = LoadFromObject(object, file); - } - } - jin.close(); - } while (jarentry != null); - } catch (final UnknownHostException ex) - { - ex.printStackTrace(); - if (raiseGUI) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - - System.err.println( - "Couldn't locate Jalview XML file : " + ex + "\n"); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.couldnt_locate", - new String[] - { file }), - MessageManager.getString("label.url_not_found"), - JvOptionPane.WARNING_MESSAGE); - } - }); - } - ; - } catch (Exception ex) - { - System.err.println("Exception whilst loading jalview XML file : "); - ex.printStackTrace(); - if (raiseGUI) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.error_loading_file_params", new String[] - { file }), - MessageManager - .getString("label.error_loading_jalview_file"), - JvOptionPane.WARNING_MESSAGE); - } - }); - } - } - - return af; - } - - AlignFrame LoadFromObject(JalviewModel object, String file) - { - Vector seqids = new Vector(); - SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); - Sequence[] vamsasSeq = vamsasSet.getSequence(); - - JalviewModelSequence jms = object.getJalviewModelSequence(); - - // //////////////////////////////// - // LOAD SEQUENCES - jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length]; - JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); - for (int i = 0; i < vamsasSeq.length; i++) - { - jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), - vamsasSeq[i].getSequence()); - jseqs[i].setStart(JSEQ[i].getStart()); - jseqs[i].setEnd(JSEQ[i].getEnd()); - seqids.add(jseqs[i]); - } - - // /SequenceFeatures are added to the DatasetSequence, - // so we must create the dataset before loading features - // /////////////////////////////// - jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs); - al.setDataset(null); - // /////////////////////////////// - - for (int i = 0; i < vamsasSeq.length; i++) - { - if (JSEQ[i].getFeaturesCount() > 0) - { - Features[] features = JSEQ[i].getFeatures(); - for (int f = 0; f < features.length; f++) - { - SequenceFeature sf = new SequenceFeature(features[f].getType(), - features[f].getDescription(), features[f].getBegin(), - features[f].getEnd(), null); - sf.setStatus(features[f].getStatus()); - al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); - } - } - if (JSEQ[i].getPdbidsCount() > 0) - { - Pdbids[] ids = JSEQ[i].getPdbids(); - for (int p = 0; p < ids.length; p++) - { - jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); - entry.setId(ids[p].getId()); - if (ids[p].getType() != null) - { - if (ids[p].getType().equalsIgnoreCase("PDB")) - { - entry.setType(PDBEntry.Type.PDB); - } - else - { - entry.setType(PDBEntry.Type.FILE); - } - } - al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) - .registerPDBEntry(entry); - } - - } - } - - // /////////////////////////////// - // //////////////////////////////// - // LOAD ANNOTATIONS - if (vamsasSet.getAnnotation() != null) - { - Annotation[] an = vamsasSet.getAnnotation(); - - for (int i = 0; i < an.length; i++) - { - AnnotationElement[] ae = an[i].getAnnotationElement(); - jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al - .getWidth()]; - - for (int aa = 0; aa < ae.length; aa++) - { - anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation( - ae[aa].getDisplayCharacter(), ae[aa].getDescription(), - ae[aa].getSecondaryStructure().charAt(0), - ae[aa].getValue()); - } - - jalview.datamodel.AlignmentAnnotation jaa = null; - - if (an[i].getGraph()) - { - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot, 0, 0, - jalview.datamodel.AlignmentAnnotation.BAR_GRAPH); - } - else - { - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot); - } - - al.addAnnotation(jaa); - } - } - - // /////////////////////////////// - // LOAD VIEWPORT - Viewport[] views = jms.getViewport(); - Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER - - AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight()); - - af.setFileName(file, FileFormat.Jalview); - - for (int i = 0; i < JSEQ.length; i++) - { - af.viewport.setSequenceColour( - af.viewport.getAlignment().getSequenceAt(i), - new java.awt.Color(JSEQ[i].getColour())); - } - - // af.changeColour() ); - // /////////////////////// - // LOAD GROUPS - if (jms.getJGroupCount() > 0) - { - JGroup[] groups = jms.getJGroup(); - - for (int i = 0; i < groups.length; i++) - { - ColourSchemeI cs = null; - - if (groups[i].getColour() != null) - { - if (groups[i].getColour().startsWith("ucs")) - { - cs = GetUserColourScheme(jms, groups[i].getColour()); - } - else - { - cs = ColourSchemeProperty.getColourScheme(al, - groups[i].getColour()); - } - } - int pidThreshold = groups[i].getPidThreshold(); - - Vector seqs = new Vector(); - int[] ids = groups[i].getSeq(); - - for (int s = 0; s < ids.length; s++) - { - seqs.addElement(seqids.elementAt(ids[s])); - } - - jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup( - seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(), - groups[i].getDisplayText(), groups[i].getColourText(), - groups[i].getStart(), groups[i].getEnd()); - sg.getGroupColourScheme().setThreshold(pidThreshold, true); - - sg.setOutlineColour( - new java.awt.Color(groups[i].getOutlineColour())); - - if (groups[i].getConsThreshold() != 0) - { - Conservation c = new Conservation("All", sg.getSequences(null), 0, - sg.getWidth() - 1); - c.calculate(); - c.verdict(false, 25); - sg.cs.setConservation(c); - } - - al.addGroup(sg); - } - } - - af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), - view.getHeight()); - af.viewport.getRanges().setStartRes(view.getStartRes()); - // startSeq set in af.alignPanel.updateLayout below - af.viewport.setShowAnnotation(view.getShowAnnotation()); - af.viewport.setAbovePIDThreshold(view.getPidSelected()); - af.viewport.setColourText(view.getShowColourText()); - af.viewport.setConservationSelected(view.getConservationSelected()); - af.viewport.setShowJVSuffix(view.getShowFullId()); - af.viewport.setFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), view.getFontSize()), true); - - af.viewport.setRenderGaps(view.getRenderGaps()); - af.viewport.setWrapAlignment(view.getWrapAlignment()); - - af.viewport.setShowAnnotation(view.isShowAnnotation()); - af.viewport.setShowBoxes(view.getShowBoxes()); - af.viewport.setShowText(view.getShowText()); - - ColourSchemeI cs = null; - - if (view.getBgColour() != null) - { - if (view.getBgColour().startsWith("ucs")) - { - cs = GetUserColourScheme(jms, view.getBgColour()); - } - else - { - cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour()); - } - - // if (cs != null) - // { - // cs.setThreshold(view.getPidThreshold(), true); - // cs.setConsensus(af.viewport.getSequenceConsensusHash()); - // } - } - - af.viewport.getResidueShading().setThreshold(view.getPidThreshold(), - true); - af.viewport.getResidueShading() - .setConsensus(af.viewport.getSequenceConsensusHash()); - af.viewport.setColourAppliesToAllGroups(false); - af.alignPanel.updateLayout(); - af.changeColour(cs); - if (view.getConservationSelected() && cs != null) - { - af.viewport.getResidueShading() - .setConservationInc(view.getConsThreshold()); - } - - af.viewport.setColourAppliesToAllGroups(true); - af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures()); - - if (jms.getFeatureSettings() != null) - { - Hashtable featuresDisplayed = new Hashtable(); - Hashtable featureColours = new Hashtable(); - String[] renderOrder = new String[jms.getFeatureSettings() - .getSettingCount()]; - for (int fs = 0; fs < jms.getFeatureSettings() - .getSettingCount(); fs++) - { - Setting setting = jms.getFeatureSettings().getSetting(fs); - - featureColours.put(setting.getType(), - new java.awt.Color(setting.getColour())); - - renderOrder[fs] = setting.getType(); - - if (setting.getDisplay()) - { - featuresDisplayed.put(setting.getType(), - new Integer(setting.getColour())); - } - } - FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, - new Hashtable(), featureColours, 1.0f, null); - af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(frs); - } - - af.setMenusFromViewport(af.viewport); - - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), - view.getHeight()); - - // LOAD TREES - // ///////////////////////////////////// - if (jms.getTreeCount() > 0) - { - try - { - for (int t = 0; t < jms.getTreeCount(); t++) - { - - Tree tree = jms.getTree(t); - - TreePanel tp = af.showNewickTree( - new jalview.io.NewickFile(tree.getNewick()), - tree.getTitle(), tree.getWidth(), tree.getHeight(), - tree.getXpos(), tree.getYpos()); - - tp.fitToWindow.setState(tree.getFitToWindow()); - tp.fitToWindow_actionPerformed(null); - - if (tree.getFontName() != null) - { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), - tree.getFontStyle(), tree.getFontSize())); - } - else - { - tp.setTreeFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), tree.getFontSize())); - } - - tp.showPlaceholders(tree.getMarkUnlinked()); - tp.showBootstrap(tree.getShowBootstrap()); - tp.showDistances(tree.getShowDistances()); - - tp.getTreeCanvas().setThreshold(tree.getThreshold()); - - if (tree.getCurrentTree()) - { - af.viewport.setCurrentTree(tp.getTree()); - } - } - - } catch (Exception ex) - { - ex.printStackTrace(); - } - - } - - return af; - } -} diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index d81a6b0..adf4447 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -33,6 +33,7 @@ import jalview.io.vamsas.Datasetsequence; import jalview.io.vamsas.DatastoreItem; import jalview.io.vamsas.DatastoreRegistry; import jalview.io.vamsas.Rangetype; +import jalview.project.Jalview2XML; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -1311,7 +1312,8 @@ public class VamsasAppDatastore // client data is shared over all app clients try { - jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML(); + // jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML(); + Jalview2XML fromxml = new Jalview2XML(); fromxml.attemptversion1parse = false; fromxml.setUniqueSetSuffix(""); fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString @@ -1360,7 +1362,7 @@ public class VamsasAppDatastore // user data overrides data shared over all app clients ? try { - jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML(); + Jalview2XML fromxml = new Jalview2XML(); fromxml.attemptversion1parse = false; fromxml.setUniqueSetSuffix(""); fromxml.setSkipList(skipList); @@ -1531,7 +1533,7 @@ public class VamsasAppDatastore { try { - jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML(); + Jalview2XML jxml = new Jalview2XML(); jxml.setObjectMappingTables(mapKeysToString(vobj2jv), mapValuesToString(jv2vobj)); jxml.setSkipList(skipList); diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index 290c4a4..028378f 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -245,16 +245,7 @@ public class GDesktop extends JFrame @Override public void actionPerformed(ActionEvent e) { - saveState_actionPerformed(true); - } - }); - JMenuItem saveAsJaxb = new JMenuItem("Save Project as JAXB"); - saveAsJaxb.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - saveState_actionPerformed(false); + saveState_actionPerformed(); } }); loadState.setText(MessageManager.getString("action.load_project")); @@ -263,16 +254,7 @@ public class GDesktop extends JFrame @Override public void actionPerformed(ActionEvent e) { - loadState_actionPerformed(true); - } - }); - JMenuItem loadAsJaxb = new JMenuItem("Load Project as JAXB"); - loadAsJaxb.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - loadState_actionPerformed(false); + loadState_actionPerformed(); } }); inputMenu.setText(MessageManager.getString("label.input_alignment")); @@ -442,9 +424,7 @@ public class GDesktop extends JFrame FileMenu.add(inputSequence); FileMenu.addSeparator(); FileMenu.add(saveState); - FileMenu.add(saveAsJaxb); FileMenu.add(loadState); - FileMenu.add(loadAsJaxb); FileMenu.addSeparator(); FileMenu.add(quit); HelpMenu.add(aboutMenuItem); @@ -586,16 +566,6 @@ public class GDesktop extends JFrame * @param e * DOCUMENT ME! */ - public void SaveState_actionPerformed(ActionEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ protected void preferences_actionPerformed(ActionEvent e) { } @@ -606,17 +576,11 @@ public class GDesktop extends JFrame * @param e * DOCUMENT ME! */ - public void saveState_actionPerformed(boolean asCastor) + public void saveState_actionPerformed() { } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - public void loadState_actionPerformed(boolean asCastor) + public void loadState_actionPerformed() { } diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index e546789..b153d9f 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -49,7 +49,6 @@ import jalview.gui.AppVarna; import jalview.gui.ChimeraViewFrame; import jalview.gui.Desktop; import jalview.gui.FeatureRenderer; -import jalview.gui.Jalview2XML_V1; import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; import jalview.gui.PaintRefresher; @@ -2643,16 +2642,7 @@ public class Jalview2XML ex.printStackTrace(System.err); if (attemptversion1parse) { - // Is Version 1 Jar file? - try - { - af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider); - } catch (Exception ex2) - { - System.err.println("Exception whilst loading as jalviewXMLV1:"); - ex2.printStackTrace(); - af = null; - } + // used to attempt to parse as V1 castor-generated xml } if (Desktop.instance != null) { diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr deleted file mode 100644 index e1100a8..0000000 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ /dev/null @@ -1,53 +0,0 @@ -#Thu Dec 14 09:10:14 GMT 2017 -jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor -jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor -jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor -jalview.schemabinding.version2.CalcIdParam=jalview.schemabinding.version2.descriptors.CalcIdParamDescriptor -jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor -jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor -jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor -jalview.schemabinding.version2.OtherData=jalview.schemabinding.version2.descriptors.OtherDataDescriptor -jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor -jalview.schemabinding.version2.AlcodonFrame=jalview.schemabinding.version2.descriptors.AlcodonFrameDescriptor -jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor -jalview.schemabinding.version2.FeatureMatcherSet=jalview.schemabinding.version2.descriptors.FeatureMatcherSetDescriptor -jalview.schemabinding.version2.SecondaryStructure=jalview.schemabinding.version2.descriptors.SecondaryStructureDescriptor -jalview.schemabinding.version2.MatchCondition=jalview.schemabinding.version2.descriptors.MatchConditionDescriptor -jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor -jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor -jalview.schemabinding.version2.RnaViewer=jalview.schemabinding.version2.descriptors.RnaViewerDescriptor -jalview.schemabinding.version2.MapListType=jalview.schemabinding.version2.descriptors.MapListTypeDescriptor -jalview.schemabinding.version2.Property=jalview.schemabinding.version2.descriptors.PropertyDescriptor -jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor -jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor -jalview.schemabinding.version2.AlcodMap=jalview.schemabinding.version2.descriptors.AlcodMapDescriptor -jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor -jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor -jalview.schemabinding.version2.MatcherSet=jalview.schemabinding.version2.descriptors.MatcherSetDescriptor -jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor -jalview.schemabinding.version2.WebServiceParameterSet=jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor -jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor -jalview.schemabinding.version2.Filter=jalview.schemabinding.version2.descriptors.FilterDescriptor -jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor -jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor -jalview.schemabinding.version2.AnnotationColourScheme=jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor -jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor -jalview.schemabinding.version2.CompoundMatcher=jalview.schemabinding.version2.descriptors.CompoundMatcherDescriptor -jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor -jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor -jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor -jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor -jalview.schemabinding.version2.UserColours=jalview.schemabinding.version2.descriptors.UserColoursDescriptor -jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor -jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor -jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descriptors.MapListFromDescriptor -jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor -jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor -jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor -jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor -jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor -jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor -jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor -jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor -jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor -jalview.schemabinding.version2.FeatureMatcher=jalview.schemabinding.version2.descriptors.FeatureMatcherDescriptor diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java deleted file mode 100644 index e2522a1..0000000 --- a/src/jalview/schemabinding/version2/AlcodMap.java +++ /dev/null @@ -1,192 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class AlcodMap. - * - * @version $Revision$ $Date$ - */ -public class AlcodMap implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * internal jalview id for the dnasq for this mapping. - * - */ - private java.lang.String _dnasq; - - /** - * a Mapping entry and an associated protein sequence - * - */ - private jalview.schemabinding.version2.Mapping _mapping; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodMap() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'dnasq'. The field 'dnasq' has the following - * description: internal jalview id for the dnasq for this mapping. - * - * - * @return the value of field 'Dnasq'. - */ - public java.lang.String getDnasq() - { - return this._dnasq; - } - - /** - * Returns the value of field 'mapping'. The field 'mapping' has the following - * description: a Mapping entry and an associated protein sequence - * - * - * @return the value of field 'Mapping'. - */ - public jalview.schemabinding.version2.Mapping getMapping() - { - return this._mapping; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'dnasq'. The field 'dnasq' has the following - * description: internal jalview id for the dnasq for this mapping. - * - * - * @param dnasq - * the value of field 'dnasq'. - */ - public void setDnasq(final java.lang.String dnasq) - { - this._dnasq = dnasq; - } - - /** - * Sets the value of field 'mapping'. The field 'mapping' has the following - * description: a Mapping entry and an associated protein sequence - * - * - * @param mapping - * the value of field 'mapping'. - */ - public void setMapping( - final jalview.schemabinding.version2.Mapping mapping) - { - this._mapping = mapping; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.AlcodMap - */ - public static jalview.schemabinding.version2.AlcodMap unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AlcodMap) Unmarshaller - .unmarshal(jalview.schemabinding.version2.AlcodMap.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java deleted file mode 100644 index 3bd1cbb..0000000 --- a/src/jalview/schemabinding/version2/Alcodon.java +++ /dev/null @@ -1,275 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Alcodon. - * - * @version $Revision$ $Date$ - */ -public class Alcodon implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _pos1. - */ - private long _pos1; - - /** - * keeps track of state for field: _pos1 - */ - private boolean _has_pos1; - - /** - * Field _pos2. - */ - private long _pos2; - - /** - * keeps track of state for field: _pos2 - */ - private boolean _has_pos2; - - /** - * Field _pos3. - */ - private long _pos3; - - /** - * keeps track of state for field: _pos3 - */ - private boolean _has_pos3; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Alcodon() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deletePos1() - { - this._has_pos1 = false; - } - - /** - */ - public void deletePos2() - { - this._has_pos2 = false; - } - - /** - */ - public void deletePos3() - { - this._has_pos3 = false; - } - - /** - * Returns the value of field 'pos1'. - * - * @return the value of field 'Pos1'. - */ - public long getPos1() - { - return this._pos1; - } - - /** - * Returns the value of field 'pos2'. - * - * @return the value of field 'Pos2'. - */ - public long getPos2() - { - return this._pos2; - } - - /** - * Returns the value of field 'pos3'. - * - * @return the value of field 'Pos3'. - */ - public long getPos3() - { - return this._pos3; - } - - /** - * Method hasPos1. - * - * @return true if at least one Pos1 has been added - */ - public boolean hasPos1() - { - return this._has_pos1; - } - - /** - * Method hasPos2. - * - * @return true if at least one Pos2 has been added - */ - public boolean hasPos2() - { - return this._has_pos2; - } - - /** - * Method hasPos3. - * - * @return true if at least one Pos3 has been added - */ - public boolean hasPos3() - { - return this._has_pos3; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'pos1'. - * - * @param pos1 - * the value of field 'pos1'. - */ - public void setPos1(final long pos1) - { - this._pos1 = pos1; - this._has_pos1 = true; - } - - /** - * Sets the value of field 'pos2'. - * - * @param pos2 - * the value of field 'pos2'. - */ - public void setPos2(final long pos2) - { - this._pos2 = pos2; - this._has_pos2 = true; - } - - /** - * Sets the value of field 'pos3'. - * - * @param pos3 - * the value of field 'pos3'. - */ - public void setPos3(final long pos3) - { - this._pos3 = pos3; - this._has_pos3 = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Alcodo - */ - public static jalview.schemabinding.version2.Alcodon unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Alcodon.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java deleted file mode 100644 index 218e07e..0000000 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ /dev/null @@ -1,466 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class AlcodonFrame. - * - * @version $Revision$ $Date$ - */ -public class AlcodonFrame implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _alcodonList. - */ - private java.util.Vector _alcodonList; - - /** - * Field _alcodMapList. - */ - private java.util.Vector _alcodMapList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodonFrame() - { - super(); - this._alcodonList = new java.util.Vector(); - this._alcodMapList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - this._alcodMapList.addElement(vAlcodMap); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodMap(final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - this._alcodMapList.add(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonList.addElement(vAlcodon); - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodon(final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonList.add(index, vAlcodon); - } - - /** - * Method enumerateAlcodMap. - * - * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap - * elements - */ - public java.util.Enumeration enumerateAlcodMap() - { - return this._alcodMapList.elements(); - } - - /** - * Method enumerateAlcodon. - * - * @return an Enumeration over all jalview.schemabinding.version2.Alcodon - * elements - */ - public java.util.Enumeration enumerateAlcodon() - { - return this._alcodonList.elements(); - } - - /** - * Method getAlcodMap. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.AlcodMap at the - * given index - */ - public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) - { - throw new IndexOutOfBoundsException("getAlcodMap: Index value '" - + index + "' not in range [0.." - + (this._alcodMapList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AlcodMap) _alcodMapList - .get(index); - } - - /** - * Method getAlcodMap.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.AlcodMap[] getAlcodMap() - { - jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; - return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList - .toArray(array); - } - - /** - * Method getAlcodMapCount. - * - * @return the size of this collection - */ - public int getAlcodMapCount() - { - return this._alcodMapList.size(); - } - - /** - * Method getAlcodon. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Alcodon at the - * given index - */ - public jalview.schemabinding.version2.Alcodon getAlcodon(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) - { - throw new IndexOutOfBoundsException("getAlcodon: Index value '" - + index + "' not in range [0.." - + (this._alcodonList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); - } - - /** - * Method getAlcodon.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Alcodon[] getAlcodon() - { - jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; - return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList - .toArray(array); - } - - /** - * Method getAlcodonCount. - * - * @return the size of this collection - */ - public int getAlcodonCount() - { - return this._alcodonList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method removeAlcodMap. - * - * @param vAlcodMap - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - { - boolean removed = _alcodMapList.remove(vAlcodMap); - return removed; - } - - /** - * Method removeAlcodMapAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( - final int index) - { - java.lang.Object obj = this._alcodMapList.remove(index); - return (jalview.schemabinding.version2.AlcodMap) obj; - } - - /** - * Method removeAlcodon. - * - * @param vAlcodon - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) - { - boolean removed = _alcodonList.remove(vAlcodon); - return removed; - } - - /** - * Method removeAlcodonAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Alcodon removeAlcodonAt( - final int index) - { - java.lang.Object obj = this._alcodonList.remove(index); - return (jalview.schemabinding.version2.Alcodon) obj; - } - - /** - */ - public void removeAllAlcodMap() - { - this._alcodMapList.clear(); - } - - /** - */ - public void removeAllAlcodon() - { - this._alcodonList.clear(); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlcodMap(final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) - { - throw new IndexOutOfBoundsException("setAlcodMap: Index value '" - + index + "' not in range [0.." - + (this._alcodMapList.size() - 1) + "]"); - } - - this._alcodMapList.set(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodMapArray - */ - public void setAlcodMap( - final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) - { - // -- copy array - _alcodMapList.clear(); - - for (int i = 0; i < vAlcodMapArray.length; i++) - { - this._alcodMapList.add(vAlcodMapArray[i]); - } - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlcodon(final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) - { - throw new IndexOutOfBoundsException("setAlcodon: Index value '" - + index + "' not in range [0.." - + (this._alcodonList.size() - 1) + "]"); - } - - this._alcodonList.set(index, vAlcodon); - } - - /** - * - * - * @param vAlcodonArray - */ - public void setAlcodon( - final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) - { - // -- copy array - _alcodonList.clear(); - - for (int i = 0; i < vAlcodonArray.length; i++) - { - this._alcodonList.add(vAlcodonArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.AlcodonFrame - */ - public static jalview.schemabinding.version2.AlcodonFrame unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller - .unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java deleted file mode 100644 index 2fead37..0000000 --- a/src/jalview/schemabinding/version2/Annotation.java +++ /dev/null @@ -1,1396 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Annotation. - * - * @version $Revision$ $Date$ - */ -public class Annotation implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _graph. - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _graphType. - */ - private int _graphType; - - /** - * keeps track of state for field: _graphType - */ - private boolean _has_graphType; - - /** - * Field _sequenceRef. - */ - private java.lang.String _sequenceRef; - - /** - * Field _groupRef. - */ - private java.lang.String _groupRef; - - /** - * Field _graphColour. - */ - private int _graphColour; - - /** - * keeps track of state for field: _graphColour - */ - private boolean _has_graphColour; - - /** - * Field _graphGroup. - */ - private int _graphGroup; - - /** - * keeps track of state for field: _graphGroup - */ - private boolean _has_graphGroup; - - /** - * height in pixels for the graph if this is a graph-type annotation. - */ - private int _graphHeight; - - /** - * keeps track of state for field: _graphHeight - */ - private boolean _has_graphHeight; - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _scoreOnly. - */ - private boolean _scoreOnly = false; - - /** - * keeps track of state for field: _scoreOnly - */ - private boolean _has_scoreOnly; - - /** - * Field _score. - */ - private double _score; - - /** - * keeps track of state for field: _score - */ - private boolean _has_score; - - /** - * Field _visible. - */ - private boolean _visible; - - /** - * keeps track of state for field: _visible - */ - private boolean _has_visible; - - /** - * Field _centreColLabels. - */ - private boolean _centreColLabels; - - /** - * keeps track of state for field: _centreColLabels - */ - private boolean _has_centreColLabels; - - /** - * Field _scaleColLabels. - */ - private boolean _scaleColLabels; - - /** - * keeps track of state for field: _scaleColLabels - */ - private boolean _has_scaleColLabels; - - /** - * Field _showAllColLabels. - */ - private boolean _showAllColLabels; - - /** - * keeps track of state for field: _showAllColLabels - */ - private boolean _has_showAllColLabels; - - /** - * is an autocalculated annotation row - */ - private boolean _autoCalculated = false; - - /** - * keeps track of state for field: _autoCalculated - */ - private boolean _has_autoCalculated; - - /** - * is to be shown below the alignment - introduced in Jalview 2.8 for - * visualizing T-COFFEE alignment scores - */ - private boolean _belowAlignment = true; - - /** - * keeps track of state for field: _belowAlignment - */ - private boolean _has_belowAlignment; - - /** - * Optional string identifier used to group sets of annotation produced by a - * particular calculation. Values are opaque strings but have semantic meaning - * to Jalview's renderer, data importer and calculation system. - */ - private java.lang.String _calcId; - - /** - * Field _annotationElementList. - */ - private java.util.Vector _annotationElementList; - - /** - * Field _label. - */ - private java.lang.String _label; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _thresholdLine. - */ - private jalview.schemabinding.version2.ThresholdLine _thresholdLine; - - /** - * Field _propertyList. - */ - private java.util.Vector _propertyList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Annotation() - { - super(); - this._annotationElementList = new java.util.Vector(); - this._propertyList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotationElement( - final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - this._annotationElementList.addElement(vAnnotationElement); - } - - /** - * - * - * @param index - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotationElement( - final int index, - final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - this._annotationElementList.add(index, vAnnotationElement); - } - - /** - * - * - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addProperty( - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.addElement(vProperty); - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addProperty(final int index, - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.add(index, vProperty); - } - - /** - */ - public void deleteAutoCalculated() - { - this._has_autoCalculated = false; - } - - /** - */ - public void deleteBelowAlignment() - { - this._has_belowAlignment = false; - } - - /** - */ - public void deleteCentreColLabels() - { - this._has_centreColLabels = false; - } - - /** - */ - public void deleteGraph() - { - this._has_graph = false; - } - - /** - */ - public void deleteGraphColour() - { - this._has_graphColour = false; - } - - /** - */ - public void deleteGraphGroup() - { - this._has_graphGroup = false; - } - - /** - */ - public void deleteGraphHeight() - { - this._has_graphHeight = false; - } - - /** - */ - public void deleteGraphType() - { - this._has_graphType = false; - } - - /** - */ - public void deleteScaleColLabels() - { - this._has_scaleColLabels = false; - } - - /** - */ - public void deleteScore() - { - this._has_score = false; - } - - /** - */ - public void deleteScoreOnly() - { - this._has_scoreOnly = false; - } - - /** - */ - public void deleteShowAllColLabels() - { - this._has_showAllColLabels = false; - } - - /** - */ - public void deleteVisible() - { - this._has_visible = false; - } - - /** - * Method enumerateAnnotationElement. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.AnnotationElement elements - */ - public java.util.Enumeration enumerateAnnotationElement() - { - return this._annotationElementList.elements(); - } - - /** - * Method enumerateProperty. - * - * @return an Enumeration over all jalview.schemabinding.version2.Property - * elements - */ - public java.util.Enumeration enumerateProperty() - { - return this._propertyList.elements(); - } - - /** - * Method getAnnotationElement. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.AnnotationElement - * at the given index - */ - public jalview.schemabinding.version2.AnnotationElement getAnnotationElement( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationElementList.size()) - { - throw new IndexOutOfBoundsException( - "getAnnotationElement: Index value '" + index - + "' not in range [0.." - + (this._annotationElementList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList - .get(index); - } - - /** - * Method getAnnotationElement.Returns the contents of the collection in an - * Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() - { - jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; - return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList - .toArray(array); - } - - /** - * Method getAnnotationElementCount. - * - * @return the size of this collection - */ - public int getAnnotationElementCount() - { - return this._annotationElementList.size(); - } - - /** - * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has - * the following description: is an autocalculated annotation row - * - * @return the value of field 'AutoCalculated'. - */ - public boolean getAutoCalculated() - { - return this._autoCalculated; - } - - /** - * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has - * the following description: is to be shown below the alignment - introduced - * in Jalview 2.8 for visualizing T-COFFEE alignment scores - * - * @return the value of field 'BelowAlignment'. - */ - public boolean getBelowAlignment() - { - return this._belowAlignment; - } - - /** - * Returns the value of field 'calcId'. The field 'calcId' has the following - * description: Optional string identifier used to group sets of annotation - * produced by a particular calculation. Values are opaque strings but have - * semantic meaning to Jalview's renderer, data importer and calculation - * system. - * - * @return the value of field 'CalcId'. - */ - public java.lang.String getCalcId() - { - return this._calcId; - } - - /** - * Returns the value of field 'centreColLabels'. - * - * @return the value of field 'CentreColLabels'. - */ - public boolean getCentreColLabels() - { - return this._centreColLabels; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean getGraph() - { - return this._graph; - } - - /** - * Returns the value of field 'graphColour'. - * - * @return the value of field 'GraphColour'. - */ - public int getGraphColour() - { - return this._graphColour; - } - - /** - * Returns the value of field 'graphGroup'. - * - * @return the value of field 'GraphGroup'. - */ - public int getGraphGroup() - { - return this._graphGroup; - } - - /** - * Returns the value of field 'graphHeight'. The field 'graphHeight' has the - * following description: height in pixels for the graph if this is a - * graph-type annotation. - * - * @return the value of field 'GraphHeight'. - */ - public int getGraphHeight() - { - return this._graphHeight; - } - - /** - * Returns the value of field 'graphType'. - * - * @return the value of field 'GraphType'. - */ - public int getGraphType() - { - return this._graphType; - } - - /** - * Returns the value of field 'groupRef'. - * - * @return the value of field 'GroupRef'. - */ - public java.lang.String getGroupRef() - { - return this._groupRef; - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel() - { - return this._label; - } - - /** - * Method getProperty. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Property at the - * given index - */ - public jalview.schemabinding.version2.Property getProperty(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException("getProperty: Index value '" - + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Property) _propertyList - .get(index); - } - - /** - * Method getProperty.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Property[] getProperty() - { - jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0]; - return (jalview.schemabinding.version2.Property[]) this._propertyList - .toArray(array); - } - - /** - * Method getPropertyCount. - * - * @return the size of this collection - */ - public int getPropertyCount() - { - return this._propertyList.size(); - } - - /** - * Returns the value of field 'scaleColLabels'. - * - * @return the value of field 'ScaleColLabels'. - */ - public boolean getScaleColLabels() - { - return this._scaleColLabels; - } - - /** - * Returns the value of field 'score'. - * - * @return the value of field 'Score'. - */ - public double getScore() - { - return this._score; - } - - /** - * Returns the value of field 'scoreOnly'. - * - * @return the value of field 'ScoreOnly'. - */ - public boolean getScoreOnly() - { - return this._scoreOnly; - } - - /** - * Returns the value of field 'sequenceRef'. - * - * @return the value of field 'SequenceRef'. - */ - public java.lang.String getSequenceRef() - { - return this._sequenceRef; - } - - /** - * Returns the value of field 'showAllColLabels'. - * - * @return the value of field 'ShowAllColLabels'. - */ - public boolean getShowAllColLabels() - { - return this._showAllColLabels; - } - - /** - * Returns the value of field 'thresholdLine'. - * - * @return the value of field 'ThresholdLine'. - */ - public jalview.schemabinding.version2.ThresholdLine getThresholdLine() - { - return this._thresholdLine; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean getVisible() - { - return this._visible; - } - - /** - * Method hasAutoCalculated. - * - * @return true if at least one AutoCalculated has been added - */ - public boolean hasAutoCalculated() - { - return this._has_autoCalculated; - } - - /** - * Method hasBelowAlignment. - * - * @return true if at least one BelowAlignment has been added - */ - public boolean hasBelowAlignment() - { - return this._has_belowAlignment; - } - - /** - * Method hasCentreColLabels. - * - * @return true if at least one CentreColLabels has been added - */ - public boolean hasCentreColLabels() - { - return this._has_centreColLabels; - } - - /** - * Method hasGraph. - * - * @return true if at least one Graph has been added - */ - public boolean hasGraph() - { - return this._has_graph; - } - - /** - * Method hasGraphColour. - * - * @return true if at least one GraphColour has been added - */ - public boolean hasGraphColour() - { - return this._has_graphColour; - } - - /** - * Method hasGraphGroup. - * - * @return true if at least one GraphGroup has been added - */ - public boolean hasGraphGroup() - { - return this._has_graphGroup; - } - - /** - * Method hasGraphHeight. - * - * @return true if at least one GraphHeight has been added - */ - public boolean hasGraphHeight() - { - return this._has_graphHeight; - } - - /** - * Method hasGraphType. - * - * @return true if at least one GraphType has been added - */ - public boolean hasGraphType() - { - return this._has_graphType; - } - - /** - * Method hasScaleColLabels. - * - * @return true if at least one ScaleColLabels has been added - */ - public boolean hasScaleColLabels() - { - return this._has_scaleColLabels; - } - - /** - * Method hasScore. - * - * @return true if at least one Score has been added - */ - public boolean hasScore() - { - return this._has_score; - } - - /** - * Method hasScoreOnly. - * - * @return true if at least one ScoreOnly has been added - */ - public boolean hasScoreOnly() - { - return this._has_scoreOnly; - } - - /** - * Method hasShowAllColLabels. - * - * @return true if at least one ShowAllColLabels has been added - */ - public boolean hasShowAllColLabels() - { - return this._has_showAllColLabels; - } - - /** - * Method hasVisible. - * - * @return true if at least one Visible has been added - */ - public boolean hasVisible() - { - return this._has_visible; - } - - /** - * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has - * the following description: is an autocalculated annotation row - * - * @return the value of field 'AutoCalculated'. - */ - public boolean isAutoCalculated() - { - return this._autoCalculated; - } - - /** - * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has - * the following description: is to be shown below the alignment - introduced - * in Jalview 2.8 for visualizing T-COFFEE alignment scores - * - * @return the value of field 'BelowAlignment'. - */ - public boolean isBelowAlignment() - { - return this._belowAlignment; - } - - /** - * Returns the value of field 'centreColLabels'. - * - * @return the value of field 'CentreColLabels'. - */ - public boolean isCentreColLabels() - { - return this._centreColLabels; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean isGraph() - { - return this._graph; - } - - /** - * Returns the value of field 'scaleColLabels'. - * - * @return the value of field 'ScaleColLabels'. - */ - public boolean isScaleColLabels() - { - return this._scaleColLabels; - } - - /** - * Returns the value of field 'scoreOnly'. - * - * @return the value of field 'ScoreOnly'. - */ - public boolean isScoreOnly() - { - return this._scoreOnly; - } - - /** - * Returns the value of field 'showAllColLabels'. - * - * @return the value of field 'ShowAllColLabels'. - */ - public boolean isShowAllColLabels() - { - return this._showAllColLabels; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean isVisible() - { - return this._visible; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAnnotationElement() - { - this._annotationElementList.clear(); - } - - /** - */ - public void removeAllProperty() - { - this._propertyList.clear(); - } - - /** - * Method removeAnnotationElement. - * - * @param vAnnotationElement - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotationElement( - final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - { - boolean removed = _annotationElementList.remove(vAnnotationElement); - return removed; - } - - /** - * Method removeAnnotationElementAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt( - final int index) - { - java.lang.Object obj = this._annotationElementList.remove(index); - return (jalview.schemabinding.version2.AnnotationElement) obj; - } - - /** - * Method removeProperty. - * - * @param vProperty - * @return true if the object was removed from the collection. - */ - public boolean removeProperty( - final jalview.schemabinding.version2.Property vProperty) - { - boolean removed = _propertyList.remove(vProperty); - return removed; - } - - /** - * Method removePropertyAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Property removePropertyAt( - final int index) - { - java.lang.Object obj = this._propertyList.remove(index); - return (jalview.schemabinding.version2.Property) obj; - } - - /** - * - * - * @param index - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAnnotationElement( - final int index, - final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationElementList.size()) - { - throw new IndexOutOfBoundsException( - "setAnnotationElement: Index value '" + index - + "' not in range [0.." - + (this._annotationElementList.size() - 1) + "]"); - } - - this._annotationElementList.set(index, vAnnotationElement); - } - - /** - * - * - * @param vAnnotationElementArray - */ - public void setAnnotationElement( - final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) - { - // -- copy array - _annotationElementList.clear(); - - for (int i = 0; i < vAnnotationElementArray.length; i++) - { - this._annotationElementList.add(vAnnotationElementArray[i]); - } - } - - /** - * Sets the value of field 'autoCalculated'. The field 'autoCalculated' has - * the following description: is an autocalculated annotation row - * - * @param autoCalculated - * the value of field 'autoCalculated'. - */ - public void setAutoCalculated(final boolean autoCalculated) - { - this._autoCalculated = autoCalculated; - this._has_autoCalculated = true; - } - - /** - * Sets the value of field 'belowAlignment'. The field 'belowAlignment' has - * the following description: is to be shown below the alignment - introduced - * in Jalview 2.8 for visualizing T-COFFEE alignment scores - * - * @param belowAlignment - * the value of field 'belowAlignment'. - */ - public void setBelowAlignment(final boolean belowAlignment) - { - this._belowAlignment = belowAlignment; - this._has_belowAlignment = true; - } - - /** - * Sets the value of field 'calcId'. The field 'calcId' has the following - * description: Optional string identifier used to group sets of annotation - * produced by a particular calculation. Values are opaque strings but have - * semantic meaning to Jalview's renderer, data importer and calculation - * system. - * - * @param calcId - * the value of field 'calcId'. - */ - public void setCalcId(final java.lang.String calcId) - { - this._calcId = calcId; - } - - /** - * Sets the value of field 'centreColLabels'. - * - * @param centreColLabels - * the value of field 'centreColLabels'. - */ - public void setCentreColLabels(final boolean centreColLabels) - { - this._centreColLabels = centreColLabels; - this._has_centreColLabels = true; - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'graph'. - * - * @param graph - * the value of field 'graph'. - */ - public void setGraph(final boolean graph) - { - this._graph = graph; - this._has_graph = true; - } - - /** - * Sets the value of field 'graphColour'. - * - * @param graphColour - * the value of field 'graphColour'. - */ - public void setGraphColour(final int graphColour) - { - this._graphColour = graphColour; - this._has_graphColour = true; - } - - /** - * Sets the value of field 'graphGroup'. - * - * @param graphGroup - * the value of field 'graphGroup'. - */ - public void setGraphGroup(final int graphGroup) - { - this._graphGroup = graphGroup; - this._has_graphGroup = true; - } - - /** - * Sets the value of field 'graphHeight'. The field 'graphHeight' has the - * following description: height in pixels for the graph if this is a - * graph-type annotation. - * - * @param graphHeight - * the value of field 'graphHeight'. - */ - public void setGraphHeight(final int graphHeight) - { - this._graphHeight = graphHeight; - this._has_graphHeight = true; - } - - /** - * Sets the value of field 'graphType'. - * - * @param graphType - * the value of field 'graphType'. - */ - public void setGraphType(final int graphType) - { - this._graphType = graphType; - this._has_graphType = true; - } - - /** - * Sets the value of field 'groupRef'. - * - * @param groupRef - * the value of field 'groupRef'. - */ - public void setGroupRef(final java.lang.String groupRef) - { - this._groupRef = groupRef; - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'label'. - * - * @param label - * the value of field 'label'. - */ - public void setLabel(final java.lang.String label) - { - this._label = label; - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setProperty(final int index, - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException("setProperty: Index value '" - + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - this._propertyList.set(index, vProperty); - } - - /** - * - * - * @param vPropertyArray - */ - public void setProperty( - final jalview.schemabinding.version2.Property[] vPropertyArray) - { - // -- copy array - _propertyList.clear(); - - for (int i = 0; i < vPropertyArray.length; i++) - { - this._propertyList.add(vPropertyArray[i]); - } - } - - /** - * Sets the value of field 'scaleColLabels'. - * - * @param scaleColLabels - * the value of field 'scaleColLabels'. - */ - public void setScaleColLabels(final boolean scaleColLabels) - { - this._scaleColLabels = scaleColLabels; - this._has_scaleColLabels = true; - } - - /** - * Sets the value of field 'score'. - * - * @param score - * the value of field 'score'. - */ - public void setScore(final double score) - { - this._score = score; - this._has_score = true; - } - - /** - * Sets the value of field 'scoreOnly'. - * - * @param scoreOnly - * the value of field 'scoreOnly'. - */ - public void setScoreOnly(final boolean scoreOnly) - { - this._scoreOnly = scoreOnly; - this._has_scoreOnly = true; - } - - /** - * Sets the value of field 'sequenceRef'. - * - * @param sequenceRef - * the value of field 'sequenceRef'. - */ - public void setSequenceRef(final java.lang.String sequenceRef) - { - this._sequenceRef = sequenceRef; - } - - /** - * Sets the value of field 'showAllColLabels'. - * - * @param showAllColLabels - * the value of field 'showAllColLabels' - */ - public void setShowAllColLabels(final boolean showAllColLabels) - { - this._showAllColLabels = showAllColLabels; - this._has_showAllColLabels = true; - } - - /** - * Sets the value of field 'thresholdLine'. - * - * @param thresholdLine - * the value of field 'thresholdLine'. - */ - public void setThresholdLine( - final jalview.schemabinding.version2.ThresholdLine thresholdLine) - { - this._thresholdLine = thresholdLine; - } - - /** - * Sets the value of field 'visible'. - * - * @param visible - * the value of field 'visible'. - */ - public void setVisible(final boolean visible) - { - this._visible = visible; - this._has_visible = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Annotation - */ - public static jalview.schemabinding.version2.Annotation unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Annotation) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Annotation.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/AnnotationColourScheme.java b/src/jalview/schemabinding/version2/AnnotationColourScheme.java deleted file mode 100644 index 2f76e76..0000000 --- a/src/jalview/schemabinding/version2/AnnotationColourScheme.java +++ /dev/null @@ -1,497 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class AnnotationColourScheme. - * - * @version $Revision$ $Date$ - */ -public class AnnotationColourScheme implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _aboveThreshold. - */ - private int _aboveThreshold; - - /** - * keeps track of state for field: _aboveThreshold - */ - private boolean _has_aboveThreshold; - - /** - * Field _annotation. - */ - private java.lang.String _annotation; - - /** - * Field _minColour. - */ - private int _minColour; - - /** - * keeps track of state for field: _minColour - */ - private boolean _has_minColour; - - /** - * Field _maxColour. - */ - private int _maxColour; - - /** - * keeps track of state for field: _maxColour - */ - private boolean _has_maxColour; - - /** - * Field _colourScheme. - */ - private java.lang.String _colourScheme; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _perSequence. - */ - private boolean _perSequence; - - /** - * keeps track of state for field: _perSequence - */ - private boolean _has_perSequence; - - /** - * Field _predefinedColours. - */ - private boolean _predefinedColours; - - /** - * keeps track of state for field: _predefinedColours - */ - private boolean _has_predefinedColours; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationColourScheme() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteAboveThreshold() - { - this._has_aboveThreshold = false; - } - - /** - */ - public void deleteMaxColour() - { - this._has_maxColour = false; - } - - /** - */ - public void deleteMinColour() - { - this._has_minColour = false; - } - - /** - */ - public void deletePerSequence() - { - this._has_perSequence = false; - } - - /** - */ - public void deletePredefinedColours() - { - this._has_predefinedColours = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - * Returns the value of field 'aboveThreshold'. - * - * @return the value of field 'AboveThreshold'. - */ - public int getAboveThreshold() - { - return this._aboveThreshold; - } - - /** - * Returns the value of field 'annotation'. - * - * @return the value of field 'Annotation'. - */ - public java.lang.String getAnnotation() - { - return this._annotation; - } - - /** - * Returns the value of field 'colourScheme'. - * - * @return the value of field 'ColourScheme'. - */ - public java.lang.String getColourScheme() - { - return this._colourScheme; - } - - /** - * Returns the value of field 'maxColour'. - * - * @return the value of field 'MaxColour'. - */ - public int getMaxColour() - { - return this._maxColour; - } - - /** - * Returns the value of field 'minColour'. - * - * @return the value of field 'MinColour'. - */ - public int getMinColour() - { - return this._minColour; - } - - /** - * Returns the value of field 'perSequence'. - * - * @return the value of field 'PerSequence'. - */ - public boolean getPerSequence() - { - return this._perSequence; - } - - /** - * Returns the value of field 'predefinedColours'. - * - * @return the value of field 'PredefinedColours'. - */ - public boolean getPredefinedColours() - { - return this._predefinedColours; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Method hasAboveThreshold. - * - * @return true if at least one AboveThreshold has been added - */ - public boolean hasAboveThreshold() - { - return this._has_aboveThreshold; - } - - /** - * Method hasMaxColour. - * - * @return true if at least one MaxColour has been added - */ - public boolean hasMaxColour() - { - return this._has_maxColour; - } - - /** - * Method hasMinColour. - * - * @return true if at least one MinColour has been added - */ - public boolean hasMinColour() - { - return this._has_minColour; - } - - /** - * Method hasPerSequence. - * - * @return true if at least one PerSequence has been added - */ - public boolean hasPerSequence() - { - return this._has_perSequence; - } - - /** - * Method hasPredefinedColours. - * - * @return true if at least one PredefinedColours has been added - */ - public boolean hasPredefinedColours() - { - return this._has_predefinedColours; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Returns the value of field 'perSequence'. - * - * @return the value of field 'PerSequence'. - */ - public boolean isPerSequence() - { - return this._perSequence; - } - - /** - * Returns the value of field 'predefinedColours'. - * - * @return the value of field 'PredefinedColours'. - */ - public boolean isPredefinedColours() - { - return this._predefinedColours; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'aboveThreshold'. - * - * @param aboveThreshold - * the value of field 'aboveThreshold'. - */ - public void setAboveThreshold(final int aboveThreshold) - { - this._aboveThreshold = aboveThreshold; - this._has_aboveThreshold = true; - } - - /** - * Sets the value of field 'annotation'. - * - * @param annotation - * the value of field 'annotation'. - */ - public void setAnnotation(final java.lang.String annotation) - { - this._annotation = annotation; - } - - /** - * Sets the value of field 'colourScheme'. - * - * @param colourScheme - * the value of field 'colourScheme'. - */ - public void setColourScheme(final java.lang.String colourScheme) - { - this._colourScheme = colourScheme; - } - - /** - * Sets the value of field 'maxColour'. - * - * @param maxColour - * the value of field 'maxColour'. - */ - public void setMaxColour(final int maxColour) - { - this._maxColour = maxColour; - this._has_maxColour = true; - } - - /** - * Sets the value of field 'minColour'. - * - * @param minColour - * the value of field 'minColour'. - */ - public void setMinColour(final int minColour) - { - this._minColour = minColour; - this._has_minColour = true; - } - - /** - * Sets the value of field 'perSequence'. - * - * @param perSequence - * the value of field 'perSequence'. - */ - public void setPerSequence(final boolean perSequence) - { - this._perSequence = perSequence; - this._has_perSequence = true; - } - - /** - * Sets the value of field 'predefinedColours'. - * - * @param predefinedColours - * the value of field 'predefinedColours'. - */ - public void setPredefinedColours(final boolean predefinedColours) - { - this._predefinedColours = predefinedColours; - this._has_predefinedColours = true; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold - * the value of field 'threshold'. - */ - public void setThreshold(final float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.AnnotationColourScheme - */ - public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.AnnotationColourScheme.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java deleted file mode 100644 index 350ebce..0000000 --- a/src/jalview/schemabinding/version2/AnnotationColours.java +++ /dev/null @@ -1,128 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class AnnotationColours. - * - * @version $Revision$ $Date$ - */ -public class AnnotationColours extends AnnotationColourScheme implements - java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationColours() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.AnnotationColourScheme - */ - public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.AnnotationColours.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java deleted file mode 100644 index 2a765ea..0000000 --- a/src/jalview/schemabinding/version2/AnnotationElement.java +++ /dev/null @@ -1,356 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class AnnotationElement. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElement implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _position. - */ - private int _position; - - /** - * keeps track of state for field: _position - */ - private boolean _has_position; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _displayCharacter. - */ - private java.lang.String _displayCharacter; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _secondaryStructure. - */ - private java.lang.String _secondaryStructure; - - /** - * Field _value. - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationElement() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deletePosition() - { - this._has_position = false; - } - - /** - */ - public void deleteValue() - { - this._has_value = false; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'displayCharacter'. - * - * @return the value of field 'DisplayCharacter'. - */ - public java.lang.String getDisplayCharacter() - { - return this._displayCharacter; - } - - /** - * Returns the value of field 'position'. - * - * @return the value of field 'Position'. - */ - public int getPosition() - { - return this._position; - } - - /** - * Returns the value of field 'secondaryStructure'. - * - * @return the value of field 'SecondaryStructure'. - */ - public java.lang.String getSecondaryStructure() - { - return this._secondaryStructure; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public float getValue() - { - return this._value; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasPosition. - * - * @return true if at least one Position has been added - */ - public boolean hasPosition() - { - return this._has_position; - } - - /** - * Method hasValue. - * - * @return true if at least one Value has been added - */ - public boolean hasValue() - { - return this._has_value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'displayCharacter'. - * - * @param displayCharacter - * the value of field 'displayCharacter' - */ - public void setDisplayCharacter(final java.lang.String displayCharacter) - { - this._displayCharacter = displayCharacter; - } - - /** - * Sets the value of field 'position'. - * - * @param position - * the value of field 'position'. - */ - public void setPosition(final int position) - { - this._position = position; - this._has_position = true; - } - - /** - * Sets the value of field 'secondaryStructure'. - * - * @param secondaryStructure - * the value of field 'secondaryStructure'. - */ - public void setSecondaryStructure( - final java.lang.String secondaryStructure) - { - this._secondaryStructure = secondaryStructure; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final float value) - { - this._value = value; - this._has_value = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.AnnotationElement - */ - public static jalview.schemabinding.version2.AnnotationElement unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.AnnotationElement.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/CalcIdParam.java b/src/jalview/schemabinding/version2/CalcIdParam.java deleted file mode 100644 index 57d6986..0000000 --- a/src/jalview/schemabinding/version2/CalcIdParam.java +++ /dev/null @@ -1,300 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class CalcIdParam. - * - * @version $Revision$ $Date$ - */ -public class CalcIdParam extends WebServiceParameterSet implements - java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * handle for the calculation which uses this parameter set - * - */ - private java.lang.String _calcId; - - /** - * should the calculation be performed immediately after loading in order to - * refresh results - * - */ - private boolean _needsUpdate = false; - - /** - * keeps track of state for field: _needsUpdate - */ - private boolean _has_needsUpdate; - - /** - * should the calculation be automatically performed on edits - * - */ - private boolean _autoUpdate; - - /** - * keeps track of state for field: _autoUpdate - */ - private boolean _has_autoUpdate; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public CalcIdParam() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteAutoUpdate() - { - this._has_autoUpdate = false; - } - - /** - */ - public void deleteNeedsUpdate() - { - this._has_needsUpdate = false; - } - - /** - * Returns the value of field 'autoUpdate'. The field 'autoUpdate' has the - * following description: should the calculation be automatically performed on - * edits - * - * - * @return the value of field 'AutoUpdate'. - */ - public boolean getAutoUpdate() - { - return this._autoUpdate; - } - - /** - * Returns the value of field 'calcId'. The field 'calcId' has the following - * description: handle for the calculation which uses this parameter set - * - * - * @return the value of field 'CalcId'. - */ - public java.lang.String getCalcId() - { - return this._calcId; - } - - /** - * Returns the value of field 'needsUpdate'. The field 'needsUpdate' has the - * following description: should the calculation be performed immediately - * after loading in order to refresh results - * - * - * @return the value of field 'NeedsUpdate'. - */ - public boolean getNeedsUpdate() - { - return this._needsUpdate; - } - - /** - * Method hasAutoUpdate. - * - * @return true if at least one AutoUpdate has been added - */ - public boolean hasAutoUpdate() - { - return this._has_autoUpdate; - } - - /** - * Method hasNeedsUpdate. - * - * @return true if at least one NeedsUpdate has been added - */ - public boolean hasNeedsUpdate() - { - return this._has_needsUpdate; - } - - /** - * Returns the value of field 'autoUpdate'. The field 'autoUpdate' has the - * following description: should the calculation be automatically performed on - * edits - * - * - * @return the value of field 'AutoUpdate'. - */ - public boolean isAutoUpdate() - { - return this._autoUpdate; - } - - /** - * Returns the value of field 'needsUpdate'. The field 'needsUpdate' has the - * following description: should the calculation be performed immediately - * after loading in order to refresh results - * - * - * @return the value of field 'NeedsUpdate'. - */ - public boolean isNeedsUpdate() - { - return this._needsUpdate; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'autoUpdate'. The field 'autoUpdate' has the - * following description: should the calculation be automatically performed on - * edits - * - * - * @param autoUpdate - * the value of field 'autoUpdate'. - */ - public void setAutoUpdate(final boolean autoUpdate) - { - this._autoUpdate = autoUpdate; - this._has_autoUpdate = true; - } - - /** - * Sets the value of field 'calcId'. The field 'calcId' has the following - * description: handle for the calculation which uses this parameter set - * - * - * @param calcId - * the value of field 'calcId'. - */ - public void setCalcId(final java.lang.String calcId) - { - this._calcId = calcId; - } - - /** - * Sets the value of field 'needsUpdate'. The field 'needsUpdate' has the - * following description: should the calculation be performed immediately - * after loading in order to refresh results - * - * - * @param needsUpdate - * the value of field 'needsUpdate'. - */ - public void setNeedsUpdate(final boolean needsUpdate) - { - this._needsUpdate = needsUpdate; - this._has_needsUpdate = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.CalcIdParam - */ - public static jalview.schemabinding.version2.CalcIdParam unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.CalcIdParam) Unmarshaller - .unmarshal(jalview.schemabinding.version2.CalcIdParam.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java deleted file mode 100644 index d1c7297..0000000 --- a/src/jalview/schemabinding/version2/Colour.java +++ /dev/null @@ -1,708 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Colour. - * - * @version $Revision$ $Date$ - */ -public class Colour implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Single letter residue code for an alignment colour scheme, or feature type - * for a feature colour scheme - */ - private java.lang.String _name; - - /** - * Field _RGB. - */ - private java.lang.String _RGB; - - /** - * Field _minRGB. - */ - private java.lang.String _minRGB; - - /** - * Field _noValueColour. - */ - private jalview.schemabinding.version2.types.NoValueColour _noValueColour = jalview.schemabinding.version2.types.NoValueColour - .valueOf("Min"); - - /** - * Field _threshType. - */ - private jalview.schemabinding.version2.types.ColourThreshTypeType _threshType; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - /** - * name of feature attribute to colour by, or attribute and sub-attribute - */ - private java.util.Vector _attributeNameList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Colour() - { - super(); - setNoValueColour(jalview.schemabinding.version2.types.NoValueColour - .valueOf("Min")); - this._attributeNameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.addElement(vAttributeName); - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.add(index, vAttributeName); - } - - /** - */ - public void deleteAutoScale() - { - this._has_autoScale = false; - } - - /** - */ - public void deleteColourByLabel() - { - this._has_colourByLabel = false; - } - - /** - */ - public void deleteMax() - { - this._has_max = false; - } - - /** - */ - public void deleteMin() - { - this._has_min = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - * Method enumerateAttributeName. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateAttributeName() - { - return this._attributeNameList.elements(); - } - - /** - * Method getAttributeName. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getAttributeName(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("getAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - return (java.lang.String) _attributeNameList.get(index); - } - - /** - * Method getAttributeName.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getAttributeName() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._attributeNameList.toArray(array); - } - - /** - * Method getAttributeNameCount. - * - * @return the size of this collection - */ - public int getAttributeNameCount() - { - return this._attributeNameList.size(); - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel() - { - return this._colourByLabel; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax() - { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin() - { - return this._min; - } - - /** - * Returns the value of field 'minRGB'. - * - * @return the value of field 'MinRGB'. - */ - public java.lang.String getMinRGB() - { - return this._minRGB; - } - - /** - * Returns the value of field 'name'. The field 'name' has the following - * description: Single letter residue code for an alignment colour scheme, or - * feature type for a feature colour scheme - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'noValueColour'. - * - * @return the value of field 'NoValueColour'. - */ - public jalview.schemabinding.version2.types.NoValueColour getNoValueColour() - { - return this._noValueColour; - } - - /** - * Returns the value of field 'RGB'. - * - * @return the value of field 'RGB'. - */ - public java.lang.String getRGB() - { - return this._RGB; - } - - /** - * Returns the value of field 'threshType'. - * - * @return the value of field 'ThreshType'. - */ - public jalview.schemabinding.version2.types.ColourThreshTypeType getThreshType() - { - return this._threshType; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale() - { - return this._has_autoScale; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel() - { - return this._has_colourByLabel; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax() - { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin() - { - return this._has_min; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel() - { - return this._colourByLabel; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAttributeName() - { - this._attributeNameList.clear(); - } - - /** - * Method removeAttributeName. - * - * @param vAttributeName - * @return true if the object was removed from the collection. - */ - public boolean removeAttributeName(final java.lang.String vAttributeName) - { - boolean removed = _attributeNameList.remove(vAttributeName); - return removed; - } - - /** - * Method removeAttributeNameAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeAttributeNameAt(final int index) - { - java.lang.Object obj = this._attributeNameList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("setAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - this._attributeNameList.set(index, vAttributeName); - } - - /** - * - * - * @param vAttributeNameArray - */ - public void setAttributeName(final java.lang.String[] vAttributeNameArray) - { - // -- copy array - _attributeNameList.clear(); - - for (int i = 0; i < vAttributeNameArray.length; i++) - { - this._attributeNameList.add(vAttributeNameArray[i]); - } - } - - /** - * Sets the value of field 'autoScale'. - * - * @param autoScale - * the value of field 'autoScale'. - */ - public void setAutoScale(final boolean autoScale) - { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * Sets the value of field 'colourByLabel'. - * - * @param colourByLabel - * the value of field 'colourByLabel'. - */ - public void setColourByLabel(final boolean colourByLabel) - { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = true; - } - - /** - * Sets the value of field 'max'. - * - * @param max - * the value of field 'max'. - */ - public void setMax(final float max) - { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min - * the value of field 'min'. - */ - public void setMin(final float min) - { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'minRGB'. - * - * @param minRGB - * the value of field 'minRGB'. - */ - public void setMinRGB(final java.lang.String minRGB) - { - this._minRGB = minRGB; - } - - /** - * Sets the value of field 'name'. The field 'name' has the following - * description: Single letter residue code for an alignment colour scheme, or - * feature type for a feature colour scheme - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'noValueColour'. - * - * @param noValueColour - * the value of field 'noValueColour'. - */ - public void setNoValueColour( - final jalview.schemabinding.version2.types.NoValueColour noValueColour) - { - this._noValueColour = noValueColour; - } - - /** - * Sets the value of field 'RGB'. - * - * @param RGB - * the value of field 'RGB'. - */ - public void setRGB(final java.lang.String RGB) - { - this._RGB = RGB; - } - - /** - * Sets the value of field 'threshType'. - * - * @param threshType - * the value of field 'threshType'. - */ - public void setThreshType( - final jalview.schemabinding.version2.types.ColourThreshTypeType threshType) - { - this._threshType = threshType; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold - * the value of field 'threshold'. - */ - public void setThreshold(final float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Colour - */ - public static jalview.schemabinding.version2.Colour unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Colour) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Colour.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/CompoundMatcher.java b/src/jalview/schemabinding/version2/CompoundMatcher.java deleted file mode 100644 index 27714e2..0000000 --- a/src/jalview/schemabinding/version2/CompoundMatcher.java +++ /dev/null @@ -1,374 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class CompoundMatcher. - * - * @version $Revision$ $Date$ - */ -public class CompoundMatcher implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * If true, matchers are AND-ed, if false they are OR-ed - */ - private boolean _and; - - /** - * keeps track of state for field: _and - */ - private boolean _has_and; - - /** - * Field _matcherSetList. - */ - private java.util.Vector _matcherSetList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public CompoundMatcher() - { - super(); - this._matcherSetList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMatcherSet( - final jalview.schemabinding.version2.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._matcherSetList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addMatcherSet has a maximum of 2"); - } - - this._matcherSetList.addElement(vMatcherSet); - } - - /** - * - * - * @param index - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMatcherSet(final int index, - final jalview.schemabinding.version2.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._matcherSetList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addMatcherSet has a maximum of 2"); - } - - this._matcherSetList.add(index, vMatcherSet); - } - - /** - */ - public void deleteAnd() - { - this._has_and = false; - } - - /** - * Method enumerateMatcherSet. - * - * @return an Enumeration over all jalview.schemabinding.version2.MatcherSet - * elements - */ - public java.util.Enumeration enumerateMatcherSet() - { - return this._matcherSetList.elements(); - } - - /** - * Returns the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @return the value of field 'And'. - */ - public boolean getAnd() - { - return this._and; - } - - /** - * Method getMatcherSet. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.MatcherSet at the - * given index - */ - public jalview.schemabinding.version2.MatcherSet getMatcherSet( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._matcherSetList.size()) - { - throw new IndexOutOfBoundsException( - "getMatcherSet: Index value '" + index + "' not in range [0.." - + (this._matcherSetList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.MatcherSet) _matcherSetList - .get(index); - } - - /** - * Method getMatcherSet.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.MatcherSet[] getMatcherSet() - { - jalview.schemabinding.version2.MatcherSet[] array = new jalview.schemabinding.version2.MatcherSet[0]; - return (jalview.schemabinding.version2.MatcherSet[]) this._matcherSetList - .toArray(array); - } - - /** - * Method getMatcherSetCount. - * - * @return the size of this collection - */ - public int getMatcherSetCount() - { - return this._matcherSetList.size(); - } - - /** - * Method hasAnd. - * - * @return true if at least one And has been added - */ - public boolean hasAnd() - { - return this._has_and; - } - - /** - * Returns the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @return the value of field 'And'. - */ - public boolean isAnd() - { - return this._and; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllMatcherSet() - { - this._matcherSetList.clear(); - } - - /** - * Method removeMatcherSet. - * - * @param vMatcherSet - * @return true if the object was removed from the collection. - */ - public boolean removeMatcherSet( - final jalview.schemabinding.version2.MatcherSet vMatcherSet) - { - boolean removed = _matcherSetList.remove(vMatcherSet); - return removed; - } - - /** - * Method removeMatcherSetAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MatcherSet removeMatcherSetAt( - final int index) - { - java.lang.Object obj = this._matcherSetList.remove(index); - return (jalview.schemabinding.version2.MatcherSet) obj; - } - - /** - * Sets the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @param and - * the value of field 'and'. - */ - public void setAnd(final boolean and) - { - this._and = and; - this._has_and = true; - } - - /** - * - * - * @param index - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setMatcherSet(final int index, - final jalview.schemabinding.version2.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._matcherSetList.size()) - { - throw new IndexOutOfBoundsException( - "setMatcherSet: Index value '" + index + "' not in range [0.." - + (this._matcherSetList.size() - 1) + "]"); - } - - this._matcherSetList.set(index, vMatcherSet); - } - - /** - * - * - * @param vMatcherSetArray - */ - public void setMatcherSet( - final jalview.schemabinding.version2.MatcherSet[] vMatcherSetArray) - { - // -- copy array - _matcherSetList.clear(); - - for (int i = 0; i < vMatcherSetArray.length; i++) - { - this._matcherSetList.add(vMatcherSetArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.CompoundMatcher - */ - public static jalview.schemabinding.version2.CompoundMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.CompoundMatcher) Unmarshaller - .unmarshal(jalview.schemabinding.version2.CompoundMatcher.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java deleted file mode 100644 index 85997ff..0000000 --- a/src/jalview/schemabinding/version2/DBRef.java +++ /dev/null @@ -1,233 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class DBRef. - * - * @version $Revision$ $Date$ - */ -public class DBRef implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _source. - */ - private java.lang.String _source; - - /** - * Field _version. - */ - private java.lang.String _version; - - /** - * Field _accessionId. - */ - private java.lang.String _accessionId; - - /** - * Field _mapping. - */ - private jalview.schemabinding.version2.Mapping _mapping; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public DBRef() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'accessionId'. - * - * @return the value of field 'AccessionId'. - */ - public java.lang.String getAccessionId() - { - return this._accessionId; - } - - /** - * Returns the value of field 'mapping'. - * - * @return the value of field 'Mapping'. - */ - public jalview.schemabinding.version2.Mapping getMapping() - { - return this._mapping; - } - - /** - * Returns the value of field 'source'. - * - * @return the value of field 'Source'. - */ - public java.lang.String getSource() - { - return this._source; - } - - /** - * Returns the value of field 'version'. - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion() - { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'accessionId'. - * - * @param accessionId - * the value of field 'accessionId'. - */ - public void setAccessionId(final java.lang.String accessionId) - { - this._accessionId = accessionId; - } - - /** - * Sets the value of field 'mapping'. - * - * @param mapping - * the value of field 'mapping'. - */ - public void setMapping( - final jalview.schemabinding.version2.Mapping mapping) - { - this._mapping = mapping; - } - - /** - * Sets the value of field 'source'. - * - * @param source - * the value of field 'source'. - */ - public void setSource(final java.lang.String source) - { - this._source = source; - } - - /** - * Sets the value of field 'version'. - * - * @param version - * the value of field 'version'. - */ - public void setVersion(final java.lang.String version) - { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.DBRef - */ - public static jalview.schemabinding.version2.DBRef unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal( - jalview.schemabinding.version2.DBRef.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java deleted file mode 100644 index 9e484d5..0000000 --- a/src/jalview/schemabinding/version2/Feature.java +++ /dev/null @@ -1,548 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Feature. - * - * @version $Revision$ $Date$ - */ -public class Feature implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _begin. - */ - private int _begin; - - /** - * keeps track of state for field: _begin - */ - private boolean _has_begin; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _status. - */ - private java.lang.String _status; - - /** - * Field _featureGroup. - */ - private java.lang.String _featureGroup; - - /** - * Field _score. - */ - private float _score; - - /** - * keeps track of state for field: _score - */ - private boolean _has_score; - - /** - * Field _otherDataList. - */ - private java.util.Vector _otherDataList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Feature() - { - super(); - this._otherDataList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addOtherData( - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - this._otherDataList.addElement(vOtherData); - } - - /** - * - * - * @param index - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addOtherData(final int index, - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - this._otherDataList.add(index, vOtherData); - } - - /** - */ - public void deleteBegin() - { - this._has_begin = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteScore() - { - this._has_score = false; - } - - /** - * Method enumerateOtherData. - * - * @return an Enumeration over all jalview.schemabinding.version2.OtherData - * elements - */ - public java.util.Enumeration enumerateOtherData() - { - return this._otherDataList.elements(); - } - - /** - * Returns the value of field 'begin'. - * - * @return the value of field 'Begin'. - */ - public int getBegin() - { - return this._begin; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'featureGroup'. - * - * @return the value of field 'FeatureGroup'. - */ - public java.lang.String getFeatureGroup() - { - return this._featureGroup; - } - - /** - * Method getOtherData. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.OtherData at the - * given index - */ - public jalview.schemabinding.version2.OtherData getOtherData( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._otherDataList.size()) - { - throw new IndexOutOfBoundsException("getOtherData: Index value '" - + index + "' not in range [0.." - + (this._otherDataList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.OtherData) _otherDataList - .get(index); - } - - /** - * Method getOtherData.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.OtherData[] getOtherData() - { - jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0]; - return (jalview.schemabinding.version2.OtherData[]) this._otherDataList - .toArray(array); - } - - /** - * Method getOtherDataCount. - * - * @return the size of this collection - */ - public int getOtherDataCount() - { - return this._otherDataList.size(); - } - - /** - * Returns the value of field 'score'. - * - * @return the value of field 'Score'. - */ - public float getScore() - { - return this._score; - } - - /** - * Returns the value of field 'status'. - * - * @return the value of field 'Status'. - */ - public java.lang.String getStatus() - { - return this._status; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method hasBegin. - * - * @return true if at least one Begin has been added - */ - public boolean hasBegin() - { - return this._has_begin; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasScore. - * - * @return true if at least one Score has been added - */ - public boolean hasScore() - { - return this._has_score; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllOtherData() - { - this._otherDataList.clear(); - } - - /** - * Method removeOtherData. - * - * @param vOtherData - * @return true if the object was removed from the collection. - */ - public boolean removeOtherData( - final jalview.schemabinding.version2.OtherData vOtherData) - { - boolean removed = _otherDataList.remove(vOtherData); - return removed; - } - - /** - * Method removeOtherDataAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.OtherData removeOtherDataAt( - final int index) - { - java.lang.Object obj = this._otherDataList.remove(index); - return (jalview.schemabinding.version2.OtherData) obj; - } - - /** - * Sets the value of field 'begin'. - * - * @param begin - * the value of field 'begin'. - */ - public void setBegin(final int begin) - { - this._begin = begin; - this._has_begin = true; - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'featureGroup'. - * - * @param featureGroup - * the value of field 'featureGroup'. - */ - public void setFeatureGroup(final java.lang.String featureGroup) - { - this._featureGroup = featureGroup; - } - - /** - * - * - * @param index - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setOtherData(final int index, - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._otherDataList.size()) - { - throw new IndexOutOfBoundsException("setOtherData: Index value '" - + index + "' not in range [0.." - + (this._otherDataList.size() - 1) + "]"); - } - - this._otherDataList.set(index, vOtherData); - } - - /** - * - * - * @param vOtherDataArray - */ - public void setOtherData( - final jalview.schemabinding.version2.OtherData[] vOtherDataArray) - { - // -- copy array - _otherDataList.clear(); - - for (int i = 0; i < vOtherDataArray.length; i++) - { - this._otherDataList.add(vOtherDataArray[i]); - } - } - - /** - * Sets the value of field 'score'. - * - * @param score - * the value of field 'score'. - */ - public void setScore(final float score) - { - this._score = score; - this._has_score = true; - } - - /** - * Sets the value of field 'status'. - * - * @param status - * the value of field 'status'. - */ - public void setStatus(final java.lang.String status) - { - this._status = status; - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Featur - */ - public static jalview.schemabinding.version2.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Feature.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/FeatureMatcher.java b/src/jalview/schemabinding/version2/FeatureMatcher.java deleted file mode 100644 index 4d29cab..0000000 --- a/src/jalview/schemabinding/version2/FeatureMatcher.java +++ /dev/null @@ -1,383 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class FeatureMatcher. - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcher implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _by. - */ - private jalview.schemabinding.version2.types.FeatureMatcherByType _by; - - /** - * name of feature attribute to filter on, or attribute and sub-attribute - */ - private java.util.Vector _attributeNameList; - - /** - * Field _condition. - */ - private java.lang.String _condition; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureMatcher() - { - super(); - this._attributeNameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.addElement(vAttributeName); - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.add(index, vAttributeName); - } - - /** - * Method enumerateAttributeName. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateAttributeName() - { - return this._attributeNameList.elements(); - } - - /** - * Method getAttributeName. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getAttributeName(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("getAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - return (java.lang.String) _attributeNameList.get(index); - } - - /** - * Method getAttributeName.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getAttributeName() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._attributeNameList.toArray(array); - } - - /** - * Method getAttributeNameCount. - * - * @return the size of this collection - */ - public int getAttributeNameCount() - { - return this._attributeNameList.size(); - } - - /** - * Returns the value of field 'by'. - * - * @return the value of field 'By'. - */ - public jalview.schemabinding.version2.types.FeatureMatcherByType getBy() - { - return this._by; - } - - /** - * Returns the value of field 'condition'. - * - * @return the value of field 'Condition'. - */ - public java.lang.String getCondition() - { - return this._condition; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue() - { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAttributeName() - { - this._attributeNameList.clear(); - } - - /** - * Method removeAttributeName. - * - * @param vAttributeName - * @return true if the object was removed from the collection. - */ - public boolean removeAttributeName(final java.lang.String vAttributeName) - { - boolean removed = _attributeNameList.remove(vAttributeName); - return removed; - } - - /** - * Method removeAttributeNameAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeAttributeNameAt(final int index) - { - java.lang.Object obj = this._attributeNameList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("setAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - this._attributeNameList.set(index, vAttributeName); - } - - /** - * - * - * @param vAttributeNameArray - */ - public void setAttributeName(final java.lang.String[] vAttributeNameArray) - { - // -- copy array - _attributeNameList.clear(); - - for (int i = 0; i < vAttributeNameArray.length; i++) - { - this._attributeNameList.add(vAttributeNameArray[i]); - } - } - - /** - * Sets the value of field 'by'. - * - * @param by - * the value of field 'by'. - */ - public void setBy( - final jalview.schemabinding.version2.types.FeatureMatcherByType by) - { - this._by = by; - } - - /** - * Sets the value of field 'condition'. - * - * @param condition - * the value of field 'condition'. - */ - public void setCondition(final java.lang.String condition) - { - this._condition = condition; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final java.lang.String value) - { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.FeatureMatcher - */ - public static jalview.schemabinding.version2.FeatureMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.FeatureMatcher) Unmarshaller - .unmarshal(jalview.schemabinding.version2.FeatureMatcher.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/FeatureMatcherSet.java b/src/jalview/schemabinding/version2/FeatureMatcherSet.java deleted file mode 100644 index 2d79a98..0000000 --- a/src/jalview/schemabinding/version2/FeatureMatcherSet.java +++ /dev/null @@ -1,200 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * A feature match condition, which may be simple or compound - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcherSet implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * Field _matchCondition. - */ - private MatchCondition _matchCondition; - - /** - * Field _compoundMatcher. - */ - private CompoundMatcher _compoundMatcher; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureMatcherSet() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'choiceValue'. The field 'choiceValue' has the - * following description: Internal choice value storage - * - * @return the value of field 'ChoiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } - - /** - * Returns the value of field 'compoundMatcher'. - * - * @return the value of field 'CompoundMatcher'. - */ - public CompoundMatcher getCompoundMatcher() - { - return this._compoundMatcher; - } - - /** - * Returns the value of field 'matchCondition'. - * - * @return the value of field 'MatchCondition'. - */ - public MatchCondition getMatchCondition() - { - return this._matchCondition; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'compoundMatcher'. - * - * @param compoundMatcher - * the value of field 'compoundMatcher'. - */ - public void setCompoundMatcher(final CompoundMatcher compoundMatcher) - { - this._compoundMatcher = compoundMatcher; - this._choiceValue = compoundMatcher; - } - - /** - * Sets the value of field 'matchCondition'. - * - * @param matchCondition - * the value of field 'matchCondition'. - */ - public void setMatchCondition(final MatchCondition matchCondition) - { - this._matchCondition = matchCondition; - this._choiceValue = matchCondition; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.FeatureMatcherSet - */ - public static jalview.schemabinding.version2.FeatureMatcherSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.FeatureMatcherSet) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.FeatureMatcherSet.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java deleted file mode 100644 index fa75e76..0000000 --- a/src/jalview/schemabinding/version2/FeatureSettings.java +++ /dev/null @@ -1,462 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class FeatureSettings. - * - * @version $Revision$ $Date$ - */ -public class FeatureSettings implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _settingList. - */ - private java.util.Vector _settingList; - - /** - * Field _groupList. - */ - private java.util.Vector _groupList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureSettings() - { - super(); - this._settingList = new java.util.Vector(); - this._groupList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addGroup(final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException - { - this._groupList.addElement(vGroup); - } - - /** - * - * - * @param index - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addGroup(final int index, - final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException - { - this._groupList.add(index, vGroup); - } - - /** - * - * - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSetting( - final jalview.schemabinding.version2.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - this._settingList.addElement(vSetting); - } - - /** - * - * - * @param index - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSetting(final int index, - final jalview.schemabinding.version2.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - this._settingList.add(index, vSetting); - } - - /** - * Method enumerateGroup. - * - * @return an Enumeration over all jalview.schemabinding.version2.Group - * elements - */ - public java.util.Enumeration enumerateGroup() - { - return this._groupList.elements(); - } - - /** - * Method enumerateSetting. - * - * @return an Enumeration over all jalview.schemabinding.version2.Setting - * elements - */ - public java.util.Enumeration enumerateSetting() - { - return this._settingList.elements(); - } - - /** - * Method getGroup. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Group at the given - * index - */ - public jalview.schemabinding.version2.Group getGroup(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._groupList.size()) - { - throw new IndexOutOfBoundsException("getGroup: Index value '" + index - + "' not in range [0.." + (this._groupList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Group) _groupList.get(index); - } - - /** - * Method getGroup.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Group[] getGroup() - { - jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0]; - return (jalview.schemabinding.version2.Group[]) this._groupList - .toArray(array); - } - - /** - * Method getGroupCount. - * - * @return the size of this collection - */ - public int getGroupCount() - { - return this._groupList.size(); - } - - /** - * Method getSetting. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Setting at the - * given index - */ - public jalview.schemabinding.version2.Setting getSetting(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._settingList.size()) - { - throw new IndexOutOfBoundsException("getSetting: Index value '" - + index + "' not in range [0.." - + (this._settingList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Setting) _settingList.get(index); - } - - /** - * Method getSetting.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Setting[] getSetting() - { - jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0]; - return (jalview.schemabinding.version2.Setting[]) this._settingList - .toArray(array); - } - - /** - * Method getSettingCount. - * - * @return the size of this collection - */ - public int getSettingCount() - { - return this._settingList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllGroup() - { - this._groupList.clear(); - } - - /** - */ - public void removeAllSetting() - { - this._settingList.clear(); - } - - /** - * Method removeGroup. - * - * @param vGroup - * @return true if the object was removed from the collection. - */ - public boolean removeGroup( - final jalview.schemabinding.version2.Group vGroup) - { - boolean removed = _groupList.remove(vGroup); - return removed; - } - - /** - * Method removeGroupAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Group removeGroupAt(final int index) - { - java.lang.Object obj = this._groupList.remove(index); - return (jalview.schemabinding.version2.Group) obj; - } - - /** - * Method removeSetting. - * - * @param vSetting - * @return true if the object was removed from the collection. - */ - public boolean removeSetting( - final jalview.schemabinding.version2.Setting vSetting) - { - boolean removed = _settingList.remove(vSetting); - return removed; - } - - /** - * Method removeSettingAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Setting removeSettingAt( - final int index) - { - java.lang.Object obj = this._settingList.remove(index); - return (jalview.schemabinding.version2.Setting) obj; - } - - /** - * - * - * @param index - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setGroup(final int index, - final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._groupList.size()) - { - throw new IndexOutOfBoundsException("setGroup: Index value '" + index - + "' not in range [0.." + (this._groupList.size() - 1) + "]"); - } - - this._groupList.set(index, vGroup); - } - - /** - * - * - * @param vGroupArray - */ - public void setGroup( - final jalview.schemabinding.version2.Group[] vGroupArray) - { - // -- copy array - _groupList.clear(); - - for (int i = 0; i < vGroupArray.length; i++) - { - this._groupList.add(vGroupArray[i]); - } - } - - /** - * - * - * @param index - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSetting(final int index, - final jalview.schemabinding.version2.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._settingList.size()) - { - throw new IndexOutOfBoundsException("setSetting: Index value '" - + index + "' not in range [0.." - + (this._settingList.size() - 1) + "]"); - } - - this._settingList.set(index, vSetting); - } - - /** - * - * - * @param vSettingArray - */ - public void setSetting( - final jalview.schemabinding.version2.Setting[] vSettingArray) - { - // -- copy array - _settingList.clear(); - - for (int i = 0; i < vSettingArray.length; i++) - { - this._settingList.add(vSettingArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.FeatureSettings - */ - public static jalview.schemabinding.version2.FeatureSettings unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.FeatureSettings.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java deleted file mode 100644 index 5d17512..0000000 --- a/src/jalview/schemabinding/version2/Features.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Features. - * - * @version $Revision$ $Date$ - */ -public class Features extends Feature implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Features() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Featur - */ - public static jalview.schemabinding.version2.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Features.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Filter.java b/src/jalview/schemabinding/version2/Filter.java deleted file mode 100644 index 45323a7..0000000 --- a/src/jalview/schemabinding/version2/Filter.java +++ /dev/null @@ -1,181 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Filter. - * - * @version $Revision$ $Date$ - */ -public class Filter implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _featureType. - */ - private java.lang.String _featureType; - - /** - * Field _matcherSet. - */ - private jalview.schemabinding.version2.MatcherSet _matcherSet; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Filter() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'featureType'. - * - * @return the value of field 'FeatureType'. - */ - public java.lang.String getFeatureType() - { - return this._featureType; - } - - /** - * Returns the value of field 'matcherSet'. - * - * @return the value of field 'MatcherSet'. - */ - public jalview.schemabinding.version2.MatcherSet getMatcherSet() - { - return this._matcherSet; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'featureType'. - * - * @param featureType - * the value of field 'featureType'. - */ - public void setFeatureType(final java.lang.String featureType) - { - this._featureType = featureType; - } - - /** - * Sets the value of field 'matcherSet'. - * - * @param matcherSet - * the value of field 'matcherSet'. - */ - public void setMatcherSet( - final jalview.schemabinding.version2.MatcherSet matcherSet) - { - this._matcherSet = matcherSet; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Filter - */ - public static jalview.schemabinding.version2.Filter unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Filter) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Filter.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java deleted file mode 100644 index ec1af95..0000000 --- a/src/jalview/schemabinding/version2/Group.java +++ /dev/null @@ -1,213 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Group. - * - * @version $Revision$ $Date$ - */ -public class Group implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _display. - */ - private boolean _display; - - /** - * keeps track of state for field: _display - */ - private boolean _has_display; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Group() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteDisplay() - { - this._has_display = false; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean getDisplay() - { - return this._display; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Method hasDisplay. - * - * @return true if at least one Display has been added - */ - public boolean hasDisplay() - { - return this._has_display; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean isDisplay() - { - return this._display; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'display'. - * - * @param display - * the value of field 'display'. - */ - public void setDisplay(final boolean display) - { - this._display = display; - this._has_display = true; - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Group - */ - public static jalview.schemabinding.version2.Group unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Group.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java deleted file mode 100644 index beac4e0..0000000 --- a/src/jalview/schemabinding/version2/HiddenColumns.java +++ /dev/null @@ -1,227 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class HiddenColumns. - * - * @version $Revision$ $Date$ - */ -public class HiddenColumns implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public HiddenColumns() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.HiddenColumns - */ - public static jalview.schemabinding.version2.HiddenColumns unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller - .unmarshal(jalview.schemabinding.version2.HiddenColumns.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java deleted file mode 100644 index 962569f..0000000 --- a/src/jalview/schemabinding/version2/JGroup.java +++ /dev/null @@ -1,1260 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JGroup. - * - * @version $Revision$ $Date$ - */ -public class JGroup implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _colour. - */ - private java.lang.String _colour; - - /** - * Field _consThreshold. - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold. - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _outlineColour. - */ - private int _outlineColour; - - /** - * keeps track of state for field: _outlineColour - */ - private boolean _has_outlineColour; - - /** - * Field _displayBoxes. - */ - private boolean _displayBoxes; - - /** - * keeps track of state for field: _displayBoxes - */ - private boolean _has_displayBoxes; - - /** - * Field _displayText. - */ - private boolean _displayText; - - /** - * keeps track of state for field: _displayText - */ - private boolean _has_displayText; - - /** - * Field _colourText. - */ - private boolean _colourText; - - /** - * keeps track of state for field: _colourText - */ - private boolean _has_colourText; - - /** - * Field _textCol1. - */ - private int _textCol1; - - /** - * keeps track of state for field: _textCol1 - */ - private boolean _has_textCol1; - - /** - * Field _textCol2. - */ - private int _textCol2; - - /** - * keeps track of state for field: _textCol2 - */ - private boolean _has_textCol2; - - /** - * Field _textColThreshold. - */ - private int _textColThreshold; - - /** - * keeps track of state for field: _textColThreshold - */ - private boolean _has_textColThreshold; - - /** - * Field _showUnconserved. - */ - private boolean _showUnconserved; - - /** - * keeps track of state for field: _showUnconserved - */ - private boolean _has_showUnconserved; - - /** - * Field _ignoreGapsinConsensus. - */ - private boolean _ignoreGapsinConsensus = true; - - /** - * keeps track of state for field: _ignoreGapsinConsensus - */ - private boolean _has_ignoreGapsinConsensus; - - /** - * Field _showConsensusHistogram. - */ - private boolean _showConsensusHistogram = true; - - /** - * keeps track of state for field: _showConsensusHistogram - */ - private boolean _has_showConsensusHistogram; - - /** - * Field _showSequenceLogo. - */ - private boolean _showSequenceLogo = false; - - /** - * keeps track of state for field: _showSequenceLogo - */ - private boolean _has_showSequenceLogo; - - /** - * Field _normaliseSequenceLogo. - */ - private boolean _normaliseSequenceLogo = false; - - /** - * keeps track of state for field: _normaliseSequenceLogo - */ - private boolean _has_normaliseSequenceLogo; - - /** - * Optional sequence group ID (only needs to be unique for this alignment) - * - */ - private java.lang.String _id; - - /** - * Field _seqList. - */ - private java.util.Vector _seqList; - - /** - * Field _annotationColours. - */ - private jalview.schemabinding.version2.AnnotationColours _annotationColours; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JGroup() - { - super(); - this._seqList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSeq(final java.lang.String vSeq) - throws java.lang.IndexOutOfBoundsException - { - this._seqList.addElement(vSeq); - } - - /** - * - * - * @param index - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSeq(final int index, final java.lang.String vSeq) - throws java.lang.IndexOutOfBoundsException - { - this._seqList.add(index, vSeq); - } - - /** - */ - public void deleteColourText() - { - this._has_colourText = false; - } - - /** - */ - public void deleteConsThreshold() - { - this._has_consThreshold = false; - } - - /** - */ - public void deleteDisplayBoxes() - { - this._has_displayBoxes = false; - } - - /** - */ - public void deleteDisplayText() - { - this._has_displayText = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteIgnoreGapsinConsensus() - { - this._has_ignoreGapsinConsensus = false; - } - - /** - */ - public void deleteNormaliseSequenceLogo() - { - this._has_normaliseSequenceLogo = false; - } - - /** - */ - public void deleteOutlineColour() - { - this._has_outlineColour = false; - } - - /** - */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } - - /** - */ - public void deleteShowConsensusHistogram() - { - this._has_showConsensusHistogram = false; - } - - /** - */ - public void deleteShowSequenceLogo() - { - this._has_showSequenceLogo = false; - } - - /** - */ - public void deleteShowUnconserved() - { - this._has_showUnconserved = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - */ - public void deleteTextCol1() - { - this._has_textCol1 = false; - } - - /** - */ - public void deleteTextCol2() - { - this._has_textCol2 = false; - } - - /** - */ - public void deleteTextColThreshold() - { - this._has_textColThreshold = false; - } - - /** - * Method enumerateSeq. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateSeq() - { - return this._seqList.elements(); - } - - /** - * Returns the value of field 'annotationColours'. - * - * @return the value of field 'AnnotationColours'. - */ - public jalview.schemabinding.version2.AnnotationColours getAnnotationColours() - { - return this._annotationColours; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public java.lang.String getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'colourText'. - * - * @return the value of field 'ColourText'. - */ - public boolean getColourText() - { - return this._colourText; - } - - /** - * Returns the value of field 'consThreshold'. - * - * @return the value of field 'ConsThreshold'. - */ - public int getConsThreshold() - { - return this._consThreshold; - } - - /** - * Returns the value of field 'displayBoxes'. - * - * @return the value of field 'DisplayBoxes'. - */ - public boolean getDisplayBoxes() - { - return this._displayBoxes; - } - - /** - * Returns the value of field 'displayText'. - * - * @return the value of field 'DisplayText'. - */ - public boolean getDisplayText() - { - return this._displayText; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'id'. The field 'id' has the following - * description: Optional sequence group ID (only needs to be unique for this - * alignment) - * - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean getIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'normaliseSequenceLogo'. - * - * @return the value of field 'NormaliseSequenceLogo'. - */ - public boolean getNormaliseSequenceLogo() - { - return this._normaliseSequenceLogo; - } - - /** - * Returns the value of field 'outlineColour'. - * - * @return the value of field 'OutlineColour'. - */ - public int getOutlineColour() - { - return this._outlineColour; - } - - /** - * Returns the value of field 'pidThreshold'. - * - * @return the value of field 'PidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } - - /** - * Method getSeq. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getSeq(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._seqList.size()) - { - throw new IndexOutOfBoundsException("getSeq: Index value '" + index - + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - return (java.lang.String) _seqList.get(index); - } - - /** - * Method getSeq.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getSeq() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._seqList.toArray(array); - } - - /** - * Method getSeqCount. - * - * @return the size of this collection - */ - public int getSeqCount() - { - return this._seqList.size(); - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean getShowConsensusHistogram() - { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean getShowSequenceLogo() - { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean getShowUnconserved() - { - return this._showUnconserved; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Returns the value of field 'textCol1'. - * - * @return the value of field 'TextCol1'. - */ - public int getTextCol1() - { - return this._textCol1; - } - - /** - * Returns the value of field 'textCol2'. - * - * @return the value of field 'TextCol2'. - */ - public int getTextCol2() - { - return this._textCol2; - } - - /** - * Returns the value of field 'textColThreshold'. - * - * @return the value of field 'TextColThreshold'. - */ - public int getTextColThreshold() - { - return this._textColThreshold; - } - - /** - * Method hasColourText. - * - * @return true if at least one ColourText has been added - */ - public boolean hasColourText() - { - return this._has_colourText; - } - - /** - * Method hasConsThreshold. - * - * @return true if at least one ConsThreshold has been added - */ - public boolean hasConsThreshold() - { - return this._has_consThreshold; - } - - /** - * Method hasDisplayBoxes. - * - * @return true if at least one DisplayBoxes has been added - */ - public boolean hasDisplayBoxes() - { - return this._has_displayBoxes; - } - - /** - * Method hasDisplayText. - * - * @return true if at least one DisplayText has been added - */ - public boolean hasDisplayText() - { - return this._has_displayText; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasIgnoreGapsinConsensus. - * - * @return true if at least one IgnoreGapsinConsensus has been added - */ - public boolean hasIgnoreGapsinConsensus() - { - return this._has_ignoreGapsinConsensus; - } - - /** - * Method hasNormaliseSequenceLogo. - * - * @return true if at least one NormaliseSequenceLogo has been added - */ - public boolean hasNormaliseSequenceLogo() - { - return this._has_normaliseSequenceLogo; - } - - /** - * Method hasOutlineColour. - * - * @return true if at least one OutlineColour has been added - */ - public boolean hasOutlineColour() - { - return this._has_outlineColour; - } - - /** - * Method hasPidThreshold. - * - * @return true if at least one PidThreshold has been added - */ - public boolean hasPidThreshold() - { - return this._has_pidThreshold; - } - - /** - * Method hasShowConsensusHistogram. - * - * @return true if at least one ShowConsensusHistogram has been added - */ - public boolean hasShowConsensusHistogram() - { - return this._has_showConsensusHistogram; - } - - /** - * Method hasShowSequenceLogo. - * - * @return true if at least one ShowSequenceLogo has been added - */ - public boolean hasShowSequenceLogo() - { - return this._has_showSequenceLogo; - } - - /** - * Method hasShowUnconserved. - * - * @return true if at least one ShowUnconserved has been added - */ - public boolean hasShowUnconserved() - { - return this._has_showUnconserved; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method hasTextCol1. - * - * @return true if at least one TextCol1 has been added - */ - public boolean hasTextCol1() - { - return this._has_textCol1; - } - - /** - * Method hasTextCol2. - * - * @return true if at least one TextCol2 has been added - */ - public boolean hasTextCol2() - { - return this._has_textCol2; - } - - /** - * Method hasTextColThreshold. - * - * @return true if at least one TextColThreshold has been added - */ - public boolean hasTextColThreshold() - { - return this._has_textColThreshold; - } - - /** - * Returns the value of field 'colourText'. - * - * @return the value of field 'ColourText'. - */ - public boolean isColourText() - { - return this._colourText; - } - - /** - * Returns the value of field 'displayBoxes'. - * - * @return the value of field 'DisplayBoxes'. - */ - public boolean isDisplayBoxes() - { - return this._displayBoxes; - } - - /** - * Returns the value of field 'displayText'. - * - * @return the value of field 'DisplayText'. - */ - public boolean isDisplayText() - { - return this._displayText; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean isIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'normaliseSequenceLogo'. - * - * @return the value of field 'NormaliseSequenceLogo'. - */ - public boolean isNormaliseSequenceLogo() - { - return this._normaliseSequenceLogo; - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean isShowConsensusHistogram() - { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean isShowSequenceLogo() - { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean isShowUnconserved() - { - return this._showUnconserved; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSeq() - { - this._seqList.clear(); - } - - /** - * Method removeSeq. - * - * @param vSeq - * @return true if the object was removed from the collection. - */ - public boolean removeSeq(final java.lang.String vSeq) - { - boolean removed = _seqList.remove(vSeq); - return removed; - } - - /** - * Method removeSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeSeqAt(final int index) - { - java.lang.Object obj = this._seqList.remove(index); - return (java.lang.String) obj; - } - - /** - * Sets the value of field 'annotationColours'. - * - * @param annotationColours - * the value of field 'annotationColours'. - */ - public void setAnnotationColours( - final jalview.schemabinding.version2.AnnotationColours annotationColours) - { - this._annotationColours = annotationColours; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final java.lang.String colour) - { - this._colour = colour; - } - - /** - * Sets the value of field 'colourText'. - * - * @param colourText - * the value of field 'colourText'. - */ - public void setColourText(final boolean colourText) - { - this._colourText = colourText; - this._has_colourText = true; - } - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold - * the value of field 'consThreshold'. - */ - public void setConsThreshold(final int consThreshold) - { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } - - /** - * Sets the value of field 'displayBoxes'. - * - * @param displayBoxes - * the value of field 'displayBoxes'. - */ - public void setDisplayBoxes(final boolean displayBoxes) - { - this._displayBoxes = displayBoxes; - this._has_displayBoxes = true; - } - - /** - * Sets the value of field 'displayText'. - * - * @param displayText - * the value of field 'displayText'. - */ - public void setDisplayText(final boolean displayText) - { - this._displayText = displayText; - this._has_displayText = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'id'. The field 'id' has the following description: - * Optional sequence group ID (only needs to be unique for this alignment) - * - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'ignoreGapsinConsensus'. - * - * @param ignoreGapsinConsensus - * the value of field 'ignoreGapsinConsensus'. - */ - public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus) - { - this._ignoreGapsinConsensus = ignoreGapsinConsensus; - this._has_ignoreGapsinConsensus = true; - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'normaliseSequenceLogo'. - * - * @param normaliseSequenceLogo - * the value of field 'normaliseSequenceLogo'. - */ - public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo) - { - this._normaliseSequenceLogo = normaliseSequenceLogo; - this._has_normaliseSequenceLogo = true; - } - - /** - * Sets the value of field 'outlineColour'. - * - * @param outlineColour - * the value of field 'outlineColour'. - */ - public void setOutlineColour(final int outlineColour) - { - this._outlineColour = outlineColour; - this._has_outlineColour = true; - } - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold - * the value of field 'pidThreshold'. - */ - public void setPidThreshold(final int pidThreshold) - { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } - - /** - * - * - * @param index - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSeq(final int index, final java.lang.String vSeq) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._seqList.size()) - { - throw new IndexOutOfBoundsException("setSeq: Index value '" + index - + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - this._seqList.set(index, vSeq); - } - - /** - * - * - * @param vSeqArray - */ - public void setSeq(final java.lang.String[] vSeqArray) - { - // -- copy array - _seqList.clear(); - - for (int i = 0; i < vSeqArray.length; i++) - { - this._seqList.add(vSeqArray[i]); - } - } - - /** - * Sets the value of field 'showConsensusHistogram'. - * - * @param showConsensusHistogram - * the value of field 'showConsensusHistogram'. - */ - public void setShowConsensusHistogram(final boolean showConsensusHistogram) - { - this._showConsensusHistogram = showConsensusHistogram; - this._has_showConsensusHistogram = true; - } - - /** - * Sets the value of field 'showSequenceLogo'. - * - * @param showSequenceLogo - * the value of field 'showSequenceLogo' - */ - public void setShowSequenceLogo(final boolean showSequenceLogo) - { - this._showSequenceLogo = showSequenceLogo; - this._has_showSequenceLogo = true; - } - - /** - * Sets the value of field 'showUnconserved'. - * - * @param showUnconserved - * the value of field 'showUnconserved'. - */ - public void setShowUnconserved(final boolean showUnconserved) - { - this._showUnconserved = showUnconserved; - this._has_showUnconserved = true; - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Sets the value of field 'textCol1'. - * - * @param textCol1 - * the value of field 'textCol1'. - */ - public void setTextCol1(final int textCol1) - { - this._textCol1 = textCol1; - this._has_textCol1 = true; - } - - /** - * Sets the value of field 'textCol2'. - * - * @param textCol2 - * the value of field 'textCol2'. - */ - public void setTextCol2(final int textCol2) - { - this._textCol2 = textCol2; - this._has_textCol2 = true; - } - - /** - * Sets the value of field 'textColThreshold'. - * - * @param textColThreshold - * the value of field 'textColThreshold' - */ - public void setTextColThreshold(final int textColThreshold) - { - this._textColThreshold = textColThreshold; - this._has_textColThreshold = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.JGroup - */ - public static jalview.schemabinding.version2.JGroup unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal( - jalview.schemabinding.version2.JGroup.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java deleted file mode 100644 index 7c6308e..0000000 --- a/src/jalview/schemabinding/version2/JSeq.java +++ /dev/null @@ -1,1097 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JSeq. - * - * @version $Revision$ $Date$ - */ -public class JSeq implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _hidden. - */ - private boolean _hidden; - - /** - * keeps track of state for field: _hidden - */ - private boolean _has_hidden; - - /** - * Field _viewreference. - */ - private boolean _viewreference; - - /** - * keeps track of state for field: _viewreference - */ - private boolean _has_viewreference; - - /** - * Field _featuresList. - */ - private java.util.Vector _featuresList; - - /** - * Field _pdbidsList. - */ - private java.util.Vector _pdbidsList; - - /** - * Field _hiddenSequencesList. - */ - private java.util.Vector _hiddenSequencesList; - - /** - * Reference to a viewer showing RNA structure for this sequence. Schema - * supports one viewer showing multiple annotations for multiple sequences, - * though currently only one annotation for one sequence (gapped or trimmed) - * is used - * - */ - private java.util.Vector _rnaViewerList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JSeq() - { - super(); - this._featuresList = new java.util.Vector(); - this._pdbidsList = new java.util.Vector(); - this._hiddenSequencesList = new java.util.Vector(); - this._rnaViewerList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFeatures( - final jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.addElement(vFeatures); - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFeatures(final int index, - final jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.add(index, vFeatures); - } - - /** - * - * - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenSequences(final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenSequencesList.addElement(new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param index - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenSequences(final int index, final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenSequencesList.add(index, new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - this._pdbidsList.addElement(vPdbids); - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final int index, - final jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - this._pdbidsList.add(index, vPdbids); - } - - /** - * - * - * @param vRnaViewer - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addRnaViewer( - final jalview.schemabinding.version2.RnaViewer vRnaViewer) - throws java.lang.IndexOutOfBoundsException - { - this._rnaViewerList.addElement(vRnaViewer); - } - - /** - * - * - * @param index - * @param vRnaViewer - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addRnaViewer(final int index, - final jalview.schemabinding.version2.RnaViewer vRnaViewer) - throws java.lang.IndexOutOfBoundsException - { - this._rnaViewerList.add(index, vRnaViewer); - } - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteHidden() - { - this._has_hidden = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - */ - public void deleteViewreference() - { - this._has_viewreference = false; - } - - /** - * Method enumerateFeatures. - * - * @return an Enumeration over all jalview.schemabinding.version2.Features - * elements - */ - public java.util.Enumeration enumerateFeatures() - { - return this._featuresList.elements(); - } - - /** - * Method enumerateHiddenSequences. - * - * @return an Enumeration over all int elements - */ - public java.util.Enumeration enumerateHiddenSequences() - { - return this._hiddenSequencesList.elements(); - } - - /** - * Method enumeratePdbids. - * - * @return an Enumeration over all jalview.schemabinding.version2.Pdbids - * elements - */ - public java.util.Enumeration enumeratePdbids() - { - return this._pdbidsList.elements(); - } - - /** - * Method enumerateRnaViewer. - * - * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer - * elements - */ - public java.util.Enumeration enumerateRnaViewer() - { - return this._rnaViewerList.elements(); - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Method getFeatures. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Features at the - * given index - */ - public jalview.schemabinding.version2.Features getFeatures(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) - { - throw new IndexOutOfBoundsException("getFeatures: Index value '" - + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Features) _featuresList - .get(index); - } - - /** - * Method getFeatures.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Features[] getFeatures() - { - jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0]; - return (jalview.schemabinding.version2.Features[]) this._featuresList - .toArray(array); - } - - /** - * Method getFeaturesCount. - * - * @return the size of this collection - */ - public int getFeaturesCount() - { - return this._featuresList.size(); - } - - /** - * Returns the value of field 'hidden'. - * - * @return the value of field 'Hidden'. - */ - public boolean getHidden() - { - return this._hidden; - } - - /** - * Method getHiddenSequences. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the int at the given index - */ - public int getHiddenSequences(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenSequencesList.size()) - { - throw new IndexOutOfBoundsException( - "getHiddenSequences: Index value '" + index - + "' not in range [0.." - + (this._hiddenSequencesList.size() - 1) + "]"); - } - - return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue(); - } - - /** - * Method getHiddenSequences.Returns the contents of the collection in an - * Array. - * - * @return this collection as an Array - */ - public int[] getHiddenSequences() - { - int size = this._hiddenSequencesList.size(); - int[] array = new int[size]; - java.util.Iterator iter = _hiddenSequencesList.iterator(); - for (int index = 0; index < size; index++) - { - array[index] = ((java.lang.Integer) iter.next()).intValue(); - } - return array; - } - - /** - * Method getHiddenSequencesCount. - * - * @return the size of this collection - */ - public int getHiddenSequencesCount() - { - return this._hiddenSequencesList.size(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Method getPdbids. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Pdbids at the given - * index - */ - public jalview.schemabinding.version2.Pdbids getPdbids(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) - { - throw new IndexOutOfBoundsException("getPdbids: Index value '" - + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index); - } - - /** - * Method getPdbids.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Pdbids[] getPdbids() - { - jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0]; - return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList - .toArray(array); - } - - /** - * Method getPdbidsCount. - * - * @return the size of this collection - */ - public int getPdbidsCount() - { - return this._pdbidsList.size(); - } - - /** - * Method getRnaViewer. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.RnaViewer at the - * given index - */ - public jalview.schemabinding.version2.RnaViewer getRnaViewer( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._rnaViewerList.size()) - { - throw new IndexOutOfBoundsException("getRnaViewer: Index value '" - + index + "' not in range [0.." - + (this._rnaViewerList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList - .get(index); - } - - /** - * Method getRnaViewer.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.RnaViewer[] getRnaViewer() - { - jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0]; - return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList - .toArray(array); - } - - /** - * Method getRnaViewerCount. - * - * @return the size of this collection - */ - public int getRnaViewerCount() - { - return this._rnaViewerList.size(); - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Returns the value of field 'viewreference'. - * - * @return the value of field 'Viewreference'. - */ - public boolean getViewreference() - { - return this._viewreference; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasHidden. - * - * @return true if at least one Hidden has been added - */ - public boolean hasHidden() - { - return this._has_hidden; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method hasViewreference. - * - * @return true if at least one Viewreference has been added - */ - public boolean hasViewreference() - { - return this._has_viewreference; - } - - /** - * Returns the value of field 'hidden'. - * - * @return the value of field 'Hidden'. - */ - public boolean isHidden() - { - return this._hidden; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * Returns the value of field 'viewreference'. - * - * @return the value of field 'Viewreference'. - */ - public boolean isViewreference() - { - return this._viewreference; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllFeatures() - { - this._featuresList.clear(); - } - - /** - */ - public void removeAllHiddenSequences() - { - this._hiddenSequencesList.clear(); - } - - /** - */ - public void removeAllPdbids() - { - this._pdbidsList.clear(); - } - - /** - */ - public void removeAllRnaViewer() - { - this._rnaViewerList.clear(); - } - - /** - * Method removeFeatures. - * - * @param vFeatures - * @return true if the object was removed from the collection. - */ - public boolean removeFeatures( - final jalview.schemabinding.version2.Features vFeatures) - { - boolean removed = _featuresList.remove(vFeatures); - return removed; - } - - /** - * Method removeFeaturesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Features removeFeaturesAt( - final int index) - { - java.lang.Object obj = this._featuresList.remove(index); - return (jalview.schemabinding.version2.Features) obj; - } - - /** - * Method removeHiddenSequences. - * - * @param vHiddenSequences - * @return true if the object was removed from the collection. - */ - public boolean removeHiddenSequences(final int vHiddenSequences) - { - boolean removed = _hiddenSequencesList.remove(new java.lang.Integer( - vHiddenSequences)); - return removed; - } - - /** - * Method removeHiddenSequencesAt. - * - * @param index - * @return the element removed from the collection - */ - public int removeHiddenSequencesAt(final int index) - { - java.lang.Object obj = this._hiddenSequencesList.remove(index); - return ((java.lang.Integer) obj).intValue(); - } - - /** - * Method removePdbids. - * - * @param vPdbids - * @return true if the object was removed from the collection. - */ - public boolean removePdbids( - final jalview.schemabinding.version2.Pdbids vPdbids) - { - boolean removed = _pdbidsList.remove(vPdbids); - return removed; - } - - /** - * Method removePdbidsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Pdbids removePdbidsAt( - final int index) - { - java.lang.Object obj = this._pdbidsList.remove(index); - return (jalview.schemabinding.version2.Pdbids) obj; - } - - /** - * Method removeRnaViewer. - * - * @param vRnaViewer - * @return true if the object was removed from the collection. - */ - public boolean removeRnaViewer( - final jalview.schemabinding.version2.RnaViewer vRnaViewer) - { - boolean removed = _rnaViewerList.remove(vRnaViewer); - return removed; - } - - /** - * Method removeRnaViewerAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt( - final int index) - { - java.lang.Object obj = this._rnaViewerList.remove(index); - return (jalview.schemabinding.version2.RnaViewer) obj; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setFeatures(final int index, - final jalview.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) - { - throw new IndexOutOfBoundsException("setFeatures: Index value '" - + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); - } - - this._featuresList.set(index, vFeatures); - } - - /** - * - * - * @param vFeaturesArray - */ - public void setFeatures( - final jalview.schemabinding.version2.Features[] vFeaturesArray) - { - // -- copy array - _featuresList.clear(); - - for (int i = 0; i < vFeaturesArray.length; i++) - { - this._featuresList.add(vFeaturesArray[i]); - } - } - - /** - * Sets the value of field 'hidden'. - * - * @param hidden - * the value of field 'hidden'. - */ - public void setHidden(final boolean hidden) - { - this._hidden = hidden; - this._has_hidden = true; - } - - /** - * - * - * @param index - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setHiddenSequences(final int index, final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenSequencesList.size()) - { - throw new IndexOutOfBoundsException( - "setHiddenSequences: Index value '" + index - + "' not in range [0.." - + (this._hiddenSequencesList.size() - 1) + "]"); - } - - this._hiddenSequencesList.set(index, new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param vHiddenSequencesArray - */ - public void setHiddenSequences(final int[] vHiddenSequencesArray) - { - // -- copy array - _hiddenSequencesList.clear(); - - for (int i = 0; i < vHiddenSequencesArray.length; i++) - { - this._hiddenSequencesList.add(new java.lang.Integer( - vHiddenSequencesArray[i])); - } - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbids(final int index, - final jalview.schemabinding.version2.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) - { - throw new IndexOutOfBoundsException("setPdbids: Index value '" - + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); - } - - this._pdbidsList.set(index, vPdbids); - } - - /** - * - * - * @param vPdbidsArray - */ - public void setPdbids( - final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) - { - // -- copy array - _pdbidsList.clear(); - - for (int i = 0; i < vPdbidsArray.length; i++) - { - this._pdbidsList.add(vPdbidsArray[i]); - } - } - - /** - * - * - * @param index - * @param vRnaViewer - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setRnaViewer(final int index, - final jalview.schemabinding.version2.RnaViewer vRnaViewer) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._rnaViewerList.size()) - { - throw new IndexOutOfBoundsException("setRnaViewer: Index value '" - + index + "' not in range [0.." - + (this._rnaViewerList.size() - 1) + "]"); - } - - this._rnaViewerList.set(index, vRnaViewer); - } - - /** - * - * - * @param vRnaViewerArray - */ - public void setRnaViewer( - final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray) - { - // -- copy array - _rnaViewerList.clear(); - - for (int i = 0; i < vRnaViewerArray.length; i++) - { - this._rnaViewerList.add(vRnaViewerArray[i]); - } - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Sets the value of field 'viewreference'. - * - * @param viewreference - * the value of field 'viewreference'. - */ - public void setViewreference(final boolean viewreference) - { - this._viewreference = viewreference; - this._has_viewreference = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.JSeq - */ - public static jalview.schemabinding.version2.JSeq unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal( - jalview.schemabinding.version2.JSeq.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java deleted file mode 100644 index c13ef64..0000000 --- a/src/jalview/schemabinding/version2/JalviewModel.java +++ /dev/null @@ -1,235 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewModel. - * - * @version $Revision$ $Date$ - */ -public class JalviewModel implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _creationDate. - */ - private java.util.Date _creationDate; - - /** - * Field _version. - */ - private java.lang.String _version; - - /** - * Field _vamsasModel. - */ - private jalview.schemabinding.version2.VamsasModel _vamsasModel; - - /** - * Field _jalviewModelSequence. - */ - private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModel() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'creationDate'. - * - * @return the value of field 'CreationDate'. - */ - public java.util.Date getCreationDate() - { - return this._creationDate; - } - - /** - * Returns the value of field 'jalviewModelSequence'. - * - * @return the value of field 'JalviewModelSequence'. - */ - public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence() - { - return this._jalviewModelSequence; - } - - /** - * Returns the value of field 'vamsasModel'. - * - * @return the value of field 'VamsasModel'. - */ - public jalview.schemabinding.version2.VamsasModel getVamsasModel() - { - return this._vamsasModel; - } - - /** - * Returns the value of field 'version'. - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion() - { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'creationDate'. - * - * @param creationDate - * the value of field 'creationDate'. - */ - public void setCreationDate(final java.util.Date creationDate) - { - this._creationDate = creationDate; - } - - /** - * Sets the value of field 'jalviewModelSequence'. - * - * @param jalviewModelSequence - * the value of field 'jalviewModelSequence'. - */ - public void setJalviewModelSequence( - final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence) - { - this._jalviewModelSequence = jalviewModelSequence; - } - - /** - * Sets the value of field 'vamsasModel'. - * - * @param vamsasModel - * the value of field 'vamsasModel'. - */ - public void setVamsasModel( - final jalview.schemabinding.version2.VamsasModel vamsasModel) - { - this._vamsasModel = vamsasModel; - } - - /** - * Sets the value of field 'version'. - * - * @param version - * the value of field 'version'. - */ - public void setVersion(final java.lang.String version) - { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.JalviewModel - */ - public static jalview.schemabinding.version2.JalviewModel unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JalviewModel) Unmarshaller - .unmarshal(jalview.schemabinding.version2.JalviewModel.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java deleted file mode 100644 index c7c02c5..0000000 --- a/src/jalview/schemabinding/version2/JalviewModelSequence.java +++ /dev/null @@ -1,986 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewModelSequence. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelSequence implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _JSeqList. - */ - private java.util.Vector _JSeqList; - - /** - * Field _JGroupList. - */ - private java.util.Vector _JGroupList; - - /** - * Field _viewportList. - */ - private java.util.Vector _viewportList; - - /** - * Field _userColoursList. - */ - private java.util.Vector _userColoursList; - - /** - * Field _treeList. - */ - private java.util.Vector _treeList; - - /** - * Field _featureSettings. - */ - private jalview.schemabinding.version2.FeatureSettings _featureSettings; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModelSequence() - { - super(); - this._JSeqList = new java.util.Vector(); - this._JGroupList = new java.util.Vector(); - this._viewportList = new java.util.Vector(); - this._userColoursList = new java.util.Vector(); - this._treeList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - this._JGroupList.addElement(vJGroup); - } - - /** - * - * - * @param index - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJGroup(final int index, - final jalview.schemabinding.version2.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - this._JGroupList.add(index, vJGroup); - } - - /** - * - * - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - this._JSeqList.addElement(vJSeq); - } - - /** - * - * - * @param index - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJSeq(final int index, - final jalview.schemabinding.version2.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - this._JSeqList.add(index, vJSeq); - } - - /** - * - * - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final jalview.schemabinding.version2.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.addElement(vTree); - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final int index, - final jalview.schemabinding.version2.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.add(index, vTree); - } - - /** - * - * - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addUserColours( - final jalview.schemabinding.version2.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - this._userColoursList.addElement(vUserColours); - } - - /** - * - * - * @param index - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addUserColours(final int index, - final jalview.schemabinding.version2.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - this._userColoursList.add(index, vUserColours); - } - - /** - * - * - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addViewport( - final jalview.schemabinding.version2.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - this._viewportList.addElement(vViewport); - } - - /** - * - * - * @param index - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addViewport(final int index, - final jalview.schemabinding.version2.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - this._viewportList.add(index, vViewport); - } - - /** - * Method enumerateJGroup. - * - * @return an Enumeration over all jalview.schemabinding.version2.JGroup - * elements - */ - public java.util.Enumeration enumerateJGroup() - { - return this._JGroupList.elements(); - } - - /** - * Method enumerateJSeq. - * - * @return an Enumeration over all jalview.schemabinding.version2.JSeq - * elements - */ - public java.util.Enumeration enumerateJSeq() - { - return this._JSeqList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all jalview.schemabinding.version2.Tree - * elements - */ - public java.util.Enumeration enumerateTree() - { - return this._treeList.elements(); - } - - /** - * Method enumerateUserColours. - * - * @return an Enumeration over all jalview.schemabinding.version2.UserColours - * elements - */ - public java.util.Enumeration enumerateUserColours() - { - return this._userColoursList.elements(); - } - - /** - * Method enumerateViewport. - * - * @return an Enumeration over all jalview.schemabinding.version2.Viewport - * elements - */ - public java.util.Enumeration enumerateViewport() - { - return this._viewportList.elements(); - } - - /** - * Returns the value of field 'featureSettings'. - * - * @return the value of field 'FeatureSettings'. - */ - public jalview.schemabinding.version2.FeatureSettings getFeatureSettings() - { - return this._featureSettings; - } - - /** - * Method getJGroup. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.JGroup at the given - * index - */ - public jalview.schemabinding.version2.JGroup getJGroup(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JGroupList.size()) - { - throw new IndexOutOfBoundsException("getJGroup: Index value '" - + index + "' not in range [0.." - + (this._JGroupList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index); - } - - /** - * Method getJGroup.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.JGroup[] getJGroup() - { - jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0]; - return (jalview.schemabinding.version2.JGroup[]) this._JGroupList - .toArray(array); - } - - /** - * Method getJGroupCount. - * - * @return the size of this collection - */ - public int getJGroupCount() - { - return this._JGroupList.size(); - } - - /** - * Method getJSeq. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.JSeq at the given - * index - */ - public jalview.schemabinding.version2.JSeq getJSeq(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JSeqList.size()) - { - throw new IndexOutOfBoundsException("getJSeq: Index value '" + index - + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index); - } - - /** - * Method getJSeq.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.JSeq[] getJSeq() - { - jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0]; - return (jalview.schemabinding.version2.JSeq[]) this._JSeqList - .toArray(array); - } - - /** - * Method getJSeqCount. - * - * @return the size of this collection - */ - public int getJSeqCount() - { - return this._JSeqList.size(); - } - - /** - * Method getTree. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Tree at the given - * index - */ - public jalview.schemabinding.version2.Tree getTree(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("getTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Tree) _treeList.get(index); - } - - /** - * Method getTree.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Tree[] getTree() - { - jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0]; - return (jalview.schemabinding.version2.Tree[]) this._treeList - .toArray(array); - } - - /** - * Method getTreeCount. - * - * @return the size of this collection - */ - public int getTreeCount() - { - return this._treeList.size(); - } - - /** - * Method getUserColours. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.UserColours at the - * given index - */ - public jalview.schemabinding.version2.UserColours getUserColours( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._userColoursList.size()) - { - throw new IndexOutOfBoundsException("getUserColours: Index value '" - + index + "' not in range [0.." - + (this._userColoursList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.UserColours) _userColoursList - .get(index); - } - - /** - * Method getUserColours.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.UserColours[] getUserColours() - { - jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0]; - return (jalview.schemabinding.version2.UserColours[]) this._userColoursList - .toArray(array); - } - - /** - * Method getUserColoursCount. - * - * @return the size of this collection - */ - public int getUserColoursCount() - { - return this._userColoursList.size(); - } - - /** - * Method getViewport. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Viewport at the - * given index - */ - public jalview.schemabinding.version2.Viewport getViewport(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._viewportList.size()) - { - throw new IndexOutOfBoundsException("getViewport: Index value '" - + index + "' not in range [0.." - + (this._viewportList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Viewport) _viewportList - .get(index); - } - - /** - * Method getViewport.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Viewport[] getViewport() - { - jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0]; - return (jalview.schemabinding.version2.Viewport[]) this._viewportList - .toArray(array); - } - - /** - * Method getViewportCount. - * - * @return the size of this collection - */ - public int getViewportCount() - { - return this._viewportList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllJGroup() - { - this._JGroupList.clear(); - } - - /** - */ - public void removeAllJSeq() - { - this._JSeqList.clear(); - } - - /** - */ - public void removeAllTree() - { - this._treeList.clear(); - } - - /** - */ - public void removeAllUserColours() - { - this._userColoursList.clear(); - } - - /** - */ - public void removeAllViewport() - { - this._viewportList.clear(); - } - - /** - * Method removeJGroup. - * - * @param vJGroup - * @return true if the object was removed from the collection. - */ - public boolean removeJGroup( - final jalview.schemabinding.version2.JGroup vJGroup) - { - boolean removed = _JGroupList.remove(vJGroup); - return removed; - } - - /** - * Method removeJGroupAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.JGroup removeJGroupAt( - final int index) - { - java.lang.Object obj = this._JGroupList.remove(index); - return (jalview.schemabinding.version2.JGroup) obj; - } - - /** - * Method removeJSeq. - * - * @param vJSeq - * @return true if the object was removed from the collection. - */ - public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq) - { - boolean removed = _JSeqList.remove(vJSeq); - return removed; - } - - /** - * Method removeJSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index) - { - java.lang.Object obj = this._JSeqList.remove(index); - return (jalview.schemabinding.version2.JSeq) obj; - } - - /** - * Method removeTree. - * - * @param vTree - * @return true if the object was removed from the collection. - */ - public boolean removeTree(final jalview.schemabinding.version2.Tree vTree) - { - boolean removed = _treeList.remove(vTree); - return removed; - } - - /** - * Method removeTreeAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Tree removeTreeAt(final int index) - { - java.lang.Object obj = this._treeList.remove(index); - return (jalview.schemabinding.version2.Tree) obj; - } - - /** - * Method removeUserColours. - * - * @param vUserColours - * @return true if the object was removed from the collection. - */ - public boolean removeUserColours( - final jalview.schemabinding.version2.UserColours vUserColours) - { - boolean removed = _userColoursList.remove(vUserColours); - return removed; - } - - /** - * Method removeUserColoursAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.UserColours removeUserColoursAt( - final int index) - { - java.lang.Object obj = this._userColoursList.remove(index); - return (jalview.schemabinding.version2.UserColours) obj; - } - - /** - * Method removeViewport. - * - * @param vViewport - * @return true if the object was removed from the collection. - */ - public boolean removeViewport( - final jalview.schemabinding.version2.Viewport vViewport) - { - boolean removed = _viewportList.remove(vViewport); - return removed; - } - - /** - * Method removeViewportAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Viewport removeViewportAt( - final int index) - { - java.lang.Object obj = this._viewportList.remove(index); - return (jalview.schemabinding.version2.Viewport) obj; - } - - /** - * Sets the value of field 'featureSettings'. - * - * @param featureSettings - * the value of field 'featureSettings'. - */ - public void setFeatureSettings( - final jalview.schemabinding.version2.FeatureSettings featureSettings) - { - this._featureSettings = featureSettings; - } - - /** - * - * - * @param index - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setJGroup(final int index, - final jalview.schemabinding.version2.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JGroupList.size()) - { - throw new IndexOutOfBoundsException("setJGroup: Index value '" - + index + "' not in range [0.." - + (this._JGroupList.size() - 1) + "]"); - } - - this._JGroupList.set(index, vJGroup); - } - - /** - * - * - * @param vJGroupArray - */ - public void setJGroup( - final jalview.schemabinding.version2.JGroup[] vJGroupArray) - { - // -- copy array - _JGroupList.clear(); - - for (int i = 0; i < vJGroupArray.length; i++) - { - this._JGroupList.add(vJGroupArray[i]); - } - } - - /** - * - * - * @param index - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setJSeq(final int index, - final jalview.schemabinding.version2.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JSeqList.size()) - { - throw new IndexOutOfBoundsException("setJSeq: Index value '" + index - + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); - } - - this._JSeqList.set(index, vJSeq); - } - - /** - * - * - * @param vJSeqArray - */ - public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray) - { - // -- copy array - _JSeqList.clear(); - - for (int i = 0; i < vJSeqArray.length; i++) - { - this._JSeqList.add(vJSeqArray[i]); - } - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setTree(final int index, - final jalview.schemabinding.version2.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("setTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - this._treeList.set(index, vTree); - } - - /** - * - * - * @param vTreeArray - */ - public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray) - { - // -- copy array - _treeList.clear(); - - for (int i = 0; i < vTreeArray.length; i++) - { - this._treeList.add(vTreeArray[i]); - } - } - - /** - * - * - * @param index - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setUserColours(final int index, - final jalview.schemabinding.version2.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._userColoursList.size()) - { - throw new IndexOutOfBoundsException("setUserColours: Index value '" - + index + "' not in range [0.." - + (this._userColoursList.size() - 1) + "]"); - } - - this._userColoursList.set(index, vUserColours); - } - - /** - * - * - * @param vUserColoursArray - */ - public void setUserColours( - final jalview.schemabinding.version2.UserColours[] vUserColoursArray) - { - // -- copy array - _userColoursList.clear(); - - for (int i = 0; i < vUserColoursArray.length; i++) - { - this._userColoursList.add(vUserColoursArray[i]); - } - } - - /** - * - * - * @param index - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setViewport(final int index, - final jalview.schemabinding.version2.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._viewportList.size()) - { - throw new IndexOutOfBoundsException("setViewport: Index value '" - + index + "' not in range [0.." - + (this._viewportList.size() - 1) + "]"); - } - - this._viewportList.set(index, vViewport); - } - - /** - * - * - * @param vViewportArray - */ - public void setViewport( - final jalview.schemabinding.version2.Viewport[] vViewportArray) - { - // -- copy array - _viewportList.clear(); - - for (int i = 0; i < vViewportArray.length; i++) - { - this._viewportList.add(vViewportArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence - */ - public static jalview.schemabinding.version2.JalviewModelSequence unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.JalviewModelSequence.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java deleted file mode 100644 index c8d52ac..0000000 --- a/src/jalview/schemabinding/version2/JalviewUserColours.java +++ /dev/null @@ -1,505 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewUserColours. - * - * @version $Revision$ $Date$ - */ -public class JalviewUserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _schemeName. - */ - private java.lang.String _schemeName; - - /** - * Jalview colour scheme document version. - * - */ - private java.lang.String _version; - - /** - * Field _colourList. - */ - private java.util.Vector _colourList; - - /** - * Field _filterList. - */ - private java.util.Vector _filterList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewUserColours() - { - super(); - this._colourList = new java.util.Vector(); - this._filterList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addColour(final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - this._colourList.addElement(vColour); - } - - /** - * - * - * @param index - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addColour(final int index, final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - this._colourList.add(index, vColour); - } - - /** - * - * - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFilter(final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - this._filterList.addElement(vFilter); - } - - /** - * - * - * @param index - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFilter(final int index, final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - this._filterList.add(index, vFilter); - } - - /** - * Method enumerateColour. - * - * @return an Enumeration over all Colour elements - */ - public java.util.Enumeration enumerateColour() - { - return this._colourList.elements(); - } - - /** - * Method enumerateFilter. - * - * @return an Enumeration over all Filter elements - */ - public java.util.Enumeration enumerateFilter() - { - return this._filterList.elements(); - } - - /** - * Method getColour. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the Colour at the given index - */ - public Colour getColour(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._colourList.size()) - { - throw new IndexOutOfBoundsException( - "getColour: Index value '" + index + "' not in range [0.." - + (this._colourList.size() - 1) + "]"); - } - - return (Colour) _colourList.get(index); - } - - /** - * Method getColour.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Colour[] getColour() - { - Colour[] array = new Colour[0]; - return (Colour[]) this._colourList.toArray(array); - } - - /** - * Method getColourCount. - * - * @return the size of this collection - */ - public int getColourCount() - { - return this._colourList.size(); - } - - /** - * Method getFilter. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the Filter at the given index - */ - public Filter getFilter(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._filterList.size()) - { - throw new IndexOutOfBoundsException( - "getFilter: Index value '" + index + "' not in range [0.." - + (this._filterList.size() - 1) + "]"); - } - - return (Filter) _filterList.get(index); - } - - /** - * Method getFilter.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Filter[] getFilter() - { - Filter[] array = new Filter[0]; - return (Filter[]) this._filterList.toArray(array); - } - - /** - * Method getFilterCount. - * - * @return the size of this collection - */ - public int getFilterCount() - { - return this._filterList.size(); - } - - /** - * Returns the value of field 'schemeName'. - * - * @return the value of field 'SchemeName'. - */ - public java.lang.String getSchemeName() - { - return this._schemeName; - } - - /** - * Returns the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document version. - * - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion() - { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllColour() - { - this._colourList.clear(); - } - - /** - */ - public void removeAllFilter() - { - this._filterList.clear(); - } - - /** - * Method removeColour. - * - * @param vColour - * @return true if the object was removed from the collection. - */ - public boolean removeColour(final Colour vColour) - { - boolean removed = _colourList.remove(vColour); - return removed; - } - - /** - * Method removeColourAt. - * - * @param index - * @return the element removed from the collection - */ - public Colour removeColourAt(final int index) - { - java.lang.Object obj = this._colourList.remove(index); - return (Colour) obj; - } - - /** - * Method removeFilter. - * - * @param vFilter - * @return true if the object was removed from the collection. - */ - public boolean removeFilter(final Filter vFilter) - { - boolean removed = _filterList.remove(vFilter); - return removed; - } - - /** - * Method removeFilterAt. - * - * @param index - * @return the element removed from the collection - */ - public Filter removeFilterAt(final int index) - { - java.lang.Object obj = this._filterList.remove(index); - return (Filter) obj; - } - - /** - * - * - * @param index - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setColour(final int index, final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._colourList.size()) - { - throw new IndexOutOfBoundsException( - "setColour: Index value '" + index + "' not in range [0.." - + (this._colourList.size() - 1) + "]"); - } - - this._colourList.set(index, vColour); - } - - /** - * - * - * @param vColourArray - */ - public void setColour(final Colour[] vColourArray) - { - // -- copy array - _colourList.clear(); - - for (int i = 0; i < vColourArray.length; i++) - { - this._colourList.add(vColourArray[i]); - } - } - - /** - * - * - * @param index - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setFilter(final int index, final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._filterList.size()) - { - throw new IndexOutOfBoundsException( - "setFilter: Index value '" + index + "' not in range [0.." - + (this._filterList.size() - 1) + "]"); - } - - this._filterList.set(index, vFilter); - } - - /** - * - * - * @param vFilterArray - */ - public void setFilter(final Filter[] vFilterArray) - { - // -- copy array - _filterList.clear(); - - for (int i = 0; i < vFilterArray.length; i++) - { - this._filterList.add(vFilterArray[i]); - } - } - - /** - * Sets the value of field 'schemeName'. - * - * @param schemeName - * the value of field 'schemeName'. - */ - public void setSchemeName(final java.lang.String schemeName) - { - this._schemeName = schemeName; - } - - /** - * Sets the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document version. - * - * - * @param version - * the value of field 'version'. - */ - public void setVersion(final java.lang.String version) - { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours - */ - public static jalview.schemabinding.version2.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.JalviewUserColours.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java deleted file mode 100644 index 67bf1dc..0000000 --- a/src/jalview/schemabinding/version2/MapListFrom.java +++ /dev/null @@ -1,227 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * a region from start to end inclusive - * - * @version $Revision$ $Date$ - */ -public class MapListFrom implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListFrom() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.MapListFrom - */ - public static jalview.schemabinding.version2.MapListFrom unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MapListFrom) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MapListFrom.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java deleted file mode 100644 index e59baf8..0000000 --- a/src/jalview/schemabinding/version2/MapListTo.java +++ /dev/null @@ -1,227 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * a region from start to end inclusive - * - * @version $Revision$ $Date$ - */ -public class MapListTo implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _start. - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListTo() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.MapListTo - */ - public static jalview.schemabinding.version2.MapListTo unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MapListTo) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MapListTo.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java deleted file mode 100644 index cfb0752..0000000 --- a/src/jalview/schemabinding/version2/MapListType.java +++ /dev/null @@ -1,597 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * developed after mapRangeType from - * http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes - * - * This effectively represents a java.util.MapList object - * - * - * @version $Revision$ $Date$ - */ -public class MapListType implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * number of dictionary symbol widths involved in each mapped position on this - * sequence (for example, 3 for a dna sequence exon region that is being - * mapped to a protein sequence). This is optional, since the unit can be - * usually be inferred from the dictionary type of each sequence involved in - * the mapping. - */ - private long _mapFromUnit; - - /** - * keeps track of state for field: _mapFromUnit - */ - private boolean _has_mapFromUnit; - - /** - * number of dictionary symbol widths involved in each mapped position on this - * sequence (for example, 3 for a dna sequence exon region that is being - * mapped to a protein sequence). This is optional, since the unit can be - * usually be inferred from the dictionary type of each sequence involved in - * the mapping. - */ - private long _mapToUnit; - - /** - * keeps track of state for field: _mapToUnit - */ - private boolean _has_mapToUnit; - - /** - * a region from start to end inclusive - */ - private java.util.Vector _mapListFromList; - - /** - * a region from start to end inclusive - */ - private java.util.Vector _mapListToList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListType() - { - super(); - this._mapListFromList = new java.util.Vector(); - this._mapListToList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMapListFrom( - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException - { - this._mapListFromList.addElement(vMapListFrom); - } - - /** - * - * - * @param index - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMapListFrom(final int index, - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException - { - this._mapListFromList.add(index, vMapListFrom); - } - - /** - * - * - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMapListTo( - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException - { - this._mapListToList.addElement(vMapListTo); - } - - /** - * - * - * @param index - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMapListTo(final int index, - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException - { - this._mapListToList.add(index, vMapListTo); - } - - /** - */ - public void deleteMapFromUnit() - { - this._has_mapFromUnit = false; - } - - /** - */ - public void deleteMapToUnit() - { - this._has_mapToUnit = false; - } - - /** - * Method enumerateMapListFrom. - * - * @return an Enumeration over all jalview.schemabinding.version2.MapListFrom - * elements - */ - public java.util.Enumeration enumerateMapListFrom() - { - return this._mapListFromList.elements(); - } - - /** - * Method enumerateMapListTo. - * - * @return an Enumeration over all jalview.schemabinding.version2.MapListTo - * elements - */ - public java.util.Enumeration enumerateMapListTo() - { - return this._mapListToList.elements(); - } - - /** - * Returns the value of field 'mapFromUnit'. The field 'mapFromUnit' has the - * following description: number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna sequence exon - * region that is being mapped to a protein sequence). This is optional, since - * the unit can be usually be inferred from the dictionary type of each - * sequence involved in the mapping. - * - * @return the value of field 'MapFromUnit'. - */ - public long getMapFromUnit() - { - return this._mapFromUnit; - } - - /** - * Method getMapListFrom. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.MapListFrom at the - * given index - */ - public jalview.schemabinding.version2.MapListFrom getMapListFrom( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._mapListFromList.size()) - { - throw new IndexOutOfBoundsException("getMapListFrom: Index value '" - + index + "' not in range [0.." - + (this._mapListFromList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.MapListFrom) _mapListFromList - .get(index); - } - - /** - * Method getMapListFrom.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.MapListFrom[] getMapListFrom() - { - jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0]; - return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList - .toArray(array); - } - - /** - * Method getMapListFromCount. - * - * @return the size of this collection - */ - public int getMapListFromCount() - { - return this._mapListFromList.size(); - } - - /** - * Method getMapListTo. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.MapListTo at the - * given index - */ - public jalview.schemabinding.version2.MapListTo getMapListTo( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._mapListToList.size()) - { - throw new IndexOutOfBoundsException("getMapListTo: Index value '" - + index + "' not in range [0.." - + (this._mapListToList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.MapListTo) _mapListToList - .get(index); - } - - /** - * Method getMapListTo.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.MapListTo[] getMapListTo() - { - jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0]; - return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList - .toArray(array); - } - - /** - * Method getMapListToCount. - * - * @return the size of this collection - */ - public int getMapListToCount() - { - return this._mapListToList.size(); - } - - /** - * Returns the value of field 'mapToUnit'. The field 'mapToUnit' has the - * following description: number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna sequence exon - * region that is being mapped to a protein sequence). This is optional, since - * the unit can be usually be inferred from the dictionary type of each - * sequence involved in the mapping. - * - * @return the value of field 'MapToUnit'. - */ - public long getMapToUnit() - { - return this._mapToUnit; - } - - /** - * Method hasMapFromUnit. - * - * @return true if at least one MapFromUnit has been added - */ - public boolean hasMapFromUnit() - { - return this._has_mapFromUnit; - } - - /** - * Method hasMapToUnit. - * - * @return true if at least one MapToUnit has been added - */ - public boolean hasMapToUnit() - { - return this._has_mapToUnit; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllMapListFrom() - { - this._mapListFromList.clear(); - } - - /** - */ - public void removeAllMapListTo() - { - this._mapListToList.clear(); - } - - /** - * Method removeMapListFrom. - * - * @param vMapListFrom - * @return true if the object was removed from the collection. - */ - public boolean removeMapListFrom( - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - { - boolean removed = _mapListFromList.remove(vMapListFrom); - return removed; - } - - /** - * Method removeMapListFromAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MapListFrom removeMapListFromAt( - final int index) - { - java.lang.Object obj = this._mapListFromList.remove(index); - return (jalview.schemabinding.version2.MapListFrom) obj; - } - - /** - * Method removeMapListTo. - * - * @param vMapListTo - * @return true if the object was removed from the collection. - */ - public boolean removeMapListTo( - final jalview.schemabinding.version2.MapListTo vMapListTo) - { - boolean removed = _mapListToList.remove(vMapListTo); - return removed; - } - - /** - * Method removeMapListToAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MapListTo removeMapListToAt( - final int index) - { - java.lang.Object obj = this._mapListToList.remove(index); - return (jalview.schemabinding.version2.MapListTo) obj; - } - - /** - * Sets the value of field 'mapFromUnit'. The field 'mapFromUnit' has the - * following description: number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna sequence exon - * region that is being mapped to a protein sequence). This is optional, since - * the unit can be usually be inferred from the dictionary type of each - * sequence involved in the mapping. - * - * @param mapFromUnit - * the value of field 'mapFromUnit'. - */ - public void setMapFromUnit(final long mapFromUnit) - { - this._mapFromUnit = mapFromUnit; - this._has_mapFromUnit = true; - } - - /** - * - * - * @param index - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setMapListFrom(final int index, - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._mapListFromList.size()) - { - throw new IndexOutOfBoundsException("setMapListFrom: Index value '" - + index + "' not in range [0.." - + (this._mapListFromList.size() - 1) + "]"); - } - - this._mapListFromList.set(index, vMapListFrom); - } - - /** - * - * - * @param vMapListFromArray - */ - public void setMapListFrom( - final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) - { - // -- copy array - _mapListFromList.clear(); - - for (int i = 0; i < vMapListFromArray.length; i++) - { - this._mapListFromList.add(vMapListFromArray[i]); - } - } - - /** - * - * - * @param index - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setMapListTo(final int index, - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._mapListToList.size()) - { - throw new IndexOutOfBoundsException("setMapListTo: Index value '" - + index + "' not in range [0.." - + (this._mapListToList.size() - 1) + "]"); - } - - this._mapListToList.set(index, vMapListTo); - } - - /** - * - * - * @param vMapListToArray - */ - public void setMapListTo( - final jalview.schemabinding.version2.MapListTo[] vMapListToArray) - { - // -- copy array - _mapListToList.clear(); - - for (int i = 0; i < vMapListToArray.length; i++) - { - this._mapListToList.add(vMapListToArray[i]); - } - } - - /** - * Sets the value of field 'mapToUnit'. The field 'mapToUnit' has the - * following description: number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna sequence exon - * region that is being mapped to a protein sequence). This is optional, since - * the unit can be usually be inferred from the dictionary type of each - * sequence involved in the mapping. - * - * @param mapToUnit - * the value of field 'mapToUnit'. - */ - public void setMapToUnit(final long mapToUnit) - { - this._mapToUnit = mapToUnit; - this._has_mapToUnit = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.MapListType - */ - public static jalview.schemabinding.version2.MapListType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MapListType) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MapListType.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java deleted file mode 100644 index 9d71e1d..0000000 --- a/src/jalview/schemabinding/version2/Mapping.java +++ /dev/null @@ -1,173 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Mapping. - * - * @version $Revision$ $Date$ - */ -public class Mapping extends jalview.schemabinding.version2.MapListType - implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * Field _mappingChoice. - */ - private jalview.schemabinding.version2.MappingChoice _mappingChoice; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Mapping() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'choiceValue'. The field 'choiceValue' has the - * following description: Internal choice value storage - * - * @return the value of field 'ChoiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } - - /** - * Returns the value of field 'mappingChoice'. - * - * @return the value of field 'MappingChoice'. - */ - public jalview.schemabinding.version2.MappingChoice getMappingChoice() - { - return this._mappingChoice; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'mappingChoice'. - * - * @param mappingChoice - * the value of field 'mappingChoice'. - */ - public void setMappingChoice( - final jalview.schemabinding.version2.MappingChoice mappingChoice) - { - this._mappingChoice = mappingChoice; - this._choiceValue = mappingChoice; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.MapListType - */ - public static jalview.schemabinding.version2.MapListType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MapListType) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Mapping.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java deleted file mode 100644 index e50efa7..0000000 --- a/src/jalview/schemabinding/version2/MappingChoice.java +++ /dev/null @@ -1,182 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class MappingChoice. - * - * @version $Revision$ $Date$ - */ -public class MappingChoice implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _sequence. - */ - private jalview.schemabinding.version2.Sequence _sequence; - - /** - * Field _dseqFor. - */ - private java.lang.String _dseqFor; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MappingChoice() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'dseqFor'. - * - * @return the value of field 'DseqFor'. - */ - public java.lang.String getDseqFor() - { - return this._dseqFor; - } - - /** - * Returns the value of field 'sequence'. - * - * @return the value of field 'Sequence'. - */ - public jalview.schemabinding.version2.Sequence getSequence() - { - return this._sequence; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'dseqFor'. - * - * @param dseqFor - * the value of field 'dseqFor'. - */ - public void setDseqFor(final java.lang.String dseqFor) - { - this._dseqFor = dseqFor; - } - - /** - * Sets the value of field 'sequence'. - * - * @param sequence - * the value of field 'sequence'. - */ - public void setSequence( - final jalview.schemabinding.version2.Sequence sequence) - { - this._sequence = sequence; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.MappingChoice - */ - public static jalview.schemabinding.version2.MappingChoice unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MappingChoice) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MappingChoice.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/MatchCondition.java b/src/jalview/schemabinding/version2/MatchCondition.java deleted file mode 100644 index af2f3f5..0000000 --- a/src/jalview/schemabinding/version2/MatchCondition.java +++ /dev/null @@ -1,126 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class MatchCondition. - * - * @version $Revision$ $Date$ - */ -public class MatchCondition extends FeatureMatcher - implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MatchCondition() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.FeatureMatcher - */ - public static jalview.schemabinding.version2.FeatureMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.FeatureMatcher) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MatchCondition.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/MatcherSet.java b/src/jalview/schemabinding/version2/MatcherSet.java deleted file mode 100644 index 6fde9e4..0000000 --- a/src/jalview/schemabinding/version2/MatcherSet.java +++ /dev/null @@ -1,126 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * optional filter(s) applied to the feature type - * - * @version $Revision$ $Date$ - */ -public class MatcherSet extends FeatureMatcherSet - implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MatcherSet() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.FeatureMatcherSet - */ - public static jalview.schemabinding.version2.FeatureMatcherSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.FeatureMatcherSet) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MatcherSet.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java deleted file mode 100644 index 31797fe..0000000 --- a/src/jalview/schemabinding/version2/OtherData.java +++ /dev/null @@ -1,199 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class OtherData. - * - * @version $Revision$ $Date$ - */ -public class OtherData implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _key. - */ - private java.lang.String _key; - - /** - * key2 may be used for a sub-attribute of key - */ - private java.lang.String _key2; - - /** - * Field _value. - */ - private java.lang.String _value; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public OtherData() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'key'. - * - * @return the value of field 'Key'. - */ - public java.lang.String getKey( - ) { - return this._key; - } - - /** - * Returns the value of field 'key2'. The field 'key2' has the - * following description: key2 may be used for a sub-attribute - * of key - * - * @return the value of field 'Key2'. - */ - public java.lang.String getKey2( - ) { - return this._key2; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue( - ) { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'key'. - * - * @param key the value of field 'key'. - */ - public void setKey( - final java.lang.String key) { - this._key = key; - } - - /** - * Sets the value of field 'key2'. The field 'key2' has the - * following description: key2 may be used for a sub-attribute - * of key - * - * @param key2 the value of field 'key2'. - */ - public void setKey2( - final java.lang.String key2) { - this._key2 = key2; - } - - /** - * Sets the value of field 'value'. - * - * @param value the value of field 'value'. - */ - public void setValue( - final java.lang.String value) { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.OtherData - */ - public static jalview.schemabinding.version2.OtherData unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java deleted file mode 100644 index 65de364..0000000 --- a/src/jalview/schemabinding/version2/Pdbentry.java +++ /dev/null @@ -1,375 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Pdbentry. - * - * @version $Revision$ $Date$ - */ -public class Pdbentry implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _file. - */ - private java.lang.String _file; - - /** - * Field _items. - */ - private java.util.Vector _items; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Pdbentry() - { - super(); - this._items = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbentryItem( - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.addElement(vPdbentryItem); - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbentryItem(final int index, - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.add(index, vPdbentryItem); - } - - /** - * Method enumeratePdbentryItem. - * - * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem - * elements - */ - public java.util.Enumeration enumeratePdbentryItem() - { - return this._items.elements(); - } - - /** - * Returns the value of field 'file'. - * - * @return the value of field 'File'. - */ - public java.lang.String getFile() - { - return this._file; - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Method getPdbentryItem. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.PdbentryItem at the - * given inde - */ - public jalview.schemabinding.version2.PdbentryItem getPdbentryItem( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._items.size()) - { - throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" - + index + "' not in range [0.." + (this._items.size() - 1) - + "]"); - } - - return (jalview.schemabinding.version2.PdbentryItem) _items.get(index); - } - - /** - * Method getPdbentryItem.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem() - { - jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0]; - return (jalview.schemabinding.version2.PdbentryItem[]) this._items - .toArray(array); - } - - /** - * Method getPdbentryItemCount. - * - * @return the size of this collection - */ - public int getPdbentryItemCount() - { - return this._items.size(); - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllPdbentryItem() - { - this._items.clear(); - } - - /** - * Method removePdbentryItem. - * - * @param vPdbentryItem - * @return true if the object was removed from the collection. - */ - public boolean removePdbentryItem( - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - { - boolean removed = _items.remove(vPdbentryItem); - return removed; - } - - /** - * Method removePdbentryItemAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt( - final int index) - { - java.lang.Object obj = this._items.remove(index); - return (jalview.schemabinding.version2.PdbentryItem) obj; - } - - /** - * Sets the value of field 'file'. - * - * @param file - * the value of field 'file'. - */ - public void setFile(final java.lang.String file) - { - this._file = file; - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbentryItem(final int index, - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._items.size()) - { - throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" - + index + "' not in range [0.." + (this._items.size() - 1) - + "]"); - } - - this._items.set(index, vPdbentryItem); - } - - /** - * - * - * @param vPdbentryItemArray - */ - public void setPdbentryItem( - final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) - { - // -- copy array - _items.clear(); - - for (int i = 0; i < vPdbentryItemArray.length; i++) - { - this._items.add(vPdbentryItemArray[i]); - } - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Pdbentry - */ - public static jalview.schemabinding.version2.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Pdbentry) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Pdbentry.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java deleted file mode 100644 index 5554b49..0000000 --- a/src/jalview/schemabinding/version2/PdbentryItem.java +++ /dev/null @@ -1,204 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -/** - * Class PdbentryItem. - * - * @version $Revision$ $Date$ - */ -public class PdbentryItem implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _propertyList. - */ - private java.util.Vector _propertyList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbentryItem() - { - super(); - this._propertyList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addProperty( - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.addElement(vProperty); - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addProperty(final int index, - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.add(index, vProperty); - } - - /** - * Method enumerateProperty. - * - * @return an Enumeration over all jalview.schemabinding.version2.Property - * elements - */ - public java.util.Enumeration enumerateProperty() - { - return this._propertyList.elements(); - } - - /** - * Method getProperty. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Property at the - * given index - */ - public jalview.schemabinding.version2.Property getProperty(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException("getProperty: Index value '" - + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Property) _propertyList - .get(index); - } - - /** - * Method getProperty.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Property[] getProperty() - { - jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0]; - return (jalview.schemabinding.version2.Property[]) this._propertyList - .toArray(array); - } - - /** - * Method getPropertyCount. - * - * @return the size of this collection - */ - public int getPropertyCount() - { - return this._propertyList.size(); - } - - /** - */ - public void removeAllProperty() - { - this._propertyList.clear(); - } - - /** - * Method removeProperty. - * - * @param vProperty - * @return true if the object was removed from the collection. - */ - public boolean removeProperty( - final jalview.schemabinding.version2.Property vProperty) - { - boolean removed = _propertyList.remove(vProperty); - return removed; - } - - /** - * Method removePropertyAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Property removePropertyAt( - final int index) - { - java.lang.Object obj = this._propertyList.remove(index); - return (jalview.schemabinding.version2.Property) obj; - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setProperty(final int index, - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException("setProperty: Index value '" - + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - this._propertyList.set(index, vProperty); - } - - /** - * - * - * @param vPropertyArray - */ - public void setProperty( - final jalview.schemabinding.version2.Property[] vPropertyArray) - { - // -- copy array - _propertyList.clear(); - - for (int i = 0; i < vPropertyArray.length; i++) - { - this._propertyList.add(vPropertyArray[i]); - } - } - -} diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java deleted file mode 100644 index 978df5b..0000000 --- a/src/jalview/schemabinding/version2/Pdbids.java +++ /dev/null @@ -1,303 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Pdbids. - * - * @version $Revision$ $Date$ - */ -public class Pdbids extends jalview.schemabinding.version2.Pdbentry - implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _structureStateList. - */ - private java.util.Vector _structureStateList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Pdbids() - { - super(); - this._structureStateList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addStructureState( - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException - { - this._structureStateList.addElement(vStructureState); - } - - /** - * - * - * @param index - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addStructureState( - final int index, - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException - { - this._structureStateList.add(index, vStructureState); - } - - /** - * Method enumerateStructureState. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.StructureState elements - */ - public java.util.Enumeration enumerateStructureState() - { - return this._structureStateList.elements(); - } - - /** - * Method getStructureState. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.StructureState at - * the given index - */ - public jalview.schemabinding.version2.StructureState getStructureState( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._structureStateList.size()) - { - throw new IndexOutOfBoundsException( - "getStructureState: Index value '" + index - + "' not in range [0.." - + (this._structureStateList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.StructureState) _structureStateList - .get(index); - } - - /** - * Method getStructureState.Returns the contents of the collection in an - * Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.StructureState[] getStructureState() - { - jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0]; - return (jalview.schemabinding.version2.StructureState[]) this._structureStateList - .toArray(array); - } - - /** - * Method getStructureStateCount. - * - * @return the size of this collection - */ - public int getStructureStateCount() - { - return this._structureStateList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllStructureState() - { - this._structureStateList.clear(); - } - - /** - * Method removeStructureState. - * - * @param vStructureState - * @return true if the object was removed from the collection. - */ - public boolean removeStructureState( - final jalview.schemabinding.version2.StructureState vStructureState) - { - boolean removed = _structureStateList.remove(vStructureState); - return removed; - } - - /** - * Method removeStructureStateAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.StructureState removeStructureStateAt( - final int index) - { - java.lang.Object obj = this._structureStateList.remove(index); - return (jalview.schemabinding.version2.StructureState) obj; - } - - /** - * - * - * @param index - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setStructureState( - final int index, - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._structureStateList.size()) - { - throw new IndexOutOfBoundsException( - "setStructureState: Index value '" + index - + "' not in range [0.." - + (this._structureStateList.size() - 1) + "]"); - } - - this._structureStateList.set(index, vStructureState); - } - - /** - * - * - * @param vStructureStateArray - */ - public void setStructureState( - final jalview.schemabinding.version2.StructureState[] vStructureStateArray) - { - // -- copy array - _structureStateList.clear(); - - for (int i = 0; i < vStructureStateArray.length; i++) - { - this._structureStateList.add(vStructureStateArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Pdbentry - */ - public static jalview.schemabinding.version2.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Pdbentry) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Pdbids.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java deleted file mode 100644 index dbf96bf..0000000 --- a/src/jalview/schemabinding/version2/Property.java +++ /dev/null @@ -1,181 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Property. - * - * @version $Revision$ $Date$ - */ -public class Property implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Property() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue() - { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final java.lang.String value) - { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Property - */ - public static jalview.schemabinding.version2.Property unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Property) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Property.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/RnaViewer.java b/src/jalview/schemabinding/version2/RnaViewer.java deleted file mode 100644 index 543d053..0000000 --- a/src/jalview/schemabinding/version2/RnaViewer.java +++ /dev/null @@ -1,668 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Reference to a viewer showing RNA structure for this sequence. Schema - * supports one viewer showing multiple annotations for multiple sequences, - * though currently only one annotation for one sequence (gapped or trimmed) is - * used - * - * - * @version $Revision$ $Date$ - */ -public class RnaViewer implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * An id unique to the RNA viewer panel - * - */ - private java.lang.String _viewId; - - /** - * horizontal position of split pane divider - * - */ - private int _dividerLocation; - - /** - * keeps track of state for field: _dividerLocation - */ - private boolean _has_dividerLocation; - - /** - * Index of the selected structure in the viewer panel - * - */ - private int _selectedRna; - - /** - * keeps track of state for field: _selectedRna - */ - private boolean _has_selectedRna; - - /** - * Field _width. - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height. - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _xpos. - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos. - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _secondaryStructureList. - */ - private java.util.Vector _secondaryStructureList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public RnaViewer() - { - super(); - this._secondaryStructureList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vSecondaryStructure - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSecondaryStructure( - final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) - throws java.lang.IndexOutOfBoundsException - { - this._secondaryStructureList.addElement(vSecondaryStructure); - } - - /** - * - * - * @param index - * @param vSecondaryStructure - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSecondaryStructure( - final int index, - final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) - throws java.lang.IndexOutOfBoundsException - { - this._secondaryStructureList.add(index, vSecondaryStructure); - } - - /** - */ - public void deleteDividerLocation() - { - this._has_dividerLocation = false; - } - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deleteSelectedRna() - { - this._has_selectedRna = false; - } - - /** - */ - public void deleteWidth() - { - this._has_width = false; - } - - /** - */ - public void deleteXpos() - { - this._has_xpos = false; - } - - /** - */ - public void deleteYpos() - { - this._has_ypos = false; - } - - /** - * Method enumerateSecondaryStructure. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.SecondaryStructure elements - */ - public java.util.Enumeration enumerateSecondaryStructure() - { - return this._secondaryStructureList.elements(); - } - - /** - * Returns the value of field 'dividerLocation'. The field 'dividerLocation' - * has the following description: horizontal position of split pane divider - * - * - * @return the value of field 'DividerLocation'. - */ - public int getDividerLocation() - { - return this._dividerLocation; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Method getSecondaryStructure. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.SecondaryStructure - * at the given index - */ - public jalview.schemabinding.version2.SecondaryStructure getSecondaryStructure( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._secondaryStructureList.size()) - { - throw new IndexOutOfBoundsException( - "getSecondaryStructure: Index value '" + index - + "' not in range [0.." - + (this._secondaryStructureList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.SecondaryStructure) _secondaryStructureList - .get(index); - } - - /** - * Method getSecondaryStructure.Returns the contents of the collection in an - * Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.SecondaryStructure[] getSecondaryStructure() - { - jalview.schemabinding.version2.SecondaryStructure[] array = new jalview.schemabinding.version2.SecondaryStructure[0]; - return (jalview.schemabinding.version2.SecondaryStructure[]) this._secondaryStructureList - .toArray(array); - } - - /** - * Method getSecondaryStructureCount. - * - * @return the size of this collection - */ - public int getSecondaryStructureCount() - { - return this._secondaryStructureList.size(); - } - - /** - * Returns the value of field 'selectedRna'. The field 'selectedRna' has the - * following description: Index of the selected structure in the viewer panel - * - * - * @return the value of field 'SelectedRna'. - */ - public int getSelectedRna() - { - return this._selectedRna; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle() - { - return this._title; - } - - /** - * Returns the value of field 'viewId'. The field 'viewId' has the following - * description: An id unique to the RNA viewer panel - * - * - * @return the value of field 'ViewId'. - */ - public java.lang.String getViewId() - { - return this._viewId; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth() - { - return this._width; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos() - { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos() - { - return this._ypos; - } - - /** - * Method hasDividerLocation. - * - * @return true if at least one DividerLocation has been added - */ - public boolean hasDividerLocation() - { - return this._has_dividerLocation; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasSelectedRna. - * - * @return true if at least one SelectedRna has been added - */ - public boolean hasSelectedRna() - { - return this._has_selectedRna; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth() - { - return this._has_width; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos() - { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos() - { - return this._has_ypos; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSecondaryStructure() - { - this._secondaryStructureList.clear(); - } - - /** - * Method removeSecondaryStructure. - * - * @param vSecondaryStructure - * @return true if the object was removed from the collection. - */ - public boolean removeSecondaryStructure( - final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) - { - boolean removed = _secondaryStructureList.remove(vSecondaryStructure); - return removed; - } - - /** - * Method removeSecondaryStructureAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.SecondaryStructure removeSecondaryStructureAt( - final int index) - { - java.lang.Object obj = this._secondaryStructureList.remove(index); - return (jalview.schemabinding.version2.SecondaryStructure) obj; - } - - /** - * Sets the value of field 'dividerLocation'. The field 'dividerLocation' has - * the following description: horizontal position of split pane divider - * - * - * @param dividerLocation - * the value of field 'dividerLocation'. - */ - public void setDividerLocation(final int dividerLocation) - { - this._dividerLocation = dividerLocation; - this._has_dividerLocation = true; - } - - /** - * Sets the value of field 'height'. - * - * @param height - * the value of field 'height'. - */ - public void setHeight(final int height) - { - this._height = height; - this._has_height = true; - } - - /** - * - * - * @param index - * @param vSecondaryStructure - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSecondaryStructure( - final int index, - final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._secondaryStructureList.size()) - { - throw new IndexOutOfBoundsException( - "setSecondaryStructure: Index value '" + index - + "' not in range [0.." - + (this._secondaryStructureList.size() - 1) + "]"); - } - - this._secondaryStructureList.set(index, vSecondaryStructure); - } - - /** - * - * - * @param vSecondaryStructureArray - */ - public void setSecondaryStructure( - final jalview.schemabinding.version2.SecondaryStructure[] vSecondaryStructureArray) - { - // -- copy array - _secondaryStructureList.clear(); - - for (int i = 0; i < vSecondaryStructureArray.length; i++) - { - this._secondaryStructureList.add(vSecondaryStructureArray[i]); - } - } - - /** - * Sets the value of field 'selectedRna'. The field 'selectedRna' has the - * following description: Index of the selected structure in the viewer panel - * - * - * @param selectedRna - * the value of field 'selectedRna'. - */ - public void setSelectedRna(final int selectedRna) - { - this._selectedRna = selectedRna; - this._has_selectedRna = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title - * the value of field 'title'. - */ - public void setTitle(final java.lang.String title) - { - this._title = title; - } - - /** - * Sets the value of field 'viewId'. The field 'viewId' has the following - * description: An id unique to the RNA viewer panel - * - * - * @param viewId - * the value of field 'viewId'. - */ - public void setViewId(final java.lang.String viewId) - { - this._viewId = viewId; - } - - /** - * Sets the value of field 'width'. - * - * @param width - * the value of field 'width'. - */ - public void setWidth(final int width) - { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos - * the value of field 'xpos'. - */ - public void setXpos(final int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos - * the value of field 'ypos'. - */ - public void setYpos(final int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.RnaViewer - */ - public static jalview.schemabinding.version2.RnaViewer unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.RnaViewer) Unmarshaller - .unmarshal(jalview.schemabinding.version2.RnaViewer.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/SecondaryStructure.java b/src/jalview/schemabinding/version2/SecondaryStructure.java deleted file mode 100644 index eb88fc4..0000000 --- a/src/jalview/schemabinding/version2/SecondaryStructure.java +++ /dev/null @@ -1,290 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class SecondaryStructure. - * - * @version $Revision$ $Date$ - */ -public class SecondaryStructure implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * id attribute of Annotation in vamsasModel for the secondary structure - * annotation shown in the viewer - * - */ - private java.lang.String _annotationId; - - /** - * if true the RNA structure is shown with gaps, if false without - * - */ - private boolean _gapped; - - /** - * keeps track of state for field: _gapped - */ - private boolean _has_gapped; - - /** - * name of the project jar entry that holds the VARNA viewer state for the - * structure - * - */ - private java.lang.String _viewerState; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SecondaryStructure() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteGapped() - { - this._has_gapped = false; - } - - /** - * Returns the value of field 'annotationId'. The field 'annotationId' has the - * following description: id attribute of Annotation in vamsasModel for the - * secondary structure annotation shown in the viewer - * - * - * @return the value of field 'AnnotationId'. - */ - public java.lang.String getAnnotationId() - { - return this._annotationId; - } - - /** - * Returns the value of field 'gapped'. The field 'gapped' has the following - * description: if true the RNA structure is shown with gaps, if false without - * - * - * @return the value of field 'Gapped'. - */ - public boolean getGapped() - { - return this._gapped; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle() - { - return this._title; - } - - /** - * Returns the value of field 'viewerState'. The field 'viewerState' has the - * following description: name of the project jar entry that holds the VARNA - * viewer state for the structure - * - * - * @return the value of field 'ViewerState'. - */ - public java.lang.String getViewerState() - { - return this._viewerState; - } - - /** - * Method hasGapped. - * - * @return true if at least one Gapped has been added - */ - public boolean hasGapped() - { - return this._has_gapped; - } - - /** - * Returns the value of field 'gapped'. The field 'gapped' has the following - * description: if true the RNA structure is shown with gaps, if false without - * - * - * @return the value of field 'Gapped'. - */ - public boolean isGapped() - { - return this._gapped; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'annotationId'. The field 'annotationId' has the - * following description: id attribute of Annotation in vamsasModel for the - * secondary structure annotation shown in the viewer - * - * - * @param annotationId - * the value of field 'annotationId'. - */ - public void setAnnotationId(final java.lang.String annotationId) - { - this._annotationId = annotationId; - } - - /** - * Sets the value of field 'gapped'. The field 'gapped' has the following - * description: if true the RNA structure is shown with gaps, if false without - * - * - * @param gapped - * the value of field 'gapped'. - */ - public void setGapped(final boolean gapped) - { - this._gapped = gapped; - this._has_gapped = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title - * the value of field 'title'. - */ - public void setTitle(final java.lang.String title) - { - this._title = title; - } - - /** - * Sets the value of field 'viewerState'. The field 'viewerState' has the - * following description: name of the project jar entry that holds the VARNA - * viewer state for the structure - * - * - * @param viewerState - * the value of field 'viewerState'. - */ - public void setViewerState(final java.lang.String viewerState) - { - this._viewerState = viewerState; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.SecondaryStructure - */ - public static jalview.schemabinding.version2.SecondaryStructure unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.SecondaryStructure.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java deleted file mode 100644 index 531ca66..0000000 --- a/src/jalview/schemabinding/version2/Sequence.java +++ /dev/null @@ -1,328 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends jalview.schemabinding.version2.SequenceType - implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * dataset sequence id for this sequence. Will be created as union of - * sequences. - * - */ - private java.lang.String _dsseqid; - - /** - * Field _DBRefList. - */ - private java.util.Vector _DBRefList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Sequence() - { - super(); - this._DBRefList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - this._DBRefList.addElement(vDBRef); - } - - /** - * - * - * @param index - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addDBRef(final int index, - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - this._DBRefList.add(index, vDBRef); - } - - /** - * Method enumerateDBRef. - * - * @return an Enumeration over all jalview.schemabinding.version2.DBRef - * elements - */ - public java.util.Enumeration enumerateDBRef() - { - return this._DBRefList.elements(); - } - - /** - * Method getDBRef. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.DBRef at the given - * index - */ - public jalview.schemabinding.version2.DBRef getDBRef(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._DBRefList.size()) - { - throw new IndexOutOfBoundsException("getDBRef: Index value '" + index - + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index); - } - - /** - * Method getDBRef.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.DBRef[] getDBRef() - { - jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0]; - return (jalview.schemabinding.version2.DBRef[]) this._DBRefList - .toArray(array); - } - - /** - * Method getDBRefCount. - * - * @return the size of this collection - */ - public int getDBRefCount() - { - return this._DBRefList.size(); - } - - /** - * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following - * description: dataset sequence id for this sequence. Will be created as - * union of sequences. - * - * - * @return the value of field 'Dsseqid'. - */ - public java.lang.String getDsseqid() - { - return this._dsseqid; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllDBRef() - { - this._DBRefList.clear(); - } - - /** - * Method removeDBRef. - * - * @param vDBRef - * @return true if the object was removed from the collection. - */ - public boolean removeDBRef( - final jalview.schemabinding.version2.DBRef vDBRef) - { - boolean removed = _DBRefList.remove(vDBRef); - return removed; - } - - /** - * Method removeDBRefAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index) - { - java.lang.Object obj = this._DBRefList.remove(index); - return (jalview.schemabinding.version2.DBRef) obj; - } - - /** - * - * - * @param index - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setDBRef(final int index, - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._DBRefList.size()) - { - throw new IndexOutOfBoundsException("setDBRef: Index value '" + index - + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); - } - - this._DBRefList.set(index, vDBRef); - } - - /** - * - * - * @param vDBRefArray - */ - public void setDBRef( - final jalview.schemabinding.version2.DBRef[] vDBRefArray) - { - // -- copy array - _DBRefList.clear(); - - for (int i = 0; i < vDBRefArray.length; i++) - { - this._DBRefList.add(vDBRefArray[i]); - } - } - - /** - * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following - * description: dataset sequence id for this sequence. Will be created as - * union of sequences. - * - * - * @param dsseqid - * the value of field 'dsseqid'. - */ - public void setDsseqid(final java.lang.String dsseqid) - { - this._dsseqid = dsseqid; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.SequenceType - */ - public static jalview.schemabinding.version2.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SequenceType) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Sequence.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java deleted file mode 100644 index 8be8022..0000000 --- a/src/jalview/schemabinding/version2/SequenceSet.java +++ /dev/null @@ -1,872 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class SequenceSet. - * - * @version $Revision$ $Date$ - */ -public class SequenceSet implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _gapChar. - */ - private java.lang.String _gapChar; - - /** - * reference to set where jalview will gather the dataset sequences for all - * sequences in the set. - * - */ - private java.lang.String _datasetId; - - /** - * Field _sequenceList. - */ - private java.util.Vector _sequenceList; - - /** - * Field _annotationList. - */ - private java.util.Vector _annotationList; - - /** - * Field _sequenceSetPropertiesList. - */ - private java.util.Vector _sequenceSetPropertiesList; - - /** - * Field _alcodonFrameList. - */ - private java.util.Vector _alcodonFrameList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSet() - { - super(); - this._sequenceList = new java.util.Vector(); - this._annotationList = new java.util.Vector(); - this._sequenceSetPropertiesList = new java.util.Vector(); - this._alcodonFrameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonFrameList.addElement(vAlcodonFrame); - } - - /** - * - * - * @param index - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodonFrame(final int index, - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonFrameList.add(index, vAlcodonFrame); - } - - /** - * - * - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotation( - final jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - this._annotationList.addElement(vAnnotation); - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotation(final int index, - final jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - this._annotationList.add(index, vAnnotation); - } - - /** - * - * - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequence( - final jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceList.addElement(vSequence); - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequence(final int index, - final jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceList.add(index, vSequence); - } - - /** - * - * - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetPropertiesList.addElement(vSequenceSetProperties); - } - - /** - * - * - * @param index - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSetProperties( - final int index, - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetPropertiesList.add(index, vSequenceSetProperties); - } - - /** - * Method enumerateAlcodonFrame. - * - * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame - * elements - */ - public java.util.Enumeration enumerateAlcodonFrame() - { - return this._alcodonFrameList.elements(); - } - - /** - * Method enumerateAnnotation. - * - * @return an Enumeration over all jalview.schemabinding.version2.Annotation - * elements - */ - public java.util.Enumeration enumerateAnnotation() - { - return this._annotationList.elements(); - } - - /** - * Method enumerateSequence. - * - * @return an Enumeration over all jalview.schemabinding.version2.Sequence - * elements - */ - public java.util.Enumeration enumerateSequence() - { - return this._sequenceList.elements(); - } - - /** - * Method enumerateSequenceSetProperties. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.SequenceSetProperties elements - */ - public java.util.Enumeration enumerateSequenceSetProperties() - { - return this._sequenceSetPropertiesList.elements(); - } - - /** - * Method getAlcodonFrame. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.AlcodonFrame at the - * given inde - */ - public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonFrameList.size()) - { - throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" - + index + "' not in range [0.." - + (this._alcodonFrameList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList - .get(index); - } - - /** - * Method getAlcodonFrame.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame() - { - jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; - return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList - .toArray(array); - } - - /** - * Method getAlcodonFrameCount. - * - * @return the size of this collection - */ - public int getAlcodonFrameCount() - { - return this._alcodonFrameList.size(); - } - - /** - * Method getAnnotation. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Annotation at the - * given index - */ - public jalview.schemabinding.version2.Annotation getAnnotation( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) - { - throw new IndexOutOfBoundsException("getAnnotation: Index value '" - + index + "' not in range [0.." - + (this._annotationList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Annotation) _annotationList - .get(index); - } - - /** - * Method getAnnotation.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Annotation[] getAnnotation() - { - jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; - return (jalview.schemabinding.version2.Annotation[]) this._annotationList - .toArray(array); - } - - /** - * Method getAnnotationCount. - * - * @return the size of this collection - */ - public int getAnnotationCount() - { - return this._annotationList.size(); - } - - /** - * Returns the value of field 'datasetId'. The field 'datasetId' has the - * following description: reference to set where jalview will gather the - * dataset sequences for all sequences in the set. - * - * - * @return the value of field 'DatasetId'. - */ - public java.lang.String getDatasetId() - { - return this._datasetId; - } - - /** - * Returns the value of field 'gapChar'. - * - * @return the value of field 'GapChar'. - */ - public java.lang.String getGapChar() - { - return this._gapChar; - } - - /** - * Method getSequence. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Sequence at the - * given index - */ - public jalview.schemabinding.version2.Sequence getSequence(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) - { - throw new IndexOutOfBoundsException("getSequence: Index value '" - + index + "' not in range [0.." - + (this._sequenceList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Sequence) _sequenceList - .get(index); - } - - /** - * Method getSequence.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Sequence[] getSequence() - { - jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; - return (jalview.schemabinding.version2.Sequence[]) this._sequenceList - .toArray(array); - } - - /** - * Method getSequenceCount. - * - * @return the size of this collection - */ - public int getSequenceCount() - { - return this._sequenceList.size(); - } - - /** - * Method getSequenceSetProperties. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.SequenceSetProperties at the given - * index - */ - public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetPropertiesList.size()) - { - throw new IndexOutOfBoundsException( - "getSequenceSetProperties: Index value '" + index - + "' not in range [0.." - + (this._sequenceSetPropertiesList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList - .get(index); - } - - /** - * Method getSequenceSetProperties.Returns the contents of the collection in - * an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties() - { - jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0]; - return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList - .toArray(array); - } - - /** - * Method getSequenceSetPropertiesCount. - * - * @return the size of this collection - */ - public int getSequenceSetPropertiesCount() - { - return this._sequenceSetPropertiesList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method removeAlcodonFrame. - * - * @param vAlcodonFrame - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - { - boolean removed = _alcodonFrameList.remove(vAlcodonFrame); - return removed; - } - - /** - * Method removeAlcodonFrameAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt( - final int index) - { - java.lang.Object obj = this._alcodonFrameList.remove(index); - return (jalview.schemabinding.version2.AlcodonFrame) obj; - } - - /** - */ - public void removeAllAlcodonFrame() - { - this._alcodonFrameList.clear(); - } - - /** - */ - public void removeAllAnnotation() - { - this._annotationList.clear(); - } - - /** - */ - public void removeAllSequence() - { - this._sequenceList.clear(); - } - - /** - */ - public void removeAllSequenceSetProperties() - { - this._sequenceSetPropertiesList.clear(); - } - - /** - * Method removeAnnotation. - * - * @param vAnnotation - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotation( - final jalview.schemabinding.version2.Annotation vAnnotation) - { - boolean removed = _annotationList.remove(vAnnotation); - return removed; - } - - /** - * Method removeAnnotationAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Annotation removeAnnotationAt( - final int index) - { - java.lang.Object obj = this._annotationList.remove(index); - return (jalview.schemabinding.version2.Annotation) obj; - } - - /** - * Method removeSequence. - * - * @param vSequence - * @return true if the object was removed from the collection. - */ - public boolean removeSequence( - final jalview.schemabinding.version2.Sequence vSequence) - { - boolean removed = _sequenceList.remove(vSequence); - return removed; - } - - /** - * Method removeSequenceAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Sequence removeSequenceAt( - final int index) - { - java.lang.Object obj = this._sequenceList.remove(index); - return (jalview.schemabinding.version2.Sequence) obj; - } - - /** - * Method removeSequenceSetProperties. - * - * @param vSequenceSetProperties - * @return true if the object was removed from the collection. - */ - public boolean removeSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - { - boolean removed = _sequenceSetPropertiesList - .remove(vSequenceSetProperties); - return removed; - } - - /** - * Method removeSequenceSetPropertiesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt( - final int index) - { - java.lang.Object obj = this._sequenceSetPropertiesList.remove(index); - return (jalview.schemabinding.version2.SequenceSetProperties) obj; - } - - /** - * - * - * @param index - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlcodonFrame(final int index, - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonFrameList.size()) - { - throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" - + index + "' not in range [0.." - + (this._alcodonFrameList.size() - 1) + "]"); - } - - this._alcodonFrameList.set(index, vAlcodonFrame); - } - - /** - * - * - * @param vAlcodonFrameArray - */ - public void setAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) - { - // -- copy array - _alcodonFrameList.clear(); - - for (int i = 0; i < vAlcodonFrameArray.length; i++) - { - this._alcodonFrameList.add(vAlcodonFrameArray[i]); - } - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAnnotation(final int index, - final jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) - { - throw new IndexOutOfBoundsException("setAnnotation: Index value '" - + index + "' not in range [0.." - + (this._annotationList.size() - 1) + "]"); - } - - this._annotationList.set(index, vAnnotation); - } - - /** - * - * - * @param vAnnotationArray - */ - public void setAnnotation( - final jalview.schemabinding.version2.Annotation[] vAnnotationArray) - { - // -- copy array - _annotationList.clear(); - - for (int i = 0; i < vAnnotationArray.length; i++) - { - this._annotationList.add(vAnnotationArray[i]); - } - } - - /** - * Sets the value of field 'datasetId'. The field 'datasetId' has the - * following description: reference to set where jalview will gather the - * dataset sequences for all sequences in the set. - * - * - * @param datasetId - * the value of field 'datasetId'. - */ - public void setDatasetId(final java.lang.String datasetId) - { - this._datasetId = datasetId; - } - - /** - * Sets the value of field 'gapChar'. - * - * @param gapChar - * the value of field 'gapChar'. - */ - public void setGapChar(final java.lang.String gapChar) - { - this._gapChar = gapChar; - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSequence(final int index, - final jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) - { - throw new IndexOutOfBoundsException("setSequence: Index value '" - + index + "' not in range [0.." - + (this._sequenceList.size() - 1) + "]"); - } - - this._sequenceList.set(index, vSequence); - } - - /** - * - * - * @param vSequenceArray - */ - public void setSequence( - final jalview.schemabinding.version2.Sequence[] vSequenceArray) - { - // -- copy array - _sequenceList.clear(); - - for (int i = 0; i < vSequenceArray.length; i++) - { - this._sequenceList.add(vSequenceArray[i]); - } - } - - /** - * - * - * @param index - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSequenceSetProperties( - final int index, - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetPropertiesList.size()) - { - throw new IndexOutOfBoundsException( - "setSequenceSetProperties: Index value '" + index - + "' not in range [0.." - + (this._sequenceSetPropertiesList.size() - 1) + "]"); - } - - this._sequenceSetPropertiesList.set(index, vSequenceSetProperties); - } - - /** - * - * - * @param vSequenceSetPropertiesArray - */ - public void setSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) - { - // -- copy array - _sequenceSetPropertiesList.clear(); - - for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) - { - this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.SequenceSet - */ - public static jalview.schemabinding.version2.SequenceSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SequenceSet) Unmarshaller - .unmarshal(jalview.schemabinding.version2.SequenceSet.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/SequenceSetProperties.java b/src/jalview/schemabinding/version2/SequenceSetProperties.java deleted file mode 100644 index 3a7d172..0000000 --- a/src/jalview/schemabinding/version2/SequenceSetProperties.java +++ /dev/null @@ -1,183 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class SequenceSetProperties. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetProperties implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _key. - */ - private java.lang.String _key; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSetProperties() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'key'. - * - * @return the value of field 'Key'. - */ - public java.lang.String getKey() - { - return this._key; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue() - { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'key'. - * - * @param key - * the value of field 'key'. - */ - public void setKey(final java.lang.String key) - { - this._key = key; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final java.lang.String value) - { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.SequenceSetProperties - */ - public static jalview.schemabinding.version2.SequenceSetProperties unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.SequenceSetProperties.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java deleted file mode 100644 index f213ebb..0000000 --- a/src/jalview/schemabinding/version2/SequenceType.java +++ /dev/null @@ -1,233 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class SequenceType. - * - * @version $Revision$ $Date$ - */ -public class SequenceType implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _sequence. - */ - private java.lang.String _sequence; - - /** - * Field _name. - */ - private java.lang.String _name; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceType() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'sequence'. - * - * @return the value of field 'Sequence'. - */ - public java.lang.String getSequence() - { - return this._sequence; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'sequence'. - * - * @param sequence - * the value of field 'sequence'. - */ - public void setSequence(final java.lang.String sequence) - { - this._sequence = sequence; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.SequenceType - */ - public static jalview.schemabinding.version2.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SequenceType) Unmarshaller - .unmarshal(jalview.schemabinding.version2.SequenceType.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java deleted file mode 100644 index 59e9522..0000000 --- a/src/jalview/schemabinding/version2/Setting.java +++ /dev/null @@ -1,923 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Setting. - * - * @version $Revision$ $Date$ - */ -public class Setting implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _display. - */ - private boolean _display; - - /** - * keeps track of state for field: _display - */ - private boolean _has_display; - - /** - * Field _order. - */ - private float _order; - - /** - * keeps track of state for field: _order - */ - private boolean _has_order; - - /** - * Optional minimum colour for graduated feature colour - * - */ - private int _mincolour; - - /** - * keeps track of state for field: _mincolour - */ - private boolean _has_mincolour; - - /** - * Field _noValueColour. - */ - private jalview.schemabinding.version2.types.NoValueColour _noValueColour = jalview.schemabinding.version2.types.NoValueColour - .valueOf("Min"); - - /** - * threshold value for graduated feature colour - * - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * threshold type for graduated feature colour - * - */ - private int _threshstate; - - /** - * keeps track of state for field: _threshstate - */ - private boolean _has_threshstate; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - /** - * name of feature attribute to colour by, or attribute and sub-attribute - */ - private java.util.Vector _attributeNameList; - - /** - * optional filter(s) applied to the feature type - */ - private jalview.schemabinding.version2.MatcherSet _matcherSet; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Setting() - { - super(); - setNoValueColour(jalview.schemabinding.version2.types.NoValueColour - .valueOf("Min")); - this._attributeNameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.addElement(vAttributeName); - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.add(index, vAttributeName); - } - - /** - */ - public void deleteAutoScale() - { - this._has_autoScale = false; - } - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteColourByLabel() - { - this._has_colourByLabel = false; - } - - /** - */ - public void deleteDisplay() - { - this._has_display = false; - } - - /** - */ - public void deleteMax() - { - this._has_max = false; - } - - /** - */ - public void deleteMin() - { - this._has_min = false; - } - - /** - */ - public void deleteMincolour() - { - this._has_mincolour = false; - } - - /** - */ - public void deleteOrder() - { - this._has_order = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - */ - public void deleteThreshstate() - { - this._has_threshstate = false; - } - - /** - * Method enumerateAttributeName. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateAttributeName() - { - return this._attributeNameList.elements(); - } - - /** - * Method getAttributeName. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getAttributeName(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("getAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - return (java.lang.String) _attributeNameList.get(index); - } - - /** - * Method getAttributeName.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getAttributeName() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._attributeNameList.toArray(array); - } - - /** - * Method getAttributeNameCount. - * - * @return the size of this collection - */ - public int getAttributeNameCount() - { - return this._attributeNameList.size(); - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel() - { - return this._colourByLabel; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean getDisplay() - { - return this._display; - } - - /** - * Returns the value of field 'matcherSet'. The field 'matcherSet' has the - * following description: optional filter(s) applied to the feature type - * - * @return the value of field 'MatcherSet'. - */ - public jalview.schemabinding.version2.MatcherSet getMatcherSet() - { - return this._matcherSet; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax() - { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin() - { - return this._min; - } - - /** - * Returns the value of field 'mincolour'. The field 'mincolour' has the - * following description: Optional minimum colour for graduated feature colour - * - * - * @return the value of field 'Mincolour'. - */ - public int getMincolour() - { - return this._mincolour; - } - - /** - * Returns the value of field 'noValueColour'. - * - * @return the value of field 'NoValueColour'. - */ - public jalview.schemabinding.version2.types.NoValueColour getNoValueColour() - { - return this._noValueColour; - } - - /** - * Returns the value of field 'order'. - * - * @return the value of field 'Order'. - */ - public float getOrder() - { - return this._order; - } - - /** - * Returns the value of field 'threshold'. The field 'threshold' has the - * following description: threshold value for graduated feature colour - * - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Returns the value of field 'threshstate'. The field 'threshstate' has the - * following description: threshold type for graduated feature colour - * - * - * @return the value of field 'Threshstate'. - */ - public int getThreshstate() - { - return this._threshstate; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale() - { - return this._has_autoScale; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel() - { - return this._has_colourByLabel; - } - - /** - * Method hasDisplay. - * - * @return true if at least one Display has been added - */ - public boolean hasDisplay() - { - return this._has_display; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax() - { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin() - { - return this._has_min; - } - - /** - * Method hasMincolour. - * - * @return true if at least one Mincolour has been added - */ - public boolean hasMincolour() - { - return this._has_mincolour; - } - - /** - * Method hasOrder. - * - * @return true if at least one Order has been added - */ - public boolean hasOrder() - { - return this._has_order; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Method hasThreshstate. - * - * @return true if at least one Threshstate has been added - */ - public boolean hasThreshstate() - { - return this._has_threshstate; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel() - { - return this._colourByLabel; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean isDisplay() - { - return this._display; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAttributeName() - { - this._attributeNameList.clear(); - } - - /** - * Method removeAttributeName. - * - * @param vAttributeName - * @return true if the object was removed from the collection. - */ - public boolean removeAttributeName(final java.lang.String vAttributeName) - { - boolean removed = _attributeNameList.remove(vAttributeName); - return removed; - } - - /** - * Method removeAttributeNameAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeAttributeNameAt(final int index) - { - java.lang.Object obj = this._attributeNameList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("setAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - this._attributeNameList.set(index, vAttributeName); - } - - /** - * - * - * @param vAttributeNameArray - */ - public void setAttributeName(final java.lang.String[] vAttributeNameArray) - { - // -- copy array - _attributeNameList.clear(); - - for (int i = 0; i < vAttributeNameArray.length; i++) - { - this._attributeNameList.add(vAttributeNameArray[i]); - } - } - - /** - * Sets the value of field 'autoScale'. - * - * @param autoScale - * the value of field 'autoScale'. - */ - public void setAutoScale(final boolean autoScale) - { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'colourByLabel'. - * - * @param colourByLabel - * the value of field 'colourByLabel'. - */ - public void setColourByLabel(final boolean colourByLabel) - { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = true; - } - - /** - * Sets the value of field 'display'. - * - * @param display - * the value of field 'display'. - */ - public void setDisplay(final boolean display) - { - this._display = display; - this._has_display = true; - } - - /** - * Sets the value of field 'matcherSet'. The field 'matcherSet' has the - * following description: optional filter(s) applied to the feature type - * - * @param matcherSet - * the value of field 'matcherSet'. - */ - public void setMatcherSet( - final jalview.schemabinding.version2.MatcherSet matcherSet) - { - this._matcherSet = matcherSet; - } - - /** - * Sets the value of field 'max'. - * - * @param max - * the value of field 'max'. - */ - public void setMax(final float max) - { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min - * the value of field 'min'. - */ - public void setMin(final float min) - { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'mincolour'. The field 'mincolour' has the - * following description: Optional minimum colour for graduated feature colour - * - * - * @param mincolour - * the value of field 'mincolour'. - */ - public void setMincolour(final int mincolour) - { - this._mincolour = mincolour; - this._has_mincolour = true; - } - - /** - * Sets the value of field 'noValueColour'. - * - * @param noValueColour - * the value of field 'noValueColour'. - */ - public void setNoValueColour( - final jalview.schemabinding.version2.types.NoValueColour noValueColour) - { - this._noValueColour = noValueColour; - } - - /** - * Sets the value of field 'order'. - * - * @param order - * the value of field 'order'. - */ - public void setOrder(final float order) - { - this._order = order; - this._has_order = true; - } - - /** - * Sets the value of field 'threshold'. The field 'threshold' has the - * following description: threshold value for graduated feature colour - * - * - * @param threshold - * the value of field 'threshold'. - */ - public void setThreshold(final float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Sets the value of field 'threshstate'. The field 'threshstate' has the - * following description: threshold type for graduated feature colour - * - * - * @param threshstate - * the value of field 'threshstate'. - */ - public void setThreshstate(final int threshstate) - { - this._threshstate = threshstate; - this._has_threshstate = true; - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Settin - */ - public static jalview.schemabinding.version2.Setting unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Setting.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java deleted file mode 100644 index 186e4e6..0000000 --- a/src/jalview/schemabinding/version2/StructureState.java +++ /dev/null @@ -1,706 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class StructureState. - * - * @version $Revision$ $Date$ - */ -public class StructureState implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _visible. - */ - private boolean _visible; - - /** - * keeps track of state for field: _visible - */ - private boolean _has_visible; - - /** - * additional identifier which properly disambiguates the structure view from - * any other view with the same attributes. This is not an ID, because it is - * possible to have many references to the same physical structure view from - * different sequences in an alignment. A structureState element citing the - * same viewId will appear for each instance. - * - */ - private java.lang.String _viewId; - - /** - * Flag set if the alignment panel containing this JSeq should be included in - * those used to perform a structure superposition (since Jalview 2.7). - * - */ - private boolean _alignwithAlignPanel = true; - - /** - * keeps track of state for field: _alignwithAlignPanel - */ - private boolean _has_alignwithAlignPanel; - - /** - * Flag set if the alignment panel containing this JSeq should be included in - * those used to colour its associated sequences in this structureState(since - * Jalview 2.7). - * - */ - private boolean _colourwithAlignPanel = false; - - /** - * keeps track of state for field: _colourwithAlignPanel - */ - private boolean _has_colourwithAlignPanel; - - /** - * Flag set if the structure display is coloured by the Jmol state, rather - * than by one or more linked alignment views. - * - */ - private boolean _colourByJmol = true; - - /** - * keeps track of state for field: _colourByJmol - */ - private boolean _has_colourByJmol; - - /** - * An identifier for the viewer type, currently either JMOL or CHIMERA - * - */ - private java.lang.String _type; - - /** - * Field _width. - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height. - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _xpos. - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos. - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public StructureState() - { - super(); - setContent(""); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteAlignwithAlignPanel() - { - this._has_alignwithAlignPanel = false; - } - - /** - */ - public void deleteColourByJmol() - { - this._has_colourByJmol = false; - } - - /** - */ - public void deleteColourwithAlignPanel() - { - this._has_colourwithAlignPanel = false; - } - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deleteVisible() - { - this._has_visible = false; - } - - /** - */ - public void deleteWidth() - { - this._has_width = false; - } - - /** - */ - public void deleteXpos() - { - this._has_xpos = false; - } - - /** - */ - public void deleteYpos() - { - this._has_ypos = false; - } - - /** - * Returns the value of field 'alignwithAlignPanel'. The field - * 'alignwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * perform a structure superposition (since Jalview 2.7). - * - * - * @return the value of field 'AlignwithAlignPanel'. - */ - public boolean getAlignwithAlignPanel() - { - return this._alignwithAlignPanel; - } - - /** - * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the - * following description: Flag set if the structure display is coloured by the - * Jmol state, rather than by one or more linked alignment views. - * - * - * @return the value of field 'ColourByJmol'. - */ - public boolean getColourByJmol() - { - return this._colourByJmol; - } - - /** - * Returns the value of field 'colourwithAlignPanel'. The field - * 'colourwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * colour its associated sequences in this structureState(since Jalview 2.7). - * - * - * @return the value of field 'ColourwithAlignPanel'. - */ - public boolean getColourwithAlignPanel() - { - return this._colourwithAlignPanel; - } - - /** - * Returns the value of field 'content'. The field 'content' has the following - * description: internal content storage - * - * @return the value of field 'Content'. - */ - public java.lang.String getContent() - { - return this._content; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Returns the value of field 'type'. The field 'type' has the following - * description: An identifier for the viewer type, currently either JMOL or - * CHIMERA - * - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Returns the value of field 'viewId'. The field 'viewId' has the following - * description: additional identifier which properly disambiguates the - * structure view from any other view with the same attributes. This is not an - * ID, because it is possible to have many references to the same physical - * structure view from different sequences in an alignment. A structureState - * element citing the same viewId will appear for each instance. - * - * - * @return the value of field 'ViewId'. - */ - public java.lang.String getViewId() - { - return this._viewId; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean getVisible() - { - return this._visible; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth() - { - return this._width; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos() - { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos() - { - return this._ypos; - } - - /** - * Method hasAlignwithAlignPanel. - * - * @return true if at least one AlignwithAlignPanel has been added - */ - public boolean hasAlignwithAlignPanel() - { - return this._has_alignwithAlignPanel; - } - - /** - * Method hasColourByJmol. - * - * @return true if at least one ColourByJmol has been added - */ - public boolean hasColourByJmol() - { - return this._has_colourByJmol; - } - - /** - * Method hasColourwithAlignPanel. - * - * @return true if at least one ColourwithAlignPanel has been added - */ - public boolean hasColourwithAlignPanel() - { - return this._has_colourwithAlignPanel; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasVisible. - * - * @return true if at least one Visible has been added - */ - public boolean hasVisible() - { - return this._has_visible; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth() - { - return this._has_width; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos() - { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos() - { - return this._has_ypos; - } - - /** - * Returns the value of field 'alignwithAlignPanel'. The field - * 'alignwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * perform a structure superposition (since Jalview 2.7). - * - * - * @return the value of field 'AlignwithAlignPanel'. - */ - public boolean isAlignwithAlignPanel() - { - return this._alignwithAlignPanel; - } - - /** - * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the - * following description: Flag set if the structure display is coloured by the - * Jmol state, rather than by one or more linked alignment views. - * - * - * @return the value of field 'ColourByJmol'. - */ - public boolean isColourByJmol() - { - return this._colourByJmol; - } - - /** - * Returns the value of field 'colourwithAlignPanel'. The field - * 'colourwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * colour its associated sequences in this structureState(since Jalview 2.7). - * - * - * @return the value of field 'ColourwithAlignPanel'. - */ - public boolean isColourwithAlignPanel() - { - return this._colourwithAlignPanel; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean isVisible() - { - return this._visible; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'alignwithAlignPanel'. The field - * 'alignwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * perform a structure superposition (since Jalview 2.7). - * - * - * @param alignwithAlignPanel - * the value of field 'alignwithAlignPanel'. - */ - public void setAlignwithAlignPanel(final boolean alignwithAlignPanel) - { - this._alignwithAlignPanel = alignwithAlignPanel; - this._has_alignwithAlignPanel = true; - } - - /** - * Sets the value of field 'colourByJmol'. The field 'colourByJmol' has the - * following description: Flag set if the structure display is coloured by the - * Jmol state, rather than by one or more linked alignment views. - * - * - * @param colourByJmol - * the value of field 'colourByJmol'. - */ - public void setColourByJmol(final boolean colourByJmol) - { - this._colourByJmol = colourByJmol; - this._has_colourByJmol = true; - } - - /** - * Sets the value of field 'colourwithAlignPanel'. The field - * 'colourwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * colour its associated sequences in this structureState(since Jalview 2.7). - * - * - * @param colourwithAlignPanel - * the value of field 'colourwithAlignPanel'. - */ - public void setColourwithAlignPanel(final boolean colourwithAlignPanel) - { - this._colourwithAlignPanel = colourwithAlignPanel; - this._has_colourwithAlignPanel = true; - } - - /** - * Sets the value of field 'content'. The field 'content' has the following - * description: internal content storage - * - * @param content - * the value of field 'content'. - */ - public void setContent(final java.lang.String content) - { - this._content = content; - } - - /** - * Sets the value of field 'height'. - * - * @param height - * the value of field 'height'. - */ - public void setHeight(final int height) - { - this._height = height; - this._has_height = true; - } - - /** - * Sets the value of field 'type'. The field 'type' has the following - * description: An identifier for the viewer type, currently either JMOL or - * CHIMERA - * - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Sets the value of field 'viewId'. The field 'viewId' has the following - * description: additional identifier which properly disambiguates the - * structure view from any other view with the same attributes. This is not an - * ID, because it is possible to have many references to the same physical - * structure view from different sequences in an alignment. A structureState - * element citing the same viewId will appear for each instance. - * - * - * @param viewId - * the value of field 'viewId'. - */ - public void setViewId(final java.lang.String viewId) - { - this._viewId = viewId; - } - - /** - * Sets the value of field 'visible'. - * - * @param visible - * the value of field 'visible'. - */ - public void setVisible(final boolean visible) - { - this._visible = visible; - this._has_visible = true; - } - - /** - * Sets the value of field 'width'. - * - * @param width - * the value of field 'width'. - */ - public void setWidth(final int width) - { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos - * the value of field 'xpos'. - */ - public void setXpos(final int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos - * the value of field 'ypos'. - */ - public void setYpos(final int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.StructureState - */ - public static jalview.schemabinding.version2.StructureState unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.StructureState) Unmarshaller - .unmarshal(jalview.schemabinding.version2.StructureState.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java deleted file mode 100644 index d70d855..0000000 --- a/src/jalview/schemabinding/version2/ThresholdLine.java +++ /dev/null @@ -1,253 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class ThresholdLine. - * - * @version $Revision$ $Date$ - */ -public class ThresholdLine implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _label. - */ - private java.lang.String _label; - - /** - * Field _value. - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public ThresholdLine() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteValue() - { - this._has_value = false; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel() - { - return this._label; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public float getValue() - { - return this._value; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasValue. - * - * @return true if at least one Value has been added - */ - public boolean hasValue() - { - return this._has_value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'label'. - * - * @param label - * the value of field 'label'. - */ - public void setLabel(final java.lang.String label) - { - this._label = label; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final float value) - { - this._value = value; - this._has_value = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.ThresholdLine - */ - public static jalview.schemabinding.version2.ThresholdLine unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller - .unmarshal(jalview.schemabinding.version2.ThresholdLine.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java deleted file mode 100644 index 19b3eb1..0000000 --- a/src/jalview/schemabinding/version2/Tree.java +++ /dev/null @@ -1,878 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Tree. - * - * @version $Revision$ $Date$ - */ -public class Tree implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _fontName. - */ - private java.lang.String _fontName; - - /** - * Field _fontSize. - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle. - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _showBootstrap. - */ - private boolean _showBootstrap; - - /** - * keeps track of state for field: _showBootstrap - */ - private boolean _has_showBootstrap; - - /** - * Field _showDistances. - */ - private boolean _showDistances; - - /** - * keeps track of state for field: _showDistances - */ - private boolean _has_showDistances; - - /** - * Field _markUnlinked. - */ - private boolean _markUnlinked; - - /** - * keeps track of state for field: _markUnlinked - */ - private boolean _has_markUnlinked; - - /** - * Field _fitToWindow. - */ - private boolean _fitToWindow; - - /** - * keeps track of state for field: _fitToWindow - */ - private boolean _has_fitToWindow; - - /** - * Field _currentTree. - */ - private boolean _currentTree; - - /** - * keeps track of state for field: _currentTree - */ - private boolean _has_currentTree; - - /** - * Tree ID added for binding tree visualization settings to vamsas document - * trees in jalview 2.4.1 - * - */ - private java.lang.String _id; - - /** - * Field _width. - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height. - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _xpos. - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos. - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * Field _newick. - */ - private java.lang.String _newick; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Tree() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteCurrentTree() - { - this._has_currentTree = false; - } - - /** - */ - public void deleteFitToWindow() - { - this._has_fitToWindow = false; - } - - /** - */ - public void deleteFontSize() - { - this._has_fontSize = false; - } - - /** - */ - public void deleteFontStyle() - { - this._has_fontStyle = false; - } - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deleteMarkUnlinked() - { - this._has_markUnlinked = false; - } - - /** - */ - public void deleteShowBootstrap() - { - this._has_showBootstrap = false; - } - - /** - */ - public void deleteShowDistances() - { - this._has_showDistances = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - */ - public void deleteWidth() - { - this._has_width = false; - } - - /** - */ - public void deleteXpos() - { - this._has_xpos = false; - } - - /** - */ - public void deleteYpos() - { - this._has_ypos = false; - } - - /** - * Returns the value of field 'currentTree'. - * - * @return the value of field 'CurrentTree'. - */ - public boolean getCurrentTree() - { - return this._currentTree; - } - - /** - * Returns the value of field 'fitToWindow'. - * - * @return the value of field 'FitToWindow'. - */ - public boolean getFitToWindow() - { - return this._fitToWindow; - } - - /** - * Returns the value of field 'fontName'. - * - * @return the value of field 'FontName'. - */ - public java.lang.String getFontName() - { - return this._fontName; - } - - /** - * Returns the value of field 'fontSize'. - * - * @return the value of field 'FontSize'. - */ - public int getFontSize() - { - return this._fontSize; - } - - /** - * Returns the value of field 'fontStyle'. - * - * @return the value of field 'FontStyle'. - */ - public int getFontStyle() - { - return this._fontStyle; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Returns the value of field 'id'. The field 'id' has the following - * description: Tree ID added for binding tree visualization settings to - * vamsas document trees in jalview 2.4.1 - * - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'markUnlinked'. - * - * @return the value of field 'MarkUnlinked'. - */ - public boolean getMarkUnlinked() - { - return this._markUnlinked; - } - - /** - * Returns the value of field 'newick'. - * - * @return the value of field 'Newick'. - */ - public java.lang.String getNewick() - { - return this._newick; - } - - /** - * Returns the value of field 'showBootstrap'. - * - * @return the value of field 'ShowBootstrap'. - */ - public boolean getShowBootstrap() - { - return this._showBootstrap; - } - - /** - * Returns the value of field 'showDistances'. - * - * @return the value of field 'ShowDistances'. - */ - public boolean getShowDistances() - { - return this._showDistances; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle() - { - return this._title; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth() - { - return this._width; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos() - { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos() - { - return this._ypos; - } - - /** - * Method hasCurrentTree. - * - * @return true if at least one CurrentTree has been added - */ - public boolean hasCurrentTree() - { - return this._has_currentTree; - } - - /** - * Method hasFitToWindow. - * - * @return true if at least one FitToWindow has been added - */ - public boolean hasFitToWindow() - { - return this._has_fitToWindow; - } - - /** - * Method hasFontSize. - * - * @return true if at least one FontSize has been added - */ - public boolean hasFontSize() - { - return this._has_fontSize; - } - - /** - * Method hasFontStyle. - * - * @return true if at least one FontStyle has been added - */ - public boolean hasFontStyle() - { - return this._has_fontStyle; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasMarkUnlinked. - * - * @return true if at least one MarkUnlinked has been added - */ - public boolean hasMarkUnlinked() - { - return this._has_markUnlinked; - } - - /** - * Method hasShowBootstrap. - * - * @return true if at least one ShowBootstrap has been added - */ - public boolean hasShowBootstrap() - { - return this._has_showBootstrap; - } - - /** - * Method hasShowDistances. - * - * @return true if at least one ShowDistances has been added - */ - public boolean hasShowDistances() - { - return this._has_showDistances; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth() - { - return this._has_width; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos() - { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos() - { - return this._has_ypos; - } - - /** - * Returns the value of field 'currentTree'. - * - * @return the value of field 'CurrentTree'. - */ - public boolean isCurrentTree() - { - return this._currentTree; - } - - /** - * Returns the value of field 'fitToWindow'. - * - * @return the value of field 'FitToWindow'. - */ - public boolean isFitToWindow() - { - return this._fitToWindow; - } - - /** - * Returns the value of field 'markUnlinked'. - * - * @return the value of field 'MarkUnlinked'. - */ - public boolean isMarkUnlinked() - { - return this._markUnlinked; - } - - /** - * Returns the value of field 'showBootstrap'. - * - * @return the value of field 'ShowBootstrap'. - */ - public boolean isShowBootstrap() - { - return this._showBootstrap; - } - - /** - * Returns the value of field 'showDistances'. - * - * @return the value of field 'ShowDistances'. - */ - public boolean isShowDistances() - { - return this._showDistances; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'currentTree'. - * - * @param currentTree - * the value of field 'currentTree'. - */ - public void setCurrentTree(final boolean currentTree) - { - this._currentTree = currentTree; - this._has_currentTree = true; - } - - /** - * Sets the value of field 'fitToWindow'. - * - * @param fitToWindow - * the value of field 'fitToWindow'. - */ - public void setFitToWindow(final boolean fitToWindow) - { - this._fitToWindow = fitToWindow; - this._has_fitToWindow = true; - } - - /** - * Sets the value of field 'fontName'. - * - * @param fontName - * the value of field 'fontName'. - */ - public void setFontName(final java.lang.String fontName) - { - this._fontName = fontName; - } - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize - * the value of field 'fontSize'. - */ - public void setFontSize(final int fontSize) - { - this._fontSize = fontSize; - this._has_fontSize = true; - } - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle - * the value of field 'fontStyle'. - */ - public void setFontStyle(final int fontStyle) - { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } - - /** - * Sets the value of field 'height'. - * - * @param height - * the value of field 'height'. - */ - public void setHeight(final int height) - { - this._height = height; - this._has_height = true; - } - - /** - * Sets the value of field 'id'. The field 'id' has the following description: - * Tree ID added for binding tree visualization settings to vamsas document - * trees in jalview 2.4.1 - * - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'markUnlinked'. - * - * @param markUnlinked - * the value of field 'markUnlinked'. - */ - public void setMarkUnlinked(final boolean markUnlinked) - { - this._markUnlinked = markUnlinked; - this._has_markUnlinked = true; - } - - /** - * Sets the value of field 'newick'. - * - * @param newick - * the value of field 'newick'. - */ - public void setNewick(final java.lang.String newick) - { - this._newick = newick; - } - - /** - * Sets the value of field 'showBootstrap'. - * - * @param showBootstrap - * the value of field 'showBootstrap'. - */ - public void setShowBootstrap(final boolean showBootstrap) - { - this._showBootstrap = showBootstrap; - this._has_showBootstrap = true; - } - - /** - * Sets the value of field 'showDistances'. - * - * @param showDistances - * the value of field 'showDistances'. - */ - public void setShowDistances(final boolean showDistances) - { - this._showDistances = showDistances; - this._has_showDistances = true; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold - * the value of field 'threshold'. - */ - public void setThreshold(final float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title - * the value of field 'title'. - */ - public void setTitle(final java.lang.String title) - { - this._title = title; - } - - /** - * Sets the value of field 'width'. - * - * @param width - * the value of field 'width'. - */ - public void setWidth(final int width) - { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos - * the value of field 'xpos'. - */ - public void setXpos(final int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos - * the value of field 'ypos'. - */ - public void setYpos(final int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Tree - */ - public static jalview.schemabinding.version2.Tree unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Tree.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java deleted file mode 100644 index e4983bd..0000000 --- a/src/jalview/schemabinding/version2/UserColourScheme.java +++ /dev/null @@ -1,127 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class UserColourScheme. - * - * @version $Revision$ $Date$ - */ -public class UserColourScheme extends JalviewUserColours implements - java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColourScheme() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours - */ - public static jalview.schemabinding.version2.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.UserColourScheme.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java deleted file mode 100644 index b02d0cd..0000000 --- a/src/jalview/schemabinding/version2/UserColours.java +++ /dev/null @@ -1,182 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class UserColours. - * - * @version $Revision$ $Date$ - */ -public class UserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _userColourScheme. - */ - private jalview.schemabinding.version2.UserColourScheme _userColourScheme; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColours() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'userColourScheme'. - * - * @return the value of field 'UserColourScheme'. - */ - public jalview.schemabinding.version2.UserColourScheme getUserColourScheme() - { - return this._userColourScheme; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'userColourScheme'. - * - * @param userColourScheme - * the value of field 'userColourScheme' - */ - public void setUserColourScheme( - final jalview.schemabinding.version2.UserColourScheme userColourScheme) - { - this._userColourScheme = userColourScheme; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.UserColours - */ - public static jalview.schemabinding.version2.UserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.UserColours) Unmarshaller - .unmarshal(jalview.schemabinding.version2.UserColours.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java deleted file mode 100644 index d025824..0000000 --- a/src/jalview/schemabinding/version2/VAMSAS.java +++ /dev/null @@ -1,454 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class VAMSAS. - * - * @version $Revision$ $Date$ - */ -public class VAMSAS implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _treeList. - */ - private java.util.Vector _treeList; - - /** - * Field _sequenceSetList. - */ - private java.util.Vector _sequenceSetList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VAMSAS() - { - super(); - this._treeList = new java.util.Vector(); - this._sequenceSetList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSet( - final jalview.schemabinding.version2.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetList.addElement(vSequenceSet); - } - - /** - * - * - * @param index - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSet(final int index, - final jalview.schemabinding.version2.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetList.add(index, vSequenceSet); - } - - /** - * - * - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.addElement(vTree); - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final int index, final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.add(index, vTree); - } - - /** - * Method enumerateSequenceSet. - * - * @return an Enumeration over all jalview.schemabinding.version2.SequenceSet - * elements - */ - public java.util.Enumeration enumerateSequenceSet() - { - return this._sequenceSetList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateTree() - { - return this._treeList.elements(); - } - - /** - * Method getSequenceSet. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.SequenceSet at the - * given index - */ - public jalview.schemabinding.version2.SequenceSet getSequenceSet( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetList.size()) - { - throw new IndexOutOfBoundsException("getSequenceSet: Index value '" - + index + "' not in range [0.." - + (this._sequenceSetList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList - .get(index); - } - - /** - * Method getSequenceSet.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.SequenceSet[] getSequenceSet() - { - jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0]; - return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList - .toArray(array); - } - - /** - * Method getSequenceSetCount. - * - * @return the size of this collection - */ - public int getSequenceSetCount() - { - return this._sequenceSetList.size(); - } - - /** - * Method getTree. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getTree(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("getTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - return (java.lang.String) _treeList.get(index); - } - - /** - * Method getTree.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getTree() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._treeList.toArray(array); - } - - /** - * Method getTreeCount. - * - * @return the size of this collection - */ - public int getTreeCount() - { - return this._treeList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSequenceSet() - { - this._sequenceSetList.clear(); - } - - /** - */ - public void removeAllTree() - { - this._treeList.clear(); - } - - /** - * Method removeSequenceSet. - * - * @param vSequenceSet - * @return true if the object was removed from the collection. - */ - public boolean removeSequenceSet( - final jalview.schemabinding.version2.SequenceSet vSequenceSet) - { - boolean removed = _sequenceSetList.remove(vSequenceSet); - return removed; - } - - /** - * Method removeSequenceSetAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt( - final int index) - { - java.lang.Object obj = this._sequenceSetList.remove(index); - return (jalview.schemabinding.version2.SequenceSet) obj; - } - - /** - * Method removeTree. - * - * @param vTree - * @return true if the object was removed from the collection. - */ - public boolean removeTree(final java.lang.String vTree) - { - boolean removed = _treeList.remove(vTree); - return removed; - } - - /** - * Method removeTreeAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeTreeAt(final int index) - { - java.lang.Object obj = this._treeList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSequenceSet(final int index, - final jalview.schemabinding.version2.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetList.size()) - { - throw new IndexOutOfBoundsException("setSequenceSet: Index value '" - + index + "' not in range [0.." - + (this._sequenceSetList.size() - 1) + "]"); - } - - this._sequenceSetList.set(index, vSequenceSet); - } - - /** - * - * - * @param vSequenceSetArray - */ - public void setSequenceSet( - final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) - { - // -- copy array - _sequenceSetList.clear(); - - for (int i = 0; i < vSequenceSetArray.length; i++) - { - this._sequenceSetList.add(vSequenceSetArray[i]); - } - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setTree(final int index, final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("setTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - this._treeList.set(index, vTree); - } - - /** - * - * - * @param vTreeArray - */ - public void setTree(final java.lang.String[] vTreeArray) - { - // -- copy array - _treeList.clear(); - - for (int i = 0; i < vTreeArray.length; i++) - { - this._treeList.add(vTreeArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.VAMSAS - */ - public static jalview.schemabinding.version2.VAMSAS unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal( - jalview.schemabinding.version2.VAMSAS.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java deleted file mode 100644 index d3fe796..0000000 --- a/src/jalview/schemabinding/version2/VamsasModel.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class VamsasModel. - * - * @version $Revision$ $Date$ - */ -public class VamsasModel extends VAMSAS implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VamsasModel() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.VAMSAS - */ - public static jalview.schemabinding.version2.VAMSAS unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal( - jalview.schemabinding.version2.VamsasModel.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java deleted file mode 100644 index 159f7ae..0000000 --- a/src/jalview/schemabinding/version2/Viewport.java +++ /dev/null @@ -1,2803 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Viewport. - * - * @version $Revision$ $Date$ - */ -public class Viewport implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _conservationSelected. - */ - private boolean _conservationSelected; - - /** - * keeps track of state for field: _conservationSelected - */ - private boolean _has_conservationSelected; - - /** - * Field _pidSelected. - */ - private boolean _pidSelected; - - /** - * keeps track of state for field: _pidSelected - */ - private boolean _has_pidSelected; - - /** - * Field _bgColour. - */ - private java.lang.String _bgColour; - - /** - * Field _consThreshold. - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold. - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * Field _showFullId. - */ - private boolean _showFullId; - - /** - * keeps track of state for field: _showFullId - */ - private boolean _has_showFullId; - - /** - * Field _rightAlignIds. - */ - private boolean _rightAlignIds; - - /** - * keeps track of state for field: _rightAlignIds - */ - private boolean _has_rightAlignIds; - - /** - * Field _showText. - */ - private boolean _showText; - - /** - * keeps track of state for field: _showText - */ - private boolean _has_showText; - - /** - * Field _showColourText. - */ - private boolean _showColourText; - - /** - * keeps track of state for field: _showColourText - */ - private boolean _has_showColourText; - - /** - * Field _showUnconserved. - */ - private boolean _showUnconserved = false; - - /** - * keeps track of state for field: _showUnconserved - */ - private boolean _has_showUnconserved; - - /** - * Field _showBoxes. - */ - private boolean _showBoxes; - - /** - * keeps track of state for field: _showBoxes - */ - private boolean _has_showBoxes; - - /** - * Field _wrapAlignment. - */ - private boolean _wrapAlignment; - - /** - * keeps track of state for field: _wrapAlignment - */ - private boolean _has_wrapAlignment; - - /** - * Field _renderGaps. - */ - private boolean _renderGaps; - - /** - * keeps track of state for field: _renderGaps - */ - private boolean _has_renderGaps; - - /** - * Field _showSequenceFeatures. - */ - private boolean _showSequenceFeatures; - - /** - * keeps track of state for field: _showSequenceFeatures - */ - private boolean _has_showSequenceFeatures; - - /** - * Field _showNPfeatureTooltip. - */ - private boolean _showNPfeatureTooltip; - - /** - * keeps track of state for field: _showNPfeatureTooltip - */ - private boolean _has_showNPfeatureTooltip; - - /** - * Field _showDbRefTooltip. - */ - private boolean _showDbRefTooltip; - - /** - * keeps track of state for field: _showDbRefTooltip - */ - private boolean _has_showDbRefTooltip; - - /** - * Field _followHighlight. - */ - private boolean _followHighlight = true; - - /** - * keeps track of state for field: _followHighlight - */ - private boolean _has_followHighlight; - - /** - * Field _followSelection. - */ - private boolean _followSelection = true; - - /** - * keeps track of state for field: _followSelection - */ - private boolean _has_followSelection; - - /** - * Field _showAnnotation. - */ - private boolean _showAnnotation; - - /** - * keeps track of state for field: _showAnnotation - */ - private boolean _has_showAnnotation; - - /** - * Field _centreColumnLabels. - */ - private boolean _centreColumnLabels = false; - - /** - * keeps track of state for field: _centreColumnLabels - */ - private boolean _has_centreColumnLabels; - - /** - * Field _showGroupConservation. - */ - private boolean _showGroupConservation = false; - - /** - * keeps track of state for field: _showGroupConservation - */ - private boolean _has_showGroupConservation; - - /** - * Field _showGroupConsensus. - */ - private boolean _showGroupConsensus = false; - - /** - * keeps track of state for field: _showGroupConsensus - */ - private boolean _has_showGroupConsensus; - - /** - * Field _showConsensusHistogram. - */ - private boolean _showConsensusHistogram = true; - - /** - * keeps track of state for field: _showConsensusHistogram - */ - private boolean _has_showConsensusHistogram; - - /** - * Field _showSequenceLogo. - */ - private boolean _showSequenceLogo = false; - - /** - * keeps track of state for field: _showSequenceLogo - */ - private boolean _has_showSequenceLogo; - - /** - * Field _normaliseSequenceLogo. - */ - private boolean _normaliseSequenceLogo = false; - - /** - * keeps track of state for field: _normaliseSequenceLogo - */ - private boolean _has_normaliseSequenceLogo; - - /** - * Field _ignoreGapsinConsensus. - */ - private boolean _ignoreGapsinConsensus = true; - - /** - * keeps track of state for field: _ignoreGapsinConsensus - */ - private boolean _has_ignoreGapsinConsensus; - - /** - * Field _startRes. - */ - private int _startRes; - - /** - * keeps track of state for field: _startRes - */ - private boolean _has_startRes; - - /** - * Field _startSeq. - */ - private int _startSeq; - - /** - * keeps track of state for field: _startSeq - */ - private boolean _has_startSeq; - - /** - * Field _fontName. - */ - private java.lang.String _fontName; - - /** - * Field _fontSize. - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle. - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - /** - * Field _scaleProteinAsCdna. - */ - private boolean _scaleProteinAsCdna = true; - - /** - * keeps track of state for field: _scaleProteinAsCdna - */ - private boolean _has_scaleProteinAsCdna; - - /** - * Field _viewName. - */ - private java.lang.String _viewName; - - /** - * Field _sequenceSetId. - */ - private java.lang.String _sequenceSetId; - - /** - * Field _gatheredViews. - */ - private boolean _gatheredViews; - - /** - * keeps track of state for field: _gatheredViews - */ - private boolean _has_gatheredViews; - - /** - * Field _textCol1. - */ - private int _textCol1; - - /** - * keeps track of state for field: _textCol1 - */ - private boolean _has_textCol1; - - /** - * Field _textCol2. - */ - private int _textCol2; - - /** - * keeps track of state for field: _textCol2 - */ - private boolean _has_textCol2; - - /** - * Field _textColThreshold. - */ - private int _textColThreshold; - - /** - * keeps track of state for field: _textColThreshold - */ - private boolean _has_textColThreshold; - - /** - * unique id used by jalview to synchronize between stored and instantiated - * views - * - */ - private java.lang.String _id; - - /** - * The viewport id of this viewport's (cdna/protein) coding complement, if any - * - */ - private java.lang.String _complementId; - - /** - * Field _width. - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height. - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _xpos. - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos. - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _annotationColours. - */ - private jalview.schemabinding.version2.AnnotationColours _annotationColours; - - /** - * Field _hiddenColumnsList. - */ - private java.util.Vector _hiddenColumnsList; - - /** - * Field _calcIdParamList. - */ - private java.util.Vector _calcIdParamList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Viewport() - { - super(); - this._hiddenColumnsList = new java.util.Vector(); - this._calcIdParamList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vCalcIdParam - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addCalcIdParam( - final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) - throws java.lang.IndexOutOfBoundsException - { - this._calcIdParamList.addElement(vCalcIdParam); - } - - /** - * - * - * @param index - * @param vCalcIdParam - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addCalcIdParam(final int index, - final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) - throws java.lang.IndexOutOfBoundsException - { - this._calcIdParamList.add(index, vCalcIdParam); - } - - /** - * - * - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenColumnsList.addElement(vHiddenColumns); - } - - /** - * - * - * @param index - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenColumns(final int index, - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenColumnsList.add(index, vHiddenColumns); - } - - /** - */ - public void deleteCentreColumnLabels() - { - this._has_centreColumnLabels = false; - } - - /** - */ - public void deleteConsThreshold() - { - this._has_consThreshold = false; - } - - /** - */ - public void deleteConservationSelected() - { - this._has_conservationSelected = false; - } - - /** - */ - public void deleteFollowHighlight() - { - this._has_followHighlight = false; - } - - /** - */ - public void deleteFollowSelection() - { - this._has_followSelection = false; - } - - /** - */ - public void deleteFontSize() - { - this._has_fontSize = false; - } - - /** - */ - public void deleteFontStyle() - { - this._has_fontStyle = false; - } - - /** - */ - public void deleteGatheredViews() - { - this._has_gatheredViews = false; - } - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deleteIgnoreGapsinConsensus() - { - this._has_ignoreGapsinConsensus = false; - } - - /** - */ - public void deleteNormaliseSequenceLogo() - { - this._has_normaliseSequenceLogo = false; - } - - /** - */ - public void deletePidSelected() - { - this._has_pidSelected = false; - } - - /** - */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } - - /** - */ - public void deleteRenderGaps() - { - this._has_renderGaps = false; - } - - /** - */ - public void deleteRightAlignIds() - { - this._has_rightAlignIds = false; - } - - /** - */ - public void deleteScaleProteinAsCdna() - { - this._has_scaleProteinAsCdna = false; - } - - /** - */ - public void deleteShowAnnotation() - { - this._has_showAnnotation = false; - } - - /** - */ - public void deleteShowBoxes() - { - this._has_showBoxes = false; - } - - /** - */ - public void deleteShowColourText() - { - this._has_showColourText = false; - } - - /** - */ - public void deleteShowConsensusHistogram() - { - this._has_showConsensusHistogram = false; - } - - /** - */ - public void deleteShowDbRefTooltip() - { - this._has_showDbRefTooltip = false; - } - - /** - */ - public void deleteShowFullId() - { - this._has_showFullId = false; - } - - /** - */ - public void deleteShowGroupConsensus() - { - this._has_showGroupConsensus = false; - } - - /** - */ - public void deleteShowGroupConservation() - { - this._has_showGroupConservation = false; - } - - /** - */ - public void deleteShowNPfeatureTooltip() - { - this._has_showNPfeatureTooltip = false; - } - - /** - */ - public void deleteShowSequenceFeatures() - { - this._has_showSequenceFeatures = false; - } - - /** - */ - public void deleteShowSequenceLogo() - { - this._has_showSequenceLogo = false; - } - - /** - */ - public void deleteShowText() - { - this._has_showText = false; - } - - /** - */ - public void deleteShowUnconserved() - { - this._has_showUnconserved = false; - } - - /** - */ - public void deleteStartRes() - { - this._has_startRes = false; - } - - /** - */ - public void deleteStartSeq() - { - this._has_startSeq = false; - } - - /** - */ - public void deleteTextCol1() - { - this._has_textCol1 = false; - } - - /** - */ - public void deleteTextCol2() - { - this._has_textCol2 = false; - } - - /** - */ - public void deleteTextColThreshold() - { - this._has_textColThreshold = false; - } - - /** - */ - public void deleteWidth() - { - this._has_width = false; - } - - /** - */ - public void deleteWrapAlignment() - { - this._has_wrapAlignment = false; - } - - /** - */ - public void deleteXpos() - { - this._has_xpos = false; - } - - /** - */ - public void deleteYpos() - { - this._has_ypos = false; - } - - /** - * Method enumerateCalcIdParam. - * - * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam - * elements - */ - public java.util.Enumeration enumerateCalcIdParam() - { - return this._calcIdParamList.elements(); - } - - /** - * Method enumerateHiddenColumns. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.HiddenColumns elements - */ - public java.util.Enumeration enumerateHiddenColumns() - { - return this._hiddenColumnsList.elements(); - } - - /** - * Returns the value of field 'annotationColours'. - * - * @return the value of field 'AnnotationColours'. - */ - public jalview.schemabinding.version2.AnnotationColours getAnnotationColours() - { - return this._annotationColours; - } - - /** - * Returns the value of field 'bgColour'. - * - * @return the value of field 'BgColour'. - */ - public java.lang.String getBgColour() - { - return this._bgColour; - } - - /** - * Method getCalcIdParam. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.CalcIdParam at the - * given index - */ - public jalview.schemabinding.version2.CalcIdParam getCalcIdParam( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._calcIdParamList.size()) - { - throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" - + index + "' not in range [0.." - + (this._calcIdParamList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList - .get(index); - } - - /** - * Method getCalcIdParam.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam() - { - jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0]; - return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList - .toArray(array); - } - - /** - * Method getCalcIdParamCount. - * - * @return the size of this collection - */ - public int getCalcIdParamCount() - { - return this._calcIdParamList.size(); - } - - /** - * Returns the value of field 'centreColumnLabels'. - * - * @return the value of field 'CentreColumnLabels'. - */ - public boolean getCentreColumnLabels() - { - return this._centreColumnLabels; - } - - /** - * Returns the value of field 'complementId'. The field 'complementId' has the - * following description: The viewport id of this viewport's (cdna/protein) - * coding complement, if any - * - * - * @return the value of field 'ComplementId'. - */ - public java.lang.String getComplementId() - { - return this._complementId; - } - - /** - * Returns the value of field 'consThreshold'. - * - * @return the value of field 'ConsThreshold'. - */ - public int getConsThreshold() - { - return this._consThreshold; - } - - /** - * Returns the value of field 'conservationSelected'. - * - * @return the value of field 'ConservationSelected'. - */ - public boolean getConservationSelected() - { - return this._conservationSelected; - } - - /** - * Returns the value of field 'followHighlight'. - * - * @return the value of field 'FollowHighlight'. - */ - public boolean getFollowHighlight() - { - return this._followHighlight; - } - - /** - * Returns the value of field 'followSelection'. - * - * @return the value of field 'FollowSelection'. - */ - public boolean getFollowSelection() - { - return this._followSelection; - } - - /** - * Returns the value of field 'fontName'. - * - * @return the value of field 'FontName'. - */ - public java.lang.String getFontName() - { - return this._fontName; - } - - /** - * Returns the value of field 'fontSize'. - * - * @return the value of field 'FontSize'. - */ - public int getFontSize() - { - return this._fontSize; - } - - /** - * Returns the value of field 'fontStyle'. - * - * @return the value of field 'FontStyle'. - */ - public int getFontStyle() - { - return this._fontStyle; - } - - /** - * Returns the value of field 'gatheredViews'. - * - * @return the value of field 'GatheredViews'. - */ - public boolean getGatheredViews() - { - return this._gatheredViews; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Method getHiddenColumns. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.HiddenColumns at - * the given index - */ - public jalview.schemabinding.version2.HiddenColumns getHiddenColumns( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenColumnsList.size()) - { - throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" - + index + "' not in range [0.." - + (this._hiddenColumnsList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList - .get(index); - } - - /** - * Method getHiddenColumns.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() - { - jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0]; - return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList - .toArray(array); - } - - /** - * Method getHiddenColumnsCount. - * - * @return the size of this collection - */ - public int getHiddenColumnsCount() - { - return this._hiddenColumnsList.size(); - } - - /** - * Returns the value of field 'id'. The field 'id' has the following - * description: unique id used by jalview to synchronize between stored and - * instantiated views - * - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean getIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'normaliseSequenceLogo'. - * - * @return the value of field 'NormaliseSequenceLogo'. - */ - public boolean getNormaliseSequenceLogo() - { - return this._normaliseSequenceLogo; - } - - /** - * Returns the value of field 'pidSelected'. - * - * @return the value of field 'PidSelected'. - */ - public boolean getPidSelected() - { - return this._pidSelected; - } - - /** - * Returns the value of field 'pidThreshold'. - * - * @return the value of field 'PidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } - - /** - * Returns the value of field 'renderGaps'. - * - * @return the value of field 'RenderGaps'. - */ - public boolean getRenderGaps() - { - return this._renderGaps; - } - - /** - * Returns the value of field 'rightAlignIds'. - * - * @return the value of field 'RightAlignIds'. - */ - public boolean getRightAlignIds() - { - return this._rightAlignIds; - } - - /** - * Returns the value of field 'scaleProteinAsCdna'. - * - * @return the value of field 'ScaleProteinAsCdna'. - */ - public boolean getScaleProteinAsCdna() - { - return this._scaleProteinAsCdna; - } - - /** - * Returns the value of field 'sequenceSetId'. - * - * @return the value of field 'SequenceSetId'. - */ - public java.lang.String getSequenceSetId() - { - return this._sequenceSetId; - } - - /** - * Returns the value of field 'showAnnotation'. - * - * @return the value of field 'ShowAnnotation'. - */ - public boolean getShowAnnotation() - { - return this._showAnnotation; - } - - /** - * Returns the value of field 'showBoxes'. - * - * @return the value of field 'ShowBoxes'. - */ - public boolean getShowBoxes() - { - return this._showBoxes; - } - - /** - * Returns the value of field 'showColourText'. - * - * @return the value of field 'ShowColourText'. - */ - public boolean getShowColourText() - { - return this._showColourText; - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean getShowConsensusHistogram() - { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showDbRefTooltip'. - * - * @return the value of field 'ShowDbRefTooltip'. - */ - public boolean getShowDbRefTooltip() - { - return this._showDbRefTooltip; - } - - /** - * Returns the value of field 'showFullId'. - * - * @return the value of field 'ShowFullId'. - */ - public boolean getShowFullId() - { - return this._showFullId; - } - - /** - * Returns the value of field 'showGroupConsensus'. - * - * @return the value of field 'ShowGroupConsensus'. - */ - public boolean getShowGroupConsensus() - { - return this._showGroupConsensus; - } - - /** - * Returns the value of field 'showGroupConservation'. - * - * @return the value of field 'ShowGroupConservation'. - */ - public boolean getShowGroupConservation() - { - return this._showGroupConservation; - } - - /** - * Returns the value of field 'showNPfeatureTooltip'. - * - * @return the value of field 'ShowNPfeatureTooltip'. - */ - public boolean getShowNPfeatureTooltip() - { - return this._showNPfeatureTooltip; - } - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return the value of field 'ShowSequenceFeatures'. - */ - public boolean getShowSequenceFeatures() - { - return this._showSequenceFeatures; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean getShowSequenceLogo() - { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showText'. - * - * @return the value of field 'ShowText'. - */ - public boolean getShowText() - { - return this._showText; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean getShowUnconserved() - { - return this._showUnconserved; - } - - /** - * Returns the value of field 'startRes'. - * - * @return the value of field 'StartRes'. - */ - public int getStartRes() - { - return this._startRes; - } - - /** - * Returns the value of field 'startSeq'. - * - * @return the value of field 'StartSeq'. - */ - public int getStartSeq() - { - return this._startSeq; - } - - /** - * Returns the value of field 'textCol1'. - * - * @return the value of field 'TextCol1'. - */ - public int getTextCol1() - { - return this._textCol1; - } - - /** - * Returns the value of field 'textCol2'. - * - * @return the value of field 'TextCol2'. - */ - public int getTextCol2() - { - return this._textCol2; - } - - /** - * Returns the value of field 'textColThreshold'. - * - * @return the value of field 'TextColThreshold'. - */ - public int getTextColThreshold() - { - return this._textColThreshold; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle() - { - return this._title; - } - - /** - * Returns the value of field 'viewName'. - * - * @return the value of field 'ViewName'. - */ - public java.lang.String getViewName() - { - return this._viewName; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth() - { - return this._width; - } - - /** - * Returns the value of field 'wrapAlignment'. - * - * @return the value of field 'WrapAlignment'. - */ - public boolean getWrapAlignment() - { - return this._wrapAlignment; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos() - { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos() - { - return this._ypos; - } - - /** - * Method hasCentreColumnLabels. - * - * @return true if at least one CentreColumnLabels has been adde - */ - public boolean hasCentreColumnLabels() - { - return this._has_centreColumnLabels; - } - - /** - * Method hasConsThreshold. - * - * @return true if at least one ConsThreshold has been added - */ - public boolean hasConsThreshold() - { - return this._has_consThreshold; - } - - /** - * Method hasConservationSelected. - * - * @return true if at least one ConservationSelected has been added - */ - public boolean hasConservationSelected() - { - return this._has_conservationSelected; - } - - /** - * Method hasFollowHighlight. - * - * @return true if at least one FollowHighlight has been added - */ - public boolean hasFollowHighlight() - { - return this._has_followHighlight; - } - - /** - * Method hasFollowSelection. - * - * @return true if at least one FollowSelection has been added - */ - public boolean hasFollowSelection() - { - return this._has_followSelection; - } - - /** - * Method hasFontSize. - * - * @return true if at least one FontSize has been added - */ - public boolean hasFontSize() - { - return this._has_fontSize; - } - - /** - * Method hasFontStyle. - * - * @return true if at least one FontStyle has been added - */ - public boolean hasFontStyle() - { - return this._has_fontStyle; - } - - /** - * Method hasGatheredViews. - * - * @return true if at least one GatheredViews has been added - */ - public boolean hasGatheredViews() - { - return this._has_gatheredViews; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasIgnoreGapsinConsensus. - * - * @return true if at least one IgnoreGapsinConsensus has been added - */ - public boolean hasIgnoreGapsinConsensus() - { - return this._has_ignoreGapsinConsensus; - } - - /** - * Method hasNormaliseSequenceLogo. - * - * @return true if at least one NormaliseSequenceLogo has been added - */ - public boolean hasNormaliseSequenceLogo() - { - return this._has_normaliseSequenceLogo; - } - - /** - * Method hasPidSelected. - * - * @return true if at least one PidSelected has been added - */ - public boolean hasPidSelected() - { - return this._has_pidSelected; - } - - /** - * Method hasPidThreshold. - * - * @return true if at least one PidThreshold has been added - */ - public boolean hasPidThreshold() - { - return this._has_pidThreshold; - } - - /** - * Method hasRenderGaps. - * - * @return true if at least one RenderGaps has been added - */ - public boolean hasRenderGaps() - { - return this._has_renderGaps; - } - - /** - * Method hasRightAlignIds. - * - * @return true if at least one RightAlignIds has been added - */ - public boolean hasRightAlignIds() - { - return this._has_rightAlignIds; - } - - /** - * Method hasScaleProteinAsCdna. - * - * @return true if at least one ScaleProteinAsCdna has been adde - */ - public boolean hasScaleProteinAsCdna() - { - return this._has_scaleProteinAsCdna; - } - - /** - * Method hasShowAnnotation. - * - * @return true if at least one ShowAnnotation has been added - */ - public boolean hasShowAnnotation() - { - return this._has_showAnnotation; - } - - /** - * Method hasShowBoxes. - * - * @return true if at least one ShowBoxes has been added - */ - public boolean hasShowBoxes() - { - return this._has_showBoxes; - } - - /** - * Method hasShowColourText. - * - * @return true if at least one ShowColourText has been added - */ - public boolean hasShowColourText() - { - return this._has_showColourText; - } - - /** - * Method hasShowConsensusHistogram. - * - * @return true if at least one ShowConsensusHistogram has been added - */ - public boolean hasShowConsensusHistogram() - { - return this._has_showConsensusHistogram; - } - - /** - * Method hasShowDbRefTooltip. - * - * @return true if at least one ShowDbRefTooltip has been added - */ - public boolean hasShowDbRefTooltip() - { - return this._has_showDbRefTooltip; - } - - /** - * Method hasShowFullId. - * - * @return true if at least one ShowFullId has been added - */ - public boolean hasShowFullId() - { - return this._has_showFullId; - } - - /** - * Method hasShowGroupConsensus. - * - * @return true if at least one ShowGroupConsensus has been adde - */ - public boolean hasShowGroupConsensus() - { - return this._has_showGroupConsensus; - } - - /** - * Method hasShowGroupConservation. - * - * @return true if at least one ShowGroupConservation has been added - */ - public boolean hasShowGroupConservation() - { - return this._has_showGroupConservation; - } - - /** - * Method hasShowNPfeatureTooltip. - * - * @return true if at least one ShowNPfeatureTooltip has been added - */ - public boolean hasShowNPfeatureTooltip() - { - return this._has_showNPfeatureTooltip; - } - - /** - * Method hasShowSequenceFeatures. - * - * @return true if at least one ShowSequenceFeatures has been added - */ - public boolean hasShowSequenceFeatures() - { - return this._has_showSequenceFeatures; - } - - /** - * Method hasShowSequenceLogo. - * - * @return true if at least one ShowSequenceLogo has been added - */ - public boolean hasShowSequenceLogo() - { - return this._has_showSequenceLogo; - } - - /** - * Method hasShowText. - * - * @return true if at least one ShowText has been added - */ - public boolean hasShowText() - { - return this._has_showText; - } - - /** - * Method hasShowUnconserved. - * - * @return true if at least one ShowUnconserved has been added - */ - public boolean hasShowUnconserved() - { - return this._has_showUnconserved; - } - - /** - * Method hasStartRes. - * - * @return true if at least one StartRes has been added - */ - public boolean hasStartRes() - { - return this._has_startRes; - } - - /** - * Method hasStartSeq. - * - * @return true if at least one StartSeq has been added - */ - public boolean hasStartSeq() - { - return this._has_startSeq; - } - - /** - * Method hasTextCol1. - * - * @return true if at least one TextCol1 has been added - */ - public boolean hasTextCol1() - { - return this._has_textCol1; - } - - /** - * Method hasTextCol2. - * - * @return true if at least one TextCol2 has been added - */ - public boolean hasTextCol2() - { - return this._has_textCol2; - } - - /** - * Method hasTextColThreshold. - * - * @return true if at least one TextColThreshold has been added - */ - public boolean hasTextColThreshold() - { - return this._has_textColThreshold; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth() - { - return this._has_width; - } - - /** - * Method hasWrapAlignment. - * - * @return true if at least one WrapAlignment has been added - */ - public boolean hasWrapAlignment() - { - return this._has_wrapAlignment; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos() - { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos() - { - return this._has_ypos; - } - - /** - * Returns the value of field 'centreColumnLabels'. - * - * @return the value of field 'CentreColumnLabels'. - */ - public boolean isCentreColumnLabels() - { - return this._centreColumnLabels; - } - - /** - * Returns the value of field 'conservationSelected'. - * - * @return the value of field 'ConservationSelected'. - */ - public boolean isConservationSelected() - { - return this._conservationSelected; - } - - /** - * Returns the value of field 'followHighlight'. - * - * @return the value of field 'FollowHighlight'. - */ - public boolean isFollowHighlight() - { - return this._followHighlight; - } - - /** - * Returns the value of field 'followSelection'. - * - * @return the value of field 'FollowSelection'. - */ - public boolean isFollowSelection() - { - return this._followSelection; - } - - /** - * Returns the value of field 'gatheredViews'. - * - * @return the value of field 'GatheredViews'. - */ - public boolean isGatheredViews() - { - return this._gatheredViews; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean isIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'normaliseSequenceLogo'. - * - * @return the value of field 'NormaliseSequenceLogo'. - */ - public boolean isNormaliseSequenceLogo() - { - return this._normaliseSequenceLogo; - } - - /** - * Returns the value of field 'pidSelected'. - * - * @return the value of field 'PidSelected'. - */ - public boolean isPidSelected() - { - return this._pidSelected; - } - - /** - * Returns the value of field 'renderGaps'. - * - * @return the value of field 'RenderGaps'. - */ - public boolean isRenderGaps() - { - return this._renderGaps; - } - - /** - * Returns the value of field 'rightAlignIds'. - * - * @return the value of field 'RightAlignIds'. - */ - public boolean isRightAlignIds() - { - return this._rightAlignIds; - } - - /** - * Returns the value of field 'scaleProteinAsCdna'. - * - * @return the value of field 'ScaleProteinAsCdna'. - */ - public boolean isScaleProteinAsCdna() - { - return this._scaleProteinAsCdna; - } - - /** - * Returns the value of field 'showAnnotation'. - * - * @return the value of field 'ShowAnnotation'. - */ - public boolean isShowAnnotation() - { - return this._showAnnotation; - } - - /** - * Returns the value of field 'showBoxes'. - * - * @return the value of field 'ShowBoxes'. - */ - public boolean isShowBoxes() - { - return this._showBoxes; - } - - /** - * Returns the value of field 'showColourText'. - * - * @return the value of field 'ShowColourText'. - */ - public boolean isShowColourText() - { - return this._showColourText; - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean isShowConsensusHistogram() - { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showDbRefTooltip'. - * - * @return the value of field 'ShowDbRefTooltip'. - */ - public boolean isShowDbRefTooltip() - { - return this._showDbRefTooltip; - } - - /** - * Returns the value of field 'showFullId'. - * - * @return the value of field 'ShowFullId'. - */ - public boolean isShowFullId() - { - return this._showFullId; - } - - /** - * Returns the value of field 'showGroupConsensus'. - * - * @return the value of field 'ShowGroupConsensus'. - */ - public boolean isShowGroupConsensus() - { - return this._showGroupConsensus; - } - - /** - * Returns the value of field 'showGroupConservation'. - * - * @return the value of field 'ShowGroupConservation'. - */ - public boolean isShowGroupConservation() - { - return this._showGroupConservation; - } - - /** - * Returns the value of field 'showNPfeatureTooltip'. - * - * @return the value of field 'ShowNPfeatureTooltip'. - */ - public boolean isShowNPfeatureTooltip() - { - return this._showNPfeatureTooltip; - } - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return the value of field 'ShowSequenceFeatures'. - */ - public boolean isShowSequenceFeatures() - { - return this._showSequenceFeatures; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean isShowSequenceLogo() - { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showText'. - * - * @return the value of field 'ShowText'. - */ - public boolean isShowText() - { - return this._showText; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean isShowUnconserved() - { - return this._showUnconserved; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * Returns the value of field 'wrapAlignment'. - * - * @return the value of field 'WrapAlignment'. - */ - public boolean isWrapAlignment() - { - return this._wrapAlignment; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllCalcIdParam() - { - this._calcIdParamList.clear(); - } - - /** - */ - public void removeAllHiddenColumns() - { - this._hiddenColumnsList.clear(); - } - - /** - * Method removeCalcIdParam. - * - * @param vCalcIdParam - * @return true if the object was removed from the collection. - */ - public boolean removeCalcIdParam( - final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) - { - boolean removed = _calcIdParamList.remove(vCalcIdParam); - return removed; - } - - /** - * Method removeCalcIdParamAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt( - final int index) - { - java.lang.Object obj = this._calcIdParamList.remove(index); - return (jalview.schemabinding.version2.CalcIdParam) obj; - } - - /** - * Method removeHiddenColumns. - * - * @param vHiddenColumns - * @return true if the object was removed from the collection. - */ - public boolean removeHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - { - boolean removed = _hiddenColumnsList.remove(vHiddenColumns); - return removed; - } - - /** - * Method removeHiddenColumnsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt( - final int index) - { - java.lang.Object obj = this._hiddenColumnsList.remove(index); - return (jalview.schemabinding.version2.HiddenColumns) obj; - } - - /** - * Sets the value of field 'annotationColours'. - * - * @param annotationColours - * the value of field 'annotationColours'. - */ - public void setAnnotationColours( - final jalview.schemabinding.version2.AnnotationColours annotationColours) - { - this._annotationColours = annotationColours; - } - - /** - * Sets the value of field 'bgColour'. - * - * @param bgColour - * the value of field 'bgColour'. - */ - public void setBgColour(final java.lang.String bgColour) - { - this._bgColour = bgColour; - } - - /** - * - * - * @param index - * @param vCalcIdParam - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setCalcIdParam(final int index, - final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._calcIdParamList.size()) - { - throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" - + index + "' not in range [0.." - + (this._calcIdParamList.size() - 1) + "]"); - } - - this._calcIdParamList.set(index, vCalcIdParam); - } - - /** - * - * - * @param vCalcIdParamArray - */ - public void setCalcIdParam( - final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) - { - // -- copy array - _calcIdParamList.clear(); - - for (int i = 0; i < vCalcIdParamArray.length; i++) - { - this._calcIdParamList.add(vCalcIdParamArray[i]); - } - } - - /** - * Sets the value of field 'centreColumnLabels'. - * - * @param centreColumnLabels - * the value of field 'centreColumnLabels'. - */ - public void setCentreColumnLabels(final boolean centreColumnLabels) - { - this._centreColumnLabels = centreColumnLabels; - this._has_centreColumnLabels = true; - } - - /** - * Sets the value of field 'complementId'. The field 'complementId' has the - * following description: The viewport id of this viewport's (cdna/protein) - * coding complement, if any - * - * - * @param complementId - * the value of field 'complementId'. - */ - public void setComplementId(final java.lang.String complementId) - { - this._complementId = complementId; - } - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold - * the value of field 'consThreshold'. - */ - public void setConsThreshold(final int consThreshold) - { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } - - /** - * Sets the value of field 'conservationSelected'. - * - * @param conservationSelected - * the value of field 'conservationSelected'. - */ - public void setConservationSelected(final boolean conservationSelected) - { - this._conservationSelected = conservationSelected; - this._has_conservationSelected = true; - } - - /** - * Sets the value of field 'followHighlight'. - * - * @param followHighlight - * the value of field 'followHighlight'. - */ - public void setFollowHighlight(final boolean followHighlight) - { - this._followHighlight = followHighlight; - this._has_followHighlight = true; - } - - /** - * Sets the value of field 'followSelection'. - * - * @param followSelection - * the value of field 'followSelection'. - */ - public void setFollowSelection(final boolean followSelection) - { - this._followSelection = followSelection; - this._has_followSelection = true; - } - - /** - * Sets the value of field 'fontName'. - * - * @param fontName - * the value of field 'fontName'. - */ - public void setFontName(final java.lang.String fontName) - { - this._fontName = fontName; - } - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize - * the value of field 'fontSize'. - */ - public void setFontSize(final int fontSize) - { - this._fontSize = fontSize; - this._has_fontSize = true; - } - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle - * the value of field 'fontStyle'. - */ - public void setFontStyle(final int fontStyle) - { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } - - /** - * Sets the value of field 'gatheredViews'. - * - * @param gatheredViews - * the value of field 'gatheredViews'. - */ - public void setGatheredViews(final boolean gatheredViews) - { - this._gatheredViews = gatheredViews; - this._has_gatheredViews = true; - } - - /** - * Sets the value of field 'height'. - * - * @param height - * the value of field 'height'. - */ - public void setHeight(final int height) - { - this._height = height; - this._has_height = true; - } - - /** - * - * - * @param index - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setHiddenColumns(final int index, - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenColumnsList.size()) - { - throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" - + index + "' not in range [0.." - + (this._hiddenColumnsList.size() - 1) + "]"); - } - - this._hiddenColumnsList.set(index, vHiddenColumns); - } - - /** - * - * - * @param vHiddenColumnsArray - */ - public void setHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) - { - // -- copy array - _hiddenColumnsList.clear(); - - for (int i = 0; i < vHiddenColumnsArray.length; i++) - { - this._hiddenColumnsList.add(vHiddenColumnsArray[i]); - } - } - - /** - * Sets the value of field 'id'. The field 'id' has the following description: - * unique id used by jalview to synchronize between stored and instantiated - * views - * - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'ignoreGapsinConsensus'. - * - * @param ignoreGapsinConsensus - * the value of field 'ignoreGapsinConsensus'. - */ - public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus) - { - this._ignoreGapsinConsensus = ignoreGapsinConsensus; - this._has_ignoreGapsinConsensus = true; - } - - /** - * Sets the value of field 'normaliseSequenceLogo'. - * - * @param normaliseSequenceLogo - * the value of field 'normaliseSequenceLogo'. - */ - public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo) - { - this._normaliseSequenceLogo = normaliseSequenceLogo; - this._has_normaliseSequenceLogo = true; - } - - /** - * Sets the value of field 'pidSelected'. - * - * @param pidSelected - * the value of field 'pidSelected'. - */ - public void setPidSelected(final boolean pidSelected) - { - this._pidSelected = pidSelected; - this._has_pidSelected = true; - } - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold - * the value of field 'pidThreshold'. - */ - public void setPidThreshold(final int pidThreshold) - { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } - - /** - * Sets the value of field 'renderGaps'. - * - * @param renderGaps - * the value of field 'renderGaps'. - */ - public void setRenderGaps(final boolean renderGaps) - { - this._renderGaps = renderGaps; - this._has_renderGaps = true; - } - - /** - * Sets the value of field 'rightAlignIds'. - * - * @param rightAlignIds - * the value of field 'rightAlignIds'. - */ - public void setRightAlignIds(final boolean rightAlignIds) - { - this._rightAlignIds = rightAlignIds; - this._has_rightAlignIds = true; - } - - /** - * Sets the value of field 'scaleProteinAsCdna'. - * - * @param scaleProteinAsCdna - * the value of field 'scaleProteinAsCdna'. - */ - public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna) - { - this._scaleProteinAsCdna = scaleProteinAsCdna; - this._has_scaleProteinAsCdna = true; - } - - /** - * Sets the value of field 'sequenceSetId'. - * - * @param sequenceSetId - * the value of field 'sequenceSetId'. - */ - public void setSequenceSetId(final java.lang.String sequenceSetId) - { - this._sequenceSetId = sequenceSetId; - } - - /** - * Sets the value of field 'showAnnotation'. - * - * @param showAnnotation - * the value of field 'showAnnotation'. - */ - public void setShowAnnotation(final boolean showAnnotation) - { - this._showAnnotation = showAnnotation; - this._has_showAnnotation = true; - } - - /** - * Sets the value of field 'showBoxes'. - * - * @param showBoxes - * the value of field 'showBoxes'. - */ - public void setShowBoxes(final boolean showBoxes) - { - this._showBoxes = showBoxes; - this._has_showBoxes = true; - } - - /** - * Sets the value of field 'showColourText'. - * - * @param showColourText - * the value of field 'showColourText'. - */ - public void setShowColourText(final boolean showColourText) - { - this._showColourText = showColourText; - this._has_showColourText = true; - } - - /** - * Sets the value of field 'showConsensusHistogram'. - * - * @param showConsensusHistogram - * the value of field 'showConsensusHistogram'. - */ - public void setShowConsensusHistogram(final boolean showConsensusHistogram) - { - this._showConsensusHistogram = showConsensusHistogram; - this._has_showConsensusHistogram = true; - } - - /** - * Sets the value of field 'showDbRefTooltip'. - * - * @param showDbRefTooltip - * the value of field 'showDbRefTooltip' - */ - public void setShowDbRefTooltip(final boolean showDbRefTooltip) - { - this._showDbRefTooltip = showDbRefTooltip; - this._has_showDbRefTooltip = true; - } - - /** - * Sets the value of field 'showFullId'. - * - * @param showFullId - * the value of field 'showFullId'. - */ - public void setShowFullId(final boolean showFullId) - { - this._showFullId = showFullId; - this._has_showFullId = true; - } - - /** - * Sets the value of field 'showGroupConsensus'. - * - * @param showGroupConsensus - * the value of field 'showGroupConsensus'. - */ - public void setShowGroupConsensus(final boolean showGroupConsensus) - { - this._showGroupConsensus = showGroupConsensus; - this._has_showGroupConsensus = true; - } - - /** - * Sets the value of field 'showGroupConservation'. - * - * @param showGroupConservation - * the value of field 'showGroupConservation'. - */ - public void setShowGroupConservation(final boolean showGroupConservation) - { - this._showGroupConservation = showGroupConservation; - this._has_showGroupConservation = true; - } - - /** - * Sets the value of field 'showNPfeatureTooltip'. - * - * @param showNPfeatureTooltip - * the value of field 'showNPfeatureTooltip'. - */ - public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip) - { - this._showNPfeatureTooltip = showNPfeatureTooltip; - this._has_showNPfeatureTooltip = true; - } - - /** - * Sets the value of field 'showSequenceFeatures'. - * - * @param showSequenceFeatures - * the value of field 'showSequenceFeatures'. - */ - public void setShowSequenceFeatures(final boolean showSequenceFeatures) - { - this._showSequenceFeatures = showSequenceFeatures; - this._has_showSequenceFeatures = true; - } - - /** - * Sets the value of field 'showSequenceLogo'. - * - * @param showSequenceLogo - * the value of field 'showSequenceLogo' - */ - public void setShowSequenceLogo(final boolean showSequenceLogo) - { - this._showSequenceLogo = showSequenceLogo; - this._has_showSequenceLogo = true; - } - - /** - * Sets the value of field 'showText'. - * - * @param showText - * the value of field 'showText'. - */ - public void setShowText(final boolean showText) - { - this._showText = showText; - this._has_showText = true; - } - - /** - * Sets the value of field 'showUnconserved'. - * - * @param showUnconserved - * the value of field 'showUnconserved'. - */ - public void setShowUnconserved(final boolean showUnconserved) - { - this._showUnconserved = showUnconserved; - this._has_showUnconserved = true; - } - - /** - * Sets the value of field 'startRes'. - * - * @param startRes - * the value of field 'startRes'. - */ - public void setStartRes(final int startRes) - { - this._startRes = startRes; - this._has_startRes = true; - } - - /** - * Sets the value of field 'startSeq'. - * - * @param startSeq - * the value of field 'startSeq'. - */ - public void setStartSeq(final int startSeq) - { - this._startSeq = startSeq; - this._has_startSeq = true; - } - - /** - * Sets the value of field 'textCol1'. - * - * @param textCol1 - * the value of field 'textCol1'. - */ - public void setTextCol1(final int textCol1) - { - this._textCol1 = textCol1; - this._has_textCol1 = true; - } - - /** - * Sets the value of field 'textCol2'. - * - * @param textCol2 - * the value of field 'textCol2'. - */ - public void setTextCol2(final int textCol2) - { - this._textCol2 = textCol2; - this._has_textCol2 = true; - } - - /** - * Sets the value of field 'textColThreshold'. - * - * @param textColThreshold - * the value of field 'textColThreshold' - */ - public void setTextColThreshold(final int textColThreshold) - { - this._textColThreshold = textColThreshold; - this._has_textColThreshold = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title - * the value of field 'title'. - */ - public void setTitle(final java.lang.String title) - { - this._title = title; - } - - /** - * Sets the value of field 'viewName'. - * - * @param viewName - * the value of field 'viewName'. - */ - public void setViewName(final java.lang.String viewName) - { - this._viewName = viewName; - } - - /** - * Sets the value of field 'width'. - * - * @param width - * the value of field 'width'. - */ - public void setWidth(final int width) - { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'wrapAlignment'. - * - * @param wrapAlignment - * the value of field 'wrapAlignment'. - */ - public void setWrapAlignment(final boolean wrapAlignment) - { - this._wrapAlignment = wrapAlignment; - this._has_wrapAlignment = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos - * the value of field 'xpos'. - */ - public void setXpos(final int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos - * the value of field 'ypos'. - */ - public void setYpos(final int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.schemabinding.version2.Viewport - */ - public static jalview.schemabinding.version2.Viewport unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Viewport) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Viewport.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/WebServiceParameterSet.java b/src/jalview/schemabinding/version2/WebServiceParameterSet.java deleted file mode 100644 index 72d2f82..0000000 --- a/src/jalview/schemabinding/version2/WebServiceParameterSet.java +++ /dev/null @@ -1,436 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class WebServiceParameterSet. - * - * @version $Revision$ $Date$ - */ -public class WebServiceParameterSet implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * The short name for the parameter set. This will be shown amongst the other - * presets for the web service. - * - */ - private java.lang.String _name; - - /** - * A Jalview Web Service Parameter Set container version number. Version 1 - * created for storing Jaba user presets. - * - */ - private java.lang.String _version; - - /** - * Short description - as utf8 encoded text. This is usually displayed in the - * body of an HTML capable tooltip, so HTML tags may be embedded using - * standard UTF8 encoding. - * - */ - private java.lang.String _description; - - /** - * URL for which the parameter set is valid. Jalview will use it to match up - * parameter sets to service instances that can parse the parameter set - * payload. - * - */ - private java.util.Vector _serviceURLList; - - /** - * UTF8 encoded string to be processed into a specific web services' parameter - * set. Note - newlines may be important to the structure of this file. - * - */ - private java.lang.String _parameters; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public WebServiceParameterSet() - { - super(); - this._serviceURLList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vServiceURL - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addServiceURL(final java.lang.String vServiceURL) - throws java.lang.IndexOutOfBoundsException - { - this._serviceURLList.addElement(vServiceURL); - } - - /** - * - * - * @param index - * @param vServiceURL - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addServiceURL(final int index, - final java.lang.String vServiceURL) - throws java.lang.IndexOutOfBoundsException - { - this._serviceURLList.add(index, vServiceURL); - } - - /** - * Method enumerateServiceURL. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateServiceURL() - { - return this._serviceURLList.elements(); - } - - /** - * Returns the value of field 'description'. The field 'description' has the - * following description: Short description - as utf8 encoded text. This is - * usually displayed in the body of an HTML capable tooltip, so HTML tags may - * be embedded using standard UTF8 encoding. - * - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'name'. The field 'name' has the following - * description: The short name for the parameter set. This will be shown - * amongst the other presets for the web service. - * - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'parameters'. The field 'parameters' has the - * following description: UTF8 encoded string to be processed into a specific - * web services' parameter set. Note - newlines may be important to the - * structure of this file. - * - * - * @return the value of field 'Parameters'. - */ - public java.lang.String getParameters() - { - return this._parameters; - } - - /** - * Method getServiceURL. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getServiceURL(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._serviceURLList.size()) - { - throw new IndexOutOfBoundsException("getServiceURL: Index value '" - + index + "' not in range [0.." - + (this._serviceURLList.size() - 1) + "]"); - } - - return (java.lang.String) _serviceURLList.get(index); - } - - /** - * Method getServiceURL.Returns the contents of the collection in an Array. - *

- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getServiceURL() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._serviceURLList.toArray(array); - } - - /** - * Method getServiceURLCount. - * - * @return the size of this collection - */ - public int getServiceURLCount() - { - return this._serviceURLList.size(); - } - - /** - * Returns the value of field 'version'. The field 'version' has the following - * description: A Jalview Web Service Parameter Set container version number. - * Version 1 created for storing Jaba user presets. - * - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion() - { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllServiceURL() - { - this._serviceURLList.clear(); - } - - /** - * Method removeServiceURL. - * - * @param vServiceURL - * @return true if the object was removed from the collection. - */ - public boolean removeServiceURL(final java.lang.String vServiceURL) - { - boolean removed = _serviceURLList.remove(vServiceURL); - return removed; - } - - /** - * Method removeServiceURLAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeServiceURLAt(final int index) - { - java.lang.Object obj = this._serviceURLList.remove(index); - return (java.lang.String) obj; - } - - /** - * Sets the value of field 'description'. The field 'description' has the - * following description: Short description - as utf8 encoded text. This is - * usually displayed in the body of an HTML capable tooltip, so HTML tags may - * be embedded using standard UTF8 encoding. - * - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'name'. The field 'name' has the following - * description: The short name for the parameter set. This will be shown - * amongst the other presets for the web service. - * - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'parameters'. The field 'parameters' has the - * following description: UTF8 encoded string to be processed into a specific - * web services' parameter set. Note - newlines may be important to the - * structure of this file. - * - * - * @param parameters - * the value of field 'parameters'. - */ - public void setParameters(final java.lang.String parameters) - { - this._parameters = parameters; - } - - /** - * - * - * @param index - * @param vServiceURL - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setServiceURL(final int index, - final java.lang.String vServiceURL) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._serviceURLList.size()) - { - throw new IndexOutOfBoundsException("setServiceURL: Index value '" - + index + "' not in range [0.." - + (this._serviceURLList.size() - 1) + "]"); - } - - this._serviceURLList.set(index, vServiceURL); - } - - /** - * - * - * @param vServiceURLArray - */ - public void setServiceURL(final java.lang.String[] vServiceURLArray) - { - // -- copy array - _serviceURLList.clear(); - - for (int i = 0; i < vServiceURLArray.length; i++) - { - this._serviceURLList.add(vServiceURLArray[i]); - } - } - - /** - * Sets the value of field 'version'. The field 'version' has the following - * description: A Jalview Web Service Parameter Set container version number. - * Version 1 created for storing Jaba user presets. - * - * - * @param version - * the value of field 'version'. - */ - public void setVersion(final java.lang.String version) - { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled - * jalview.schemabinding.version2.WebServiceParameterSet - */ - public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.WebServiceParameterSet.class, - reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java deleted file mode 100644 index 1447978..0000000 --- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java +++ /dev/null @@ -1,247 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AlcodMap; - -/** - * Class AlcodMapDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlcodMapDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodMapDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "alcodMap"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _dnasq - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_dnasq", "dnasq", - 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 - { - AlcodMap target = (AlcodMap) object; - return target.getDnasq(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AlcodMap target = (AlcodMap) object; - target.setDnasq((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _dnasq - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _mapping - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Mapping.class, "_mapping", - "Mapping", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AlcodMap target = (AlcodMap) object; - return target.getMapping(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AlcodMap target = (AlcodMap) object; - target.setMapping((jalview.schemabinding.version2.Mapping) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Mapping(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mapping - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AlcodMap.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java deleted file mode 100644 index c1a0eab..0000000 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java +++ /dev/null @@ -1,313 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Alcodon; - -/** - * Class AlcodonDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlcodonDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodonDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "alcodon"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _pos1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_pos1", "pos1", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos1()) - { - return null; - } - return new java.lang.Long(target.getPos1()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePos1(); - return; - } - target.setPos1(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pos1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _pos2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_pos2", "pos2", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos2()) - { - return null; - } - return new java.lang.Long(target.getPos2()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePos2(); - return; - } - target.setPos2(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pos2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _pos3 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_pos3", "pos3", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos3()) - { - return null; - } - return new java.lang.Long(target.getPos3()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePos3(); - return; - } - target.setPos3(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pos3 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Alcodon.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java deleted file mode 100644 index 919941e..0000000 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java +++ /dev/null @@ -1,267 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AlcodonFrame; - -/** - * Class AlcodonFrameDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlcodonFrameDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodonFrameDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "AlcodonFrame"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _alcodonList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Alcodon.class, "_alcodonList", - "alcodon", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AlcodonFrame target = (AlcodonFrame) object; - return target.getAlcodon(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AlcodonFrame target = (AlcodonFrame) object; - target.addAlcodon((jalview.schemabinding.version2.Alcodon) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - AlcodonFrame target = (AlcodonFrame) object; - target.removeAllAlcodon(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Alcodon(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _alcodonList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _alcodMapList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", - "alcodMap", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AlcodonFrame target = (AlcodonFrame) object; - return target.getAlcodMap(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AlcodonFrame target = (AlcodonFrame) object; - target.addAlcodMap((jalview.schemabinding.version2.AlcodMap) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - AlcodonFrame target = (AlcodonFrame) object; - target.removeAllAlcodMap(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AlcodMap(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _alcodMapList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AlcodonFrame.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java deleted file mode 100644 index 804b49e..0000000 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java +++ /dev/null @@ -1,573 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AnnotationColourScheme; - -/** - * Class AnnotationColourSchemeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationColourSchemeDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationColourSchemeDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "AnnotationColourScheme"; - _elementDefinition = false; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _aboveThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - if (!target.hasAboveThreshold()) - { - return null; - } - return new java.lang.Integer(target.getAboveThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAboveThreshold(); - return; - } - target.setAboveThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _aboveThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _annotation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_annotation", "annotation", - 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 - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - return target.getAnnotation(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - target.setAnnotation((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _annotation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _minColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_minColour", "minColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - if (!target.hasMinColour()) - { - return null; - } - return new java.lang.Integer(target.getMinColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMinColour(); - return; - } - target.setMinColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _minColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _maxColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_maxColour", "maxColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - if (!target.hasMaxColour()) - { - return null; - } - return new java.lang.Integer(target.getMaxColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMaxColour(); - return; - } - target.setMaxColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _maxColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _colourScheme - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_colourScheme", "colourScheme", - 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 - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - return target.getColourScheme(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - target.setColourScheme((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourScheme - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_threshold", "threshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - if (!target.hasThreshold()) - { - return null; - } - return new java.lang.Float(target.getThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshold(); - return; - } - target.setThreshold(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _perSequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_perSequence", "perSequence", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - if (!target.hasPerSequence()) - { - return null; - } - return (target.getPerSequence() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePerSequence(); - return; - } - target.setPerSequence(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _perSequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _predefinedColours - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_predefinedColours", - "predefinedColours", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - if (!target.hasPredefinedColours()) - { - return null; - } - return (target.getPredefinedColours() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColourScheme target = (AnnotationColourScheme) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePredefinedColours(); - return; - } - target.setPredefinedColours(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _predefinedColours - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AnnotationColourScheme.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java deleted file mode 100644 index 5739d90..0000000 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java +++ /dev/null @@ -1,149 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AnnotationColours; - -/** - * Class AnnotationColoursDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationColoursDescriptor - extends - jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationColoursDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "AnnotationColours"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AnnotationColours.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java deleted file mode 100644 index e2331f4..0000000 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java +++ /dev/null @@ -1,1298 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Annotation; - -/** - * Class AnnotationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Annotation"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _graph - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_graph", "graph", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraph()) - { - return null; - } - return (target.getGraph() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setGraph(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graph - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _graphType - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_graphType", "graphType", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphType()) - { - return null; - } - return new java.lang.Integer(target.getGraphType()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGraphType(); - return; - } - target.setGraphType(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graphType - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _sequenceRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_sequenceRef", "sequenceRef", - 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 - { - Annotation target = (Annotation) object; - return target.getSequenceRef(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setSequenceRef((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _sequenceRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _groupRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_groupRef", "groupRef", - 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 - { - Annotation target = (Annotation) object; - return target.getGroupRef(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setGroupRef((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _groupRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _graphColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_graphColour", "graphColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphColour()) - { - return null; - } - return new java.lang.Integer(target.getGraphColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGraphColour(); - return; - } - target.setGraphColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graphColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _graphGroup - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_graphGroup", "graphGroup", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphGroup()) - { - return null; - } - return new java.lang.Integer(target.getGraphGroup()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGraphGroup(); - return; - } - target.setGraphGroup(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graphGroup - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _graphHeight - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_graphHeight", "graphHeight", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphHeight()) - { - return null; - } - return new java.lang.Integer(target.getGraphHeight()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGraphHeight(); - return; - } - target.setGraphHeight(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graphHeight - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _id - 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 - { - Annotation target = (Annotation) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _scoreOnly - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScoreOnly()) - { - return null; - } - return (target.getScoreOnly() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScoreOnly(); - return; - } - target.setScoreOnly(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _scoreOnly - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _score - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Double.TYPE, "_score", "score", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScore()) - { - return null; - } - return new java.lang.Double(target.getScore()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScore(); - return; - } - target.setScore(((java.lang.Double) value).doubleValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _score - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.DoubleValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.DoubleValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-1.7976931348623157E308); - typeValidator.setMaxInclusive(1.7976931348623157E308); - } - desc.setValidator(fieldValidator); - // -- _visible - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_visible", "visible", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasVisible()) - { - return null; - } - return (target.getVisible() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteVisible(); - return; - } - target.setVisible(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _visible - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _centreColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasCentreColLabels()) - { - return null; - } - return (target.getCentreColLabels() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteCentreColLabels(); - return; - } - target.setCentreColLabels(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _centreColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _scaleColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScaleColLabels()) - { - return null; - } - return (target.getScaleColLabels() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScaleColLabels(); - return; - } - target.setScaleColLabels(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _scaleColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showAllColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showAllColLabels", - "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasShowAllColLabels()) - { - return null; - } - return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowAllColLabels(); - return; - } - target.setShowAllColLabels(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showAllColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _autoCalculated - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasAutoCalculated()) - { - return null; - } - return (target.getAutoCalculated() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAutoCalculated(); - return; - } - target.setAutoCalculated(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _autoCalculated - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _belowAlignment - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_belowAlignment", "belowAlignment", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasBelowAlignment()) - { - return null; - } - return (target.getBelowAlignment() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteBelowAlignment(); - return; - } - target.setBelowAlignment(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _belowAlignment - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _calcId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_calcId", "calcId", - 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 - { - Annotation target = (Annotation) object; - return target.getCalcId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setCalcId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _calcId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _annotationElementList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AnnotationElement.class, - "_annotationElementList", "annotationElement", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getAnnotationElement(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.removeAllAnnotationElement(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AnnotationElement(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _annotationElementList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _label - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_label", "label", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getLabel(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setLabel((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _thresholdLine - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.ThresholdLine.class, - "_thresholdLine", "thresholdLine", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getThresholdLine(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.ThresholdLine(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _thresholdLine - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Property.class, "_propertyList", - "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getProperty(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.addProperty((jalview.schemabinding.version2.Property) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.removeAllProperty(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Annotation.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java deleted file mode 100644 index 4416bbf..0000000 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java +++ /dev/null @@ -1,464 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.AnnotationElement; - -/** - * Class AnnotationElementDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElementDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationElementDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "annotationElement"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _position - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_position", "position", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasPosition()) - { - return null; - } - return new java.lang.Integer(target.getPosition()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setPosition(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _position - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasColour()) - { - return null; - } - return new java.lang.Integer(target.getColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColour(); - return; - } - target.setColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _displayCharacter - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_displayCharacter", - "displayCharacter", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDisplayCharacter(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - target.setDisplayCharacter((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _displayCharacter - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _secondaryStructure - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_secondaryStructure", - "secondaryStructure", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getSecondaryStructure(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - target.setSecondaryStructure((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _secondaryStructure - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - typeValidator.setLength(1); - } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_value", "value", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasValue()) - { - return null; - } - return new java.lang.Float(target.getValue()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteValue(); - return; - } - target.setValue(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AnnotationElement.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java b/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java deleted file mode 100644 index 6dbea24..0000000 --- a/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java +++ /dev/null @@ -1,313 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.CalcIdParam; - -/** - * Class CalcIdParamDescriptor. - * - * @version $Revision$ $Date$ - */ -public class CalcIdParamDescriptor - extends - jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public CalcIdParamDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "calcIdParam"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _calcId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_calcId", "calcId", - 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 - { - CalcIdParam target = (CalcIdParam) object; - return target.getCalcId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - CalcIdParam target = (CalcIdParam) object; - target.setCalcId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _calcId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _needsUpdate - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_needsUpdate", "needsUpdate", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - CalcIdParam target = (CalcIdParam) object; - if (!target.hasNeedsUpdate()) - { - return null; - } - return (target.getNeedsUpdate() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - CalcIdParam target = (CalcIdParam) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteNeedsUpdate(); - return; - } - target.setNeedsUpdate(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _needsUpdate - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _autoUpdate - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_autoUpdate", "autoUpdate", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - CalcIdParam target = (CalcIdParam) object; - if (!target.hasAutoUpdate()) - { - return null; - } - return (target.getAutoUpdate() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - CalcIdParam target = (CalcIdParam) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setAutoUpdate(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _autoUpdate - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.CalcIdParam.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java deleted file mode 100644 index cca4ef1..0000000 --- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java +++ /dev/null @@ -1,719 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Colour; - -/** - * Class ColourDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ColourDescriptor - extends org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public ColourDescriptor() - { - super(); - _xmlName = "colour"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "Name", - 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 - { - Colour target = (Colour) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _RGB - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_RGB", "RGB", - 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 - { - Colour target = (Colour) object; - return target.getRGB(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setRGB((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _RGB - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _minRGB - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_minRGB", "minRGB", - 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 - { - Colour target = (Colour) object; - return target.getMinRGB(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setMinRGB((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _minRGB - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _noValueColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.types.NoValueColour.class, - "_noValueColour", "noValueColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getNoValueColour(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setNoValueColour( - (jalview.schemabinding.version2.types.NoValueColour) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - handler = new org.exolab.castor.xml.handlers.EnumFieldHandler( - jalview.schemabinding.version2.types.NoValueColour.class, - handler); - desc.setImmutable(true); - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _noValueColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _threshType - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.types.ColourThreshTypeType.class, - "_threshType", "threshType", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getThreshType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setThreshType( - (jalview.schemabinding.version2.types.ColourThreshTypeType) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - handler = new org.exolab.castor.xml.handlers.EnumFieldHandler( - jalview.schemabinding.version2.types.ColourThreshTypeType.class, - handler); - desc.setImmutable(true); - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshType - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_threshold", "threshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasThreshold()) - { - return null; - } - return new java.lang.Float(target.getThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshold(); - return; - } - target.setThreshold(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _max - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_max", "max", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasMax()) - { - return null; - } - return new java.lang.Float(target.getMax()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMax(); - return; - } - target.setMax(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _max - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _min - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_min", "min", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasMin()) - { - return null; - } - return new java.lang.Float(target.getMin()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMin(); - return; - } - target.setMin(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _min - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _colourByLabel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasColourByLabel()) - { - return null; - } - return (target.getColourByLabel() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColourByLabel(); - return; - } - target.setColourByLabel( - ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourByLabel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _autoScale - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_autoScale", "autoScale", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasAutoScale()) - { - return null; - } - return (target.getAutoScale() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAutoScale(); - return; - } - target.setAutoScale(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _autoScale - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _attributeNameList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_attributeNameList", "attributeName", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getAttributeName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.addAttributeName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.removeAllAttributeName(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _attributeNameList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - fieldValidator.setMaxOccurs(2); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Colour.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/CompoundMatcherDescriptor.java b/src/jalview/schemabinding/version2/descriptors/CompoundMatcherDescriptor.java deleted file mode 100644 index 2402d68..0000000 --- a/src/jalview/schemabinding/version2/descriptors/CompoundMatcherDescriptor.java +++ /dev/null @@ -1,270 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.CompoundMatcher; - -/** - * Class CompoundMatcherDescriptor. - * - * @version $Revision$ $Date$ - */ -public class CompoundMatcherDescriptor - extends org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public CompoundMatcherDescriptor() - { - super(); - _xmlName = "compoundMatcher"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _and - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_and", "and", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - CompoundMatcher target = (CompoundMatcher) object; - if (!target.hasAnd()) - { - return null; - } - return (target.getAnd() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - CompoundMatcher target = (CompoundMatcher) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setAnd(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _and - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _matcherSetList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MatcherSet.class, - "_matcherSetList", "matcherSet", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - CompoundMatcher target = (CompoundMatcher) object; - return target.getMatcherSet(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - CompoundMatcher target = (CompoundMatcher) object; - target.addMatcherSet( - (jalview.schemabinding.version2.MatcherSet) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) - throws IllegalStateException, IllegalArgumentException - { - try - { - CompoundMatcher target = (CompoundMatcher) object; - target.removeAllMatcherSet(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MatcherSet(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _matcherSetList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(2); - fieldValidator.setMaxOccurs(2); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.CompoundMatcher.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java deleted file mode 100644 index e896d7a..0000000 --- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java +++ /dev/null @@ -1,333 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.DBRef; - -/** - * Class DBRefDescriptor. - * - * @version $Revision$ $Date$ - */ -public class DBRefDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public DBRefDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "DBRef"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _source - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_source", "source", - 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 - { - DBRef target = (DBRef) object; - return target.getSource(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - DBRef target = (DBRef) object; - target.setSource((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _source - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_version", "version", - 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 - { - DBRef target = (DBRef) object; - return target.getVersion(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - DBRef target = (DBRef) object; - target.setVersion((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _accessionId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_accessionId", "accessionId", - 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 - { - DBRef target = (DBRef) object; - return target.getAccessionId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - DBRef target = (DBRef) object; - target.setAccessionId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _accessionId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _mapping - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Mapping.class, "_mapping", - "Mapping", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getMapping(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - DBRef target = (DBRef) object; - target.setMapping((jalview.schemabinding.version2.Mapping) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Mapping(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mapping - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.DBRef.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java deleted file mode 100644 index 64ed3a5..0000000 --- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java +++ /dev/null @@ -1,564 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Feature; - -/** - * Class FeatureDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeatureDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "feature"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _begin - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_begin", "begin", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasBegin()) - { - return null; - } - return new java.lang.Integer(target.getBegin()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setBegin(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _begin - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_type", "type", - 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 - { - Feature target = (Feature) object; - return target.getType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.setType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - 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 - { - Feature target = (Feature) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _status - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_status", "status", - 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 - { - Feature target = (Feature) object; - return target.getStatus(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.setStatus((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _status - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _featureGroup - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_featureGroup", "featureGroup", - 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 - { - Feature target = (Feature) object; - return target.getFeatureGroup(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.setFeatureGroup((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _featureGroup - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _score - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_score", "score", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasScore()) - { - return null; - } - return new java.lang.Float(target.getScore()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScore(); - return; - } - target.setScore(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _score - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _otherDataList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.OtherData.class, - "_otherDataList", "otherData", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getOtherData(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.addOtherData((jalview.schemabinding.version2.OtherData) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.removeAllOtherData(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.OtherData(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _otherDataList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Feature.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureMatcherDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureMatcherDescriptor.java deleted file mode 100644 index 2df2f5b..0000000 --- a/src/jalview/schemabinding/version2/descriptors/FeatureMatcherDescriptor.java +++ /dev/null @@ -1,356 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.FeatureMatcher; - -/** - * Class FeatureMatcherDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcherDescriptor - extends org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureMatcherDescriptor() - { - super(); - _nsURI = "www.jalview.org/colours"; - _xmlName = "FeatureMatcher"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _by - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.types.FeatureMatcherByType.class, - "_by", "by", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureMatcher target = (FeatureMatcher) object; - return target.getBy(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureMatcher target = (FeatureMatcher) object; - target.setBy( - (jalview.schemabinding.version2.types.FeatureMatcherByType) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - handler = new org.exolab.castor.xml.handlers.EnumFieldHandler( - jalview.schemabinding.version2.types.FeatureMatcherByType.class, - handler); - desc.setImmutable(true); - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _by - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _attributeNameList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_attributeNameList", "attributeName", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureMatcher target = (FeatureMatcher) object; - return target.getAttributeName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureMatcher target = (FeatureMatcher) object; - target.addAttributeName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureMatcher target = (FeatureMatcher) object; - target.removeAllAttributeName(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _attributeNameList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - fieldValidator.setMaxOccurs(2); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _condition - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_condition", "condition", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureMatcher target = (FeatureMatcher) object; - return target.getCondition(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureMatcher target = (FeatureMatcher) object; - target.setCondition((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _condition - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_value", "value", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureMatcher target = (FeatureMatcher) object; - return target.getValue(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureMatcher target = (FeatureMatcher) object; - target.setValue((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.FeatureMatcher.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureMatcherSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureMatcherSetDescriptor.java deleted file mode 100644 index b3d19bb..0000000 --- a/src/jalview/schemabinding/version2/descriptors/FeatureMatcherSetDescriptor.java +++ /dev/null @@ -1,258 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -import jalview.schemabinding.version2.CompoundMatcher; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.FeatureMatcherSet; -import jalview.schemabinding.version2.MatchCondition; - -/** - * Class FeatureMatcherSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcherSetDescriptor - extends org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureMatcherSetDescriptor() - { - super(); - _nsURI = "www.jalview.org/colours"; - _xmlName = "FeatureMatcherSet"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _matchCondition - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - MatchCondition.class, "_matchCondition", "matchCondition", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - @Override - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureMatcherSet target = (FeatureMatcherSet) object; - return target.getMatchCondition(); - } - - @Override - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureMatcherSet target = (FeatureMatcherSet) object; - target.setMatchCondition((MatchCondition) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - @Override - public java.lang.Object newInstance(java.lang.Object parent) - { - return new MatchCondition(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _matchCondition - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _compoundMatcher - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - CompoundMatcher.class, "_compoundMatcher", "compoundMatcher", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - @Override - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureMatcherSet target = (FeatureMatcherSet) object; - return target.getCompoundMatcher(); - } - - @Override - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureMatcherSet target = (FeatureMatcherSet) object; - target.setCompoundMatcher((CompoundMatcher) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - @Override - public java.lang.Object newInstance(java.lang.Object parent) - { - return new CompoundMatcher(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _compoundMatcher - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - @Override - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - @Override - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - @Override - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.FeatureMatcherSet.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - @Override - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - @Override - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - @Override - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - @Override - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - @Override - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java deleted file mode 100644 index 44bc256..0000000 --- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java +++ /dev/null @@ -1,267 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.FeatureSettings; - -/** - * Class FeatureSettingsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeatureSettingsDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureSettingsDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "FeatureSettings"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _settingList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Setting.class, "_settingList", - "setting", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureSettings target = (FeatureSettings) object; - return target.getSetting(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureSettings target = (FeatureSettings) object; - target.addSetting((jalview.schemabinding.version2.Setting) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - FeatureSettings target = (FeatureSettings) object; - target.removeAllSetting(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Setting(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _settingList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _groupList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Group.class, "_groupList", - "group", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureSettings target = (FeatureSettings) object; - return target.getGroup(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureSettings target = (FeatureSettings) object; - target.addGroup((jalview.schemabinding.version2.Group) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - FeatureSettings target = (FeatureSettings) object; - target.removeAllGroup(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Group(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _groupList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.FeatureSettings.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java deleted file mode 100644 index 107c06d..0000000 --- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java +++ /dev/null @@ -1,148 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Features; - -/** - * Class FeaturesDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeaturesDescriptor extends - jalview.schemabinding.version2.descriptors.FeatureDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeaturesDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "features"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Features.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/FilterDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FilterDescriptor.java deleted file mode 100644 index f58f9ae..0000000 --- a/src/jalview/schemabinding/version2/descriptors/FilterDescriptor.java +++ /dev/null @@ -1,246 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Filter; - -/** - * Class FilterDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FilterDescriptor - extends org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FilterDescriptor() - { - super(); - _xmlName = "filter"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _featureType - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_featureType", "featureType", - 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 - { - Filter target = (Filter) object; - return target.getFeatureType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Filter target = (Filter) object; - target.setFeatureType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _featureType - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _matcherSet - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MatcherSet.class, "_matcherSet", - "matcherSet", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Filter target = (Filter) object; - return target.getMatcherSet(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Filter target = (Filter) object; - target.setMatcherSet( - (jalview.schemabinding.version2.MatcherSet) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MatcherSet(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _matcherSet - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Filter.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java deleted file mode 100644 index 7aa6203..0000000 --- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java +++ /dev/null @@ -1,257 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Group; - -/** - * Class GroupDescriptor. - * - * @version $Revision$ $Date$ - */ -public class GroupDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public GroupDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "group"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - 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 - { - Group target = (Group) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Group target = (Group) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _display - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_display", "display", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Group target = (Group) object; - if (!target.hasDisplay()) - { - return null; - } - return (target.getDisplay() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Group target = (Group) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setDisplay(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _display - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Group.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java deleted file mode 100644 index a5607b7..0000000 --- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java +++ /dev/null @@ -1,264 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.HiddenColumns; - -/** - * Class HiddenColumnsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class HiddenColumnsDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public HiddenColumnsDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "hiddenColumns"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - HiddenColumns target = (HiddenColumns) object; - if (!target.hasStart()) - { - return null; - } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - HiddenColumns target = (HiddenColumns) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteStart(); - return; - } - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - HiddenColumns target = (HiddenColumns) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - HiddenColumns target = (HiddenColumns) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteEnd(); - return; - } - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.HiddenColumns.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java deleted file mode 100644 index 620432f..0000000 --- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java +++ /dev/null @@ -1,1275 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JGroup; - -/** - * Class JGroupDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JGroupDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JGroupDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JGroup"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasStart()) - { - return null; - } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteStart(); - return; - } - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteEnd(); - return; - } - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - 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 - { - JGroup target = (JGroup) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_colour", "colour", - 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 - { - JGroup target = (JGroup) object; - return target.getColour(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.setColour((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _consThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_consThreshold", "consThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasConsThreshold()) - { - return null; - } - return new java.lang.Integer(target.getConsThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteConsThreshold(); - return; - } - target.setConsThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _consThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _pidThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasPidThreshold()) - { - return null; - } - return new java.lang.Integer(target.getPidThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePidThreshold(); - return; - } - target.setPidThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pidThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _outlineColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_outlineColour", "outlineColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasOutlineColour()) - { - return null; - } - return new java.lang.Integer(target.getOutlineColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteOutlineColour(); - return; - } - target.setOutlineColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _outlineColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _displayBoxes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasDisplayBoxes()) - { - return null; - } - return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteDisplayBoxes(); - return; - } - target.setDisplayBoxes(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _displayBoxes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _displayText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_displayText", "displayText", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasDisplayText()) - { - return null; - } - return (target.getDisplayText() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteDisplayText(); - return; - } - target.setDisplayText(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _displayText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _colourText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_colourText", "colourText", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasColourText()) - { - return null; - } - return (target.getColourText() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColourText(); - return; - } - target.setColourText(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _textCol1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textCol1", "textCol1", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextCol1()) - { - return null; - } - return new java.lang.Integer(target.getTextCol1()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextCol1(); - return; - } - target.setTextCol1(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textCol1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _textCol2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textCol2", "textCol2", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextCol2()) - { - return null; - } - return new java.lang.Integer(target.getTextCol2()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextCol2(); - return; - } - target.setTextCol2(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textCol2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _textColThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textColThreshold", - "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextColThreshold()) - { - return null; - } - return new java.lang.Integer(target.getTextColThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextColThreshold(); - return; - } - target.setTextColThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textColThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _showUnconserved - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowUnconserved()) - { - return null; - } - return (target.getShowUnconserved() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowUnconserved(); - return; - } - target.setShowUnconserved(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showUnconserved - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _ignoreGapsinConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", - "ignoreGapsinConsensus", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasIgnoreGapsinConsensus()) - { - return null; - } - return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteIgnoreGapsinConsensus(); - return; - } - target.setIgnoreGapsinConsensus(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ignoreGapsinConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showConsensusHistogram - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showConsensusHistogram", - "showConsensusHistogram", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowConsensusHistogram()) - { - return null; - } - return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowConsensusHistogram(); - return; - } - target.setShowConsensusHistogram(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showConsensusHistogram - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showSequenceLogo - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showSequenceLogo", - "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowSequenceLogo()) - { - return null; - } - return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowSequenceLogo(); - return; - } - target.setShowSequenceLogo(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showSequenceLogo - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _normaliseSequenceLogo - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_normaliseSequenceLogo", - "normaliseSequenceLogo", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasNormaliseSequenceLogo()) - { - return null; - } - return (target.getNormaliseSequenceLogo() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteNormaliseSequenceLogo(); - return; - } - target.setNormaliseSequenceLogo(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _normaliseSequenceLogo - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _id - 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 - { - JGroup target = (JGroup) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _seqList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_seqList", "seq", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getSeq(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.addSeq((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.removeAllSeq(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _seqList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _annotationColours - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AnnotationColours.class, - "_annotationColours", "annotationColours", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getAnnotationColours(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AnnotationColours(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _annotationColours - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JGroup.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java deleted file mode 100644 index 28f23b26..0000000 --- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java +++ /dev/null @@ -1,714 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JSeq; - -/** - * Class JSeqDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JSeqDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JSeqDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JSeq"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasColour()) - { - return null; - } - return new java.lang.Integer(target.getColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColour(); - return; - } - target.setColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasStart()) - { - return null; - } - return new java.lang.Integer(target.getStart()); - } - - 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.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - - 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.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _id - 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; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _hidden - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_hidden", "hidden", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasHidden()) - { - return null; - } - return (target.getHidden() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHidden(); - return; - } - target.setHidden(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _hidden - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _viewreference - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_viewreference", "viewreference", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasViewreference()) - { - return null; - } - return (target.getViewreference() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteViewreference(); - return; - } - target.setViewreference(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _viewreference - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _featuresList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Features.class, "_featuresList", - "features", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getFeatures(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.addFeatures((jalview.schemabinding.version2.Features) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.removeAllFeatures(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Features(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _featuresList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _pdbidsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", - "pdbids", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getPdbids(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.addPdbids((jalview.schemabinding.version2.Pdbids) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.removeAllPdbids(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Pdbids(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _pdbidsList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _hiddenSequencesList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_hiddenSequencesList", - "hiddenSequences", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getHiddenSequences(); - } - - 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.addHiddenSequences(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.removeAllHiddenSequences(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _hiddenSequencesList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _rnaViewerList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.RnaViewer.class, - "_rnaViewerList", "rnaViewer", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getRnaViewer(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.addRnaViewer((jalview.schemabinding.version2.RnaViewer) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.removeAllRnaViewer(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.RnaViewer(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _rnaViewerList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JSeq.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java deleted file mode 100644 index f400c2c..0000000 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java +++ /dev/null @@ -1,341 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JalviewModel; - -/** - * Class JalviewModelDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModelDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JalviewModel"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _creationDate - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.util.Date.class, "_creationDate", "creationDate", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getCreationDate(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModel target = (JalviewModel) object; - target.setCreationDate((java.util.Date) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new java.util.Date(); - } - }; - handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler); - desc.setImmutable(true); - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _creationDate - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.DateTimeValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_version", "version", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getVersion(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModel target = (JalviewModel) object; - target.setVersion((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _vamsasModel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.VamsasModel.class, - "_vamsasModel", "vamsasModel", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getVamsasModel(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModel target = (JalviewModel) object; - target.setVamsasModel((jalview.schemabinding.version2.VamsasModel) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.VamsasModel(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _vamsasModel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _jalviewModelSequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.JalviewModelSequence.class, - "_jalviewModelSequence", "-error-if-this-is-used-", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getJalviewModelSequence(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModel target = (JalviewModel) object; - target.setJalviewModelSequence((jalview.schemabinding.version2.JalviewModelSequence) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.JalviewModelSequence(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor()); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _jalviewModelSequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JalviewModel.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java deleted file mode 100644 index e8c4ef4..0000000 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java +++ /dev/null @@ -1,474 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JalviewModelSequence; - -/** - * Class JalviewModelSequenceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelSequenceDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModelSequenceDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _JSeqList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getJSeq(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addJSeq((jalview.schemabinding.version2.JSeq) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllJSeq(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.JSeq(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _JSeqList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _JGroupList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.JGroup.class, "_JGroupList", - "JGroup", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getJGroup(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addJGroup((jalview.schemabinding.version2.JGroup) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllJGroup(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.JGroup(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _JGroupList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _viewportList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Viewport.class, "_viewportList", - "Viewport", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getViewport(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addViewport((jalview.schemabinding.version2.Viewport) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllViewport(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Viewport(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _viewportList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _userColoursList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.UserColours.class, - "_userColoursList", "UserColours", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getUserColours(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addUserColours((jalview.schemabinding.version2.UserColours) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllUserColours(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.UserColours(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _userColoursList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Tree.class, "_treeList", "tree", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getTree(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addTree((jalview.schemabinding.version2.Tree) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllTree(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Tree(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _featureSettings - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.FeatureSettings.class, - "_featureSettings", "FeatureSettings", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getFeatureSettings(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.setFeatureSettings((jalview.schemabinding.version2.FeatureSettings) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.FeatureSettings(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _featureSettings - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JalviewModelSequence.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java deleted file mode 100644 index 459d645..0000000 --- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java +++ /dev/null @@ -1,380 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -import jalview.schemabinding.version2.Colour; -import jalview.schemabinding.version2.Filter; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.JalviewUserColours; - -/** - * Class JalviewUserColoursDescriptor. - * - * @version $Revision$ $Date$ - */ -public class JalviewUserColoursDescriptor - extends org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewUserColoursDescriptor() - { - super(); - _nsURI = "www.jalview.org/colours"; - _xmlName = "JalviewUserColours"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _schemeName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_schemeName", "schemeName", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - @Override - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getSchemeName(); - } - - @Override - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.setSchemeName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - @Override - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _schemeName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_version", "Version", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - @Override - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getVersion(); - } - - @Override - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.setVersion((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - @Override - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _colourList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - Colour.class, "_colourList", "colour", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - @Override - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getColour(); - } - - @Override - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.addColour((Colour) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - @Override - public void resetValue(Object object) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.removeAllColour(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - @Override - public java.lang.Object newInstance(java.lang.Object parent) - { - return new Colour(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _colourList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _filterList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - Filter.class, "_filterList", "filter", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - @Override - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getFilter(); - } - - @Override - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.addFilter((Filter) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - @Override - public void resetValue(Object object) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.removeAllFilter(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - @Override - public java.lang.Object newInstance(java.lang.Object parent) - { - return new Filter(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _filterList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - @Override - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - @Override - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - @Override - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JalviewUserColours.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - @Override - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - @Override - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - @Override - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - @Override - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - @Override - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java deleted file mode 100644 index 529f477..0000000 --- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java +++ /dev/null @@ -1,268 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MapListFrom; - -/** - * Class MapListFromDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapListFromDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListFromDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListFrom"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListFrom target = (MapListFrom) object; - if (!target.hasStart()) - { - return null; - } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListFrom target = (MapListFrom) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListFrom target = (MapListFrom) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListFrom target = (MapListFrom) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MapListFrom.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java deleted file mode 100644 index bed082a..0000000 --- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java +++ /dev/null @@ -1,268 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MapListTo; - -/** - * Class MapListToDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapListToDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListToDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListTo"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListTo target = (MapListTo) object; - if (!target.hasStart()) - { - return null; - } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListTo target = (MapListTo) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListTo target = (MapListTo) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListTo target = (MapListTo) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MapListTo.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java deleted file mode 100644 index fc24a78..0000000 --- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java +++ /dev/null @@ -1,381 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MapListType; - -/** - * Class MapListTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapListTypeDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListTypeDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListType"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _mapFromUnit - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListType target = (MapListType) object; - if (!target.hasMapFromUnit()) - { - return null; - } - return new java.lang.Long(target.getMapFromUnit()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setMapFromUnit(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mapFromUnit - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(1L); - } - desc.setValidator(fieldValidator); - // -- _mapToUnit - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListType target = (MapListType) object; - if (!target.hasMapToUnit()) - { - return null; - } - return new java.lang.Long(target.getMapToUnit()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setMapToUnit(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mapToUnit - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(1L); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _mapListFromList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MapListFrom.class, - "_mapListFromList", "mapListFrom", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListType target = (MapListType) object; - return target.getMapListFrom(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - target.addMapListFrom((jalview.schemabinding.version2.MapListFrom) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - target.removeAllMapListFrom(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MapListFrom(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _mapListFromList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _mapListToList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MapListTo.class, - "_mapListToList", "mapListTo", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListType target = (MapListType) object; - return target.getMapListTo(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - target.addMapListTo((jalview.schemabinding.version2.MapListTo) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - target.removeAllMapListTo(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MapListTo(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _mapListToList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MapListType.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java deleted file mode 100644 index ae460af..0000000 --- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java +++ /dev/null @@ -1,243 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MappingChoice; - -/** - * Class MappingChoiceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MappingChoiceDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MappingChoiceDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _sequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Sequence.class, "_sequence", - "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MappingChoice target = (MappingChoice) object; - return target.getSequence(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MappingChoice target = (MappingChoice) object; - target.setSequence((jalview.schemabinding.version2.Sequence) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _sequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _dseqFor - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_dseqFor", "dseqFor", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MappingChoice target = (MappingChoice) object; - return target.getDseqFor(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MappingChoice target = (MappingChoice) object; - target.setDseqFor((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _dseqFor - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MappingChoice.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java deleted file mode 100644 index fab0d2e..0000000 --- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java +++ /dev/null @@ -1,202 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Mapping; - -/** - * Class MappingDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MappingDescriptor extends - jalview.schemabinding.version2.descriptors.MapListTypeDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MappingDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor()); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Mapping"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _mappingChoice - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MappingChoice.class, - "_mappingChoice", "-error-if-this-is-used-", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Mapping target = (Mapping) object; - return target.getMappingChoice(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Mapping target = (Mapping) object; - target.setMappingChoice((jalview.schemabinding.version2.MappingChoice) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MappingChoice(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor()); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mappingChoice - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Mapping.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/MatchConditionDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MatchConditionDescriptor.java deleted file mode 100644 index 8373421..0000000 --- a/src/jalview/schemabinding/version2/descriptors/MatchConditionDescriptor.java +++ /dev/null @@ -1,148 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MatchCondition; - -/** - * Class MatchConditionDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MatchConditionDescriptor extends - jalview.schemabinding.version2.descriptors.FeatureMatcherDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MatchConditionDescriptor() - { - super(); - setExtendsWithoutFlatten( - new jalview.schemabinding.version2.descriptors.FeatureMatcherDescriptor()); - _xmlName = "matchCondition"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MatchCondition.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/MatcherSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MatcherSetDescriptor.java deleted file mode 100644 index 2807f92..0000000 --- a/src/jalview/schemabinding/version2/descriptors/MatcherSetDescriptor.java +++ /dev/null @@ -1,148 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.MatcherSet; - -/** - * Class MatcherSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MatcherSetDescriptor extends - jalview.schemabinding.version2.descriptors.FeatureMatcherSetDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MatcherSetDescriptor() - { - super(); - setExtendsWithoutFlatten( - new jalview.schemabinding.version2.descriptors.FeatureMatcherSetDescriptor()); - _xmlName = "matcherSet"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MatcherSet.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java deleted file mode 100644 index ab7a626..0000000 --- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java +++ /dev/null @@ -1,272 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.OtherData; - -/** - * Class OtherDataDescriptor. - * - * @version $Revision$ $Date$ - */ -public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public OtherDataDescriptor() { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "otherData"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _key - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", 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 - { - OtherData target = (OtherData) object; - return target.getKey(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - OtherData target = (OtherData) object; - target.setKey( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _key - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _key2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key2", "key2", 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 - { - OtherData target = (OtherData) object; - return target.getKey2(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - OtherData target = (OtherData) object; - target.setKey2( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _key2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", 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 - { - OtherData target = (OtherData) object; - return target.getValue(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - OtherData target = (OtherData) object; - target.setValue( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.OtherData.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java deleted file mode 100644 index f19703a..0000000 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java +++ /dev/null @@ -1,346 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Pdbentry; - -/** - * Class PdbentryDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PdbentryDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbentryDescriptor() - { - super(); - _xmlName = "pdbentry"; - _elementDefinition = false; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _id - 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 - { - Pdbentry target = (Pdbentry) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_type", "type", - 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 - { - Pdbentry target = (Pdbentry) object; - return target.getType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.setType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _file - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_file", "file", - 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 - { - Pdbentry target = (Pdbentry) object; - return target.getFile(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.setFile((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _file - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _items - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.PdbentryItem.class, "_items", - (java.lang.String) null, org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getPdbentryItem(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.addPdbentryItem((jalview.schemabinding.version2.PdbentryItem) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.removeAllPdbentryItem(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.PdbentryItem(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor()); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _items - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Pdbentry.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java deleted file mode 100644 index 4e2fc87..0000000 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.PdbentryItem; - -/** - * Class PdbentryItemDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PdbentryItemDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbentryItemDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "pdbentry"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Property.class, "_propertyList", - "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - PdbentryItem target = (PdbentryItem) object; - return target.getProperty(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - PdbentryItem target = (PdbentryItem) object; - target.addProperty((jalview.schemabinding.version2.Property) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - PdbentryItem target = (PdbentryItem) object; - target.removeAllProperty(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.PdbentryItem.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java deleted file mode 100644 index 584607d..0000000 --- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java +++ /dev/null @@ -1,214 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Pdbids; - -/** - * Class PdbidsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PdbidsDescriptor extends - jalview.schemabinding.version2.descriptors.PdbentryDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbidsDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "pdbids"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _structureStateList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.StructureState.class, - "_structureStateList", "structureState", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Pdbids target = (Pdbids) object; - return target.getStructureState(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbids target = (Pdbids) object; - target.addStructureState((jalview.schemabinding.version2.StructureState) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Pdbids target = (Pdbids) object; - target.removeAllStructureState(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.StructureState(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _structureStateList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Pdbids.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java deleted file mode 100644 index 60d09b4..0000000 --- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java +++ /dev/null @@ -1,248 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Property; - -/** - * Class PropertyDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PropertyDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PropertyDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "property"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - 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 - { - Property target = (Property) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Property target = (Property) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_value", "value", - 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 - { - Property target = (Property) object; - return target.getValue(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Property target = (Property) object; - target.setValue((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Property.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java b/src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java deleted file mode 100644 index 3344050..0000000 --- a/src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java +++ /dev/null @@ -1,634 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.RnaViewer; - -/** - * Class RnaViewerDescriptor. - * - * @version $Revision$ $Date$ - */ -public class RnaViewerDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public RnaViewerDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "rnaViewer"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_title", "title", - 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 - { - RnaViewer target = (RnaViewer) object; - return target.getTitle(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - target.setTitle((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _viewId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_viewId", "viewId", - 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 - { - RnaViewer target = (RnaViewer) object; - return target.getViewId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - target.setViewId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _viewId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _dividerLocation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_dividerLocation", "dividerLocation", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - RnaViewer target = (RnaViewer) object; - if (!target.hasDividerLocation()) - { - return null; - } - return new java.lang.Integer(target.getDividerLocation()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteDividerLocation(); - return; - } - target.setDividerLocation(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _dividerLocation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _selectedRna - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_selectedRna", "selectedRna", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - RnaViewer target = (RnaViewer) object; - if (!target.hasSelectedRna()) - { - return null; - } - return new java.lang.Integer(target.getSelectedRna()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteSelectedRna(); - return; - } - target.setSelectedRna(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _selectedRna - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_width", "width", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - RnaViewer target = (RnaViewer) object; - if (!target.hasWidth()) - { - return null; - } - return new java.lang.Integer(target.getWidth()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWidth(); - return; - } - target.setWidth(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_height", "height", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - RnaViewer target = (RnaViewer) object; - if (!target.hasHeight()) - { - return null; - } - return new java.lang.Integer(target.getHeight()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHeight(); - return; - } - target.setHeight(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_xpos", "xpos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - RnaViewer target = (RnaViewer) object; - if (!target.hasXpos()) - { - return null; - } - return new java.lang.Integer(target.getXpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteXpos(); - return; - } - target.setXpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_ypos", "ypos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - RnaViewer target = (RnaViewer) object; - if (!target.hasYpos()) - { - return null; - } - return new java.lang.Integer(target.getYpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteYpos(); - return; - } - target.setYpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _secondaryStructureList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.SecondaryStructure.class, - "_secondaryStructureList", "secondaryStructure", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - RnaViewer target = (RnaViewer) object; - return target.getSecondaryStructure(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - target.addSecondaryStructure((jalview.schemabinding.version2.SecondaryStructure) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - RnaViewer target = (RnaViewer) object; - target.removeAllSecondaryStructure(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.SecondaryStructure(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _secondaryStructureList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.RnaViewer.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java deleted file mode 100644 index c1e46b8..0000000 --- a/src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java +++ /dev/null @@ -1,345 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.SecondaryStructure; - -/** - * Class SecondaryStructureDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SecondaryStructureDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SecondaryStructureDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "secondaryStructure"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_title", "title", - 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 - { - SecondaryStructure target = (SecondaryStructure) object; - return target.getTitle(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SecondaryStructure target = (SecondaryStructure) object; - target.setTitle((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _annotationId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_annotationId", "annotationId", - 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 - { - SecondaryStructure target = (SecondaryStructure) object; - return target.getAnnotationId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SecondaryStructure target = (SecondaryStructure) object; - target.setAnnotationId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _annotationId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _gapped - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_gapped", "gapped", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SecondaryStructure target = (SecondaryStructure) object; - if (!target.hasGapped()) - { - return null; - } - return (target.getGapped() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SecondaryStructure target = (SecondaryStructure) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGapped(); - return; - } - target.setGapped(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _gapped - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _viewerState - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_viewerState", "viewerState", - 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 - { - SecondaryStructure target = (SecondaryStructure) object; - return target.getViewerState(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SecondaryStructure target = (SecondaryStructure) object; - target.setViewerState((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _viewerState - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.SecondaryStructure.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java deleted file mode 100644 index 2303e1b..0000000 --- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java +++ /dev/null @@ -1,258 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Sequence; - -/** - * Class SequenceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceDescriptor extends - jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor()); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Sequence"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _dsseqid - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_dsseqid", "dsseqid", - 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 - { - Sequence target = (Sequence) object; - return target.getDsseqid(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Sequence target = (Sequence) object; - target.setDsseqid((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _dsseqid - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _DBRefList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.DBRef.class, "_DBRefList", - "DBRef", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getDBRef(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Sequence target = (Sequence) object; - target.addDBRef((jalview.schemabinding.version2.DBRef) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Sequence target = (Sequence) object; - target.removeAllDBRef(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.DBRef(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _DBRefList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Sequence.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java deleted file mode 100644 index cd74c6e..0000000 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java +++ /dev/null @@ -1,472 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.SequenceSet; - -/** - * Class SequenceSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSetDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "SequenceSet"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _gapChar - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_gapChar", "gapChar", - 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 - { - SequenceSet target = (SequenceSet) object; - return target.getGapChar(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.setGapChar((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _gapChar - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _datasetId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_datasetId", "datasetId", - 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 - { - SequenceSet target = (SequenceSet) object; - return target.getDatasetId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.setDatasetId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _datasetId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _sequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Sequence.class, "_sequenceList", - "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getSequence(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.addSequence((jalview.schemabinding.version2.Sequence) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.removeAllSequence(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _sequenceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _annotationList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Annotation.class, - "_annotationList", "Annotation", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getAnnotation(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.addAnnotation((jalview.schemabinding.version2.Annotation) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.removeAllAnnotation(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Annotation(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _annotationList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _sequenceSetPropertiesList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.SequenceSetProperties.class, - "_sequenceSetPropertiesList", "sequenceSetProperties", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getSequenceSetProperties(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.removeAllSequenceSetProperties(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.SequenceSetProperties(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _sequenceSetPropertiesList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _alcodonFrameList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AlcodonFrame.class, - "_alcodonFrameList", "AlcodonFrame", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getAlcodonFrame(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.removeAllAlcodonFrame(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AlcodonFrame(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _alcodonFrameList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.SequenceSet.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java deleted file mode 100644 index 409abdd..0000000 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java +++ /dev/null @@ -1,244 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.SequenceSetProperties; - -/** - * Class SequenceSetPropertiesDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetPropertiesDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSetPropertiesDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "sequenceSetProperties"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _key - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_key", "key", - 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 - { - SequenceSetProperties target = (SequenceSetProperties) object; - return target.getKey(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSetProperties target = (SequenceSetProperties) object; - target.setKey((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _key - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_value", "value", - 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 - { - SequenceSetProperties target = (SequenceSetProperties) object; - return target.getValue(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSetProperties target = (SequenceSetProperties) object; - target.setValue((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.SequenceSetProperties.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java deleted file mode 100644 index 3ee3fa9..0000000 --- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java +++ /dev/null @@ -1,339 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.SequenceType; - -/** - * Class SequenceTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceTypeDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceTypeDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "SequenceType"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _id - 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 - { - SequenceType target = (SequenceType) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceType target = (SequenceType) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - 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 - { - SequenceType target = (SequenceType) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceType target = (SequenceType) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _sequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_sequence", "sequence", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getSequence(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceType target = (SequenceType) object; - target.setSequence((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _sequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceType target = (SequenceType) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.SequenceType.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java deleted file mode 100644 index c816e43..0000000 --- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java +++ /dev/null @@ -1,905 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Setting; - -/** - * Class SettingDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SettingDescriptor - extends org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SettingDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "setting"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_type", "type", - 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 - { - Setting target = (Setting) object; - return target.getType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - target.setType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasColour()) - { - return null; - } - return new java.lang.Integer(target.getColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - 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(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _display - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_display", "display", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasDisplay()) - { - return null; - } - return (target.getDisplay() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setDisplay(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _display - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _order - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_order", "order", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasOrder()) - { - return null; - } - return new java.lang.Float(target.getOrder()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteOrder(); - return; - } - target.setOrder(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _order - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _mincolour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_mincolour", "mincolour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMincolour()) - { - return null; - } - return new java.lang.Integer(target.getMincolour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMincolour(); - return; - } - target.setMincolour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mincolour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _noValueColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.types.NoValueColour.class, - "_noValueColour", "noValueColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - return target.getNoValueColour(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - target.setNoValueColour( - (jalview.schemabinding.version2.types.NoValueColour) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - handler = new org.exolab.castor.xml.handlers.EnumFieldHandler( - jalview.schemabinding.version2.types.NoValueColour.class, - handler); - desc.setImmutable(true); - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _noValueColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_threshold", "threshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasThreshold()) - { - return null; - } - return new java.lang.Float(target.getThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshold(); - return; - } - target.setThreshold(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _threshstate - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_threshstate", "threshstate", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasThreshstate()) - { - return null; - } - return new java.lang.Integer(target.getThreshstate()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshstate(); - return; - } - target.setThreshstate(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshstate - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _max - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_max", "max", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMax()) - { - return null; - } - return new java.lang.Float(target.getMax()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMax(); - return; - } - target.setMax(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _max - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _min - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_min", "min", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMin()) - { - return null; - } - return new java.lang.Float(target.getMin()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMin(); - return; - } - target.setMin(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _min - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _colourByLabel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasColourByLabel()) - { - return null; - } - return (target.getColourByLabel() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColourByLabel(); - return; - } - target.setColourByLabel( - ((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourByLabel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _autoScale - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_autoScale", "autoScale", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasAutoScale()) - { - return null; - } - return (target.getAutoScale() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAutoScale(); - return; - } - target.setAutoScale(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _autoScale - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _attributeNameList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_attributeNameList", "attributeName", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - return target.getAttributeName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - target.addAttributeName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - target.removeAllAttributeName(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _attributeNameList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - fieldValidator.setMaxOccurs(2); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _matcherSet - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MatcherSet.class, "_matcherSet", - "matcherSet", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - return target.getMatcherSet(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - target.setMatcherSet( - (jalview.schemabinding.version2.MatcherSet) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MatcherSet(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _matcherSet - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Setting.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java deleted file mode 100644 index 16d091b..0000000 --- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java +++ /dev/null @@ -1,727 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.StructureState; - -/** - * Class StructureStateDescriptor. - * - * @version $Revision$ $Date$ - */ -public class StructureStateDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public StructureStateDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "structureState"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_content", "PCDATA", - org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - return target.getContent(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - target.setContent((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - // -- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize attribute descriptors - - // -- _visible - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_visible", "visible", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasVisible()) - { - return null; - } - return (target.getVisible() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteVisible(); - return; - } - target.setVisible(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _visible - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _viewId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_viewId", "viewId", - 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 - { - StructureState target = (StructureState) object; - return target.getViewId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - target.setViewId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _viewId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _alignwithAlignPanel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_alignwithAlignPanel", - "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasAlignwithAlignPanel()) - { - return null; - } - return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAlignwithAlignPanel(); - return; - } - target.setAlignwithAlignPanel(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _alignwithAlignPanel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _colourwithAlignPanel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_colourwithAlignPanel", - "colourwithAlignPanel", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasColourwithAlignPanel()) - { - return null; - } - return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColourwithAlignPanel(); - return; - } - target.setColourwithAlignPanel(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourwithAlignPanel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _colourByJmol - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_colourByJmol", "colourByJmol", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasColourByJmol()) - { - return null; - } - return (target.getColourByJmol() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColourByJmol(); - return; - } - target.setColourByJmol(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourByJmol - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_type", "type", - 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 - { - StructureState target = (StructureState) object; - return target.getType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - target.setType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_width", "width", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasWidth()) - { - return null; - } - return new java.lang.Integer(target.getWidth()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWidth(); - return; - } - target.setWidth(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_height", "height", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasHeight()) - { - return null; - } - return new java.lang.Integer(target.getHeight()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHeight(); - return; - } - target.setHeight(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_xpos", "xpos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasXpos()) - { - return null; - } - return new java.lang.Integer(target.getXpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteXpos(); - return; - } - target.setXpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_ypos", "ypos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasYpos()) - { - return null; - } - return new java.lang.Integer(target.getYpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteYpos(); - return; - } - target.setYpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.StructureState.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java deleted file mode 100644 index 8a863d8..0000000 --- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java +++ /dev/null @@ -1,309 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.ThresholdLine; - -/** - * Class ThresholdLineDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ThresholdLineDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public ThresholdLineDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "thresholdLine"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _label - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_label", "label", - 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 - { - ThresholdLine target = (ThresholdLine) object; - return target.getLabel(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - ThresholdLine target = (ThresholdLine) object; - target.setLabel((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_value", "value", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - ThresholdLine target = (ThresholdLine) object; - if (!target.hasValue()) - { - return null; - } - return new java.lang.Float(target.getValue()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - ThresholdLine target = (ThresholdLine) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteValue(); - return; - } - target.setValue(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - ThresholdLine target = (ThresholdLine) object; - if (!target.hasColour()) - { - return null; - } - return new java.lang.Integer(target.getColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - ThresholdLine target = (ThresholdLine) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColour(); - return; - } - target.setColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.ThresholdLine.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java deleted file mode 100644 index 8e675f3..0000000 --- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java +++ /dev/null @@ -1,995 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Tree; - -/** - * Class TreeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class TreeDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public TreeDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "tree"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _fontName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_fontName", "fontName", - 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 - { - Tree target = (Tree) object; - return target.getFontName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - target.setFontName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _fontSize - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_fontSize", "fontSize", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFontSize()) - { - return null; - } - return new java.lang.Integer(target.getFontSize()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFontSize(); - return; - } - target.setFontSize(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontSize - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _fontStyle - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_fontStyle", "fontStyle", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFontStyle()) - { - return null; - } - return new java.lang.Integer(target.getFontStyle()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFontStyle(); - return; - } - target.setFontStyle(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontStyle - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_threshold", "threshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasThreshold()) - { - return null; - } - return new java.lang.Float(target.getThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshold(); - return; - } - target.setThreshold(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _showBootstrap - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasShowBootstrap()) - { - return null; - } - return (target.getShowBootstrap() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowBootstrap(); - return; - } - target.setShowBootstrap(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showBootstrap - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showDistances - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showDistances", "showDistances", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasShowDistances()) - { - return null; - } - return (target.getShowDistances() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowDistances(); - return; - } - target.setShowDistances(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showDistances - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _markUnlinked - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasMarkUnlinked()) - { - return null; - } - return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMarkUnlinked(); - return; - } - target.setMarkUnlinked(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _markUnlinked - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _fitToWindow - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFitToWindow()) - { - return null; - } - return (target.getFitToWindow() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFitToWindow(); - return; - } - target.setFitToWindow(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fitToWindow - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _currentTree - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_currentTree", "currentTree", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasCurrentTree()) - { - return null; - } - return (target.getCurrentTree() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteCurrentTree(); - return; - } - target.setCurrentTree(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _currentTree - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - super.setIdentity(desc); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IdValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IdValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_width", "width", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasWidth()) - { - return null; - } - return new java.lang.Integer(target.getWidth()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWidth(); - return; - } - target.setWidth(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_height", "height", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasHeight()) - { - return null; - } - return new java.lang.Integer(target.getHeight()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHeight(); - return; - } - target.setHeight(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_xpos", "xpos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasXpos()) - { - return null; - } - return new java.lang.Integer(target.getXpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteXpos(); - return; - } - target.setXpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_ypos", "ypos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasYpos()) - { - return null; - } - return new java.lang.Integer(target.getYpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteYpos(); - return; - } - target.setYpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_title", "title", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getTitle(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - target.setTitle((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _newick - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_newick", "newick", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getNewick(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - target.setNewick((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _newick - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Tree.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java deleted file mode 100644 index df9ab07..0000000 --- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java +++ /dev/null @@ -1,149 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.UserColourScheme; - -/** - * Class UserColourSchemeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class UserColourSchemeDescriptor - extends - jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColourSchemeDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "UserColourScheme"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.UserColourScheme.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java deleted file mode 100644 index 53dfde4..0000000 --- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java +++ /dev/null @@ -1,246 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.UserColours; - -/** - * Class UserColoursDescriptor. - * - * @version $Revision$ $Date$ - */ -public class UserColoursDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColoursDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "UserColours"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _id - 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 - { - UserColours target = (UserColours) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - UserColours target = (UserColours) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _userColourScheme - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.UserColourScheme.class, - "_userColourScheme", "UserColourScheme", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - UserColours target = (UserColours) object; - return target.getUserColourScheme(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - UserColours target = (UserColours) object; - target.setUserColourScheme((jalview.schemabinding.version2.UserColourScheme) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.UserColourScheme(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _userColourScheme - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.UserColours.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java deleted file mode 100644 index e3470ee..0000000 --- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java +++ /dev/null @@ -1,273 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.VAMSAS; - -/** - * Class VAMSASDescriptor. - * - * @version $Revision$ $Date$ - */ -public class VAMSASDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VAMSASDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "VAMSAS"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_treeList", "Tree", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getTree(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - VAMSAS target = (VAMSAS) object; - target.addTree((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - VAMSAS target = (VAMSAS) object; - target.removeAllTree(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _sequenceSetList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.SequenceSet.class, - "_sequenceSetList", "SequenceSet", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getSequenceSet(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - VAMSAS target = (VAMSAS) object; - target.addSequenceSet((jalview.schemabinding.version2.SequenceSet) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - VAMSAS target = (VAMSAS) object; - target.removeAllSequenceSet(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.SequenceSet(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _sequenceSetList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.VAMSAS.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java deleted file mode 100644 index 3e26611..0000000 --- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java +++ /dev/null @@ -1,148 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.VamsasModel; - -/** - * Class VamsasModelDescriptor. - * - * @version $Revision$ $Date$ - */ -public class VamsasModelDescriptor extends - jalview.schemabinding.version2.descriptors.VAMSASDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VamsasModelDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "vamsasModel"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.VamsasModel.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java deleted file mode 100644 index 1df3988..0000000 --- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java +++ /dev/null @@ -1,2717 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.Viewport; - -/** - * Class ViewportDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ViewportDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public ViewportDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "Viewport"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _conservationSelected - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_conservationSelected", - "conservationSelected", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasConservationSelected()) - { - return null; - } - return (target.getConservationSelected() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteConservationSelected(); - return; - } - target.setConservationSelected(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _conservationSelected - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _pidSelected - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasPidSelected()) - { - return null; - } - return (target.getPidSelected() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePidSelected(); - return; - } - target.setPidSelected(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pidSelected - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _bgColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_bgColour", "bgColour", - 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 - { - Viewport target = (Viewport) object; - return target.getBgColour(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setBgColour((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _bgColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _consThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_consThreshold", "consThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasConsThreshold()) - { - return null; - } - return new java.lang.Integer(target.getConsThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteConsThreshold(); - return; - } - target.setConsThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _consThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _pidThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasPidThreshold()) - { - return null; - } - return new java.lang.Integer(target.getPidThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePidThreshold(); - return; - } - target.setPidThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pidThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_title", "title", - 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 - { - Viewport target = (Viewport) object; - return target.getTitle(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setTitle((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _showFullId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showFullId", "showFullId", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowFullId()) - { - return null; - } - return (target.getShowFullId() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowFullId(); - return; - } - target.setShowFullId(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showFullId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _rightAlignIds - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasRightAlignIds()) - { - return null; - } - return (target.getRightAlignIds() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteRightAlignIds(); - return; - } - target.setRightAlignIds(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _rightAlignIds - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showText", "showText", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowText()) - { - return null; - } - return (target.getShowText() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowText(); - return; - } - target.setShowText(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showColourText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showColourText", "showColourText", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowColourText()) - { - return null; - } - return (target.getShowColourText() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowColourText(); - return; - } - target.setShowColourText(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showColourText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showUnconserved - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowUnconserved()) - { - return null; - } - return (target.getShowUnconserved() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowUnconserved(); - return; - } - target.setShowUnconserved(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showUnconserved - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showBoxes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowBoxes()) - { - return null; - } - return (target.getShowBoxes() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowBoxes(); - return; - } - target.setShowBoxes(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showBoxes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _wrapAlignment - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasWrapAlignment()) - { - return null; - } - return (target.getWrapAlignment() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWrapAlignment(); - return; - } - target.setWrapAlignment(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _wrapAlignment - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _renderGaps - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasRenderGaps()) - { - return null; - } - return (target.getRenderGaps() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteRenderGaps(); - return; - } - target.setRenderGaps(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _renderGaps - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showSequenceFeatures - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showSequenceFeatures", - "showSequenceFeatures", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowSequenceFeatures()) - { - return null; - } - return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowSequenceFeatures(); - return; - } - target.setShowSequenceFeatures(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showSequenceFeatures - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showNPfeatureTooltip - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showNPfeatureTooltip", - "showNPfeatureTooltip", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowNPfeatureTooltip()) - { - return null; - } - return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowNPfeatureTooltip(); - return; - } - target.setShowNPfeatureTooltip(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showNPfeatureTooltip - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showDbRefTooltip - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showDbRefTooltip", - "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowDbRefTooltip()) - { - return null; - } - return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowDbRefTooltip(); - return; - } - target.setShowDbRefTooltip(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showDbRefTooltip - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _followHighlight - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFollowHighlight()) - { - return null; - } - return (target.getFollowHighlight() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFollowHighlight(); - return; - } - target.setFollowHighlight(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _followHighlight - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _followSelection - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_followSelection", "followSelection", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFollowSelection()) - { - return null; - } - return (target.getFollowSelection() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFollowSelection(); - return; - } - target.setFollowSelection(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _followSelection - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showAnnotation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowAnnotation()) - { - return null; - } - return (target.getShowAnnotation() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowAnnotation(); - return; - } - target.setShowAnnotation(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showAnnotation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _centreColumnLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_centreColumnLabels", - "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasCentreColumnLabels()) - { - return null; - } - return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteCentreColumnLabels(); - return; - } - target.setCentreColumnLabels(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _centreColumnLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showGroupConservation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showGroupConservation", - "showGroupConservation", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowGroupConservation()) - { - return null; - } - return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowGroupConservation(); - return; - } - target.setShowGroupConservation(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showGroupConservation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showGroupConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showGroupConsensus", - "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowGroupConsensus()) - { - return null; - } - return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowGroupConsensus(); - return; - } - target.setShowGroupConsensus(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showGroupConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showConsensusHistogram - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showConsensusHistogram", - "showConsensusHistogram", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowConsensusHistogram()) - { - return null; - } - return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowConsensusHistogram(); - return; - } - target.setShowConsensusHistogram(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showConsensusHistogram - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showSequenceLogo - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showSequenceLogo", - "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowSequenceLogo()) - { - return null; - } - return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowSequenceLogo(); - return; - } - target.setShowSequenceLogo(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showSequenceLogo - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _normaliseSequenceLogo - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_normaliseSequenceLogo", - "normaliseSequenceLogo", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasNormaliseSequenceLogo()) - { - return null; - } - return (target.getNormaliseSequenceLogo() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteNormaliseSequenceLogo(); - return; - } - target.setNormaliseSequenceLogo(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _normaliseSequenceLogo - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _ignoreGapsinConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", - "ignoreGapsinConsensus", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasIgnoreGapsinConsensus()) - { - return null; - } - return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteIgnoreGapsinConsensus(); - return; - } - target.setIgnoreGapsinConsensus(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ignoreGapsinConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _startRes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_startRes", "startRes", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasStartRes()) - { - return null; - } - return new java.lang.Integer(target.getStartRes()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteStartRes(); - return; - } - target.setStartRes(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _startRes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _startSeq - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_startSeq", "startSeq", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasStartSeq()) - { - return null; - } - return new java.lang.Integer(target.getStartSeq()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteStartSeq(); - return; - } - target.setStartSeq(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _startSeq - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _fontName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_fontName", "fontName", - 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 - { - Viewport target = (Viewport) object; - return target.getFontName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setFontName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _fontSize - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_fontSize", "fontSize", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFontSize()) - { - return null; - } - return new java.lang.Integer(target.getFontSize()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFontSize(); - return; - } - target.setFontSize(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontSize - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _fontStyle - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_fontStyle", "fontStyle", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFontStyle()) - { - return null; - } - return new java.lang.Integer(target.getFontStyle()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFontStyle(); - return; - } - target.setFontStyle(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontStyle - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _scaleProteinAsCdna - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_scaleProteinAsCdna", - "scaleProteinAsCdna", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasScaleProteinAsCdna()) - { - return null; - } - return (target.getScaleProteinAsCdna() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScaleProteinAsCdna(); - return; - } - target.setScaleProteinAsCdna(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _scaleProteinAsCdna - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _viewName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_viewName", "viewName", - 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 - { - Viewport target = (Viewport) object; - return target.getViewName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setViewName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _viewName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _sequenceSetId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_sequenceSetId", "sequenceSetId", - 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 - { - Viewport target = (Viewport) object; - return target.getSequenceSetId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setSequenceSetId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _sequenceSetId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _gatheredViews - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasGatheredViews()) - { - return null; - } - return (target.getGatheredViews() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGatheredViews(); - return; - } - target.setGatheredViews(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _gatheredViews - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _textCol1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textCol1", "textCol1", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextCol1()) - { - return null; - } - return new java.lang.Integer(target.getTextCol1()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextCol1(); - return; - } - target.setTextCol1(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textCol1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _textCol2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textCol2", "textCol2", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextCol2()) - { - return null; - } - return new java.lang.Integer(target.getTextCol2()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextCol2(); - return; - } - target.setTextCol2(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textCol2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _textColThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textColThreshold", - "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextColThreshold()) - { - return null; - } - return new java.lang.Integer(target.getTextColThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextColThreshold(); - return; - } - target.setTextColThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textColThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - super.setIdentity(desc); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IdValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IdValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _complementId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_complementId", "complementId", - 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 - { - Viewport target = (Viewport) object; - return target.getComplementId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setComplementId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _complementId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_width", "width", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasWidth()) - { - return null; - } - return new java.lang.Integer(target.getWidth()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWidth(); - return; - } - target.setWidth(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_height", "height", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasHeight()) - { - return null; - } - return new java.lang.Integer(target.getHeight()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHeight(); - return; - } - target.setHeight(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_xpos", "xpos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasXpos()) - { - return null; - } - return new java.lang.Integer(target.getXpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteXpos(); - return; - } - target.setXpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_ypos", "ypos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasYpos()) - { - return null; - } - return new java.lang.Integer(target.getYpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteYpos(); - return; - } - target.setYpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _annotationColours - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AnnotationColours.class, - "_annotationColours", "AnnotationColours", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getAnnotationColours(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AnnotationColours(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _annotationColours - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _hiddenColumnsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.HiddenColumns.class, - "_hiddenColumnsList", "hiddenColumns", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getHiddenColumns(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.addHiddenColumns((jalview.schemabinding.version2.HiddenColumns) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.removeAllHiddenColumns(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.HiddenColumns(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _hiddenColumnsList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _calcIdParamList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.CalcIdParam.class, - "_calcIdParamList", "calcIdParam", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getCalcIdParam(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.addCalcIdParam((jalview.schemabinding.version2.CalcIdParam) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.removeAllCalcIdParam(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.CalcIdParam(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _calcIdParamList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Viewport.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java deleted file mode 100644 index beb5b50..0000000 --- a/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java +++ /dev/null @@ -1,396 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.WebServiceParameterSet; - -/** - * Class WebServiceParameterSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class WebServiceParameterSetDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public WebServiceParameterSetDescriptor() - { - super(); - _nsURI = "www.jalview.org/xml/wsparamset"; - _xmlName = "WebServiceParameterSet"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - 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 - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_version", "Version", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getVersion(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.setVersion((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _serviceURLList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_serviceURLList", "serviceURL", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getServiceURL(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.addServiceURL((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.removeAllServiceURL(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _serviceURLList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _parameters - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_parameters", "parameters", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getParameters(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.setParameters((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _parameters - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.WebServiceParameterSet.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/types/.castor.cdr b/src/jalview/schemabinding/version2/types/.castor.cdr deleted file mode 100644 index d9874b6..0000000 --- a/src/jalview/schemabinding/version2/types/.castor.cdr +++ /dev/null @@ -1,5 +0,0 @@ -#Thu Dec 14 15:28:22 GMT 2017 -jalview.schemabinding.version2.types.ColourNoValueColourType=jalview.schemabinding.version2.types.descriptors.ColourNoValueColourTypeDescriptor -jalview.schemabinding.version2.types.FeatureMatcherByType=jalview.schemabinding.version2.types.descriptors.FeatureMatcherByTypeDescriptor -jalview.schemabinding.version2.types.NoValueColour=jalview.schemabinding.version2.types.descriptors.NoValueColourDescriptor -jalview.schemabinding.version2.types.ColourThreshTypeType=jalview.schemabinding.version2.types.descriptors.ColourThreshTypeTypeDescriptor diff --git a/src/jalview/schemabinding/version2/types/ColourThreshTypeType.java b/src/jalview/schemabinding/version2/types/ColourThreshTypeType.java deleted file mode 100644 index 0330411..0000000 --- a/src/jalview/schemabinding/version2/types/ColourThreshTypeType.java +++ /dev/null @@ -1,168 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.types; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.util.Hashtable; - -/** - * Class ColourThreshTypeType. - * - * @version $Revision$ $Date$ - */ -public class ColourThreshTypeType implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * The NONE type - */ - public static final int NONE_TYPE = 0; - - /** - * The instance of the NONE type - */ - public static final ColourThreshTypeType NONE = new ColourThreshTypeType(NONE_TYPE, "NONE"); - - /** - * The ABOVE type - */ - public static final int ABOVE_TYPE = 1; - - /** - * The instance of the ABOVE type - */ - public static final ColourThreshTypeType ABOVE = new ColourThreshTypeType(ABOVE_TYPE, "ABOVE"); - - /** - * The BELOW type - */ - public static final int BELOW_TYPE = 2; - - /** - * The instance of the BELOW type - */ - public static final ColourThreshTypeType BELOW = new ColourThreshTypeType(BELOW_TYPE, "BELOW"); - - /** - * Field _memberTable. - */ - private static java.util.Hashtable _memberTable = init(); - - /** - * Field type. - */ - private int type = -1; - - /** - * Field stringValue. - */ - private java.lang.String stringValue = null; - - - //----------------/ - //- Constructors -/ - //----------------/ - - private ColourThreshTypeType(final int type, final java.lang.String value) { - super(); - this.type = type; - this.stringValue = value; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method enumerate.Returns an enumeration of all possible - * instances of ColourThreshTypeType - * - * @return an Enumeration over all possible instances of - * ColourThreshTypeType - */ - public static java.util.Enumeration enumerate( - ) { - return _memberTable.elements(); - } - - /** - * Method getType.Returns the type of this ColourThreshTypeType - * - * @return the type of this ColourThreshTypeType - */ - public int getType( - ) { - return this.type; - } - - /** - * Method init. - * - * @return the initialized Hashtable for the member table - */ - private static java.util.Hashtable init( - ) { - Hashtable members = new Hashtable(); - members.put("NONE", NONE); - members.put("ABOVE", ABOVE); - members.put("BELOW", BELOW); - return members; - } - - /** - * Method readResolve. will be called during deserialization to - * replace the deserialized object with the correct constant - * instance. - * - * @return this deserialized object - */ - private java.lang.Object readResolve( - ) { - return valueOf(this.stringValue); - } - - /** - * Method toString.Returns the String representation of this - * ColourThreshTypeType - * - * @return the String representation of this ColourThreshTypeTyp - */ - public java.lang.String toString( - ) { - return this.stringValue; - } - - /** - * Method valueOf.Returns a new ColourThreshTypeType based on - * the given String value. - * - * @param string - * @return the ColourThreshTypeType value of parameter 'string' - */ - public static jalview.schemabinding.version2.types.ColourThreshTypeType valueOf( - final java.lang.String string) { - java.lang.Object obj = null; - if (string != null) { - obj = _memberTable.get(string); - } - if (obj == null) { - String err = "" + string + " is not a valid ColourThreshTypeType"; - throw new IllegalArgumentException(err); - } - return (ColourThreshTypeType) obj; - } - -} diff --git a/src/jalview/schemabinding/version2/types/FeatureMatcherByType.java b/src/jalview/schemabinding/version2/types/FeatureMatcherByType.java deleted file mode 100644 index 6e97332..0000000 --- a/src/jalview/schemabinding/version2/types/FeatureMatcherByType.java +++ /dev/null @@ -1,168 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.types; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.util.Hashtable; - -/** - * Class FeatureMatcherByType. - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcherByType implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * The byLabel type - */ - public static final int BYLABEL_TYPE = 0; - - /** - * The instance of the byLabel type - */ - public static final FeatureMatcherByType BYLABEL = new FeatureMatcherByType(BYLABEL_TYPE, "byLabel"); - - /** - * The byScore type - */ - public static final int BYSCORE_TYPE = 1; - - /** - * The instance of the byScore type - */ - public static final FeatureMatcherByType BYSCORE = new FeatureMatcherByType(BYSCORE_TYPE, "byScore"); - - /** - * The byAttribute type - */ - public static final int BYATTRIBUTE_TYPE = 2; - - /** - * The instance of the byAttribute type - */ - public static final FeatureMatcherByType BYATTRIBUTE = new FeatureMatcherByType(BYATTRIBUTE_TYPE, "byAttribute"); - - /** - * Field _memberTable. - */ - private static java.util.Hashtable _memberTable = init(); - - /** - * Field type. - */ - private int type = -1; - - /** - * Field stringValue. - */ - private java.lang.String stringValue = null; - - - //----------------/ - //- Constructors -/ - //----------------/ - - private FeatureMatcherByType(final int type, final java.lang.String value) { - super(); - this.type = type; - this.stringValue = value; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method enumerate.Returns an enumeration of all possible - * instances of FeatureMatcherByType - * - * @return an Enumeration over all possible instances of - * FeatureMatcherByType - */ - public static java.util.Enumeration enumerate( - ) { - return _memberTable.elements(); - } - - /** - * Method getType.Returns the type of this FeatureMatcherByType - * - * @return the type of this FeatureMatcherByType - */ - public int getType( - ) { - return this.type; - } - - /** - * Method init. - * - * @return the initialized Hashtable for the member table - */ - private static java.util.Hashtable init( - ) { - Hashtable members = new Hashtable(); - members.put("byLabel", BYLABEL); - members.put("byScore", BYSCORE); - members.put("byAttribute", BYATTRIBUTE); - return members; - } - - /** - * Method readResolve. will be called during deserialization to - * replace the deserialized object with the correct constant - * instance. - * - * @return this deserialized object - */ - private java.lang.Object readResolve( - ) { - return valueOf(this.stringValue); - } - - /** - * Method toString.Returns the String representation of this - * FeatureMatcherByType - * - * @return the String representation of this FeatureMatcherByTyp - */ - public java.lang.String toString( - ) { - return this.stringValue; - } - - /** - * Method valueOf.Returns a new FeatureMatcherByType based on - * the given String value. - * - * @param string - * @return the FeatureMatcherByType value of parameter 'string' - */ - public static jalview.schemabinding.version2.types.FeatureMatcherByType valueOf( - final java.lang.String string) { - java.lang.Object obj = null; - if (string != null) { - obj = _memberTable.get(string); - } - if (obj == null) { - String err = "" + string + " is not a valid FeatureMatcherByType"; - throw new IllegalArgumentException(err); - } - return (FeatureMatcherByType) obj; - } - -} diff --git a/src/jalview/schemabinding/version2/types/NoValueColour.java b/src/jalview/schemabinding/version2/types/NoValueColour.java deleted file mode 100644 index bbef3d7..0000000 --- a/src/jalview/schemabinding/version2/types/NoValueColour.java +++ /dev/null @@ -1,169 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.types; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import java.util.Hashtable; - -/** - * Graduated feature colour if no score (or attribute) value - * - * @version $Revision$ $Date$ - */ -public class NoValueColour implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * The None type - */ - public static final int NONE_TYPE = 0; - - /** - * The instance of the None type - */ - public static final NoValueColour NONE = new NoValueColour(NONE_TYPE, - "None"); - - /** - * The Min type - */ - public static final int MIN_TYPE = 1; - - /** - * The instance of the Min type - */ - public static final NoValueColour MIN = new NoValueColour(MIN_TYPE, - "Min"); - - /** - * The Max type - */ - public static final int MAX_TYPE = 2; - - /** - * The instance of the Max type - */ - public static final NoValueColour MAX = new NoValueColour(MAX_TYPE, - "Max"); - - /** - * Field _memberTable. - */ - private static java.util.Hashtable _memberTable = init(); - - /** - * Field type. - */ - private int type = -1; - - /** - * Field stringValue. - */ - private java.lang.String stringValue = null; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - private NoValueColour(final int type, final java.lang.String value) - { - super(); - this.type = type; - this.stringValue = value; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method enumerate.Returns an enumeration of all possible instances of - * NoValueColour - * - * @return an Enumeration over all possible instances of NoValueColour - */ - public static java.util.Enumeration enumerate() - { - return _memberTable.elements(); - } - - /** - * Method getType.Returns the type of this NoValueColour - * - * @return the type of this NoValueColour - */ - public int getType() - { - return this.type; - } - - /** - * Method init. - * - * @return the initialized Hashtable for the member table - */ - private static java.util.Hashtable init() - { - Hashtable members = new Hashtable(); - members.put("None", NONE); - members.put("Min", MIN); - members.put("Max", MAX); - return members; - } - - /** - * Method readResolve. will be called during deserialization to replace the - * deserialized object with the correct constant instance. - * - * @return this deserialized object - */ - private java.lang.Object readResolve() - { - return valueOf(this.stringValue); - } - - /** - * Method toString.Returns the String representation of this NoValueColour - * - * @return the String representation of this NoValueColour - */ - public java.lang.String toString() - { - return this.stringValue; - } - - /** - * Method valueOf.Returns a new NoValueColour based on the given String value. - * - * @param string - * @return the NoValueColour value of parameter 'string' - */ - public static jalview.schemabinding.version2.types.NoValueColour valueOf( - final java.lang.String string) - { - java.lang.Object obj = null; - if (string != null) - { - obj = _memberTable.get(string); - } - if (obj == null) - { - String err = "" + string + " is not a valid NoValueColour"; - throw new IllegalArgumentException(err); - } - return (NoValueColour) obj; - } - -} diff --git a/src/jalview/schemabinding/version2/types/descriptors/ColourThreshTypeTypeDescriptor.java b/src/jalview/schemabinding/version2/types/descriptors/ColourThreshTypeTypeDescriptor.java deleted file mode 100644 index f978363..0000000 --- a/src/jalview/schemabinding/version2/types/descriptors/ColourThreshTypeTypeDescriptor.java +++ /dev/null @@ -1,150 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.types.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.types.ColourThreshTypeType; - -/** - * Class ColourThreshTypeTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ColourThreshTypeTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ColourThreshTypeTypeDescriptor() { - super(); - _nsURI = "www.jalview.org/colours"; - _xmlName = "ColourThreshTypeType"; - _elementDefinition = false; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.types.ColourThreshTypeType.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/types/descriptors/FeatureMatcherByTypeDescriptor.java b/src/jalview/schemabinding/version2/types/descriptors/FeatureMatcherByTypeDescriptor.java deleted file mode 100644 index e392e76..0000000 --- a/src/jalview/schemabinding/version2/types/descriptors/FeatureMatcherByTypeDescriptor.java +++ /dev/null @@ -1,150 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.types.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.types.FeatureMatcherByType; - -/** - * Class FeatureMatcherByTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcherByTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public FeatureMatcherByTypeDescriptor() { - super(); - _nsURI = "www.jalview.org/colours"; - _xmlName = "FeatureMatcherByType"; - _elementDefinition = false; - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.types.FeatureMatcherByType.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemabinding/version2/types/descriptors/NoValueColourDescriptor.java b/src/jalview/schemabinding/version2/types/descriptors/NoValueColourDescriptor.java deleted file mode 100644 index 14c58ed..0000000 --- a/src/jalview/schemabinding/version2/types/descriptors/NoValueColourDescriptor.java +++ /dev/null @@ -1,147 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.types.descriptors; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.types.NoValueColour; - -/** - * Class NoValueColourDescriptor. - * - * @version $Revision$ $Date$ - */ -public class NoValueColourDescriptor - extends org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public NoValueColourDescriptor() - { - super(); - _nsURI = "www.jalview.org/colours"; - _xmlName = "NoValueColour"; - _elementDefinition = false; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.types.NoValueColour.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } - -} diff --git a/src/jalview/schemes/ColourSchemeLoader.java b/src/jalview/schemes/ColourSchemeLoader.java index 481f809..141ef10 100644 --- a/src/jalview/schemes/ColourSchemeLoader.java +++ b/src/jalview/schemes/ColourSchemeLoader.java @@ -114,34 +114,9 @@ public class ColourSchemeLoader } } catch (Exception ex) { - // Could be old Jalview Archive format - try - { - InputStreamReader in = new InputStreamReader( - new FileInputStream(file), "UTF-8"); - - jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours(); - - jucs = jalview.binding.JalviewUserColours.unmarshal(in); - - newColours = new Color[jucs.getColourCount()]; - - for (int i = 0; i < 24; i++) - { - newColours[i] = new Color( - Integer.parseInt(jucs.getColour(i).getRGB(), 16)); - } - ucs = new UserColourScheme(newColours); - ucs.setName(jucs.getSchemeName()); - } catch (Exception ex2) - { - ex2.printStackTrace(); - } - - if (newColours == null) - { - System.out.println("Error loading User ColourFile\n" + ex); - } + // used to try to parse a V1 Castor generated colours file + System.err.println("Failed to read colour scheme from " + filePath + + " : " + ex.toString()); } return ucs; diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index b0aaab9..bdda48d 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -38,7 +38,7 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; import jalview.io.FileLoader; -import jalview.io.Jalview2xmlTests; +import jalview.project.Jalview2xmlTests; import jalview.renderer.ResidueShaderI; import jalview.schemes.BuriedColourScheme; import jalview.schemes.FeatureColour; diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index 2b8a62f..53a0acb 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -29,8 +29,8 @@ import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.CrossRefAction; import jalview.gui.Desktop; -import jalview.gui.Jalview2XML; import jalview.gui.JvOptionPane; +import jalview.project.Jalview2XML; import jalview.util.DBRefUtils; import java.io.File; @@ -41,13 +41,13 @@ import java.util.HashMap; import java.util.List; import java.util.Map; -import junit.extensions.PA; - import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import junit.extensions.PA; + @Test(singleThreaded = true) public class CrossRef2xmlTests extends Jalview2xmlBase { diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java deleted file mode 100644 index 53bb0e7..0000000 --- a/test/jalview/io/Jalview2xmlTests.java +++ /dev/null @@ -1,1038 +0,0 @@ -/* - * 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. - */ -package jalview.io; - -import static org.testng.Assert.assertEquals; -import static org.testng.Assert.assertFalse; -import static org.testng.Assert.assertNotNull; -import static org.testng.Assert.assertNull; -import static org.testng.Assert.assertSame; -import static org.testng.Assert.assertTrue; - -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureColourI; -import jalview.api.ViewStyleI; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenSequences; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.PDBEntry.Type; -import jalview.datamodel.SequenceCollectionI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.datamodel.features.FeatureMatcher; -import jalview.datamodel.features.FeatureMatcherSet; -import jalview.datamodel.features.FeatureMatcherSetI; -import jalview.gui.AlignFrame; -import jalview.gui.AlignViewport; -import jalview.gui.AlignmentPanel; -import jalview.gui.Desktop; -import jalview.gui.FeatureRenderer; -import jalview.gui.Jalview2XML; -import jalview.gui.JvOptionPane; -import jalview.gui.PopupMenu; -import jalview.gui.SliderPanel; -import jalview.renderer.ResidueShaderI; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.FeatureColour; -import jalview.schemes.JalviewColourScheme; -import jalview.schemes.RNAHelicesColour; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TCoffeeColourScheme; -import jalview.structure.StructureImportSettings; -import jalview.util.matcher.Condition; -import jalview.viewmodel.AlignmentViewport; - -import java.awt.Color; -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.testng.Assert; -import org.testng.AssertJUnit; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - -@Test(singleThreaded = true) -public class Jalview2xmlTests extends Jalview2xmlBase -{ - - @Override - @BeforeClass(alwaysRun = true) - public void setUpJvOptionPane() - { - JvOptionPane.setInteractiveMode(false); - JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); - } - - @Test(groups = { "Functional" }) - public void testRNAStructureRecovery() throws Exception - { - String inFile = "examples/RF00031_folded.stk"; - String tfile = File.createTempFile("JalviewTest", ".jvp") - .getAbsolutePath(); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, - DataSourceType.FILE); - assertNotNull(af, "Didn't read input file " + inFile); - int olddsann = countDsAnn(af.getViewport()); - assertTrue(olddsann > 0, "Didn't find any dataset annotations"); - af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices - .toString()); - assertTrue( - af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, - "Couldn't apply RNA helices colourscheme"); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), - "Failed to store as a project."); - af.closeMenuItem_actionPerformed(true); - af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); - assertNotNull(af, "Failed to import new project"); - int newdsann = countDsAnn(af.getViewport()); - assertEquals(olddsann, newdsann, - "Differing numbers of dataset sequence annotation\nOriginally " - + olddsann + " and now " + newdsann); - System.out - .println("Read in same number of annotations as originally present (" - + olddsann + ")"); - assertTrue( - - af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, - "RNA helices colourscheme was not applied on import."); - } - - @Test(groups = { "Functional" }) - public void testTCoffeeScores() throws Exception - { - String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii"; - String tfile = File.createTempFile("JalviewTest", ".jvp") - .getAbsolutePath(); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, - DataSourceType.FILE); - assertNotNull(af, "Didn't read input file " + inFile); - af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); - assertSame(af.getViewport().getGlobalColourScheme().getClass(), - TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme"); - assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport() - .getAlignment(), af.getViewport().getGlobalColourScheme() - .getSchemeName()), "Recognise T-Coffee score from string"); - - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), - "Failed to store as a project."); - af.closeMenuItem_actionPerformed(true); - af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); - assertNotNull(af, "Failed to import new project"); - assertSame(af.getViewport().getGlobalColourScheme().getClass(), - TCoffeeColourScheme.class, - "Didn't set T-coffee colourscheme for imported project."); - System.out - .println("T-Coffee score shading successfully recovered from project."); - } - - @Test(groups = { "Functional" }) - public void testColourByAnnotScores() throws Exception - { - String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva"; - String tfile = File.createTempFile("JalviewTest", ".jvp") - .getAbsolutePath(); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, - DataSourceType.FILE); - assertNotNull(af, "Didn't read input file " + inFile); - af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); - AlignmentAnnotation[] aa = af.getViewport().getAlignment() - .getSequenceAt(0).getAnnotation("IUPredWS (Short)"); - assertTrue( - - aa != null && aa.length > 0, - "Didn't find any IUPred annotation to use to shade alignment."); - AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null, - AnnotationColourGradient.ABOVE_THRESHOLD); - AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], - null, AnnotationColourGradient.BELOW_THRESHOLD); - cs.setSeqAssociated(true); - gcs.setSeqAssociated(true); - af.changeColour(cs); - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(57); - sg.setEndRes(92); - sg.cs.setColourScheme(gcs); - af.getViewport().getAlignment().addGroup(sg); - sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false); - sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); - af.alignPanel.alignmentChanged(); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), - "Failed to store as a project."); - af.closeMenuItem_actionPerformed(true); - af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); - assertNotNull(af, "Failed to import new project"); - - // check for group and alignment colourschemes - - ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme(); - ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups() - .get(0).getColourScheme(); - assertNotNull(_rcs, "Didn't recover global colourscheme"); - assertTrue(_rcs instanceof AnnotationColourGradient, - "Didn't recover annotation colour global scheme"); - AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs; - assertTrue(__rcs.isSeqAssociated(), - "Annotation colourscheme wasn't sequence associated"); - - boolean diffseqcols = false, diffgseqcols = false; - SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); - for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) - { - if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs - .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) - { - diffseqcols = true; - } - } - assertTrue(diffseqcols, "Got Different sequence colours"); - System.out - .println("Per sequence colourscheme (Background) successfully applied and recovered."); - - assertNotNull(_rgcs, "Didn't recover group colourscheme"); - assertTrue(_rgcs instanceof AnnotationColourGradient, - "Didn't recover annotation colour group colourscheme"); - __rcs = (AnnotationColourGradient) _rgcs; - assertTrue(__rcs.isSeqAssociated(), - "Group Annotation colourscheme wasn't sequence associated"); - - for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) - { - if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs - .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f)) - { - diffgseqcols = true; - } - } - assertTrue(diffgseqcols, "Got Different group sequence colours"); - System.out - .println("Per sequence (Group) colourscheme successfully applied and recovered."); - } - - @Test(groups = { "Functional" }) - public void gatherViewsHere() throws Exception - { - int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop - .getAlignFrames().length; - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertNotNull(af, "Didn't read in the example file correctly."); - assertTrue(Desktop.getAlignFrames().length == 1 + origCount, - "Didn't gather the views in the example file."); - - } - - /** - * Test for JAL-2223 - multiple mappings in View Mapping report - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void noDuplicatePdbMappingsMade() throws Exception - { - StructureImportSettings.setProcessSecondaryStructure(true); - StructureImportSettings.setVisibleChainAnnotation(true); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertNotNull(af, "Didn't read in the example file correctly."); - - // locate Jmol viewer - // count number of PDB mappings the structure selection manager holds - - String pdbFile = af.getCurrentView().getStructureSelectionManager() - .findFileForPDBId("1A70"); - assertEquals( - af.getCurrentView().getStructureSelectionManager() - .getMapping(pdbFile).length, - 2, "Expected only two mappings for 1A70"); - - } - - @Test(groups = { "Functional" }) - public void viewRefPdbAnnotation() throws Exception - { - StructureImportSettings.setProcessSecondaryStructure(true); - StructureImportSettings.setVisibleChainAnnotation(true); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertNotNull(af, "Didn't read in the example file correctly."); - AlignmentViewPanel sps = null; - for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) - { - if ("Spinach Feredoxin Structure".equals(ap.getViewName())) - { - sps = ap; - break; - } - } - assertNotNull(sps, "Couldn't find the structure view"); - AlignmentAnnotation refan = null; - for (AlignmentAnnotation ra : sps.getAlignment() - .getAlignmentAnnotation()) - { - if (ra.graph != 0) - { - refan = ra; - break; - } - } - assertNotNull(refan, "Annotation secondary structure not found."); - SequenceI sq = sps.getAlignment().findName("1A70|"); - assertNotNull(sq, "Couldn't find 1a70 null chain"); - // compare the manually added temperature factor annotation - // to the track automatically transferred from the pdb structure on load - assertNotNull(sq.getDatasetSequence().getAnnotation(), - "1a70 has no annotation"); - for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation()) - { - AlignmentAnnotation alaa; - sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala)); - alaa.adjustForAlignment(); - if (ala.graph == refan.graph) - { - for (int p = 0; p < ala.annotations.length; p++) - { - sq.findPosition(p); - try - { - assertTrue( - (alaa.annotations[p] == null && refan.annotations[p] == null) - || alaa.annotations[p].value == refan.annotations[p].value, - "Mismatch at alignment position " + p); - } catch (NullPointerException q) - { - Assert.fail("Mismatch of alignment annotations at position " - + p + " Ref seq ann: " + refan.annotations[p] - + " alignment " + alaa.annotations[p]); - } - } - } - } - - } - - @Test(groups = { "Functional" }) - public void testCopyViewSettings() throws Exception - { - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertNotNull(af, "Didn't read in the example file correctly."); - AlignmentViewPanel sps = null, groups = null; - for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) - { - if ("Spinach Feredoxin Structure".equals(ap.getViewName())) - { - sps = ap; - } - if (ap.getViewName().contains("MAFFT")) - { - groups = ap; - } - } - assertNotNull(sps, "Couldn't find the structure view"); - assertNotNull(groups, "Couldn't find the MAFFT view"); - - ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle(); - ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle(); - AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle)); - - groups.getAlignViewport().setViewStyle(structureStyle); - AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport() - .getViewStyle())); - Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport() - .getViewStyle())); - - } - - /** - * test store and recovery of expanded views - * - * @throws Exception - */ - @Test(groups = { "Functional" }, enabled = true) - public void testStoreAndRecoverExpandedviews() throws Exception - { - Desktop.instance.closeAll_actionPerformed(null); - - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", DataSourceType.FILE); - Assert.assertEquals(Desktop.getAlignFrames().length, 1); - String afid = af.getViewport().getSequenceSetId(); - - // check FileLoader returned a reference to the one alignFrame that is - // actually on the Desktop - assertSame( - af, - Desktop.getAlignFrameFor(af.getViewport()), - "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window"); - - Desktop.explodeViews(af); - - int oldviews = Desktop.getAlignFrames().length; - Assert.assertEquals(Desktop.getAlignFrames().length, - Desktop.getAlignmentPanels(afid).length); - File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp"); - try - { - new Jalview2XML(false).saveState(tfile); - } catch (Error e) - { - Assert.fail("Didn't save the expanded view state", e); - } catch (Exception e) - { - Assert.fail("Didn't save the expanded view state", e); - } - Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) - { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); - } - af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), - DataSourceType.FILE); - Assert.assertNotNull(af); - Assert.assertEquals( - Desktop.getAlignFrames().length, - Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); - Assert.assertEquals( - Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length, - oldviews); - } - - /** - * Test save and reload of a project with a different representative sequence - * in each view. - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testStoreAndRecoverReferenceSeqSettings() throws Exception - { - Desktop.instance.closeAll_actionPerformed(null); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertNotNull(af, "Didn't read in the example file correctly."); - String afid = af.getViewport().getSequenceSetId(); - - // remember reference sequence for each panel - Map refseqs = new HashMap<>(); - - /* - * mark sequence 2, 3, 4.. in panels 1, 2, 3... - * as reference sequence for itself and the preceding sequence - */ - int n = 1; - for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) - { - AlignViewportI av = ap.getAlignViewport(); - AlignmentI alignment = ap.getAlignment(); - int repIndex = n % alignment.getHeight(); - SequenceI rep = alignment.getSequenceAt(repIndex); - refseqs.put(ap.getViewName(), rep); - - // code from mark/unmark sequence as reference in jalview.gui.PopupMenu - // todo refactor this to an alignment view controller - av.setDisplayReferenceSeq(true); - av.setColourByReferenceSeq(true); - av.getAlignment().setSeqrep(rep); - - n++; - } - File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq", - ".jvp"); - try - { - new Jalview2XML(false).saveState(tfile); - } catch (Throwable e) - { - Assert.fail("Didn't save the expanded view state", e); - } - Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) - { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); - } - - af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), - DataSourceType.FILE); - afid = af.getViewport().getSequenceSetId(); - - for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) - { - // check representative - AlignmentI alignment = ap.getAlignment(); - SequenceI rep = alignment.getSeqrep(); - Assert.assertNotNull(rep, - "Couldn't restore sequence representative from project"); - // can't use a strong equals here, because by definition, the sequence IDs - // will be different. - // could set vamsas session save/restore flag to preserve IDs across - // load/saves. - Assert.assertEquals(refseqs.get(ap.getViewName()).toString(), - rep.toString(), - "Representative wasn't the same when recovered."); - Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(), - "Display reference sequence view setting not set."); - Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(), - "Colour By Reference Seq view setting not set."); - } - } - - @Test(groups = { "Functional" }) - public void testIsVersionStringLaterThan() - { - /* - * No version / development / test / autobuild is leniently assumed to be - * compatible - */ - assertTrue(Jalview2XML.isVersionStringLaterThan(null, null)); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null)); - assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3")); - assertTrue(Jalview2XML.isVersionStringLaterThan(null, - "Development Build")); - assertTrue(Jalview2XML.isVersionStringLaterThan(null, - "DEVELOPMENT BUILD")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", - "Development Build")); - assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test")); - assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test")); - assertTrue(Jalview2XML - .isVersionStringLaterThan(null, "Automated Build")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", - "Automated Build")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", - "AUTOMATED BUILD")); - - /* - * same version returns true i.e. compatible - */ - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1")); - - /* - * later version returns true - */ - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3")); - assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1")); - - /* - * earlier version returns false - */ - assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8")); - assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3")); - assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3")); - assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1")); - assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1")); - } - - /** - * Test save and reload of a project with a different sequence group (and - * representative sequence) in each view. - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testStoreAndRecoverGroupRepSeqs() throws Exception - { - Desktop.instance.closeAll_actionPerformed(null); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/uniref50.fa", DataSourceType.FILE); - assertNotNull(af, "Didn't read in the example file correctly."); - String afid = af.getViewport().getSequenceSetId(); - // make a second view of the alignment - af.newView_actionPerformed(null); - - /* - * remember representative and hidden sequences marked - * on each panel - */ - Map repSeqs = new HashMap<>(); - Map> hiddenSeqNames = new HashMap<>(); - - /* - * mark sequence 2, 3, 4.. in panels 1, 2, 3... - * as reference sequence for itself and the preceding sequence - */ - int n = 1; - for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) - { - AlignViewportI av = ap.getAlignViewport(); - AlignmentI alignment = ap.getAlignment(); - int repIndex = n % alignment.getHeight(); - // ensure at least one preceding sequence i.e. index >= 1 - repIndex = Math.max(repIndex, 1); - SequenceI repSeq = alignment.getSequenceAt(repIndex); - repSeqs.put(ap.getViewName(), repSeq); - List hiddenNames = new ArrayList<>(); - hiddenSeqNames.put(ap.getViewName(), hiddenNames); - - /* - * have rep sequence represent itself and the one before it - * this hides the group (except for the rep seq) - */ - SequenceGroup sg = new SequenceGroup(); - sg.addSequence(repSeq, false); - SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1); - sg.addSequence(precedingSeq, false); - sg.setSeqrep(repSeq); - assertTrue(sg.getSequences().contains(repSeq)); - assertTrue(sg.getSequences().contains(precedingSeq)); - av.setSelectionGroup(sg); - assertSame(repSeq, sg.getSeqrep()); - - /* - * represent group with sequence adds to a map of hidden rep sequences - * (it does not create a group on the alignment) - */ - ((AlignmentViewport) av).hideSequences(repSeq, true); - assertSame(repSeq, sg.getSeqrep()); - assertTrue(sg.getSequences().contains(repSeq)); - assertTrue(sg.getSequences().contains(precedingSeq)); - assertTrue(alignment.getGroups().isEmpty(), "alignment has groups"); - Map hiddenRepSeqsMap = av - .getHiddenRepSequences(); - assertNotNull(hiddenRepSeqsMap); - assertEquals(1, hiddenRepSeqsMap.size()); - assertSame(sg, hiddenRepSeqsMap.get(repSeq)); - assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq)); - assertFalse(alignment.getHiddenSequences().isHidden(repSeq)); - hiddenNames.add(precedingSeq.getName()); - - n++; - } - File tfile = File - .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); - try - { - new Jalview2XML(false).saveState(tfile); - } catch (Throwable e) - { - Assert.fail("Didn't save the expanded view state", e); - } - Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) - { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); - } - - af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), - DataSourceType.FILE); - afid = af.getViewport().getSequenceSetId(); - - for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) - { - String viewName = ap.getViewName(); - AlignViewportI av = ap.getAlignViewport(); - AlignmentI alignment = ap.getAlignment(); - List groups = alignment.getGroups(); - assertNotNull(groups); - assertTrue(groups.isEmpty(), "Alignment has groups"); - Map hiddenRepSeqsMap = av - .getHiddenRepSequences(); - assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences"); - assertEquals(1, hiddenRepSeqsMap.size()); - assertEquals(repSeqs.get(viewName).getDisplayId(true), - hiddenRepSeqsMap.keySet().iterator().next() - .getDisplayId(true)); - - /* - * verify hidden sequences in restored panel - */ - List hidden = hiddenSeqNames.get(ap.getViewName()); - HiddenSequences hs = alignment.getHiddenSequences(); - assertEquals( - hidden.size(), - hs.getSize(), - "wrong number of restored hidden sequences in " - + ap.getViewName()); - } - } - - /** - * Test save and reload of PDBEntry in Jalview project - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testStoreAndRecoverPDBEntry() throws Exception - { - Desktop.instance.closeAll_actionPerformed(null); - String exampleFile = "examples/3W5V.pdb"; - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile, - DataSourceType.FILE); - assertNotNull(af, "Didn't read in the example file correctly."); - String afid = af.getViewport().getSequenceSetId(); - - AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid); - System.out.println(); - AlignmentViewPanel ap = alignPanels[0]; - String tfileBase = new File(".").getAbsolutePath().replace(".", ""); - String testFile = tfileBase + exampleFile; - AlignmentI alignment = ap.getAlignment(); - System.out.println("blah"); - SequenceI[] seqs = alignment.getSequencesArray(); - Assert.assertNotNull(seqs[0]); - Assert.assertNotNull(seqs[1]); - Assert.assertNotNull(seqs[2]); - Assert.assertNotNull(seqs[3]); - Assert.assertNotNull(seqs[0].getDatasetSequence()); - Assert.assertNotNull(seqs[1].getDatasetSequence()); - Assert.assertNotNull(seqs[2].getDatasetSequence()); - Assert.assertNotNull(seqs[3].getDatasetSequence()); - PDBEntry[] pdbEntries = new PDBEntry[4]; - pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile); - pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile); - pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile); - pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile); - Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[0]); - Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[1]); - Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[2]); - Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[3]); - - File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp"); - try - { - new Jalview2XML(false).saveState(tfile); - } catch (Throwable e) - { - Assert.fail("Didn't save the state", e); - } - Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) - { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); - } - - AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), DataSourceType.FILE); - String rfid = restoredFrame.getViewport().getSequenceSetId(); - AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid); - AlignmentViewPanel rap = rAlignPanels[0]; - AlignmentI rAlignment = rap.getAlignment(); - System.out.println("blah"); - SequenceI[] rseqs = rAlignment.getSequencesArray(); - Assert.assertNotNull(rseqs[0]); - Assert.assertNotNull(rseqs[1]); - Assert.assertNotNull(rseqs[2]); - Assert.assertNotNull(rseqs[3]); - Assert.assertNotNull(rseqs[0].getDatasetSequence()); - Assert.assertNotNull(rseqs[1].getDatasetSequence()); - Assert.assertNotNull(rseqs[2].getDatasetSequence()); - Assert.assertNotNull(rseqs[3].getDatasetSequence()); - - // The Asserts below are expected to fail until the PDB chainCode is - // recoverable from a Jalview projects - for (int chain = 0; chain < 4; chain++) - { - PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries() - .get(0); - PDBEntry expected = pdbEntries[chain]; - Assert.assertEquals(recov.getId(), expected.getId(), - "Mismatch PDB ID"); - Assert.assertEquals(recov.getChainCode(), expected.getChainCode(), - "Mismatch PDB ID"); - Assert.assertEquals(recov.getType(), expected.getType(), - "Mismatch PDBEntry 'Type'"); - Assert.assertNotNull(recov.getFile(), - "Recovered PDBEntry should have a non-null file entry"); - } - } - - /** - * Configure an alignment and a sub-group each with distinct colour schemes, - * Conservation and PID thresholds, and confirm these are restored from the - * saved project. - * - * @throws IOException - */ - @Test(groups = { "Functional" }) - public void testStoreAndRecoverColourThresholds() throws IOException - { - Desktop.instance.closeAll_actionPerformed(null); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/uniref50.fa", DataSourceType.FILE); - - AlignViewport av = af.getViewport(); - AlignmentI al = av.getAlignment(); - - /* - * Colour alignment by Buried Index, Above 10% PID, By Conservation 20% - */ - af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); - assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); - af.abovePIDThreshold_actionPerformed(true); - SliderPanel sp = SliderPanel.getSliderPanel(); - assertFalse(sp.isForConservation()); - sp.valueChanged(10); - af.conservationMenuItem_actionPerformed(true); - sp = SliderPanel.getSliderPanel(); - assertTrue(sp.isForConservation()); - sp.valueChanged(20); - ResidueShaderI rs = av.getResidueShading(); - assertEquals(rs.getThreshold(), 10); - assertTrue(rs.conservationApplied()); - assertEquals(rs.getConservationInc(), 20); - - /* - * create a group with Strand colouring, 30% Conservation - * and 40% PID threshold - */ - SequenceGroup sg = new SequenceGroup(); - sg.addSequence(al.getSequenceAt(0), false); - sg.setStartRes(15); - sg.setEndRes(25); - av.setSelectionGroup(sg); - PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); - popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand - .toString()); - assertTrue(sg.getColourScheme() instanceof StrandColourScheme); - assertEquals(al.getGroups().size(), 1); - assertSame(al.getGroups().get(0), sg); - popupMenu.conservationMenuItem_actionPerformed(true); - sp = SliderPanel.getSliderPanel(); - assertTrue(sp.isForConservation()); - sp.valueChanged(30); - popupMenu.abovePIDColour_actionPerformed(true); - sp = SliderPanel.getSliderPanel(); - assertFalse(sp.isForConservation()); - sp.valueChanged(40); - assertTrue(sg.getGroupColourScheme().conservationApplied()); - assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); - assertEquals(sg.getGroupColourScheme().getThreshold(), 40); - - /* - * save project, close windows, reload project, verify - */ - File tfile = File.createTempFile("testStoreAndRecoverColourThresholds", - ".jvp"); - tfile.deleteOnExit(); - new Jalview2XML(false).saveState(tfile); - Desktop.instance.closeAll_actionPerformed(null); - af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), - DataSourceType.FILE); - Assert.assertNotNull(af, "Failed to reload project"); - - /* - * verify alignment (background) colouring - */ - rs = af.getViewport().getResidueShading(); - assertTrue(rs.getColourScheme() instanceof BuriedColourScheme); - assertEquals(rs.getThreshold(), 10); - assertTrue(rs.conservationApplied()); - assertEquals(rs.getConservationInc(), 20); - - /* - * verify group colouring - */ - assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1); - rs = af.getViewport().getAlignment().getGroups().get(0) - .getGroupColourScheme(); - assertTrue(rs.getColourScheme() instanceof StrandColourScheme); - assertEquals(rs.getThreshold(), 40); - assertTrue(rs.conservationApplied()); - assertEquals(rs.getConservationInc(), 30); - } - - /** - * Test save and reload of feature colour schemes and filter settings - * - * @throws IOException - */ - @Test(groups = { "Functional" }) - public void testSaveLoadFeatureColoursAndFilters() throws IOException - { - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE); - SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0); - - /* - * add some features to the sequence - */ - int score = 1; - addFeatures(seq1, "type1", score++); - addFeatures(seq1, "type2", score++); - addFeatures(seq1, "type3", score++); - addFeatures(seq1, "type4", score++); - addFeatures(seq1, "type5", score++); - - /* - * set colour schemes for features - */ - FeatureRenderer fr = af.getFeatureRenderer(); - fr.findAllFeatures(true); - - // type1: red - fr.setColour("type1", new FeatureColour(Color.red)); - - // type2: by label - FeatureColourI byLabel = new FeatureColour(); - byLabel.setColourByLabel(true); - fr.setColour("type2", byLabel); - - // type3: by score above threshold - FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1, - 10); - byScore.setAboveThreshold(true); - byScore.setThreshold(2f); - fr.setColour("type3", byScore); - - // type4: by attribute AF - FeatureColourI byAF = new FeatureColour(); - byAF.setColourByLabel(true); - byAF.setAttributeName("AF"); - fr.setColour("type4", byAF); - - // type5: by attribute CSQ:PolyPhen below threshold - FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE, - 1, 10); - byPolyPhen.setBelowThreshold(true); - byPolyPhen.setThreshold(3f); - byPolyPhen.setAttributeName("CSQ", "PolyPhen"); - fr.setColour("type5", byPolyPhen); - - /* - * set filters for feature types - */ - - // filter type1 features by (label contains "x") - FeatureMatcherSetI filterByX = new FeatureMatcherSet(); - filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x")); - fr.setFeatureFilter("type1", filterByX); - - // filter type2 features by (score <= 2.4 and score > 1.1) - FeatureMatcherSetI filterByScore = new FeatureMatcherSet(); - filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4")); - filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1")); - fr.setFeatureFilter("type2", filterByScore); - - // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0) - FeatureMatcherSetI filterByXY = new FeatureMatcherSet(); - filterByXY - .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF")); - filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ", - "PolyPhen")); - fr.setFeatureFilter("type3", filterByXY); - - /* - * save as Jalview project - */ - File tfile = File.createTempFile("JalviewTest", ".jvp"); - tfile.deleteOnExit(); - String filePath = tfile.getAbsolutePath(); - assertTrue(af.saveAlignment(filePath, FileFormat.Jalview), - "Failed to store as a project."); - - /* - * close current alignment and load the saved project - */ - af.closeMenuItem_actionPerformed(true); - af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE); - assertNotNull(af, "Failed to import new project"); - - /* - * verify restored feature colour schemes and filters - */ - fr = af.getFeatureRenderer(); - FeatureColourI fc = fr.getFeatureStyle("type1"); - assertTrue(fc.isSimpleColour()); - assertEquals(fc.getColour(), Color.red); - fc = fr.getFeatureStyle("type2"); - assertTrue(fc.isColourByLabel()); - fc = fr.getFeatureStyle("type3"); - assertTrue(fc.isGraduatedColour()); - assertNull(fc.getAttributeName()); - assertTrue(fc.isAboveThreshold()); - assertEquals(fc.getThreshold(), 2f); - fc = fr.getFeatureStyle("type4"); - assertTrue(fc.isColourByLabel()); - assertTrue(fc.isColourByAttribute()); - assertEquals(fc.getAttributeName(), new String[] { "AF" }); - fc = fr.getFeatureStyle("type5"); - assertTrue(fc.isGraduatedColour()); - assertTrue(fc.isColourByAttribute()); - assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" }); - assertTrue(fc.isBelowThreshold()); - assertEquals(fc.getThreshold(), 3f); - - assertEquals(fr.getFeatureFilter("type1").toStableString(), - "Label Contains x"); - assertEquals(fr.getFeatureFilter("type2").toStableString(), - "(Score LE 2.4) AND (Score GT 1.1)"); - assertEquals(fr.getFeatureFilter("type3").toStableString(), - "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)"); - } - - private void addFeature(SequenceI seq, String featureType, int score) - { - SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2, - score, "grp"); - sf.setValue("AF", score); - sf.setValue("CSQ", new HashMap() - { - { - put("PolyPhen", Integer.toString(score)); - } - }); - seq.addSequenceFeature(sf); - } - - /** - * Adds two features of the given type to the given sequence, also setting the - * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen" - * - * @param seq - * @param featureType - * @param score - */ - private void addFeatures(SequenceI seq, String featureType, int score) - { - addFeature(seq, featureType, score++); - addFeature(seq, featureType, score); - } -} diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 089c29f..889c003 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -26,13 +26,13 @@ import static org.testng.AssertJUnit.assertTrue; import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.gui.Jalview2XML; import jalview.gui.JvOptionPane; import jalview.io.AnnotationFile; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.io.StockholmFileTest; +import jalview.project.Jalview2XML; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.RNAalifoldClient; import jalview.ws.jws2.SequenceAnnotationWSClient; @@ -118,7 +118,7 @@ public class RNAStructExportImport assertNotNull("Couldn't load test data ('" + testseqs + "')", af); // remove any existing annotation - List aal = new ArrayList(); + List aal = new ArrayList<>(); for (AlignmentAnnotation rna : af.getViewport().getAlignment() .getAlignmentAnnotation()) { @@ -259,7 +259,7 @@ public class RNAStructExportImport @Test(groups = { "Network" }) public void testRnaalifoldSettingsRecovery() { - List opts = new ArrayList(); + List opts = new ArrayList<>(); for (Argument rg : (List) rnaalifoldws.getRunnerConfig() .getArguments()) { diff --git a/utils/castor-1.1-cycle-codegen-anttask.jar b/utils/castor-1.1-cycle-codegen-anttask.jar deleted file mode 100644 index 5c59416..0000000 Binary files a/utils/castor-1.1-cycle-codegen-anttask.jar and /dev/null differ diff --git a/utils/castor-1.1-cycle-codegen.jar b/utils/castor-1.1-cycle-codegen.jar deleted file mode 100644 index 74ad927..0000000 Binary files a/utils/castor-1.1-cycle-codegen.jar and /dev/null differ