<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
<classpathentry kind="lib" path="lib/xercesImpl.jar"/>
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="output" path="classes"/>
</classpath>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<launchConfiguration type="org.eclipse.ant.AntBuilderLaunchConfigurationType">
+<stringAttribute key="process_factory_id" value="org.eclipse.ant.ui.remoteAntProcessFactory"/>
+<booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="true"/>
+<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.eclipse.ant.internal.ui.antsupport.InternalAntRunner"/>
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.ui.externaltools.launchGroup"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
+<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="/homes/jimp/prj/eclipse/VamsasClient"/>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_INSTALL_TYPE_ID" value="org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType"/>
+<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry type="4" path="1" containerPath="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry id="org.eclipse.ant.ui.classpathentry.antHome"> <memento default="true"/> </runtimeClasspathEntry> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry type="2" path="3" internalArchive="/VamsasClient/tools/castor-0.9.9M2-srcgen-ant-task.jar"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry type="2" path="3" internalArchive="/VamsasClient/lib/castor-0.9.9M2-xml.jar"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry type="2" path="3" internalArchive="/VamsasClient/lib/castor-0.9.9M2.jar"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry id="org.eclipse.ant.ui.classpathentry.extraClasspathEntries"> <memento/> </runtimeClasspathEntry> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry type="2" path="3" internalArchive="/VamsasClient/lib/log4j-1.2.8.jar"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry type="2" path="3" internalArchive="/VamsasClient/lib/xercesImpl.jar"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry type="2" path="3" internalArchive="/VamsasClient/lib/xml-apis.jar"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8"?> <runtimeClasspathEntry type="2" path="3" internalArchive="/VamsasClient/tools/commons-logging.jar"/> "/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.launching.VM_INSTALL_NAME" value="jdk"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="VamsasClient"/>
+<stringAttribute key="org.eclipse.debug.core.ATTR_REFRESH_SCOPE" value="${working_set:<?xml version="1.0" encoding="UTF-8"?> <launchConfigurationWorkingSet factoryID="org.eclipse.ui.internal.WorkingSetFactory" name="working set" editPageId="org.eclipse.ui.resourceWorkingSetPage"> <item factoryID="org.eclipse.ui.internal.model.ResourceFactory" path="/VamsasClient/src/org/vamsas/objects" type="2"/> </launchConfigurationWorkingSet> }"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${workspace_loc:/VamsasClient/build.xml}"/>
+</launchConfiguration>
<arguments>
<dictionary>
<key>LaunchConfigHandle</key>
- <value><project>/.externalToolBuilders/org.eclipse.jdt.core.javabuilder.launch</value>
- </dictionary>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
- <triggers>full,incremental,</triggers>
- <arguments>
- <dictionary>
- <key>LaunchConfigHandle</key>
<value><project>/.externalToolBuilders/Build VamsasClient [Builder].launch</value>
</dictionary>
</arguments>
-#Mon Sep 19 20:49:22 BST 2005
+#Tue Sep 20 11:30:35 BST 2005
eclipse.preferences.version=1
org.eclipse.jdt.core.codeComplete.argumentPrefixes=
org.eclipse.jdt.core.codeComplete.argumentSuffixes=
org.eclipse.jdt.core.codeComplete.localSuffixes=
org.eclipse.jdt.core.codeComplete.staticFieldPrefixes=
org.eclipse.jdt.core.codeComplete.staticFieldSuffixes=
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=disabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.2
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.4
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=warning
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=warning
+org.eclipse.jdt.core.compiler.source=1.3
org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=16
-#Mon Sep 19 20:49:22 BST 2005
+#Tue Sep 20 11:34:19 BST 2005
eclipse.preferences.version=1
formatter_settings_version=8
+internal.default.compliance=default
org.eclipse.jdt.ui.exception.name=e
org.eclipse.jdt.ui.gettersetter.use.is=true
org.eclipse.jdt.ui.javadoc=false
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
+http://www.vamsas.ac.uk/build/VamsasClient/schemas/vamsas.xsd">
+ <SequenceSet>
+ <Sequence start="1" end="167" id="a1127235554296">
+ <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
+ <name>Q899P0</name>
+ </Sequence>
+ <Sequence start="1" end="168" id="a1127235554297">
+ <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL</sequence>
+ <name>Q972M3</name>
+ </Sequence>
+ <Sequence start="1" end="167" id="a1127235554298">
+ <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
+ <name>Q81M93</name>
+ </Sequence>
+ <Sequence start="1" end="167" id="a1127235554299">
+ <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
+ <name>NODG_AZOBR</name>
+ </Sequence>
+ <Sequence start="1" end="166" id="a1127235554300">
+ <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
+ <name>Q8PS57</name>
+ </Sequence>
+ <Sequence start="1" end="167" id="a1127235554301">
+ <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
+ <name>Q8A195</name>
+ </Sequence>
+ <Sequence start="1" end="164" id="a1127235554302">
+ <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD</sequence>
+ <name>Q888G8</name>
+ </Sequence>
+ <Sequence start="1" end="164" id="a1127235554303">
+ <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD</sequence>
+ <name>Q9KRP5</name>
+ </Sequence>
+ <Sequence start="1" end="163" id="a1127235554304">
+ <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
+ <name>Q87N22</name>
+ </Sequence>
+ <Alignment gapChar="-">
+ <alignmentSequence start="1" end="167" refid="a1127235554296">
+ <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
+ <name>Q899P0</name>
+ </alignmentSequence>
+ <alignmentSequence start="1" end="168" refid="a1127235554297">
+ <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDEL--RKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWL-GNIGQANYSAAKAGVIGFTKTLAREL</sequence>
+ <name>Q972M3</name>
+ </alignmentSequence>
+ <alignmentSequence start="1" end="167" refid="a1127235554298">
+ <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKL--KALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGR--IDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
+ <name>Q81M93</name>
+ </alignmentSequence>
+ <alignmentSequence start="1" end="167" refid="a1127235554299">
+ <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALG--FKFYVAEGDVSDFESCKAMVAKIEADLGP--VDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
+ <name>NODG_AZOBR</name>
+ </alignmentSequence>
+ <alignmentSequence start="1" end="166" refid="a1127235554300">
+ <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDI--RETARMVEKEG-RKALPVSTDIRVEEDVENMISEAVDAFGR--IDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
+ <name>Q8PS57</name>
+ </alignmentSequence>
+ <alignmentSequence start="1" end="167" refid="a1127235554301">
+ <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMG--VKAKGYASNAANFEDTAKVVEEIHKDFGR--IDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
+ <name>Q8A195</name>
+ </alignmentSequence>
+ <alignmentSequence start="1" end="164" refid="a1127235554302">
+ <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKL--AKVAAQLKG---AEHLIRATDVADLTDVEALFKEVAERFGR--LDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD-</sequence>
+ <name>Q888G8</name>
+ </alignmentSequence>
+ <alignmentSequence start="1" end="164" refid="a1127235554303">
+ <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQL--AIVIEQFDS---ARVYAQKVDVSDPEQVQALVRKTVERFGR--LDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD-</sequence>
+ <name>Q9KRP5</name>
+ </alignmentSequence>
+ <alignmentSequence start="1" end="163" refid="a1127235554304">
+ <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGA--AAISEYLG----ENGKGLALNVTDVESIEATLKAINDEFGA--IDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
+ <name>Q87N22</name>
+ </alignmentSequence>
+ <Provenance>
+ <entry>
+ <User>jim</User>
+ <Action>edited</Action>
+ <Date>2005-12-21</Date>
+ </entry>
+ </Provenance>
+ </Alignment>
+ </SequenceSet>
+</VAMSAS>
<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:element name="Version" type="xs:string"/>
- <xs:annotation>
- <xs:documentation>DESCRIPTION</xs:documentation>
+ <xs:annotation>
+ <xs:documentation>Vamsas Document Version Number</xs:documentation>
</xs:annotation>
-
- <xs:complexType name="LockFile">
- <xs:simpleContent>
- <xs:extension base="xs:string"/>
- </xs:simpleContent>
- </xs:complexType>
+ <xs:element name="LockFile">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
<xs:element name="VAMSAS">
- <xs:complexType>
-
- <xs:sequence>
- <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Tree">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="newick" minOccurs="1" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="title" type="xs:string" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
</xs:complexType>
- </xs:element>
- <xs:element name="Tree">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
- <xs:element name="newick" minOccurs="1" maxOccurs="unbounded">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:string">
- <xs:attribute name="title" type="xs:string" use="optional"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
- </xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
- </xs:complexType>
</xs:element>
<xs:element name="Provenance">
<xs:complexType>
<xs:element name="Action" type="xs:string"/>
<xs:element name="Date" type="xs:date"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
-
<xs:element name="SequenceSet">
<xs:complexType>
<xs:sequence>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
<xs:sequence>
- <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="source"/>
- <xs:attribute name="version"/>
- <xs:attribute name="accessionId"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
- </xs:complexType>
+ <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="source"/>
+ <xs:attribute name="version"/>
+ <xs:attribute name="accessionId"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
+ </xs:complexType>
</xs:element>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="required"/>
+ <xs:attribute name="id" type="xs:ID" use="required"/>
<xs:attribute name="dictionary" type="xs:string"/>
</xs:extension>
</xs:complexContent>
<xs:attribute name="end" type="xs:string" use="required"/>
<xs:attribute name="begin" type="xs:string" use="required"/>
<xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
</xs:complexType>
</xs:element>
<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
<xs:attribute name="graph" type="xs:boolean" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
<xs:complexType>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
<xs:attribute name="refid" type="xs:IDREF" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:element>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="gapChar" type="xs:string" use="required"/>
+ <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
- <xs:attribute name="gapChar" type="xs:string" use="required"/>
- <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
</xs:complexType>
</xs:element>
<xs:element name="annotationElement">
<xs:element name="value" type="xs:float"/>
</xs:sequence>
<xs:attribute name="position" type="xs:int" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
</xs:complexType>
</xs:element>
- <xs:complexType name="SequenceType">
+ <xs:complexType name="SequenceType">
<xs:sequence>
<xs:element name="sequence" type="xs:string"/>
<xs:element name="name" type="xs:string"/>
<xs:attribute name="start" type="xs:int" use="required"/>
<xs:attribute name="end" type="xs:int" use="required"/>
</xs:complexType>
-
- <xs:complexType name="ApplicationData">
- <xs:sequence>
- <xs:element name="Application">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="User">
- <xs:complexType>
- <xs:attribute name="fullname" type="xs:string"/>
- <xs:attribute name="organization" type="xs:string"/>
- <xs:attribute name="data" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="name" type="xs:string"/>
- <xs:attribute name="urn" type="xs:string"/>
- <xs:attribute name="data" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:complexType>
+ <xs:element name="ApplicationData">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="Application">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="User">
+ <xs:complexType>
+ <xs:attribute name="fullname" type="xs:string"/>
+ <xs:attribute name="organization" type="xs:string"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="urn" type="xs:string"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
</xs:schema>
org.vamsas.objects.core.AnnotationElement=org.vamsas.objects.core.AnnotationEle...
org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ...
org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc...
-org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor
org.vamsas.objects.core.User=org.vamsas.objects.core.UserDescriptor
+org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor
org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn...
org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe...
org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor
//--------------------------/
/**
+ * Field _gapChar
+ */
+ private java.lang.String _gapChar;
+
+ /**
+ * Field _aligned
+ */
+ private boolean _aligned;
+
+ /**
+ * keeps track of state for field: _aligned
+ */
+ private boolean _has_aligned;
+
+ /**
* Field _id
*/
private java.lang.String _id;
} //-- void addTree(int, org.vamsas.objects.core.Tree)
/**
+ * Method deleteAligned
+ *
+ */
+ public void deleteAligned()
+ {
+ this._has_aligned= false;
+ } //-- void deleteAligned()
+
+ /**
* Method enumerateAlignmentSequence
*
*
if (obj instanceof Alignment) {
Alignment temp = (Alignment)obj;
+ if (this._gapChar != null) {
+ if (temp._gapChar == null) return false;
+ else if (!(this._gapChar.equals(temp._gapChar)))
+ return false;
+ }
+ else if (temp._gapChar != null)
+ return false;
+ if (this._aligned != temp._aligned)
+ return false;
+ if (this._has_aligned != temp._has_aligned)
+ return false;
if (this._id != null) {
if (temp._id == null) return false;
else if (!(this._id.equals(temp._id)))
} //-- boolean equals(java.lang.Object)
/**
+ * Returns the value of field 'aligned'.
+ *
+ * @return boolean
+ * @return the value of field 'aligned'.
+ */
+ public boolean getAligned()
+ {
+ return this._aligned;
+ } //-- boolean getAligned()
+
+ /**
* Returns the value of field 'alignmentAnnotations'.
*
* @return AlignmentAnnotations
} //-- int getAlignmentSequenceCount()
/**
+ * Returns the value of field 'gapChar'.
+ *
+ * @return String
+ * @return the value of field 'gapChar'.
+ */
+ public java.lang.String getGapChar()
+ {
+ return this._gapChar;
+ } //-- java.lang.String getGapChar()
+
+ /**
* Returns the value of field 'id'.
*
* @return String
} //-- int getTreeCount()
/**
+ * Method hasAligned
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasAligned()
+ {
+ return this._has_aligned;
+ } //-- boolean hasAligned()
+
+ /**
* Method isValid
*
*
} //-- org.vamsas.objects.core.Tree removeTree(int)
/**
+ * Sets the value of field 'aligned'.
+ *
+ * @param aligned the value of field 'aligned'.
+ */
+ public void setAligned(boolean aligned)
+ {
+ this._aligned = aligned;
+ this._has_aligned = true;
+ } //-- void setAligned(boolean)
+
+ /**
* Sets the value of field 'alignmentAnnotations'.
*
* @param alignmentAnnotations the value of field
} //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
/**
+ * Sets the value of field 'gapChar'.
+ *
+ * @param gapChar the value of field 'gapChar'.
+ */
+ public void setGapChar(java.lang.String gapChar)
+ {
+ this._gapChar = gapChar;
+ } //-- void setGapChar(java.lang.String)
+
+ /**
* Sets the value of field 'id'.
*
* @param id the value of field 'id'.
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
+ {
+ Alignment target = (Alignment) object;
+ return target.getGapChar();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Alignment target = (Alignment) 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
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _aligned
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Alignment target = (Alignment) object;
+ if(!target.hasAligned())
+ return null;
+ return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Alignment target = (Alignment) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteAligned();
+ return;
+ }
+ target.setAligned( ((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: _aligned
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ BooleanValidator typeValidator = new 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);
this.identity = desc;
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.Serializable;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Class ProvenanceItem.
- *
- * @version $Revision$ $Date$
- */
-public class ProvenanceItem implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _entry
- */
- private org.vamsas.objects.core.Entry _entry;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ProvenanceItem()
- {
- super();
- } //-- org.vamsas.objects.core.ProvenanceItem()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'entry'.
- *
- * @return Entry
- * @return the value of field 'entry'.
- */
- public org.vamsas.objects.core.Entry getEntry()
- {
- return this._entry;
- } //-- org.vamsas.objects.core.Entry getEntry()
-
- /**
- * Sets the value of field 'entry'.
- *
- * @param entry the value of field 'entry'.
- */
- public void setEntry(org.vamsas.objects.core.Entry entry)
- {
- this._entry = entry;
- } //-- void setEntry(org.vamsas.objects.core.Entry)
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class ProvenanceItemDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class ProvenanceItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field nsPrefix
- */
- private java.lang.String nsPrefix;
-
- /**
- * Field nsURI
- */
- private java.lang.String nsURI;
-
- /**
- * Field xmlName
- */
- private java.lang.String xmlName;
-
- /**
- * Field identity
- */
- private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ProvenanceItemDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "Provenance";
-
- //-- 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
-
- //-- _entry
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entry", "entry", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- ProvenanceItem target = (ProvenanceItem) object;
- return target.getEntry();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ProvenanceItem target = (ProvenanceItem) object;
- target.setEntry( (org.vamsas.objects.core.Entry) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Entry();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _entry
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.ProvenanceItemDescriptor()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode
- *
- *
- *
- * @return AccessMode
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
-
- /**
- * Method getExtends
- *
- *
- *
- * @return ClassDescriptor
- */
- public org.exolab.castor.mapping.ClassDescriptor getExtends()
- {
- return null;
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
-
- /**
- * Method getIdentity
- *
- *
- *
- * @return FieldDescriptor
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- return identity;
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
-
- /**
- * Method getJavaClass
- *
- *
- *
- * @return Class
- */
- public java.lang.Class getJavaClass()
- {
- return org.vamsas.objects.core.ProvenanceItem.class;
- } //-- java.lang.Class getJavaClass()
-
- /**
- * Method getNameSpacePrefix
- *
- *
- *
- * @return String
- */
- public java.lang.String getNameSpacePrefix()
- {
- return nsPrefix;
- } //-- java.lang.String getNameSpacePrefix()
-
- /**
- * Method getNameSpaceURI
- *
- *
- *
- * @return String
- */
- public java.lang.String getNameSpaceURI()
- {
- return nsURI;
- } //-- java.lang.String getNameSpaceURI()
-
- /**
- * Method getValidator
- *
- *
- *
- * @return TypeValidator
- */
- public org.exolab.castor.xml.TypeValidator getValidator()
- {
- return this;
- } //-- org.exolab.castor.xml.TypeValidator getValidator()
-
- /**
- * Method getXMLName
- *
- *
- *
- * @return String
- */
- public java.lang.String getXMLName()
- {
- return xmlName;
- } //-- java.lang.String getXMLName()
-
-}
}
};
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
}
desc.setValidator(fieldValidator);
//--------------------------/
/**
- * Field _gapChar
- */
- private java.lang.String _gapChar;
-
- /**
- * Field _aligned
- */
- private boolean _aligned;
-
- /**
- * keeps track of state for field: _aligned
- */
- private boolean _has_aligned;
-
- /**
* Field _id
*/
private java.lang.String _id;
} //-- void addTree(int, org.vamsas.objects.core.Tree)
/**
- * Method deleteAligned
- *
- */
- public void deleteAligned()
- {
- this._has_aligned= false;
- } //-- void deleteAligned()
-
- /**
* Method enumerateAlignment
*
*
if (obj instanceof SequenceSet) {
SequenceSet temp = (SequenceSet)obj;
- if (this._gapChar != null) {
- if (temp._gapChar == null) return false;
- else if (!(this._gapChar.equals(temp._gapChar)))
- return false;
- }
- else if (temp._gapChar != null)
- return false;
- if (this._aligned != temp._aligned)
- return false;
- if (this._has_aligned != temp._has_aligned)
- return false;
if (this._id != null) {
if (temp._id == null) return false;
else if (!(this._id.equals(temp._id)))
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'aligned'.
- *
- * @return boolean
- * @return the value of field 'aligned'.
- */
- public boolean getAligned()
- {
- return this._aligned;
- } //-- boolean getAligned()
-
- /**
* Method getAlignment
*
*
} //-- int getAlignmentCount()
/**
- * Returns the value of field 'gapChar'.
- *
- * @return String
- * @return the value of field 'gapChar'.
- */
- public java.lang.String getGapChar()
- {
- return this._gapChar;
- } //-- java.lang.String getGapChar()
-
- /**
* Returns the value of field 'id'.
*
* @return String
} //-- int getTreeCount()
/**
- * Method hasAligned
- *
- *
- *
- * @return boolean
- */
- public boolean hasAligned()
- {
- return this._has_aligned;
- } //-- boolean hasAligned()
-
- /**
* Method isValid
*
*
} //-- org.vamsas.objects.core.Tree removeTree(int)
/**
- * Sets the value of field 'aligned'.
- *
- * @param aligned the value of field 'aligned'.
- */
- public void setAligned(boolean aligned)
- {
- this._aligned = aligned;
- this._has_aligned = true;
- } //-- void setAligned(boolean)
-
- /**
* Method setAlignment
*
*
} //-- void setAlignment(org.vamsas.objects.core.Alignment)
/**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar the value of field 'gapChar'.
- */
- public void setGapChar(java.lang.String gapChar)
- {
- this._gapChar = gapChar;
- } //-- void setGapChar(java.lang.String)
-
- /**
* Sets the value of field 'id'.
*
* @param id the value of field 'id'.
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
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _aligned
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- if(!target.hasAligned())
- return null;
- return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAligned();
- return;
- }
- target.setAligned( ((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: _aligned
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- BooleanValidator typeValidator = new 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);
this.identity = desc;
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class TreeType.
- *
- * @version $Revision$ $Date$
- */
-public class TreeType extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _id
- */
- private java.lang.String _id;
-
- /**
- * Field _newickFormatList
- */
- private java.util.Vector _newickFormatList;
-
- /**
- * Field _provenance
- */
- private org.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public TreeType()
- {
- super();
- _newickFormatList = new Vector();
- } //-- org.vamsas.objects.core.TreeType()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addNewickFormat
- *
- *
- *
- * @param vNewickFormat
- */
- public void addNewickFormat(java.lang.String vNewickFormat)
- throws java.lang.IndexOutOfBoundsException
- {
- _newickFormatList.addElement(vNewickFormat);
- } //-- void addNewickFormat(java.lang.String)
-
- /**
- * Method addNewickFormat
- *
- *
- *
- * @param index
- * @param vNewickFormat
- */
- public void addNewickFormat(int index, java.lang.String vNewickFormat)
- throws java.lang.IndexOutOfBoundsException
- {
- _newickFormatList.insertElementAt(vNewickFormat, index);
- } //-- void addNewickFormat(int, java.lang.String)
-
- /**
- * Method enumerateNewickFormat
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateNewickFormat()
- {
- return _newickFormatList.elements();
- } //-- java.util.Enumeration enumerateNewickFormat()
-
- /**
- * Note: hashCode() has not been overriden
- *
- * @param obj
- * @return boolean
- */
- public boolean equals(java.lang.Object obj)
- {
- if ( this == obj )
- return true;
-
- if (super.equals(obj)==false)
- return false;
-
- if (obj instanceof TreeType) {
-
- TreeType temp = (TreeType)obj;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._newickFormatList != null) {
- if (temp._newickFormatList == null) return false;
- else if (!(this._newickFormatList.equals(temp._newickFormatList)))
- return false;
- }
- else if (temp._newickFormatList != null)
- return false;
- if (this._provenance != null) {
- if (temp._provenance == null) return false;
- else if (!(this._provenance.equals(temp._provenance)))
- return false;
- }
- else if (temp._provenance != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'id'.
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Method getNewickFormat
- *
- *
- *
- * @param index
- * @return String
- */
- public java.lang.String getNewickFormat(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _newickFormatList.size())) {
- throw new IndexOutOfBoundsException("getNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
- }
-
- return (String)_newickFormatList.elementAt(index);
- } //-- java.lang.String getNewickFormat(int)
-
- /**
- * Method getNewickFormat
- *
- *
- *
- * @return String
- */
- public java.lang.String[] getNewickFormat()
- {
- int size = _newickFormatList.size();
- java.lang.String[] mArray = new java.lang.String[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (String)_newickFormatList.elementAt(index);
- }
- return mArray;
- } //-- java.lang.String[] getNewickFormat()
-
- /**
- * Method getNewickFormatCount
- *
- *
- *
- * @return int
- */
- public int getNewickFormatCount()
- {
- return _newickFormatList.size();
- } //-- int getNewickFormatCount()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.objects.core.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.objects.core.Provenance getProvenance()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAllNewickFormat
- *
- */
- public void removeAllNewickFormat()
- {
- _newickFormatList.removeAllElements();
- } //-- void removeAllNewickFormat()
-
- /**
- * Method removeNewickFormat
- *
- *
- *
- * @param index
- * @return String
- */
- public java.lang.String removeNewickFormat(int index)
- {
- java.lang.Object obj = _newickFormatList.elementAt(index);
- _newickFormatList.removeElementAt(index);
- return (String)obj;
- } //-- java.lang.String removeNewickFormat(int)
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Method setNewickFormat
- *
- *
- *
- * @param index
- * @param vNewickFormat
- */
- public void setNewickFormat(int index, java.lang.String vNewickFormat)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _newickFormatList.size())) {
- throw new IndexOutOfBoundsException("setNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
- }
- _newickFormatList.setElementAt(vNewickFormat, index);
- } //-- void setNewickFormat(int, java.lang.String)
-
- /**
- * Method setNewickFormat
- *
- *
- *
- * @param newickFormatArray
- */
- public void setNewickFormat(java.lang.String[] newickFormatArray)
- {
- //-- copy array
- _newickFormatList.removeAllElements();
- for (int i = 0; i < newickFormatArray.length; i++) {
- _newickFormatList.addElement(newickFormatArray[i]);
- }
- } //-- void setNewickFormat(java.lang.String)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.objects.core.Provenance)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return TreeType
- */
- public static org.vamsas.objects.core.TreeType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.TreeType) Unmarshaller.unmarshal(org.vamsas.objects.core.TreeType.class, reader);
- } //-- org.vamsas.objects.core.TreeType unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class TreeTypeDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class TreeTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field nsPrefix
- */
- private java.lang.String nsPrefix;
-
- /**
- * Field nsURI
- */
- private java.lang.String nsURI;
-
- /**
- * Field xmlName
- */
- private java.lang.String xmlName;
-
- /**
- * Field identity
- */
- private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public TreeTypeDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "TreeType";
-
- //-- 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);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- TreeType target = (TreeType) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- TreeType target = (TreeType) 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
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _newickFormatList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormatList", "newickFormat", 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
- {
- TreeType target = (TreeType) object;
- return target.getNewickFormat();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- TreeType target = (TreeType) object;
- target.addNewickFormat( (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("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _newickFormatList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- TreeType target = (TreeType) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- TreeType target = (TreeType) object;
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Provenance();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _provenance
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.objects.core.TreeTypeDescriptor()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode
- *
- *
- *
- * @return AccessMode
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
-
- /**
- * Method getExtends
- *
- *
- *
- * @return ClassDescriptor
- */
- public org.exolab.castor.mapping.ClassDescriptor getExtends()
- {
- return null;
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
-
- /**
- * Method getIdentity
- *
- *
- *
- * @return FieldDescriptor
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- return identity;
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
-
- /**
- * Method getJavaClass
- *
- *
- *
- * @return Class
- */
- public java.lang.Class getJavaClass()
- {
- return org.vamsas.objects.core.TreeType.class;
- } //-- java.lang.Class getJavaClass()
-
- /**
- * Method getNameSpacePrefix
- *
- *
- *
- * @return String
- */
- public java.lang.String getNameSpacePrefix()
- {
- return nsPrefix;
- } //-- java.lang.String getNameSpacePrefix()
-
- /**
- * Method getNameSpaceURI
- *
- *
- *
- * @return String
- */
- public java.lang.String getNameSpaceURI()
- {
- return nsURI;
- } //-- java.lang.String getNameSpaceURI()
-
- /**
- * Method getValidator
- *
- *
- *
- * @return TypeValidator
- */
- public org.exolab.castor.xml.TypeValidator getValidator()
- {
- return this;
- } //-- org.exolab.castor.xml.TypeValidator getValidator()
-
- /**
- * Method getXMLName
- *
- *
- *
- * @return String
- */
- public java.lang.String getXMLName()
- {
- return xmlName;
- } //-- java.lang.String getXMLName()
-
-}
import java.awt.Event;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
+import java.io.IOException;
import java.util.Vector;
/**
* Toy vamsas command line client application demonstrating the API.
}
// get IClientFactory
- clientfactory = new org.vamsas.client.SimpleClientFactory(args[0]);
+ try {
+ clientfactory = new org.vamsas.client.SimpleClientFactory(args[0]);
+ } catch (IOException e) {
+ System.err.println(e+"\n"+Usage);
+ System.exit(1);
+ }
// get an Iclient with session data
app = new ClientHandle("org.vamsas.test.ExampleApplication","0.1");
git://source.jalview.org / vamsas.git / commitdiff