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Heiko Dietze
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‎OboGraphView/.classpath‎

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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="src" output="target/classes" path="src/main/java"/>
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<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
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<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
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<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
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<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
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<classpathentry kind="output" path="target/classes"/>
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</classpath>

‎OboGraphView/.project‎

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<?xml version="1.0" encoding="UTF-8"?>
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<projectDescription>
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<name>OboGraphView</name>
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<comment></comment>
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<projects>
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</projects>
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<buildSpec>
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<buildCommand>
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<name>org.eclipse.jdt.core.javabuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.m2e.core.maven2Builder</name>
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<arguments>
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</arguments>
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</buildCommand>
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</buildSpec>
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<natures>
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<nature>org.eclipse.jdt.core.javanature</nature>
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<nature>org.eclipse.m2e.core.maven2Nature</nature>
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</natures>
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</projectDescription>

‎OboGraphView/.settings/org.eclipse.jdt.core.prefs‎

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eclipse.preferences.version=1
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org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
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org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
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org.eclipse.jdt.core.compiler.compliance=1.6
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org.eclipse.jdt.core.compiler.debug.lineNumber=generate
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org.eclipse.jdt.core.compiler.debug.localVariable=generate
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org.eclipse.jdt.core.compiler.debug.sourceFile=generate
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org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
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org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
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org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
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org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
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org.eclipse.jdt.core.compiler.problem.deadCode=warning
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org.eclipse.jdt.core.compiler.problem.deprecation=warning
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org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
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org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
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org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
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org.eclipse.jdt.core.compiler.problem.emptyStatement=ignore
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org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
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org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore
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org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
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org.eclipse.jdt.core.compiler.problem.fieldHiding=ignore
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org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
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org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
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org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
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org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
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org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
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org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
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org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=ignore
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org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore
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org.eclipse.jdt.core.compiler.problem.localVariableHiding=ignore
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org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
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org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=warning
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org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=ignore
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org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=warning
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org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled
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org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
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org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=ignore
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org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning
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org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning
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org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
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org.eclipse.jdt.core.compiler.problem.nullReference=warning
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org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
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org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
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org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=ignore
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org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore
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org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
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org.eclipse.jdt.core.compiler.problem.redundantNullCheck=ignore
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org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore
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org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore
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org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
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org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore
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org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
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org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
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org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
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org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
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org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=ignore
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org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
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org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
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org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
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org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore
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org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
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org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
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org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=ignore
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org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
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org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=ignore
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org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
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org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
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org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
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org.eclipse.jdt.core.compiler.problem.unusedImport=warning
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org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
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org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
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org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=ignore
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org.eclipse.jdt.core.compiler.problem.unusedParameter=ignore
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org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
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org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
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org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
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org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
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org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
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org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
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org.eclipse.jdt.core.compiler.source=1.6

‎OboGraphView/.settings/org.eclipse.m2e.core.prefs‎

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activeProfiles=
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eclipse.preferences.version=1
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resolveWorkspaceProjects=true
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version=1

‎OboGraphView/pom.xml‎

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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>org.geneontology</groupId>
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<artifactId>OboGraphView</artifactId>
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<version>0.1.0-SNAPSHOT</version>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<version>2.3.2</version>
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<configuration>
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<source>1.6</source>
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<target>1.6</target>
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</configuration>
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</plugin>
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</plugins>
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</build>
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<repositories>
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<repository>
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<id>BerkeleyBOP</id>
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<name>Berkeley BOP maven repository</name>
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<url>http://code.berkeleybop.org/maven/repository/</url>
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<snapshots>
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<enabled>true</enabled>
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</snapshots>
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</repository>
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<repository>
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<id>BerkeleyBOPSnapshot</id>
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<url>http://code.berkeleybop.org/maven/snapshot-repository/</url>
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<snapshots>
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<enabled>true</enabled>
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</snapshots>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.8.2</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.bbop</groupId>
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<artifactId>OWLTools-Annotation</artifactId>
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<version>0.2.1-SNAPSHOT</version>
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<exclusions>
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<exclusion>
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<groupId>org.coode</groupId>
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<artifactId>oppl2</artifactId>
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</exclusion>
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<exclusion>
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<artifactId>slf4j-log4j12</artifactId>
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<groupId>org.slf4j</groupId>
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</exclusion>
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<exclusion>
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<artifactId>factplusplus</artifactId>
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<groupId>uk.ac.manchester.cs</groupId>
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</exclusion>
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<exclusion>
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<artifactId>HermiT</artifactId>
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<groupId>org.semanticweb</groupId>
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</exclusion>
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<exclusion>
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<artifactId>jcel.owlapi</artifactId>
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<groupId>jcel</groupId>
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</exclusion>
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<exclusion>
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<artifactId>sparqldl-api</artifactId>
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<groupId>de.derivo</groupId>
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</exclusion>
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<exclusion>
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<artifactId>graphdraw</artifactId>
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<groupId>uk.ac.ebi.interpro</groupId>
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</exclusion>
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<exclusion>
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<artifactId>ant</artifactId>
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<groupId>org.apache.ant</groupId>
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</exclusion>
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<exclusion>
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<artifactId>gson</artifactId>
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<groupId>com.google.code.gson</groupId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.piccolo2d</groupId>
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<artifactId>piccolo2d-core</artifactId>
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<version>1.3.1</version>
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</dependency>
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<dependency>
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<groupId>org.piccolo2d</groupId>
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<artifactId>piccolo2d-extras</artifactId>
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<version>1.3.1</version>
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</dependency>
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<dependency>
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<groupId>batik</groupId>
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<artifactId>batik-gvt</artifactId>
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<version>1.6-1</version>
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</dependency>
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<dependency>
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<groupId>batik</groupId>
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<artifactId>batik-bridge</artifactId>
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<version>1.6-1</version>
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</dependency>
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</dependencies>
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</project>

‎OboGraphView/src/main/java/org/geneontology/graph/DefaultNamedChildProvider.java‎

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package org.geneontology.graph;
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import java.util.Collection;
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import java.util.LinkedHashSet;
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import org.apache.log4j.Logger;
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import edu.umd.cs.piccolo.PNode;
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public class DefaultNamedChildProvider implements NamedChildProvider {
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//initialize logger
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protected final static Logger logger = Logger.getLogger(DefaultNamedChildProvider.class);
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protected static DefaultNamedChildProvider instance;
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public static synchronized DefaultNamedChildProvider getInstance() {
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if (instance == null)
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instance = new DefaultNamedChildProvider();
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return instance;
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}
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@Override
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public Collection<Object> getChildNames(PNode node) {
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Collection<Object> out = (Collection<Object>) node.getAttribute("_magic_properties_");
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return out;
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}
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@Override
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public PNode getNamedChild(Object name, PNode node) {
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return (PNode) node.getAttribute(name);
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}
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@Override
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public void setNamedChild(Object name, PNode node, PNode value) {
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Collection<Object> props = getChildNames(node);
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if (props == null) {
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props = new LinkedHashSet<Object>();
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node.addAttribute("_magic_properties_", props);
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}
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if (value != null) {
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if (!props.contains(name))
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props.add(name);
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} else {
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props.remove(name);
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}
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PNode oldValue = (PNode) node.getAttribute(name);
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if (oldValue != null)
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node.removeChild(oldValue);
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node.addAttribute(name, value);
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if (value != null)
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node.addChild(value);
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}
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}

‎OboGraphView/src/main/java/org/geneontology/graph/DefaultNodeFactory.java‎

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package org.geneontology.graph;
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import java.awt.Shape;
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import org.apache.log4j.Logger;
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import org.geneontology.graph.LinkDatabase.Link;
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import org.geneontology.graph.tooltip.TooltipFactory;
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import org.semanticweb.owlapi.model.OWLObject;
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public class DefaultNodeFactory implements NodeFactory {
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//initialize logger
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protected final static Logger logger = Logger.getLogger(DefaultNodeFactory.class);
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private final TypeIconManager iconManager;
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private final TypeColorManager colorManager;
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private final NodeLabelProvider labelProvider;
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private final TooltipFactory tooltipFactory;
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public DefaultNodeFactory(TypeIconManager iconManager, TypeColorManager colorManager,
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NodeLabelProvider labelProvider, TooltipFactory tooltipFactory) {
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super();
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this.iconManager = iconManager;
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this.colorManager = colorManager;
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this.labelProvider = labelProvider;
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this.tooltipFactory = tooltipFactory;
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}
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@Override
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public OELink createLink(Link link, Shape s) {
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OELink node = new OELink(link, iconManager, colorManager, s);
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node.setTooltipFactory(tooltipFactory);
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return node;
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}
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@Override
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public OENode createNode(OWLObject obj, Shape s) {
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OENode node = new OENode(obj, labelProvider, s);
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return node;
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}
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}

‎OboGraphView/src/main/java/org/geneontology/graph/DefaultNodeLabelProvider.java‎

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package org.geneontology.graph;
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import org.semanticweb.owlapi.model.OWLObject;
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import owltools.graph.OWLGraphWrapper;
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public class DefaultNodeLabelProvider implements NodeLabelProvider {
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private final OWLGraphWrapper graph;
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public DefaultNodeLabelProvider(OWLGraphWrapper graph) {
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this.graph = graph;
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}
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@Override
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public String getLabel(OWLObject lo) {
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return graph.getLabelOrDisplayId(lo);
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}
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}

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