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flick.uml
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flick.uml
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<?xml version="1.0" encoding="UTF-8"?>
<xmi:XMI xmi:version="20131001" xmlns:xmi="http:https://www.omg.org/spec/XMI/20131001" xmlns:xsi="http:https://www.w3.org/2001/XMLSchema-instance" xmlns:UMLLabProfile="http:https:///schemas/UMLLabProfile/NS/0" xmlns:ecore="http:https://www.eclipse.org/emf/2002/Ecore" xmlns:uml="http:https://www.eclipse.org/uml2/5.0.0/UML" xsi:schemaLocation="http:https:///schemas/UMLLabProfile/NS/0 pathmap:https://UMLLAB_PROFILES/UMLLab.profile.uml#UMLLabProfile-Annotation_2-UMLLabProfile">
<uml:Model xmi:id="_35f38NRXEeWg6Ki32dw_Og" name="flick">
<eAnnotations xmi:id="_4AoasNRXEeWg6Ki32dw_Og" source="http:https://ns.yatta.de/umllab">
<contents xmi:type="ecore:EAnnotation" xmi:id="_4AoasdRXEeWg6Ki32dw_Og" source="codegen">
<details xmi:id="_4AoastRXEeWg6Ki32dw_Og" key="codegenDirectory" value="/flick/resources"/>
<details xmi:id="_ChzyENRmEeWg6Ki32dw_Og" key="AssociatedSourceCode" value="/flick/src/edu/rit/flick/AbstractFlickFile.java;1556137924/1;/flick/src/edu/rit/flick/config/ConfigurationProcessor.java;575928632/1;/flick/src/edu/rit/flick/FileArchiver.java;2549822828/1;/flick/src/edu/rit/flick/FileDeflator.java;3021471743/1;/flick/src/edu/rit/flick/FileInflator.java;553955518/1;/flick/src/edu/rit/flick/FlickFile.java;1552659039/1;/flick/src/edu/rit/flick/config/Configuration.java;454714696/1;/flick/src/edu/rit/flick/config/AbstractOption.java;2707971271/1;/flick/src/edu/rit/flick/config/AbstractOptionSet.java;1092116781/1;/flick/src/edu/rit/flick/config/AbstractConfiguration.java;285232421/1;/flick/src/edu/rit/flick/config/OptionSet.java;3456057298/1;/flick/src/edu/rit/flick/config/DefaultFlag.java;1656290218/1;/flick/src/edu/rit/flick/config/DefaultOptionSet.java;4046003158/1;/flick/src/edu/rit/flick/config/DeflationConfiguration.java;1490843136/1;/flick/src/edu/rit/flick/config/DeflationOptionSet.java;2377141722/1;/flick/src/edu/rit/flick/config/Flag.java;3284223630/1;/flick/src/edu/rit/flick/config/InflationConfiguration.java;2783581404/1;/flick/src/edu/rit/flick/config/InflationOptionSet.java;873763243/1;/flick/src/edu/rit/flick/config/Option.java;4188169649/1;/flick/src/edu/rit/flick/config/StringOption.java;651186218/1;/flick/src/edu/rit/flick/DefaultFlickFile.java;162615491/1;/flick/src/edu/rit/flick/genetics/ByteConverterBiMapFactory.java;4203823801/1;/flick/src/edu/rit/flick/genetics/FastFileDeflator.java;3420644376/1;/flick/src/edu/rit/flick/genetics/FastFileArchiver.java;1600693133/1;/flick/src/edu/rit/flick/genetics/FastaFileInflator.java;3965915007/1;/flick/src/edu/rit/flick/genetics/FastaFileDeflator.java;426835781/1;/flick/src/edu/rit/flick/genetics/TetramerNotFoundException.java;651205329/1;/flick/src/edu/rit/flick/genetics/FastqFileInflator.java;2572105395/1;/flick/src/edu/rit/flick/genetics/FastqFileArchiver.java;937825628/1;/flick/src/edu/rit/flick/genetics/FastqFileDeflator.java;832334651/1;/flick/src/edu/rit/flick/genetics/FastaFileArchiver.java;2835019032/1;/flick/src/edu/rit/flick/genetics/config/FastaDeflationOptionSet.java;228972764/1;/flick/src/edu/rit/flick/genetics/config/FastaInflationOptionSet.java;4027636729/1;/flick/src/edu/rit/flick/genetics/config/FastqDeflationOptionSet.java;1646654552/1;/flick/src/edu/rit/flick/genetics/config/FastqInflationOptionSet.java;3043232986/1;/flick/src/edu/rit/flick/util/Flick.java;1747837734/1;/flick/src/edu/rit/flick/util/Unflick.java;1062280889/1;/flick/src/edu/rit/util/HexPrinter.java;1350589528/1;/flick/test/edu/rit/flick/util/FlickTest.java;2412367096/1;/flick/src/edu/rit/util/ByteBufferOutputStream.java;3802349185/1;/flick/src/edu/rit/flick/genetics/FastFileInflator.java;4069087614/1;"/>
</contents>
<contents xmi:type="ecore:EAnnotation" xmi:id="_cMTKANjqEeWpMNe4koXegA" source="preferences">
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<details xmi:id="_cMTxEtjqEeWpMNe4koXegA" key="com.yattasolutions.codegen.reverse.roundtrip.ReverseEngineerChangedFiles" value="true"/>
<details xmi:id="_cMTxE9jqEeWpMNe4koXegA" key="com.yattasolutions.codegen.reverse.roundtrip.RemoveDeletedFiles" value="true"/>
</contents>
</contents>
</eAnnotations>
<elementImport xmi:id="_5lanMNRXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#boolean"/>
</elementImport>
<elementImport xmi:id="_5lanMdRXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#byte"/>
</elementImport>
<elementImport xmi:id="_5lanMtRXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#char"/>
</elementImport>
<elementImport xmi:id="_5lanM9RXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#double"/>
</elementImport>
<elementImport xmi:id="_5lanNNRXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#float"/>
</elementImport>
<elementImport xmi:id="_5lbOQNRXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#int"/>
</elementImport>
<elementImport xmi:id="_5lbOQdRXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#long"/>
</elementImport>
<elementImport xmi:id="_5lbOQtRXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#short"/>
</elementImport>
<elementImport xmi:id="_5lbOQ9RXEeWg6Ki32dw_Og">
<importedElement xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/UMLPrimitiveTypes.library.uml#String"/>
</elementImport>
<packagedElement xmi:type="uml:Package" xmi:id="_5eQPQNRXEeWg6Ki32dw_Og" name="edu">
<packagedElement xmi:type="uml:Package" xmi:id="_5eQ2UNRXEeWg6Ki32dw_Og" name="rit">
<packagedElement xmi:type="uml:Package" xmi:id="_5eSEcNRXEeWg6Ki32dw_Og" name="flick">
<packagedElement xmi:type="uml:Class" xmi:id="_5k5CwNRXEeWg6Ki32dw_Og" name="AbstractFlickFile" isAbstract="true">
<eAnnotations xmi:id="_5k5p0NRXEeWg6Ki32dw_Og" source="http:https://ns.yatta.de/umllab">
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<details xmi:id="_5k6Q4NRXEeWg6Ki32dw_Og" key="codegenDirectory" value="/flick/src"/>
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</eAnnotations>
<ownedComment xmi:id="_6EdToNRXEeWg6Ki32dw_Og">
<body>@author Alex Aiezza
*</body>
</ownedComment>
<ownedAttribute xmi:id="_6CUloNRXEeWg6Ki32dw_Og" name="fileIn" visibility="private" isLeaf="true" type="_5928YNRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FSaENRXEeWg6Ki32dw_Og"/>
<ownedAttribute xmi:id="_6CVzwNRXEeWg6Ki32dw_Og" name="configuration" visibility="protected" isLeaf="true" type="_5l-n4NRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FSaE9RXEeWg6Ki32dw_Og"/>
<ownedAttribute xmi:id="_6CWa0dRXEeWg6Ki32dw_Og" name="flickFile" visibility="protected" isLeaf="true" type="_594KgNRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FTBIdRXEeWg6Ki32dw_Og"/>
<ownedAttribute xmi:id="_6CXB4dRXEeWg6Ki32dw_Og" name="zParams" visibility="protected" isLeaf="true" type="_595YodRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FToMNRXEeWg6Ki32dw_Og"/>
<ownedAttribute xmi:id="_6EdTodRXEeWg6Ki32dw_Og" name="fileOut" visibility="private" type="_5928YNRXEeWg6Ki32dw_Og" association="_6F0lkdRXEeWg6Ki32dw_Og"/>
<interfaceRealization xmi:id="_59704dRXEeWg6Ki32dw_Og" client="_5k5CwNRXEeWg6Ki32dw_Og" supplier="_5l5IUNRXEeWg6Ki32dw_Og" contract="_5l5IUNRXEeWg6Ki32dw_Og"/>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6Dlw8NRXEeWg6Ki32dw_Og" name="AbstractFlickFile" specification="_599DANRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6Dlw8dRXEeWg6Ki32dw_Og" name="configuration" type="_5l-n4NRXEeWg6Ki32dw_Og">
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</ownedParameter>
<ownedParameter xmi:id="_6Dlw9NRXEeWg6Ki32dw_Og" type="_5k5CwNRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
</ownedParameter>
<language>java</language>
<body>this.configuration = configuration;
final String inputPath = (String) configuration.getOption( INPUT_PATH );
final Object outputPath = configuration.getOption( OUTPUT_PATH );
fileIn = new File( inputPath );
fileOut = new File( outputPath == null ? fileIn.getPath() + getDefaultDeflatedExtension()
: (String) outputPath );
if ( fileOut.exists() )
FileUtils.deleteQuietly( fileOut );
flickFile = new ZipFile( configuration.getFlag( ARCHIVE_MODE ) ? fileOut : fileIn );
zParams = new ZipParameters();
zParams.setIncludeRootFolder( true );
zParams.setCompressionMethod( Zip4jConstants.COMP_DEFLATE );
zParams.setCompressionLevel( Zip4jConstants.DEFLATE_LEVEL_FAST );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DmYANRXEeWg6Ki32dw_Og" name="getConfiguration" specification="_5ldqgNRXEeWg6Ki32dw_Og">
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<name xsi:nil="true"/>
</ownedParameter>
<language>java</language>
<body>return configuration;
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DmYAtRXEeWg6Ki32dw_Og" name="getFileIn" specification="_5lffsNRXEeWg6Ki32dw_Og">
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<name xsi:nil="true"/>
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<language>java</language>
<body>return fileIn;
</body>
</ownedBehavior>
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<ownedParameter xmi:id="_6DmYBdRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/UMLPrimitiveTypes.library.uml#String"/>
</ownedParameter>
<language>java</language>
<body>return fileIn.getPath();
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DmYBtRXEeWg6Ki32dw_Og" name="getFileOut" specification="_5lh78tRXEeWg6Ki32dw_Og">
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<name xsi:nil="true"/>
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<language>java</language>
<body>return fileOut;
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6Dm_ENRXEeWg6Ki32dw_Og" name="getFileOutPath" specification="_5ljKEtRXEeWg6Ki32dw_Og">
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<name xsi:nil="true"/>
<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/UMLPrimitiveTypes.library.uml#String"/>
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<language>java</language>
<body>return fileOut.getPath();
</body>
</ownedBehavior>
<ownedOperation xmi:id="_5ldqgNRXEeWg6Ki32dw_Og" name="getConfiguration" method="_6DmYANRXEeWg6Ki32dw_Og">
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<body>@author Alex Aiezza
*</body>
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final Option<?> op = configuration.getOptionFromShortFormat( o );

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<body>@author Alex Aiezza
*</body>
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<body>@author Alex Aiezza
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<interfaceRealization xmi:id="_5-U2cNRXEeWg6Ki32dw_Og" client="_5mHx0NRXEeWg6Ki32dw_Og" supplier="_5nBJsNRXEeWg6Ki32dw_Og" contract="_5nBJsNRXEeWg6Ki32dw_Og"/>
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<eAnnotations xmi:id="_6AzitdRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6AzittRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<ownedParameter xmi:id="_6Ay7p9RXEeWg6Ki32dw_Og" type="_5mHx0NRXEeWg6Ki32dw_Og" direction="return"/>
</ownedOperation>
</packagedElement>
<packagedElement xmi:type="uml:Class" xmi:id="_5mPGkNRXEeWg6Ki32dw_Og" name="AbstractOptionSet" isAbstract="true">
<eAnnotations xmi:id="_5mPtoNRXEeWg6Ki32dw_Og" source="http:https://ns.yatta.de/umllab">
<contents xmi:type="ecore:EAnnotation" xmi:id="_5mPtodRXEeWg6Ki32dw_Og" source="codegen">
<details xmi:id="_5mPtotRXEeWg6Ki32dw_Og" key="codegenDirectory" value="/flick/src"/>
</contents>
</eAnnotations>
<ownedComment xmi:id="_6Efv4dRXEeWg6Ki32dw_Og">
<body>@author Alex Aiezza
*</body>
</ownedComment>
<ownedAttribute xmi:id="_6CbTUNRXEeWg6Ki32dw_Og" name="options" visibility="protected" isLeaf="true" type="_5nBJsNRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FUPQdRXEeWg6Ki32dw_Og">
<upperValue xmi:type="uml:LiteralUnlimitedNatural" xmi:id="_6CbTUdRXEeWg6Ki32dw_Og" value="*"/>
</ownedAttribute>
<interfaceRealization xmi:id="_5-Zu8tRXEeWg6Ki32dw_Og" client="_5mPGkNRXEeWg6Ki32dw_Og" supplier="_5mmS8NRXEeWg6Ki32dw_Og" contract="_5mmS8NRXEeWg6Ki32dw_Og"/>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DqCYtRXEeWg6Ki32dw_Og" name="_initializer1" specification="_5mRi0NRXEeWg6Ki32dw_Og">
<language>java</language>
<body>options = new HashSet<Option<V>>();
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DqpcNRXEeWg6Ki32dw_Og" name="getOptions" specification="_5mSJ4NRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DqpcdRXEeWg6Ki32dw_Og" type="_5nBJsNRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
<upperValue xmi:type="uml:LiteralUnlimitedNatural" xmi:id="_6DqpctRXEeWg6Ki32dw_Og" value="*"/>
</ownedParameter>
<language>java</language>
<body>return options;
</body>
</ownedBehavior>
<ownedOperation xmi:id="_5mRi0NRXEeWg6Ki32dw_Og" name="_initializer1" method="_6DqCYtRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_5mRi0dRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_5mRi0tRXEeWg6Ki32dw_Og" key="init"/>
</eAnnotations>
</ownedOperation>
<ownedOperation xmi:id="_5mSJ4NRXEeWg6Ki32dw_Og" name="getOptions" method="_6DqpcNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5mSJ4dRXEeWg6Ki32dw_Og" type="_5nBJsNRXEeWg6Ki32dw_Og" direction="return">
<upperValue xmi:type="uml:LiteralUnlimitedNatural" xmi:id="_5mSJ4tRXEeWg6Ki32dw_Og" value="*"/>
</ownedParameter>
</ownedOperation>
</packagedElement>
<packagedElement xmi:type="uml:Class" xmi:id="_5mUmINRXEeWg6Ki32dw_Og" name="AbstractConfiguration" isAbstract="true">
<eAnnotations xmi:id="_5mVNMNRXEeWg6Ki32dw_Og" source="http:https://ns.yatta.de/umllab">
<contents xmi:type="ecore:EAnnotation" xmi:id="_5mVNMdRXEeWg6Ki32dw_Og" source="codegen">
<details xmi:id="_5mVNMtRXEeWg6Ki32dw_Og" key="codegenDirectory" value="/flick/src"/>
</contents>
</eAnnotations>
<ownedComment xmi:id="_6Efv4tRXEeWg6Ki32dw_Og">
<body>@author Alex Aiezza
*</body>
</ownedComment>
<ownedAttribute xmi:id="_6CchcdRXEeWg6Ki32dw_Og" name="options" visibility="private" isLeaf="true" type="_6Av4UNRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FU2UdRXEeWg6Ki32dw_Og">
<qualifier xmi:id="_6CdIgdRXEeWg6Ki32dw_Og" type="_5nBJsNRXEeWg6Ki32dw_Og"/>
</ownedAttribute>
<ownedAttribute xmi:id="_6CdvkdRXEeWg6Ki32dw_Og" name="flags" visibility="private" isLeaf="true" isReadOnly="true">
<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#boolean"/>
<qualifier xmi:id="_6CeWoNRXEeWg6Ki32dw_Og" type="_5m5N4NRXEeWg6Ki32dw_Og"/>
</ownedAttribute>
<interfaceRealization xmi:id="_5-dZUNRXEeWg6Ki32dw_Og" client="_5mUmINRXEeWg6Ki32dw_Og" supplier="_5l-n4NRXEeWg6Ki32dw_Og" contract="_5l-n4NRXEeWg6Ki32dw_Og"/>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6Dqpc9RXEeWg6Ki32dw_Og" name="_initializer1" specification="_5mV0QNRXEeWg6Ki32dw_Og">
<language>java</language>
<body>options = new HashMap<Option<? extends Object>, Object>();
flags = new HashMap<Flag, Boolean>();
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DqpdNRXEeWg6Ki32dw_Og" name="AbstractConfiguration" specification="_5mWbUdRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DqpddRXEeWg6Ki32dw_Og" type="_5mUmINRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
</ownedParameter>
<language>java</language>
<body>registerOptionSet( new DefaultOptionSet() );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DrQgNRXEeWg6Ki32dw_Og" name="addFlag" specification="_5-eAYNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DrQgdRXEeWg6Ki32dw_Og" name="flag" type="_5m5N4NRXEeWg6Ki32dw_Og">
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<language>java</language>
<body>flags.put( flag, flag.getDefaultValue() );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6Dr3kNRXEeWg6Ki32dw_Og" name="addOption" specification="_5-fOgNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6Dr3kdRXEeWg6Ki32dw_Og" name="option" type="_5nBJsNRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_6Dr3ktRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6Dr3k9RXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<language>java</language>
<body>options.put( option, option.getDefaultValue() );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6Dr3lNRXEeWg6Ki32dw_Og" name="getFlag" specification="_5-hDsNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6Dr3ldRXEeWg6Ki32dw_Og" name="flag" type="_5m5N4NRXEeWg6Ki32dw_Og">
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<ownedParameter xmi:id="_6Dr3mNRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#boolean"/>
</ownedParameter>
<language>java</language>
<body>return flags.get( flag );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6Dr3mdRXEeWg6Ki32dw_Og" name="getOption" specification="_5-iR0NRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6Dr3mtRXEeWg6Ki32dw_Og" name="option" type="_5nBJsNRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_6Dr3m9RXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6Dr3nNRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<ownedParameter xmi:id="_6Dr3ndRXEeWg6Ki32dw_Og" type="_6Av4UNRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
</ownedParameter>
<language>java</language>
<body>return options.get( option );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DseoNRXEeWg6Ki32dw_Og" name="getOptionFromLongFormat" specification="_5mY3kNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DseodRXEeWg6Ki32dw_Og" name="optionStr">
<eAnnotations xmi:id="_6DseotRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6Dseo9RXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/UMLPrimitiveTypes.library.uml#String"/>
</ownedParameter>
<ownedParameter xmi:id="_6DsepNRXEeWg6Ki32dw_Og" type="_5nBJsNRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
</ownedParameter>
<language>java</language>
<body>return getOptionFromString( optionStr, e -> e.getLongFlag().matches( optionStr ) );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DsepdRXEeWg6Ki32dw_Og" name="getOptionFromShortFormat" specification="_5mbT0NRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DseptRXEeWg6Ki32dw_Og" name="optionStr">
<eAnnotations xmi:id="_6Dsep9RXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6DseqNRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/UMLPrimitiveTypes.library.uml#String"/>
</ownedParameter>
<ownedParameter xmi:id="_6DseqdRXEeWg6Ki32dw_Og" type="_5nBJsNRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
</ownedParameter>
<language>java</language>
<body>return getOptionFromString( optionStr, e -> e.getShortFlag().matches( optionStr ) );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DtFsNRXEeWg6Ki32dw_Og" name="getOptionFromString" specification="_6A0w0dRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DtFsdRXEeWg6Ki32dw_Og" name="optionStr">
<eAnnotations xmi:id="_6DtFstRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6DtFs9RXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/UMLPrimitiveTypes.library.uml#String"/>
</ownedParameter>
<ownedParameter xmi:id="_6DtFtNRXEeWg6Ki32dw_Og" name="predicate" type="_5-cLMdRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_6DtFtdRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6DtFttRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<ownedParameter xmi:id="_6DtFt9RXEeWg6Ki32dw_Og" type="_5nBJsNRXEeWg6Ki32dw_Og" direction="return">
<name xsi:nil="true"/>
</ownedParameter>
<language>java</language>
<body>for ( final Option<? extends Object> op : options.keySet() )
if ( predicate.test( op ) )
return op;

for ( final Option<? extends Object> op : flags.keySet() )
if ( predicate.test( op ) )
return op;

return null;
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DtFuNRXEeWg6Ki32dw_Og" name="registerOptionSet" specification="_5-lVINRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DtFudRXEeWg6Ki32dw_Og" name="optionSet" type="_5mmS8NRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_6DtFutRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6DtFu9RXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<language>java</language>
<body>for ( final Option<? extends Object> option : optionSet.getOptions() )
if ( option.isFlag() )
addFlag( (Flag) option );
else addOption( option );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6DtswNRXEeWg6Ki32dw_Og" name="setFlag" specification="_5-nKUtRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DtswdRXEeWg6Ki32dw_Og" name="flag" type="_5m5N4NRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_6DtswtRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6Dtsw9RXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<ownedParameter xmi:id="_6DtsxNRXEeWg6Ki32dw_Og" name="value">
<eAnnotations xmi:id="_6DtsxdRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6DtsxtRXEeWg6Ki32dw_Og" key="final"/>
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<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#boolean"/>
</ownedParameter>
<language>java</language>
<body>flags.put( flag, value );
</body>
</ownedBehavior>
<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6Dtsx9RXEeWg6Ki32dw_Og" name="setOption" specification="_6A2mANRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_6DtsyNRXEeWg6Ki32dw_Og" name="option" type="_5nBJsNRXEeWg6Ki32dw_Og">
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<details xmi:id="_6DtsytRXEeWg6Ki32dw_Og" key="final"/>
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</ownedParameter>
<ownedParameter xmi:id="_6Dtsy9RXEeWg6Ki32dw_Og" name="value" type="_6Av4UNRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_6DtszNRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_6DtszdRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<language>java</language>
<body>options.put( option, value );
</body>
</ownedBehavior>
<ownedOperation xmi:id="_5mV0QNRXEeWg6Ki32dw_Og" name="_initializer1" method="_6Dqpc9RXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_5mV0QdRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_5mV0QtRXEeWg6Ki32dw_Og" key="init"/>
</eAnnotations>
</ownedOperation>
<ownedOperation xmi:id="_5mWbUdRXEeWg6Ki32dw_Og" name="AbstractConfiguration" method="_6DqpdNRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_5mWbUtRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_5mWbU9RXEeWg6Ki32dw_Og" key="create"/>
</eAnnotations>
<ownedParameter xmi:id="_5mXCYNRXEeWg6Ki32dw_Og" type="_5mUmINRXEeWg6Ki32dw_Og" direction="return"/>
</ownedOperation>
<ownedOperation xmi:id="_5mY3kNRXEeWg6Ki32dw_Og" name="getOptionFromLongFormat" method="_6DseoNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5mY3kdRXEeWg6Ki32dw_Og" name="optionStr">
<eAnnotations xmi:id="_5maFsdRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
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<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/UMLPrimitiveTypes.library.uml#String"/>
</ownedParameter>
<ownedParameter xmi:id="_5-kuENRXEeWg6Ki32dw_Og" type="_5nBJsNRXEeWg6Ki32dw_Og" direction="return"/>
</ownedOperation>
<ownedOperation xmi:id="_5mbT0NRXEeWg6Ki32dw_Og" name="getOptionFromShortFormat" method="_6DsepdRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5mbT0dRXEeWg6Ki32dw_Og" name="optionStr">
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<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/UMLPrimitiveTypes.library.uml#String"/>
</ownedParameter>
<ownedParameter xmi:id="_5-kuEdRXEeWg6Ki32dw_Og" type="_5nBJsNRXEeWg6Ki32dw_Og" direction="return"/>
</ownedOperation>
<ownedOperation xmi:id="_5-eAYNRXEeWg6Ki32dw_Og" name="addFlag" method="_6DrQgNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5-eAYdRXEeWg6Ki32dw_Og" name="flag" type="_5m5N4NRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_5-encdRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_5-enctRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
</ownedOperation>
<ownedOperation xmi:id="_5-fOgNRXEeWg6Ki32dw_Og" name="addOption" method="_6Dr3kNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5-fOgdRXEeWg6Ki32dw_Og" name="option" type="_5nBJsNRXEeWg6Ki32dw_Og">
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<details xmi:id="_5-f1kdRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
</ownedOperation>
<ownedOperation xmi:id="_5-hDsNRXEeWg6Ki32dw_Og" name="getFlag" method="_6Dr3lNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5-hDsdRXEeWg6Ki32dw_Og" name="flag" type="_5m5N4NRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_5-hqwdRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_5-hqwtRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<ownedParameter xmi:id="_5-hDstRXEeWg6Ki32dw_Og" direction="return">
<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#boolean"/>
</ownedParameter>
</ownedOperation>
<ownedOperation xmi:id="_5-iR0NRXEeWg6Ki32dw_Og" name="getOption" method="_6Dr3mdRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5-iR0dRXEeWg6Ki32dw_Og" name="option" type="_5nBJsNRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_5-i44dRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_5-i44tRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<ownedParameter xmi:id="_6A0w0NRXEeWg6Ki32dw_Og" type="_6Av4UNRXEeWg6Ki32dw_Og" direction="return"/>
</ownedOperation>
<ownedOperation xmi:id="_5-lVINRXEeWg6Ki32dw_Og" name="registerOptionSet" method="_6DtFuNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5-lVIdRXEeWg6Ki32dw_Og" name="optionSet" type="_5mmS8NRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_5-l8MdRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_5-l8MtRXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
</ownedOperation>
<ownedOperation xmi:id="_5-nKUtRXEeWg6Ki32dw_Og" name="setFlag" method="_6DtswNRXEeWg6Ki32dw_Og">
<ownedParameter xmi:id="_5-nKU9RXEeWg6Ki32dw_Og" name="flag" type="_5m5N4NRXEeWg6Ki32dw_Og">
<eAnnotations xmi:id="_5-nxYtRXEeWg6Ki32dw_Og" source="http:https://www.eclipse.org/uml2/2.0.0/UML">
<details xmi:id="_5-nxY9RXEeWg6Ki32dw_Og" key="final"/>
</eAnnotations>
</ownedParameter>
<ownedParameter xmi:id="_5-nxYNRXEeWg6Ki32dw_Og" name="value">
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<body>@author Alex Aiezza
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<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#boolean"/>
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<body>return String.format( "Flag (%s)", getName() );
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<type xmi:type="uml:PrimitiveType" href="pathmap:https://UML_LIBRARIES/JavaPrimitiveTypes.library.uml#boolean"/>
<defaultValue xmi:type="uml:LiteralString" xmi:id="_6Ce9sdRXEeWg6Ki32dw_Og" value="true"/>
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<ownedAttribute xmi:id="_6CfkwNRXEeWg6Ki32dw_Og" name="INFLATION_ARCHIVE_MODE" isLeaf="true" isStatic="true" isReadOnly="true">
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<ownedAttribute xmi:id="_6CgL1NRXEeWg6Ki32dw_Og" name="DELETE_FLAG" isLeaf="true" isStatic="true" type="_5m5N4NRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FWrgdRXEeWg6Ki32dw_Og">
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<ownedAttribute xmi:id="_6Cgy4dRXEeWg6Ki32dw_Og" name="VERBOSE_FLAG" isLeaf="true" isStatic="true" type="_5m5N4NRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FXSkdRXEeWg6Ki32dw_Og">
<defaultValue xmi:type="uml:LiteralString" xmi:id="_6Cgy4tRXEeWg6Ki32dw_Og" value="new DefaultFlag( "verbose",
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<ownedAttribute xmi:id="_6CiBA9RXEeWg6Ki32dw_Og" name="OUTPUT_PATH" isLeaf="true" isStatic="true" type="_5nBJsNRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FYgsdRXEeWg6Ki32dw_Og">
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<body>options.add( ARCHIVE_MODE );

options.add( HELP_FLAG );
options.add( DELETE_FLAG );
options.add( VERBOSE_FLAG );
options.add( FORCE_FLAG );

options.add( INPUT_PATH );
options.add( OUTPUT_PATH );
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<packagedElement xmi:type="uml:Class" xmi:id="_5m1jgNRXEeWg6Ki32dw_Og" name="DeflationConfiguration">
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<ownedComment xmi:id="_6EiMINRXEeWg6Ki32dw_Og">
<body>@author Alex Aiezza
*</body>
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<language>java</language>
<body>registerOptionSet( new DeflationOptionSet() );

registerOptionSet( new FastaDeflationOptionSet() );
registerOptionSet( new FastqDeflationOptionSet() );
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<details xmi:id="_5m3_wtRXEeWg6Ki32dw_Og" key="codegenDirectory" value="/flick/src"/>
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<ownedComment xmi:id="_6EiMIdRXEeWg6Ki32dw_Og">
<body>@author Alex Aiezza
*</body>
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<generalization xmi:id="_5-vGINRXEeWg6Ki32dw_Og" general="_5mPGkNRXEeWg6Ki32dw_Og"/>
<ownedAttribute xmi:id="_6CjPINRXEeWg6Ki32dw_Og" name="NO_ZIP_FLAG" isLeaf="true" isStatic="true" type="_5m5N4NRXEeWg6Ki32dw_Og" isReadOnly="true" association="_6FZHwdRXEeWg6Ki32dw_Og">
<defaultValue xmi:type="uml:LiteralString" xmi:id="_6CjPIdRXEeWg6Ki32dw_Og" value="new DefaultFlag( "no zip", "no-zip", "", false )"/>
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<ownedBehavior xmi:type="uml:OpaqueBehavior" xmi:id="_6Dvh8dRXEeWg6Ki32dw_Og" name="_initializer1" specification="_5m3_w9RXEeWg6Ki32dw_Og">
<language>java</language>
<body>options.add( NO_ZIP_FLAG );
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<ownedOperation xmi:id="_5m3_w9RXEeWg6Ki32dw_Og" name="_initializer1" method="_6Dvh8dRXEeWg6Ki32dw_Og">
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<packagedElement xmi:type="uml:Interface" xmi:id="_5m5N4NRXEeWg6Ki32dw_Og" name="Flag">
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<details xmi:id="_5m508tRXEeWg6Ki32dw_Og" key="codegenDirectory" value="/flick/src"/>
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