Add packages, code, tests and test resources

Note: Could not include SRR390728_1.fq and
experiment/fastq_data/SRR390728_2.fq because of github size restriction.

.classpath

@@ -1,8 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry excluding="launch4j_configs/" kind="src" path="resources"/>
+	<classpathentry kind="src" path="resources"/>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="test"/>
+	<classpathentry kind="src" path="test_resources"/>
 	<classpathentry exported="true" kind="con" path="org.springsource.ide.eclipse.gradle.classpathcontainer"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk1.8.0_45">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk1.8.0_65">
 		<attributes>
 			<attribute name="owner.project.facets" value="java"/>
 		</attributes>

.gitattributes

@@ -0,0 +1 @@
+*.fq filter=lfs diff=lfs merge=lfs -text

src/edu/rit/flick/AbstractFlickFile.java

@@ -0,0 +1,90 @@
+/**
+ *  COPYRIGHT (C) 2015 Alex Aiezza. All Rights Reserved.
+ *
+ *  See the LICENSE for the specific language governing permissions and
+ *  limitations under the License provided with this project.
+ */
+package edu.rit.flick;
+
+import static edu.rit.flick.config.DefaultOptionSet.ARCHIVE_MODE;
+import static edu.rit.flick.config.DefaultOptionSet.INPUT_PATH;
+import static edu.rit.flick.config.DefaultOptionSet.OUTPUT_PATH;
+
+import java.io.File;
+
+import net.lingala.zip4j.core.ZipFile;
+import net.lingala.zip4j.exception.ZipException;
+import net.lingala.zip4j.model.ZipParameters;
+import net.lingala.zip4j.util.Zip4jConstants;
+
+import org.apache.commons.io.FileUtils;
+
+import edu.rit.flick.config.Configuration;
+
+/**
+ * @author Alex Aiezza
+ *
+ */
+public abstract class AbstractFlickFile implements FlickFile
+{
+    private final File            fileIn, fileOut;
+
+    protected final Configuration configuration;
+
+    protected final ZipFile       flickFile;
+
+    protected final ZipParameters zParams;
+
+    public AbstractFlickFile( final Configuration configuration ) throws ZipException
+    {
+        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 );
+    }
+
+    @Override
+    public Configuration getConfiguration()
+    {
+        return configuration;
+    }
+
+    @Override
+    public File getFileIn()
+    {
+        return fileIn;
+    }
+
+    @Override
+    public String getFileInPath()
+    {
+        return fileIn.getPath();
+    }
+
+    @Override
+    public File getFileOut()
+    {
+        return fileOut;
+    }
+
+    @Override
+    public String getFileOutPath()
+    {
+        return fileOut.getPath();
+    }
+}