diff --git a/.classpath b/.classpath
index 1bfe994..da54680 100644
--- a/.classpath
+++ b/.classpath
@@ -1,14 +1,14 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/build.gradle b/build.gradle
index c8bc4ae..b932a8f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -2,7 +2,7 @@ apply plugin: 'java'
apply plugin: 'eclipse'
group = 'rit'
-version = 0.3
+version = 0.4
jar.baseName = 'flick'
// def uploadSite = 'ftp.bioinformatics.rit.edu'
@@ -83,6 +83,7 @@ dependencies {
compile 'com.google.guava:guava:18.0'
compile 'net.lingala.zip4j:zip4j:1.3.2'
compile 'it.unimi.dsi:dsiutils:2.2.4'
+ compile 'org.springframework:spring-context:4.2.5.RELEASE'
testCompile 'junit:junit:4.+'
testCompile 'junit-addons:junit-addons:1.+'
diff --git a/src/edu/rit/flick/AbstractFlickFile.java b/src/edu/rit/flick/AbstractFlickFile.java
index 8a66ecc..f4bee7b 100644
--- a/src/edu/rit/flick/AbstractFlickFile.java
+++ b/src/edu/rit/flick/AbstractFlickFile.java
@@ -20,6 +20,7 @@
import com.google.common.io.Files;
import edu.rit.flick.config.Configuration;
+import edu.rit.flick.config.FileArchiverExtensionRegistry;
import net.lingala.zip4j.core.ZipFile;
import net.lingala.zip4j.exception.ZipException;
import net.lingala.zip4j.model.ZipParameters;
@@ -31,19 +32,22 @@
*/
public abstract class AbstractFlickFile implements FlickFile
{
- public static final String FILE_NOT_FOUND_EXCEPTION_MESSAGE = "file not found";
+ public static final String FILE_NOT_FOUND_EXCEPTION_MESSAGE = "file not found";
- private static final String FILE_ALREADY_EXISTS_AS_DIRECTORY_EXCEPTION = "already exists as directory";
+ private static final String FILE_ALREADY_EXISTS_AS_DIRECTORY_EXCEPTION = "already exists as directory";
- private static final String CANT_OVERWRITE_EXISTING_FILE_WITHOT_FORCE_FLAG = "\n can't overwrite existing file without --force flag";
+ private static final String CANT_OVERWRITE_EXISTING_FILE_WITHOT_FORCE_FLAG = "\n can't overwrite existing file without --force flag";
- protected final File fileIn, fileOut;
+ protected final File fileIn, fileOut;
- protected final Configuration configuration;
+ protected final Configuration configuration;
- protected final ZipFile flickFile;
+ protected final ZipFile flickFile;
- protected final ZipParameters zParams;
+ protected final ZipParameters zParams;
+
+ protected final FileArchiverExtensionRegistry REGISTRY = FileArchiverExtensionRegistry
+ .getInstance();
public AbstractFlickFile( final Configuration configuration )
throws ZipException,
@@ -52,8 +56,6 @@ public AbstractFlickFile( final Configuration configuration )
{
this.configuration = configuration;
- init();
-
final String inputPath = (String) configuration.getOption( INPUT_PATH );
final Object outputPath = configuration.getOption( OUTPUT_PATH );
@@ -120,7 +122,4 @@ public String getFileOutPath()
{
return fileOut.getPath();
}
-
- protected void init()
- {}
}
diff --git a/src/edu/rit/flick/DefaultFlickFile.java b/src/edu/rit/flick/DefaultFlickFile.java
index f2e4aaa..1432108 100644
--- a/src/edu/rit/flick/DefaultFlickFile.java
+++ b/src/edu/rit/flick/DefaultFlickFile.java
@@ -24,17 +24,12 @@
import java.util.List;
import java.util.concurrent.atomic.LongAdder;
import java.util.stream.Collectors;
-import java.util.stream.Stream;
import org.apache.commons.io.FileUtils;
import com.google.common.io.Files;
import edu.rit.flick.config.Configuration;
-import edu.rit.flick.genetics.FastaFileDeflator;
-import edu.rit.flick.genetics.FastaFileInflator;
-import edu.rit.flick.genetics.FastqFileDeflator;
-import edu.rit.flick.genetics.FastqFileInflator;
import net.lingala.zip4j.core.HeaderReader;
import net.lingala.zip4j.exception.ZipException;
import net.lingala.zip4j.model.CentralDirectory;
@@ -60,10 +55,6 @@ public class DefaultFlickFile extends AbstractFlickFile
private static final String FILE_COULD_NOT_BE_DELETED_WARNING_FORMAT = "File '%s' could not be deleted.%n";
- private List fileDeflators;
-
- private List fileInflators;
-
/**
* @param configuration
* @throws ZipException
@@ -78,31 +69,6 @@ public DefaultFlickFile( final Configuration configuration )
super( configuration );
}
- @Override
- protected void init()
- {
- fileDeflators = new ArrayList();
- fileInflators = new ArrayList();
-
- if ( configuration.getFlag( ARCHIVE_MODE ) == DEFLATION_ARCHIVE_MODE )
- addDefaultFileDeflators();
- else if ( configuration.getFlag( ARCHIVE_MODE ) == INFLATION_ARCHIVE_MODE )
- addDefaultFileInflators();
- }
-
-
- private final void addDefaultFileDeflators()
- {
- registerFileDeflator( new FastaFileDeflator() );
- registerFileDeflator( new FastqFileDeflator() );
- }
-
- private final void addDefaultFileInflators()
- {
- registerFileInflator( new FastaFileInflator() );
- registerFileInflator( new FastqFileInflator() );
- }
-
private File archiveFile( final File file, final boolean onlyFile )
{
double time = 0;
@@ -112,32 +78,33 @@ private File archiveFile( final File file, final boolean onlyFile )
{
final String fileExt = "." + Files.getFileExtension( file.getPath() );
- if ( getExtensions().contains( fileExt ) )
- if ( configuration.getFlag( ARCHIVE_MODE ) == DEFLATION_ARCHIVE_MODE &&
- !configuration.getFlag( NO_ZIP_FLAG ) )
+ if ( configuration.getFlag( ARCHIVE_MODE ) == DEFLATION_ARCHIVE_MODE &&
+ !configuration.getFlag( NO_ZIP_FLAG ) )
+ {
+ final FileDeflator fileDeflator = REGISTRY.getFileDeflator( fileExt );
+ if ( fileDeflator != null )
{
- for ( final FileDeflator deflator : fileDeflators )
- if ( deflator.getExtensions().contains( fileExt ) )
- {
- final long t1 = System.currentTimeMillis();
- if ( onlyFile && configuration.getOption( OUTPUT_PATH ) != null )
- archivedFile = deflator.deflate( configuration, file,
- new File( (String) configuration.getOption( OUTPUT_PATH ) ) );
- else archivedFile = deflator.deflate( configuration, file );
- time = ( System.currentTimeMillis() - t1 ) / 1000d;
- }
- } else if ( configuration.getFlag( ARCHIVE_MODE ) == INFLATION_ARCHIVE_MODE &&
- !configuration.getFlag( KEEP_ZIPPED_FLAG ) )
- for ( final FileInflator inflator : fileInflators )
- if ( inflator.getExtensions().contains( fileExt ) )
- {
- final long t1 = System.currentTimeMillis();
- if ( onlyFile && configuration.getOption( OUTPUT_PATH ) != null )
- archivedFile = inflator.inflate( configuration, file,
- new File( (String) configuration.getOption( OUTPUT_PATH ) ) );
- else archivedFile = inflator.inflate( configuration, file );
- time = ( System.currentTimeMillis() - t1 ) / 1000d;
- }
+ final long t1 = System.currentTimeMillis();
+ if ( onlyFile && configuration.getOption( OUTPUT_PATH ) != null )
+ archivedFile = fileDeflator.deflate( configuration, file,
+ new File( (String) configuration.getOption( OUTPUT_PATH ) ) );
+ else archivedFile = fileDeflator.deflate( configuration, file );
+ time = ( System.currentTimeMillis() - t1 ) / 1000d;
+ }
+ } else if ( configuration.getFlag( ARCHIVE_MODE ) == INFLATION_ARCHIVE_MODE &&
+ !configuration.getFlag( KEEP_ZIPPED_FLAG ) )
+ {
+ final FileInflator fileInflator = REGISTRY.getFileInflator( fileExt );
+ if ( fileInflator != null )
+ {
+ final long t1 = System.currentTimeMillis();
+ if ( onlyFile && configuration.getOption( OUTPUT_PATH ) != null )
+ archivedFile = fileInflator.inflate( configuration, file,
+ new File( (String) configuration.getOption( OUTPUT_PATH ) ) );
+ else archivedFile = fileInflator.inflate( configuration, file );
+ time = ( System.currentTimeMillis() - t1 ) / 1000d;
+ }
+ }
if ( archivedFile != null )
if ( configuration.getFlag( VERBOSE_FLAG ) )
@@ -241,27 +208,16 @@ public String getDefaultDeflatedExtension()
{
final String fileExt = "." + Files.getFileExtension( fileIn.getPath() );
- if ( configuration.getFlag( ARCHIVE_MODE ) == DEFLATION_ARCHIVE_MODE )
- {
- for ( final FileDeflator fd : fileDeflators )
- if ( fd.getExtensions().contains( fileExt ) )
- return fd.getDefaultDeflatedExtension();
- } else if ( configuration.getFlag( ARCHIVE_MODE ) == INFLATION_ARCHIVE_MODE )
- {
- for ( final FileInflator fi : fileInflators )
- if ( fi.getExtensions().contains( fileExt ) )
- return Files.getFileExtension(
- fileIn.getPath().replaceAll( fi.getDefaultDeflatedExtension(), "" ) );
- }
+ final String deflatedExtension = REGISTRY.getDeflatedExtension( fileExt );
- return DEFAULT_DEFLATED_EXTENSION;
- }
+ if ( deflatedExtension != null )
+ if ( configuration.getFlag( ARCHIVE_MODE ) == DEFLATION_ARCHIVE_MODE )
+ return deflatedExtension;
+ else if ( configuration.getFlag( ARCHIVE_MODE ) == INFLATION_ARCHIVE_MODE )
+ return Files
+ .getFileExtension( fileIn.getPath().replaceAll( deflatedExtension, "" ) );
- @Override
- public List getExtensions()
- {
- return Stream.concat( fileInflators.stream(), fileDeflators.stream() )
- .flatMap( fA -> fA.getExtensions().stream() ).collect( Collectors.toList() );
+ return DEFAULT_DEFLATED_EXTENSION;
}
@Override
@@ -346,25 +302,4 @@ public File inflate( final Configuration configuration, final File fileIn, final
return fileOut;
}
-
- private void registerFileArchiver(
- final F fileArchiver,
- final List fileArchivers )
- {
- if ( fileArchivers.contains( fileArchiver ) )
- // TODO nope
- return;
-
- fileArchivers.add( fileArchiver );
- }
-
- public void registerFileDeflator( final FileDeflator fileDeflator )
- {
- registerFileArchiver( fileDeflator, fileDeflators );
- }
-
- public void registerFileInflator( final FileInflator fileInflator )
- {
- registerFileArchiver( fileInflator, fileInflators );
- }
}
diff --git a/src/edu/rit/flick/FileArchiver.java b/src/edu/rit/flick/FileArchiver.java
index f48e06b..7a18f66 100644
--- a/src/edu/rit/flick/FileArchiver.java
+++ b/src/edu/rit/flick/FileArchiver.java
@@ -6,8 +6,6 @@
*/
package edu.rit.flick;
-import java.util.List;
-
/**
* @author Alex Aiezza
*
@@ -15,6 +13,4 @@
public interface FileArchiver
{
public String getDefaultDeflatedExtension();
-
- public List getExtensions();
}
diff --git a/src/edu/rit/flick/RegisterFileDeflatorInflator.java b/src/edu/rit/flick/RegisterFileDeflatorInflator.java
new file mode 100644
index 0000000..14a63ea
--- /dev/null
+++ b/src/edu/rit/flick/RegisterFileDeflatorInflator.java
@@ -0,0 +1,34 @@
+/**
+ * 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 java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+
+import edu.rit.flick.config.DeflationOptionSet;
+import edu.rit.flick.config.InflationOptionSet;
+
+/**
+ * @author Alex Aiezza
+ *
+ *
+ */
+@Retention ( RetentionPolicy.RUNTIME )
+public @interface RegisterFileDeflatorInflator
+{
+ String [] inflatedExtensions();
+
+ String deflatedExtension() default "flick";
+
+ Class fileDeflator() default FlickFile.class;
+
+ Class fileInflator() default FlickFile.class;
+
+ Class fileDeflatorOptionSet();
+
+ Class fileInflatorOptionSet();
+}
diff --git a/src/edu/rit/flick/config/DeflationConfiguration.java b/src/edu/rit/flick/config/DeflationConfiguration.java
index 122d28a..3b0495c 100644
--- a/src/edu/rit/flick/config/DeflationConfiguration.java
+++ b/src/edu/rit/flick/config/DeflationConfiguration.java
@@ -6,8 +6,8 @@
*/
package edu.rit.flick.config;
-import edu.rit.flick.genetics.config.FastaDeflationOptionSet;
-import edu.rit.flick.genetics.config.FastqDeflationOptionSet;
+import static edu.rit.flick.config.DefaultOptionSet.ARCHIVE_MODE;
+import static edu.rit.flick.config.DefaultOptionSet.DEFLATION_ARCHIVE_MODE;
/**
* @author Alex Aiezza
@@ -16,10 +16,13 @@
public class DeflationConfiguration extends AbstractConfiguration
{
{
+ for ( final DeflationOptionSet dos : FileArchiverExtensionRegistry.getInstance()
+ .getDeflationOptionSets() )
+ registerOptionSet( dos );
+
registerOptionSet( new DeflationOptionSet() );
- registerOptionSet( new FastaDeflationOptionSet() );
- registerOptionSet( new FastqDeflationOptionSet() );
+ setFlag( ARCHIVE_MODE, DEFLATION_ARCHIVE_MODE );
}
}
diff --git a/src/edu/rit/flick/config/FileArchiverExtensionRegistry.java b/src/edu/rit/flick/config/FileArchiverExtensionRegistry.java
new file mode 100644
index 0000000..e796049
--- /dev/null
+++ b/src/edu/rit/flick/config/FileArchiverExtensionRegistry.java
@@ -0,0 +1,189 @@
+/**
+ * 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.config;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+
+import org.springframework.beans.factory.annotation.AnnotatedBeanDefinition;
+import org.springframework.beans.factory.config.BeanDefinition;
+import org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider;
+import org.springframework.core.type.filter.AnnotationTypeFilter;
+
+import edu.rit.flick.FileArchiver;
+import edu.rit.flick.FileDeflator;
+import edu.rit.flick.FileInflator;
+import edu.rit.flick.RegisterFileDeflatorInflator;
+
+/**
+ * A singleton helper class for registering and storing mappings of file
+ * extensions to file archivers.
+ *
+ * @author Alex Aiezza
+ *
+ */
+public final class FileArchiverExtensionRegistry
+{
+ // Singleton
+ private static FileArchiverExtensionRegistry FILE_ARCHIVER_REGISTRY;
+
+ /**
+ * Retrieve the registry.
+ *
+ * @return The single existing instance of the FileArchiverExtensionRegistry
+ */
+ public static synchronized FileArchiverExtensionRegistry getInstance()
+ {
+ if ( FILE_ARCHIVER_REGISTRY == null )
+ FILE_ARCHIVER_REGISTRY = new FileArchiverExtensionRegistry();
+ return FILE_ARCHIVER_REGISTRY;
+ }
+
+ private final Map registry;
+
+ private final List deflationOptionSets;
+ private final List inflationOptionSets;
+
+ /**
+ * Constructs the file archiver extension registry and scans for
+ * FileArchiver classes.
+ */
+ private FileArchiverExtensionRegistry()
+ {
+ registry = new HashMap();
+ deflationOptionSets = new ArrayList();
+ inflationOptionSets = new ArrayList();
+
+ final ClassPathScanningCandidateComponentProvider scanner = new ClassPathScanningCandidateComponentProvider(
+ false )
+ {
+ @Override
+ protected boolean isCandidateComponent( AnnotatedBeanDefinition beanDefinition )
+ {
+ return beanDefinition.getMetadata().isIndependent();
+ }
+ };
+
+ scanner.addIncludeFilter( new AnnotationTypeFilter( RegisterFileDeflatorInflator.class ) );
+
+ for ( final BeanDefinition bd : scanner.findCandidateComponents( "*" ) )
+ {
+ try
+ {
+ final Class cl = Class.forName( bd.getBeanClassName() );
+ final RegisterFileDeflatorInflator fileDIP = cl
+ .getAnnotation( RegisterFileDeflatorInflator.class );
+ if ( fileDIP != null )
+ registerFileArchiverExtensions( fileDIP );
+ } catch ( Exception e )
+ {}
+ }
+ }
+
+ public FileDeflator getFileDeflator( final String extension )
+ {
+ final FileDeflatorInflator fileDIP = registry.get( extension );
+ if ( fileDIP != null )
+ return fileDIP.fileDeflator;
+
+ return null;
+ }
+
+ public FileInflator getFileInflator( final String extension )
+ {
+ final Optional fileDIo = registry.values().stream().filter(
+ fileDI -> fileDI.fileInflator.getDefaultDeflatedExtension().equals( extension ) )
+ .findFirst();
+ return fileDIo.isPresent() ? fileDIo.get().fileInflator : null;
+ }
+
+ public String getDeflatedExtension( final String extension )
+ {
+ final FileDeflatorInflator fileDIP = registry.get( extension );
+ if ( fileDIP != null )
+ return fileDIP.fileDeflator.getDefaultDeflatedExtension();
+
+ return null;
+ }
+
+ public List getExtensions( final FileArchiver fileArchiver )
+ {
+ final Optional fileDIPo = registry.values().stream()
+ .filter( fileDIP -> fileDIP.fileDeflator.equals( fileArchiver ) ||
+ fileDIP.fileInflator.equals( fileArchiver ) )
+ .findFirst();
+ return fileDIPo.isPresent() ? fileDIPo.get().extensions : null;
+ }
+
+ public List getExtensions( final Class fileArchiver )
+ {
+ final Optional fileDIPo = registry.values().stream()
+ .filter(
+ fileDIP -> fileArchiver.isAssignableFrom( fileDIP.fileDeflator.getClass() ) ||
+ fileArchiver.isAssignableFrom( fileDIP.fileInflator.getClass() ) )
+ .findFirst();
+ return fileDIPo.isPresent() ? fileDIPo.get().extensions : null;
+ }
+
+ public List getDeflationOptionSets()
+ {
+ return deflationOptionSets;
+ }
+
+ public List getInflationOptionSets()
+ {
+ return inflationOptionSets;
+ }
+
+ public synchronized void registerFileArchiverExtensions(
+ final RegisterFileDeflatorInflator fileDIP )
+ throws InstantiationException, IllegalAccessException
+ {
+ final List extensions = Arrays.asList( fileDIP.inflatedExtensions() );
+
+ for ( int e = 0; e < extensions.size(); e++ )
+ {
+ String extension = extensions.get( e );
+ if ( !extension.startsWith( "." ) )
+ extension = "." + extension;
+ if ( extension.matches( "\\.{2,}.+" ) )
+ extension = extension.replaceFirst( "\\.{2,}", "." );
+
+ extensions.set( e, extension );
+ }
+
+ for ( final String extension : extensions )
+ {
+ registry.put( extension, new FileDeflatorInflator( fileDIP.fileDeflator().newInstance(),
+ fileDIP.fileInflator().newInstance(), extensions ) );
+ }
+
+ deflationOptionSets.add( fileDIP.fileDeflatorOptionSet().newInstance() );
+ inflationOptionSets.add( fileDIP.fileInflatorOptionSet().newInstance() );
+ }
+
+ private class FileDeflatorInflator
+ {
+ private final FileDeflator fileDeflator;
+ private final FileInflator fileInflator;
+ private final List extensions;
+
+ private FileDeflatorInflator(
+ final FileDeflator fileDeflator,
+ final FileInflator fileInflator,
+ final List extensions )
+ {
+ this.fileDeflator = fileDeflator;
+ this.fileInflator = fileInflator;
+ this.extensions = extensions;
+ }
+ }
+}
diff --git a/src/edu/rit/flick/config/InflationConfiguration.java b/src/edu/rit/flick/config/InflationConfiguration.java
index 8a01124..1c3a7ce 100644
--- a/src/edu/rit/flick/config/InflationConfiguration.java
+++ b/src/edu/rit/flick/config/InflationConfiguration.java
@@ -6,8 +6,8 @@
*/
package edu.rit.flick.config;
-import edu.rit.flick.genetics.config.FastaInflationOptionSet;
-import edu.rit.flick.genetics.config.FastqInflationOptionSet;
+import static edu.rit.flick.config.DefaultOptionSet.ARCHIVE_MODE;
+import static edu.rit.flick.config.DefaultOptionSet.INFLATION_ARCHIVE_MODE;
/**
* @author Alex Aiezza
@@ -16,9 +16,12 @@
public class InflationConfiguration extends AbstractConfiguration
{
{
+ for ( final InflationOptionSet ios : FileArchiverExtensionRegistry.getInstance()
+ .getInflationOptionSets() )
+ registerOptionSet( ios );
+
registerOptionSet( new InflationOptionSet() );
- registerOptionSet( new FastaInflationOptionSet() );
- registerOptionSet( new FastqInflationOptionSet() );
+ setFlag( ARCHIVE_MODE, INFLATION_ARCHIVE_MODE );
}
}
diff --git a/src/edu/rit/flick/genetics/FastaFileArchiver.java b/src/edu/rit/flick/genetics/FastaFileArchiver.java
index b85dbb2..b23d741 100644
--- a/src/edu/rit/flick/genetics/FastaFileArchiver.java
+++ b/src/edu/rit/flick/genetics/FastaFileArchiver.java
@@ -8,10 +8,22 @@
import static java.lang.String.format;
+import edu.rit.flick.RegisterFileDeflatorInflator;
+import edu.rit.flick.genetics.config.FastaDeflationOptionSet;
+import edu.rit.flick.genetics.config.FastaInflationOptionSet;
+
/**
* @author Alex Aiezza
*
*/
+@RegisterFileDeflatorInflator (
+ deflatedExtension = FastaFileArchiver.DEFAULT_DEFLATED_FASTA_EXTENSION,
+ inflatedExtensions =
+{ "fna", "fa", "fasta" },
+ fileDeflator = FastaFileDeflator.class,
+ fileInflator = FastaFileInflator.class,
+ fileDeflatorOptionSet = FastaDeflationOptionSet.class,
+ fileInflatorOptionSet = FastaInflationOptionSet.class )
public interface FastaFileArchiver extends FastFileArchiver
{
public final static int DEFAULT_FASTA_SEQUENCE_LINE_SIZE = 80;
@@ -25,8 +37,6 @@ public interface FastaFileArchiver extends FastFileArchiver
public static final byte SEQUENCE_ID_START = '>';
- public static final String FASTA_EXTENSION = ".fna";
-
public static final String DEFAULT_DEFLATED_FASTA_EXTENSION = ".flickfa";
@Override
diff --git a/src/edu/rit/flick/genetics/FastaFileDeflator.java b/src/edu/rit/flick/genetics/FastaFileDeflator.java
index 2ea7f3e..3258273 100644
--- a/src/edu/rit/flick/genetics/FastaFileDeflator.java
+++ b/src/edu/rit/flick/genetics/FastaFileDeflator.java
@@ -14,7 +14,6 @@
import java.nio.channels.FileChannel;
import java.nio.channels.FileChannel.MapMode;
import java.util.Arrays;
-import java.util.Collections;
import java.util.List;
import edu.rit.flick.genetics.util.ByteBufferOutputStream;
@@ -115,12 +114,6 @@ protected void createOutputFiles( final File fastaFile, final String tempOutputD
}
- @Override
- public List getExtensions()
- {
- return Collections.singletonList( FASTA_EXTENSION );
- }
-
@Override
public int getFastaSequenceLineSize()
{
diff --git a/src/edu/rit/flick/genetics/FastaFileInflator.java b/src/edu/rit/flick/genetics/FastaFileInflator.java
index 44b5fe7..62310a5 100644
--- a/src/edu/rit/flick/genetics/FastaFileInflator.java
+++ b/src/edu/rit/flick/genetics/FastaFileInflator.java
@@ -10,8 +10,6 @@
import java.io.File;
import java.io.IOException;
-import java.util.Collections;
-import java.util.List;
import java.util.Scanner;
import java.util.StringTokenizer;
@@ -68,12 +66,6 @@ protected void createOutputFiles( final String tempOutputDirectory, final File f
.useDelimiter( "\\" + PIPE );
}
- @Override
- public List getExtensions()
- {
- return Collections.singletonList( DEFAULT_DEFLATED_FASTA_EXTENSION );
- }
-
@Override
public int getFastaSequenceLineSize()
{
diff --git a/src/edu/rit/flick/genetics/FastqFileArchiver.java b/src/edu/rit/flick/genetics/FastqFileArchiver.java
index a2a61f8..3439e30 100644
--- a/src/edu/rit/flick/genetics/FastqFileArchiver.java
+++ b/src/edu/rit/flick/genetics/FastqFileArchiver.java
@@ -8,10 +8,22 @@
import static java.lang.String.format;
+import edu.rit.flick.RegisterFileDeflatorInflator;
+import edu.rit.flick.genetics.config.FastqDeflationOptionSet;
+import edu.rit.flick.genetics.config.FastqInflationOptionSet;
+
/**
* @author Alex Aiezza
*
*/
+@RegisterFileDeflatorInflator (
+ deflatedExtension = FastqFileArchiver.DEFAULT_DEFLATED_FASTQ_EXTENSION,
+ inflatedExtensions =
+{ "fq", "fastq" },
+ fileDeflator = FastqFileDeflator.class,
+ fileInflator = FastqFileInflator.class,
+ fileDeflatorOptionSet = FastqDeflationOptionSet.class,
+ fileInflatorOptionSet = FastqInflationOptionSet.class )
public interface FastqFileArchiver extends FastFileArchiver
{
public static final String SEQUENCE_SCORE_FILE = "Scores.txt";
@@ -21,8 +33,6 @@ public interface FastqFileArchiver extends FastFileArchiver
public static final byte SEQUENCE_ID_START = '@';
public static final byte COMMENT_START = '+';
- public static final String FASTQ_EXTENSION = ".fq";
-
public static final String DEFAULT_DEFLATED_FASTQ_EXTENSION = ".flickfq";
public static final String META_COMMENT_SAME_AS_SEQUENCE_ID = "commentSameAsSequenceId";
diff --git a/src/edu/rit/flick/genetics/FastqFileDeflator.java b/src/edu/rit/flick/genetics/FastqFileDeflator.java
index 5825450..afd3ec3 100644
--- a/src/edu/rit/flick/genetics/FastqFileDeflator.java
+++ b/src/edu/rit/flick/genetics/FastqFileDeflator.java
@@ -15,7 +15,6 @@
import java.nio.channels.FileChannel;
import java.nio.channels.FileChannel.MapMode;
import java.util.Arrays;
-import java.util.Collections;
import java.util.List;
import edu.rit.flick.genetics.util.ByteBufferOutputStream;
@@ -63,12 +62,6 @@ protected void createOutputFiles( final File fastqFile, final String tempOutputD
new FileOutputStream( tempOutputDirectory + COMMENTS_FILE ), DEFAULT_BUFFER );
}
- @Override
- public List getExtensions()
- {
- return Collections.singletonList( FASTQ_EXTENSION );
- }
-
@Override
protected List getSequenceEscapes()
{
diff --git a/src/edu/rit/flick/genetics/FastqFileInflator.java b/src/edu/rit/flick/genetics/FastqFileInflator.java
index ad2edd4..8e1e026 100644
--- a/src/edu/rit/flick/genetics/FastqFileInflator.java
+++ b/src/edu/rit/flick/genetics/FastqFileInflator.java
@@ -12,8 +12,6 @@
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
-import java.util.Collections;
-import java.util.List;
import java.util.Scanner;
import it.unimi.dsi.io.ByteBufferInputStream;
@@ -86,12 +84,6 @@ public synchronized int read() throws IOException
scoreFis.close();
}
- @Override
- public List getExtensions()
- {
- return Collections.singletonList( DEFAULT_DEFLATED_FASTQ_EXTENSION );
- }
-
public void getNextLength() throws IOException
{
if ( lengthfile.available() > 0 )
diff --git a/src/edu/rit/flick/util/Flick.java b/src/edu/rit/flick/util/Flick.java
index a663a1b..49137c2 100644
--- a/src/edu/rit/flick/util/Flick.java
+++ b/src/edu/rit/flick/util/Flick.java
@@ -6,8 +6,6 @@
*/
package edu.rit.flick.util;
-import static edu.rit.flick.config.DefaultOptionSet.ARCHIVE_MODE;
-import static edu.rit.flick.config.DefaultOptionSet.DEFLATION_ARCHIVE_MODE;
import static edu.rit.flick.config.DefaultOptionSet.HELP_FLAG;
import java.io.BufferedReader;
@@ -39,15 +37,12 @@ public class Flick
Flick.class.getClassLoader().getResourceAsStream( FLICK_USAGE_FILE ) ) );
br.lines().forEach( line -> usage.append( line ).append( "\n" ) );
USAGE_FORMAT = usage.toString();
-
- // TODO Map file extensions to deflators.
}
public static void main( final String... args )
{
final Configuration configuration = new DeflationConfiguration();
ConfigurationProcessor.processConfiguration( configuration, args );
- configuration.setFlag( ARCHIVE_MODE, DEFLATION_ARCHIVE_MODE );
if ( args.length <= 0 || configuration.getFlag( HELP_FLAG ) )
{
diff --git a/src/edu/rit/flick/util/Unflick.java b/src/edu/rit/flick/util/Unflick.java
index 4193211..6d9895e 100644
--- a/src/edu/rit/flick/util/Unflick.java
+++ b/src/edu/rit/flick/util/Unflick.java
@@ -6,9 +6,7 @@
*/
package edu.rit.flick.util;
-import static edu.rit.flick.config.DefaultOptionSet.ARCHIVE_MODE;
import static edu.rit.flick.config.DefaultOptionSet.HELP_FLAG;
-import static edu.rit.flick.config.DefaultOptionSet.INFLATION_ARCHIVE_MODE;
import java.io.BufferedReader;
import java.io.InputStreamReader;
@@ -45,7 +43,6 @@ public static void main( final String... args )
{
final Configuration configuration = new InflationConfiguration();
ConfigurationProcessor.processConfiguration( configuration, args );
- configuration.setFlag( ARCHIVE_MODE, INFLATION_ARCHIVE_MODE );
if ( args.length <= 0 || configuration.getFlag( HELP_FLAG ) )
{
diff --git a/test/edu/rit/flick/util/FlickTest.java b/test/edu/rit/flick/util/FlickTest.java
index 64eda11..6f3b532 100644
--- a/test/edu/rit/flick/util/FlickTest.java
+++ b/test/edu/rit/flick/util/FlickTest.java
@@ -43,6 +43,7 @@
import edu.rit.flick.AbstractFlickFile;
import edu.rit.flick.DefaultFlickFile;
+import edu.rit.flick.config.FileArchiverExtensionRegistry;
import edu.rit.flick.genetics.FastaFileArchiver;
import edu.rit.flick.genetics.FastqFileArchiver;
import it.unimi.dsi.io.ByteBufferInputStream;
@@ -54,26 +55,29 @@
*/
public class FlickTest
{
- private static final String VERBOSE_FLAG = "--verbose";
+ private static final String VERBOSE_FLAG = "--verbose";
- private static final String HELP_FLAG = "--help";
+ private static final String HELP_FLAG = "--help";
- private static final String FILES_DO_NOT_MATCH_ERROR_FORMAT = "%n File '%s' is different from%n file '%s'%n at byte# %d%n";
+ private static final String FILES_DO_NOT_MATCH_ERROR_FORMAT = "%n File '%s' is different from%n file '%s'%n at byte# %d%n";
- private static final String TEST_RESOURCES_FOLDER = "test_resources" +
+ private static final String TEST_RESOURCES_FOLDER = "test_resources" +
File.separator;
- private static final String RESOURCES_FOLDER = "resources" +
+ private static final String RESOURCES_FOLDER = "resources" +
File.separator;
- private static final String FULL_FASTA_EXTENSION = ".fasta";
+ private static final String FULL_FASTA_EXTENSION = ".fasta";
- private static final String FULL_FASTQ_EXTENSION = ".fastq";
+ private static final String FULL_FASTQ_EXTENSION = ".fastq";
- private static final ByteArrayOutputStream outContent = new ByteArrayOutputStream();
- private static final ByteArrayOutputStream errContent = new ByteArrayOutputStream();
+ private static final FileArchiverExtensionRegistry REGISTRY = FileArchiverExtensionRegistry
+ .getInstance();
- private static PrintStream oldOut, oldErr;
+ private static final ByteArrayOutputStream outContent = new ByteArrayOutputStream();
+ private static final ByteArrayOutputStream errContent = new ByteArrayOutputStream();
+
+ private static PrintStream oldOut, oldErr;
@AfterClass
public static void cleanUpStreams() throws IOException
@@ -258,9 +262,10 @@ public void testDirectory( final String directory )
private final void testFASTAfile( final String fileBase )
{
originalFile = getFile( TEST_RESOURCES_FOLDER,
- fileBase + FastaFileArchiver.FASTA_EXTENSION );
- flickedFile = getFile( TEST_RESOURCES_FOLDER, fileBase + FastaFileArchiver.FASTA_EXTENSION +
- FastaFileArchiver.DEFAULT_DEFLATED_FASTA_EXTENSION );
+ fileBase + REGISTRY.getExtensions( FastaFileArchiver.class ).get( 0 ) );
+ flickedFile = getFile( TEST_RESOURCES_FOLDER,
+ fileBase + REGISTRY.getExtensions( FastaFileArchiver.class ).get( 0 ) +
+ FastaFileArchiver.DEFAULT_DEFLATED_FASTA_EXTENSION );
unflickedFile = getFile( TEST_RESOURCES_FOLDER, fileBase + FULL_FASTA_EXTENSION );
try
@@ -275,9 +280,10 @@ private final void testFASTAfile( final String fileBase )
private final void testFASTQfile( final String fileBase )
{
originalFile = getFile( TEST_RESOURCES_FOLDER,
- fileBase + FastqFileArchiver.FASTQ_EXTENSION );
- flickedFile = getFile( TEST_RESOURCES_FOLDER, fileBase + FastqFileArchiver.FASTQ_EXTENSION +
- FastqFileArchiver.DEFAULT_DEFLATED_FASTQ_EXTENSION );
+ fileBase + REGISTRY.getExtensions( FastqFileArchiver.class ).get( 0 ) );
+ flickedFile = getFile( TEST_RESOURCES_FOLDER,
+ fileBase + REGISTRY.getExtensions( FastqFileArchiver.class ).get( 0 ) +
+ FastqFileArchiver.DEFAULT_DEFLATED_FASTQ_EXTENSION );
unflickedFile = getFile( TEST_RESOURCES_FOLDER, fileBase + FULL_FASTQ_EXTENSION );
try