Rename project

mikessh · Feb 16, 2015 · ca4e2a6 · ca4e2a6
1 parent 8466f3b
commit ca4e2a6
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Showing 131 changed files with 499 additions and 516 deletions.
diff --git a/pom.xml b/pom.xml
@@ -3,10 +3,10 @@
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>com.milaboratory</groupId>
-    <artifactId>migec2</artifactId>
+    <artifactId>oncomigec</artifactId>
     <version>1.0-SNAPSHOT</version>
     <packaging>jar</packaging>
-    <name>MIGEC2</name>
+    <name>OncoMIGEC</name>
 
     <repositories>
         <repository>
@@ -167,7 +167,7 @@
                 <configuration>
                     <archive>
                         <manifest>
-                            <mainClass>com.milaboratory.migec2.pipeline.MigecCli</mainClass>
+                            <mainClass>com.milaboratory.oncomigec.pipeline.MigecCli</mainClass>
                             <addDefaultImplementationEntries>
                                 true
                             </addDefaultImplementationEntries>
@@ -228,7 +228,7 @@
                                 </transformer>
                                 <transformer
                                         implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                                    <mainClass>com.milaboratory.migec2.pipeline.MigecCli</mainClass>
+                                    <mainClass>com.milaboratory.oncomigec.pipeline.MigecCli</mainClass>
                                 </transformer>
                             </transformers>
                             <shadedArtifactAttached>true</shadedArtifactAttached>

diff --git a/...2/model/classifier/TrainClassifier.groovy → ...c/model/classifier/TrainClassifier.groovy b/...2/model/classifier/TrainClassifier.groovy → ...c/model/classifier/TrainClassifier.groovy
@@ -16,10 +16,10 @@
  * Last modified on 23.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.classifier
+package com.milaboratory.oncomigec.model.classifier
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet
-import com.milaboratory.migec2.model.variant.Variant
+import com.milaboratory.oncomigec.model.variant.Variant
 import weka.core.Instance
 
 def cli = new CliBuilder(usage: "TrainClassifier [options] control_variants input_vardump output_prefix\n" +

diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java b/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java
diff --git a/src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java b/src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java
diff --git a/...2/core/align/entity/PAlignmentResult.java → ...c/core/align/entity/PAlignmentResult.java b/...2/core/align/entity/PAlignmentResult.java → ...c/core/align/entity/PAlignmentResult.java
@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.entity;
+package com.milaboratory.oncomigec.core.align.entity;
 
 import com.milaboratory.core.sequence.Range;
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 import java.util.List;
 

diff --git a/...2/core/align/entity/SAlignmentResult.java → ...c/core/align/entity/SAlignmentResult.java b/...2/core/align/entity/SAlignmentResult.java → ...c/core/align/entity/SAlignmentResult.java
@@ -13,13 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.entity;
+package com.milaboratory.oncomigec.core.align.entity;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 import java.util.ArrayList;
 import java.util.List;

diff --git a/...ry/migec2/core/align/kmer/KMerFinder.java → ...oncomigec/core/align/kmer/KMerFinder.java b/...ry/migec2/core/align/kmer/KMerFinder.java → ...oncomigec/core/align/kmer/KMerFinder.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 import com.milaboratory.util.IntArrayList;
 
 public class KMerFinder {

diff --git a/...ec2/core/align/kmer/KMerFinderResult.java → ...gec/core/align/kmer/KMerFinderResult.java b/...ec2/core/align/kmer/KMerFinderResult.java → ...gec/core/align/kmer/KMerFinderResult.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 public class KMerFinderResult {
     private final double information;

diff --git a/...atory/migec2/core/align/kmer/KmerMap.java → ...ry/oncomigec/core/align/kmer/KmerMap.java b/...atory/migec2/core/align/kmer/KmerMap.java → ...ry/oncomigec/core/align/kmer/KmerMap.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
 //
 // Adapted from KAnalyze package, see

diff --git a/...ory/migec2/core/align/kmer/KmerUtils.java → .../oncomigec/core/align/kmer/KmerUtils.java b/...ory/migec2/core/align/kmer/KmerUtils.java → .../oncomigec/core/align/kmer/KmerUtils.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public class KmerUtils {
     private final int k;

diff --git a/.../migec2/core/align/processor/Aligner.java → ...comigec/core/align/processor/Aligner.java b/.../migec2/core/align/processor/Aligner.java → ...comigec/core/align/processor/Aligner.java
@@ -13,12 +13,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.processor;
+package com.milaboratory.oncomigec.core.align.processor;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.entity.PAlignmentResult;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public interface Aligner {
     /**

diff --git a/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java
@@ -0,0 +1,7 @@
+package com.milaboratory.oncomigec.core.align.processor;
+
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+
+public interface AlignerFactory <T extends Aligner> {
+    public T fromReferenceLibrary(ReferenceLibrary referenceLibrary);
+}
diff --git a/...rocessor/AlignerFactoryWithReference.java → ...rocessor/AlignerFactoryWithReference.java b/...rocessor/AlignerFactoryWithReference.java → ...rocessor/AlignerFactoryWithReference.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.align.processor;
+package com.milaboratory.oncomigec.core.align.processor;
 
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public class AlignerFactoryWithReference<T extends Aligner> {
     private final ReferenceLibrary referenceLibrary;

diff --git a/...rocessor/aligners/AlignmentEvaluator.java → ...rocessor/aligners/AlignmentEvaluator.java b/...rocessor/aligners/AlignmentEvaluator.java → ...rocessor/aligners/AlignmentEvaluator.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 

diff --git a/...sor/aligners/DummyAlignmentEvaluator.java → ...sor/aligners/DummyAlignmentEvaluator.java b/...sor/aligners/DummyAlignmentEvaluator.java → ...sor/aligners/DummyAlignmentEvaluator.java
@@ -16,7 +16,7 @@
  * Last modified on 19.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 

diff --git a/...cessor/aligners/ExtendedExomeAligner.java → ...cessor/aligners/ExtendedExomeAligner.java b/...cessor/aligners/ExtendedExomeAligner.java → ...cessor/aligners/ExtendedExomeAligner.java
@@ -1,17 +1,17 @@
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.alignment.AffineGapAlignmentScoring;
 import com.milaboratory.core.sequence.alignment.LocalAligner;
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.entity.PAlignmentResult;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.kmer.KMerFinder;
-import com.milaboratory.migec2.core.align.kmer.KMerFinderResult;
-import com.milaboratory.migec2.core.align.processor.Aligner;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.kmer.KMerFinder;
+import com.milaboratory.oncomigec.core.align.kmer.KMerFinderResult;
+import com.milaboratory.oncomigec.core.align.processor.Aligner;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 import java.util.ArrayList;
 import java.util.List;

diff --git a/...aligners/ExtendedExomeAlignerFactory.java → ...aligners/ExtendedExomeAlignerFactory.java b/...aligners/ExtendedExomeAlignerFactory.java → ...aligners/ExtendedExomeAlignerFactory.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
-import com.milaboratory.migec2.core.align.processor.AlignerFactory;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactory;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public class ExtendedExomeAlignerFactory implements AlignerFactory<ExtendedExomeAligner> {
     private final int k;

diff --git a/...sor/aligners/LocalAlignmentEvaluator.java → ...sor/aligners/LocalAlignmentEvaluator.java b/...sor/aligners/LocalAlignmentEvaluator.java → ...sor/aligners/LocalAlignmentEvaluator.java
@@ -14,10 +14,9 @@
  * limitations under the License.
  */
 
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
-import com.milaboratory.core.sequence.aminoacid.AminoAcidAlphabet;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 

diff --git a/...rocessor/aligners/SimpleExomeAligner.java → ...rocessor/aligners/SimpleExomeAligner.java b/...rocessor/aligners/SimpleExomeAligner.java → ...rocessor/aligners/SimpleExomeAligner.java
@@ -13,16 +13,16 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.alignment.*;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.entity.PAlignmentResult;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.processor.Aligner;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.processor.Aligner;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 import java.util.ArrayList;
 import java.util.List;

diff --git a/...r/aligners/SimpleExomeAlignerFactory.java → ...r/aligners/SimpleExomeAlignerFactory.java b/...r/aligners/SimpleExomeAlignerFactory.java → ...r/aligners/SimpleExomeAlignerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.alignment.KAlignerParameters;
-import com.milaboratory.migec2.core.align.processor.AlignerFactory;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactory;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public class SimpleExomeAlignerFactory implements AlignerFactory<SimpleExomeAligner> {
     private final KAlignerParameters parameters;

diff --git a/src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java
@@ -0,0 +1,4 @@
+package com.milaboratory.oncomigec.core.align.reference;
+
+public class KmerLibrary {
+}
diff --git a/...igec2/core/align/reference/Reference.java → ...migec/core/align/reference/Reference.java b/...igec2/core/align/reference/Reference.java → ...migec/core/align/reference/Reference.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.reference;
+package com.milaboratory.oncomigec.core.align.reference;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 

diff --git a/...ore/align/reference/ReferenceLibrary.java → ...ore/align/reference/ReferenceLibrary.java b/...ore/align/reference/ReferenceLibrary.java → ...ore/align/reference/ReferenceLibrary.java
@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.reference;
+package com.milaboratory.oncomigec.core.align.reference;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.Util;
 
 import java.io.File;
 import java.io.IOException;

diff --git a/...igec2/core/assemble/entity/Consensus.java → ...migec/core/assemble/entity/Consensus.java b/...igec2/core/assemble/entity/Consensus.java → ...migec/core/assemble/entity/Consensus.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.assemble.entity;
+package com.milaboratory.oncomigec.core.assemble.entity;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.QualityHistogram;
+import com.milaboratory.oncomigec.util.QualityHistogram;
 
 public interface Consensus {
     public int size();

diff --git a/...gec2/core/assemble/entity/PConsensus.java → ...igec/core/assemble/entity/PConsensus.java b/...gec2/core/assemble/entity/PConsensus.java → ...igec/core/assemble/entity/PConsensus.java
@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.assemble.entity;
+package com.milaboratory.oncomigec.core.assemble.entity;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.QualityHistogram;
+import com.milaboratory.oncomigec.util.QualityHistogram;
 
 public final class PConsensus implements Consensus {
     private final SConsensus consensus1, consensus2;

diff --git a/...gec2/core/assemble/entity/SConsensus.java → ...igec/core/assemble/entity/SConsensus.java b/...gec2/core/assemble/entity/SConsensus.java → ...igec/core/assemble/entity/SConsensus.java
@@ -13,12 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.assemble.entity;
+package com.milaboratory.oncomigec.core.assemble.entity;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.QualityHistogram;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.QualityHistogram;
 
 import java.util.List;
 

diff --git a/.../core/assemble/misc/AssemblerFactory.java → .../core/assemble/misc/AssemblerFactory.java b/.../core/assemble/misc/AssemblerFactory.java → .../core/assemble/misc/AssemblerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.assemble.misc;
+package com.milaboratory.oncomigec.core.assemble.misc;
 
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.assemble.processor.Assembler;
-import com.milaboratory.migec2.core.io.entity.Mig;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.assemble.processor.Assembler;
+import com.milaboratory.oncomigec.core.io.entity.Mig;
 
 public abstract class AssemblerFactory<T extends Consensus, V extends Mig> {
     protected final AssemblerParameters parameters;

diff --git a/...re/assemble/misc/AssemblerParameters.java → ...re/assemble/misc/AssemblerParameters.java b/...re/assemble/misc/AssemblerParameters.java → ...re/assemble/misc/AssemblerParameters.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.assemble.misc;
+package com.milaboratory.oncomigec.core.assemble.misc;
 
-import com.milaboratory.migec2.util.ParameterSet;
+import com.milaboratory.oncomigec.util.ParameterSet;
 import org.jdom.Element;
 
 public final class AssemblerParameters implements ParameterSet {

diff --git a/...core/assemble/misc/PAssemblerFactory.java → ...core/assemble/misc/PAssemblerFactory.java b/...core/assemble/misc/PAssemblerFactory.java → ...core/assemble/misc/PAssemblerFactory.java
@@ -1,9 +1,9 @@
-package com.milaboratory.migec2.core.assemble.misc;
+package com.milaboratory.oncomigec.core.assemble.misc;
 
-import com.milaboratory.migec2.core.assemble.entity.PConsensus;
-import com.milaboratory.migec2.core.assemble.processor.PAssembler;
-import com.milaboratory.migec2.core.assemble.processor.SAssembler;
-import com.milaboratory.migec2.core.io.entity.PMig;
+import com.milaboratory.oncomigec.core.assemble.entity.PConsensus;
+import com.milaboratory.oncomigec.core.assemble.processor.PAssembler;
+import com.milaboratory.oncomigec.core.assemble.processor.SAssembler;
+import com.milaboratory.oncomigec.core.io.entity.PMig;
 
 public final class PAssemblerFactory extends AssemblerFactory<PConsensus, PMig> {
 

diff --git a/...core/assemble/misc/SAssemblerFactory.java → ...core/assemble/misc/SAssemblerFactory.java b/...core/assemble/misc/SAssemblerFactory.java → ...core/assemble/misc/SAssemblerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.assemble.misc;
+package com.milaboratory.oncomigec.core.assemble.misc;
 
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.assemble.processor.SAssembler;
-import com.milaboratory.migec2.core.io.entity.SMig;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.assemble.processor.SAssembler;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
 
 public final class SAssemblerFactory extends AssemblerFactory<SConsensus, SMig> {
 

diff --git a/...c2/core/assemble/processor/Assembler.java → ...ec/core/assemble/processor/Assembler.java b/...c2/core/assemble/processor/Assembler.java → ...ec/core/assemble/processor/Assembler.java
@@ -13,13 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.assemble.processor;
+package com.milaboratory.oncomigec.core.assemble.processor;
 
 import cc.redberry.pipe.Processor;
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.io.entity.Mig;
-import com.milaboratory.migec2.util.ProcessorResultWrapper;
-import com.milaboratory.migec2.util.QualityHistogram;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.io.entity.Mig;
+import com.milaboratory.oncomigec.util.ProcessorResultWrapper;
+import com.milaboratory.oncomigec.util.QualityHistogram;
 
 import java.util.Collections;
 import java.util.LinkedList;