Reference moved to repseq.io

Author: dbolotin

pom.xml

@@ -56,8 +56,8 @@
 
         <dependency>
             <groupId>com.milaboratory</groupId>
-            <artifactId>milib</artifactId>
-            <version>${milib.version}</version>
+            <artifactId>repseq.io</artifactId>
+            <version>1.0.0-SNAPSHOT</version>
         </dependency>
 
         <dependency>

src/main/java/com/milaboratory/mixcr/assembler/AbstractClonalAlignerParameters.java

@@ -28,7 +28,7 @@
  */
 package com.milaboratory.mixcr.assembler;
 
-import com.milaboratory.mixcr.reference.GeneFeature;
+import io.repseq.reference.GeneFeature;
 
 public abstract class AbstractClonalAlignerParameters<T extends AbstractClonalAlignerParameters<T>>
         implements java.io.Serializable {

src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java

@@ -31,7 +31,7 @@
 import cc.redberry.pipe.OutputPortCloseable;
 import com.milaboratory.mixcr.basictypes.VDJCAlignments;
 import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader;
-import com.milaboratory.mixcr.reference.AlleleResolver;
+import io.repseq.reference.AlleleResolver;
 import com.milaboratory.util.Factory;
 
 import java.io.*;

src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java

@@ -35,8 +35,8 @@
 import com.milaboratory.mixcr.basictypes.ClonalSequence;
 import com.milaboratory.mixcr.basictypes.VDJCAlignments;
 import com.milaboratory.mixcr.basictypes.VDJCHit;
-import com.milaboratory.mixcr.reference.AlleleId;
-import com.milaboratory.mixcr.reference.GeneType;
+import io.repseq.reference.AlleleId;
+import io.repseq.reference.GeneType;
 import gnu.trove.iterator.TObjectFloatIterator;
 import gnu.trove.map.hash.TObjectFloatHashMap;
 

src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java

@@ -42,10 +42,10 @@
 import com.milaboratory.core.tree.NeighborhoodIterator;
 import com.milaboratory.core.tree.SequenceTreeMap;
 import com.milaboratory.mixcr.basictypes.*;
-import com.milaboratory.mixcr.reference.Allele;
-import com.milaboratory.mixcr.reference.AlleleId;
-import com.milaboratory.mixcr.reference.GeneFeature;
-import com.milaboratory.mixcr.reference.GeneType;
+import io.repseq.reference.Allele;
+import io.repseq.reference.AlleleId;
+import io.repseq.reference.GeneFeature;
+import io.repseq.reference.GeneType;
 import com.milaboratory.util.CanReportProgress;
 import com.milaboratory.util.Factory;
 import com.milaboratory.util.RandomUtil;
@@ -59,7 +59,7 @@
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.atomic.AtomicLong;
 
-import static com.milaboratory.mixcr.reference.GeneFeature.*;
+import static io.repseq.reference.GeneFeature.*;
 
 public final class CloneAssembler implements CanReportProgress, AutoCloseable {
     final CloneAssemblerParameters parameters;

src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java

@@ -32,7 +32,7 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import com.milaboratory.mixcr.reference.GeneFeature;
+import io.repseq.reference.GeneFeature;
 
 import java.util.Arrays;
 import java.util.regex.Matcher;

src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java

@@ -33,11 +33,11 @@
 import com.milaboratory.core.sequence.NucleotideSequence;
 import com.milaboratory.mixcr.basictypes.Clone;
 import com.milaboratory.mixcr.basictypes.VDJCHit;
-import com.milaboratory.mixcr.reference.*;
 import com.milaboratory.mixcr.vdjaligners.SingleDAligner;
 import com.milaboratory.mixcr.vdjaligners.VDJCAligner;
 import gnu.trove.iterator.TObjectFloatIterator;
 import gnu.trove.map.hash.TObjectFloatHashMap;
+import io.repseq.reference.*;
 
 import java.util.*;
 

src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java

@@ -32,8 +32,8 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
-import com.milaboratory.mixcr.reference.GeneFeature;
-import com.milaboratory.mixcr.reference.GeneType;
+import io.repseq.reference.GeneFeature;
+import io.repseq.reference.GeneType;
 import com.milaboratory.mixcr.vdjaligners.DAlignerParameters;
 
 import java.util.EnumMap;

src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java

@@ -33,7 +33,7 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.milaboratory.core.alignment.AlignmentScoring;
 import com.milaboratory.core.sequence.NucleotideSequence;
-import com.milaboratory.mixcr.reference.GeneFeature;
+import io.repseq.reference.GeneFeature;
 
 @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE,
         getterVisibility = JsonAutoDetect.Visibility.NONE)

src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java

@@ -33,7 +33,7 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.milaboratory.core.alignment.BandedAlignerParameters;
 import com.milaboratory.core.sequence.NucleotideSequence;
-import com.milaboratory.mixcr.reference.GeneFeature;
+import io.repseq.reference.GeneFeature;
 
 @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE,
         getterVisibility = JsonAutoDetect.Visibility.NONE)

src/main/java/com/milaboratory/mixcr/basictypes/Clone.java

@@ -29,8 +29,8 @@
 package com.milaboratory.mixcr.basictypes;
 
 import com.milaboratory.core.sequence.NSequenceWithQuality;
-import com.milaboratory.mixcr.reference.GeneFeature;
-import com.milaboratory.mixcr.reference.GeneType;
+import io.repseq.reference.GeneFeature;
+import io.repseq.reference.GeneType;
 import com.milaboratory.primitivio.annotations.Serializable;
 
 import java.util.EnumMap;

src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java

@@ -29,10 +29,10 @@
 package com.milaboratory.mixcr.basictypes;
 
 import cc.redberry.primitives.Filter;
-import com.milaboratory.mixcr.reference.Allele;
-import com.milaboratory.mixcr.reference.AlleleId;
-import com.milaboratory.mixcr.reference.GeneFeature;
-import com.milaboratory.mixcr.reference.GeneType;
+import io.repseq.reference.Allele;
+import io.repseq.reference.AlleleId;
+import io.repseq.reference.GeneFeature;
+import io.repseq.reference.GeneType;
 
 import java.util.*;
 

src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java

@@ -28,10 +28,10 @@
  */
 package com.milaboratory.mixcr.basictypes;
 
-import com.milaboratory.mixcr.reference.Allele;
-import com.milaboratory.mixcr.reference.AlleleResolver;
-import com.milaboratory.mixcr.reference.GeneFeature;
-import com.milaboratory.mixcr.reference.GeneType;
+import io.repseq.reference.Allele;
+import io.repseq.reference.AlleleResolver;
+import io.repseq.reference.GeneFeature;
+import io.repseq.reference.GeneType;
 import com.milaboratory.mixcr.util.VersionInfoProvider;
 import com.milaboratory.primitivio.PrimitivI;
 import com.milaboratory.primitivio.PrimitivO;

src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java

@@ -29,8 +29,8 @@
 package com.milaboratory.mixcr.basictypes;
 
 import com.milaboratory.core.sequence.NSequenceWithQuality;
-import com.milaboratory.mixcr.reference.GeneType;
-import com.milaboratory.mixcr.reference.ReferenceCompatibilityIO;
+import io.repseq.reference.GeneType;
+import io.repseq.reference.ReferenceCompatibilityIO;
 import com.milaboratory.primitivio.PrimitivI;
 import com.milaboratory.primitivio.PrimitivO;
 import com.milaboratory.primitivio.Serializer;

src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java

@@ -28,8 +28,8 @@
  */
 package com.milaboratory.mixcr.basictypes;
 
-import com.milaboratory.mixcr.reference.GeneFeature;
-import com.milaboratory.mixcr.reference.GeneType;
+import io.repseq.reference.GeneFeature;
+import io.repseq.reference.GeneType;
 
 /**
  * Parameters that can return gene features used in alignments for different gene types.

src/main/java/com/milaboratory/mixcr/basictypes/IO.java

@@ -31,9 +31,9 @@
 import com.milaboratory.core.alignment.Alignment;
 import com.milaboratory.core.sequence.NSequenceWithQuality;
 import com.milaboratory.core.sequence.NucleotideSequence;
-import com.milaboratory.mixcr.reference.Allele;
-import com.milaboratory.mixcr.reference.GeneFeature;
-import com.milaboratory.mixcr.reference.GeneType;
+import io.repseq.reference.Allele;
+import io.repseq.reference.GeneFeature;
+import io.repseq.reference.GeneType;
 import com.milaboratory.primitivio.PrimitivI;
 import com.milaboratory.primitivio.PrimitivO;
 import com.milaboratory.primitivio.Serializer;

src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java

@@ -30,10 +30,10 @@
 
 import com.milaboratory.core.io.CompressionType;
 import com.milaboratory.core.sequence.NucleotideSequence;
-import com.milaboratory.mixcr.reference.Allele;
-import com.milaboratory.mixcr.reference.AlleleId;
-import com.milaboratory.mixcr.reference.AlleleResolver;
-import com.milaboratory.mixcr.reference.GeneFeature;
+import io.repseq.reference.Allele;
+import io.repseq.reference.AlleleId;
+import io.repseq.reference.AlleleResolver;
+import io.repseq.reference.GeneFeature;
 import com.milaboratory.primitivio.PrimitivI;
 import com.milaboratory.primitivio.PrimitivO;