Migration to MiLib 1.1-SNAPSHOT.

milaboratory · Aug 19, 2015 · ba8f80e · ba8f80e
1 parent df3b7e0
commit ba8f80e
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Showing 16 changed files with 51 additions and 30 deletions.
diff --git a/pom.xml b/pom.xml
@@ -44,7 +44,7 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <milib.version>1.0.2</milib.version>
+        <milib.version>1.1-SNAPSHOT</milib.version>
     </properties>
 
     <dependencies>

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java b/src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java
@@ -43,8 +43,10 @@
 import com.milaboratory.core.io.sequence.SequenceRead;
 import com.milaboratory.core.io.sequence.SequenceReaderCloseable;
 import com.milaboratory.core.io.sequence.fasta.FastaReader;
+import com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper;
 import com.milaboratory.core.io.sequence.fastq.PairedFastqReader;
 import com.milaboratory.core.io.sequence.fastq.SingleFastqReader;
+import com.milaboratory.core.sequence.NucleotideSequence;
 import com.milaboratory.mitools.cli.Action;
 import com.milaboratory.mitools.cli.ActionHelper;
 import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter;
@@ -241,13 +243,16 @@ public String getOutputName() {
 
         public SequenceReaderCloseable<? extends SequenceRead> createReader() throws IOException {
             if (isInputPaired())
-                return new PairedFastqReader(parameters.get(0), parameters.get(1));
+                return new PairedFastqReader(parameters.get(0), parameters.get(1), true);
             else {
                 String[] s = parameters.get(0).split("\\.");
                 if (s[s.length - 1].equals("fasta"))
-                    return new FastaReader(parameters.get(0), true);
+                    return new FastaSequenceReaderWrapper(
+                            new FastaReader<>(parameters.get(0), NucleotideSequence.ALPHABET),
+                            true
+                    );
                 else
-                    return new SingleFastqReader(parameters.get(0));
+                    return new SingleFastqReader(parameters.get(0), true);
             }
         }
 

diff --git a/src/main/java/com/milaboratory/mixcr/reference/LociLibraryReader.java b/src/main/java/com/milaboratory/mixcr/reference/LociLibraryReader.java
@@ -30,6 +30,7 @@
 
 import com.milaboratory.core.mutations.Mutations;
 import com.milaboratory.core.sequence.NucleotideSequence;
+import com.milaboratory.core.sequence.SequencesUtils;
 import com.milaboratory.util.Bit2Array;
 
 import java.io.*;
@@ -252,7 +253,7 @@ private void readSequencePart(boolean compressed) throws IOException {
             inflater.end();
         } else
             seqContent = Bit2Array.readFrom(stream);
-        library.base.put(accession, from, new NucleotideSequence(seqContent));
+        library.base.put(accession, from, SequencesUtils.convertBit2ArrayToNSequence(seqContent));
     }
 
     private void readMeta() throws IOException {

diff --git a/src/main/java/com/milaboratory/mixcr/reference/LociLibraryWriter.java b/src/main/java/com/milaboratory/mixcr/reference/LociLibraryWriter.java
@@ -30,6 +30,7 @@
 
 
 import com.milaboratory.core.sequence.NucleotideSequence;
+import com.milaboratory.core.sequence.SequencesUtils;
 
 import java.io.ByteArrayOutputStream;
 import java.io.DataOutputStream;
@@ -82,13 +83,13 @@ public void writeSequencePart(String accession, int from, NucleotideSequence seq
             ByteArrayOutputStream bos = new ByteArrayOutputStream();
             final Deflater def = new Deflater(9, true);
             DeflaterOutputStream dos = new DeflaterOutputStream(bos, def);
-            sequence.getInnerData().writeTo(new DataOutputStream(dos));
+            SequencesUtils.convertNSequenceToBit2Array(sequence).writeTo(new DataOutputStream(dos));
             dos.close();
             def.end();
             stream.writeInt(bos.size());
             stream.write(bos.toByteArray());
         } else
-            sequence.getInnerData().writeTo(stream);
+            SequencesUtils.convertNSequenceToBit2Array(sequence).writeTo(stream);
     }
 
     /**

diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/KVJResultsForSingle.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/KVJResultsForSingle.java
@@ -47,7 +47,7 @@ public KVJResultsForSingle(KAlignmentResult vResult, KAlignmentResult jResult, b
         this.isRC = isRC;
     }
 
-    private static KAlignmentHit[] extractHits(float minScore, KAlignmentResult result, int maxHits) {
+    private static KAlignmentHit<?>[] extractHits(float minScore, KAlignmentResult<?> result, int maxHits) {
         int count = 0;
         for (KAlignmentHit hit : result.getHits())
             if (hit.getAlignment().getScore() > minScore) {

diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java
@@ -141,12 +141,12 @@ PAlignmentHelper createInitialHelper(PairedTarget target) {
     }
 
     static final PreVDJCHit[] zeroArray = new PreVDJCHit[0];
-    static final KAlignmentHit[] zeroKArray = new KAlignmentHit[0];
+    static final KAlignmentHit<?>[] zeroKArray = new KAlignmentHit[0];
 
     final class PAlignmentHelper {
         final PairedTarget target;
-        final KAlignmentResult[] vResults;
-        KAlignmentResult[] jResults;
+        final KAlignmentResult<?>[] vResults;
+        KAlignmentResult<?>[] jResults;
         PairedHit[] vHits, jHits;
         PairedHit bestVHits;
 
@@ -219,7 +219,7 @@ boolean hasHits() {
         /**
          * Converts two KAlignmentResults to an array of paired hits (each paired hit for a particular V of J gene)
          */
-        PairedHit[] extractDoubleHits(KAlignmentResult... results) {
+        PairedHit[] extractDoubleHits(KAlignmentResult<?>... results) {
             TIntObjectHashMap<PairedHit> hits = new TIntObjectHashMap<>();
             addHits(hits, results[0], 0);
             addHits(hits, results[1], 1);
@@ -235,7 +235,7 @@ float score() {
                     (jHits != null && jHits.length > 0 ? jHits[0].sumScore : 0.0f);
         }
 
-        void addHits(TIntObjectHashMap<PairedHit> hits, KAlignmentResult result, int index) {
+        void addHits(TIntObjectHashMap<PairedHit> hits, KAlignmentResult<?> result, int index) {
             if (result == null)
                 return;
 
@@ -395,7 +395,7 @@ static void calculateScoreAndSort(PairedHit[] hits) {
      * read.
      */
     static final class PairedHit {
-        KAlignmentHit hit0, hit1;
+        KAlignmentHit<?> hit0, hit1;
         float sumScore = -1, vEndScore = -1;
 
         PairedHit() {
@@ -488,7 +488,7 @@ private static VDJCHit[] convert(PairedHit[] preHits,
     /**
      * Calculates alignment score only for FR3 and CDR3 part of V gene.
      */
-    float calculateVEndScore(KAlignmentHit hit) {
+    float calculateVEndScore(KAlignmentHit<?> hit) {
         final Allele allele = getVAllelesToAlign().get(hit.getId());
         final int boundary = allele.getPartitioning().getRelativePosition(
                 parameters.getFeatureToAlign(GeneType.Variable),
@@ -523,7 +523,7 @@ public int compare(PairedHit o1, PairedHit o2) {
         }
     };
 
-    static VDJCHit[] combine(final List<Allele> alleles, final GeneFeature feature, final KAlignmentHit[][] hits) {
+    static VDJCHit[] combine(final List<Allele> alleles, final GeneFeature feature, final KAlignmentHit<?>[][] hits) {
         for (int i = 0; i < hits.length; i++)
             Arrays.sort(hits[i], ALLELE_ID_COMPARATOR);
         ArrayList<VDJCHit> result = new ArrayList<>();

diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java
@@ -28,7 +28,7 @@
  */
 package com.milaboratory.mixcr.assembler;
 
-import com.milaboratory.core.io.util.TestUtil;
+import com.milaboratory.core.io.util.IOTestUtil;
 import com.milaboratory.mixcr.reference.GeneFeature;
 import org.junit.Assert;
 import org.junit.Test;
@@ -42,6 +42,6 @@ public void test1() throws Exception {
 
     @Test
     public void test2() throws Exception {
-        TestUtil.assertJavaSerialization(CloneAssemblerParametersPresets.getByName("default"));
+        IOTestUtil.assertJavaSerialization(CloneAssemblerParametersPresets.getByName("default"));
     }
 }
diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java
@@ -87,10 +87,11 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException
 
         SequenceReader reader;
         if (fastqFiles.length == 1)
-            reader = new SingleFastqReader(CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[0]));
+            reader = new SingleFastqReader(CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[0]),
+                    true);
         else
             reader = new PairedFastqReader(CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[0]),
-                    CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[1]));
+                    CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[1]), true);
 
         //write alignments to byte array
         ByteArrayOutputStream alignmentsSerialized = new ByteArrayOutputStream();

diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java
@@ -87,7 +87,7 @@ public void testIsCompatible4() throws Exception {
             assert rp <= td.c1.getConcatenated().size();
             Mutations<NucleotideSequence> incompatible =
                     td.mutations.combineWith(Mutations.decode(
-                            "I" + rp + "" + NucleotideSequence.ALPHABET.symbolFromCode(rl)
+                            "I" + rp + "" + NucleotideSequence.ALPHABET.codeToSymbol(rl)
                             , NucleotideSequence.ALPHABET));
             Assert.assertFalse(td.c1.isCompatible(td.c2, incompatible));
         }

diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java
@@ -64,7 +64,7 @@ public void testSerialization1() throws Exception {
         try (SingleFastqReader reader =
                      new SingleFastqReader(
                              IOTest.class.getClassLoader()
-                                     .getResourceAsStream("sequences/sample_IGH_R1.fastq"))) {
+                                     .getResourceAsStream("sequences/sample_IGH_R1.fastq"), true)) {
 
             VDJCAlignerSJFirst aligner = new VDJCAlignerSJFirst(parameters);
 

diff --git a/src/test/java/com/milaboratory/mixcr/reference/LociLibraryIOTest.java b/src/test/java/com/milaboratory/mixcr/reference/LociLibraryIOTest.java
@@ -34,6 +34,7 @@
 import org.junit.Test;
 
 import java.io.*;
+import java.util.Arrays;
 import java.util.List;
 import java.util.UUID;
 
@@ -107,6 +108,18 @@ public void test3ReadLL() throws Exception {
         Assert.assertTrue(allele.getPartitioning() != null);
     }
 
+    @Test
+    public void test3ReadLL1() throws Exception {
+        InputStream sample = LociLibraryReader.class.getClassLoader().getResourceAsStream("reference/mi.ll");
+        LociLibrary library = LociLibraryReader.read(sample);
+        for (Allele allele : library.getAllAlleles(Species.HomoSapiens)) {
+            if (allele.getName().contains("4-61")) {
+                System.out.println(allele.isFunctional());
+                System.out.println(Arrays.toString(allele.getPartitioning().points));
+            }
+        }
+    }
+
     @Ignore
     @Test
     public void testExportLL() throws Exception {

diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java
@@ -29,7 +29,7 @@
 package com.milaboratory.mixcr.vdjaligners;
 
 import com.milaboratory.core.alignment.AffineGapAlignmentScoring;
-import com.milaboratory.core.io.util.TestUtil;
+import com.milaboratory.core.io.util.IOTestUtil;
 import com.milaboratory.mixcr.reference.GeneFeature;
 import com.milaboratory.util.GlobalObjectMappers;
 import org.junit.Test;
@@ -52,6 +52,6 @@ public void test1() throws Exception {
     public void test2() throws Exception {
         DAlignerParameters se = new DAlignerParameters(GeneFeature.DRegion,
                 30.0f, 0.85f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring());
-        TestUtil.assertJavaSerialization(se);
+        IOTestUtil.assertJavaSerialization(se);
     }
 }
diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java
@@ -64,7 +64,7 @@ public void test1() throws Exception {
                              VDJCAlignerSJFirstTest.class.getClassLoader()
                                      .getResourceAsStream("sequences/sample_IGH_R1.fastq"),
                              VDJCAlignerSJFirstTest.class.getClassLoader()
-                                     .getResourceAsStream("sequences/sample_IGH_R2.fastq"))) {
+                                     .getResourceAsStream("sequences/sample_IGH_R2.fastq"), true)) {
 
             VDJCAlignerPVFirst aligner = new VDJCAlignerPVFirst(parameters);
 

diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSJFirstTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSJFirstTest.java
@@ -55,7 +55,7 @@ public void testSerialization1() throws Exception {
         try (SingleFastqReader reader =
                      new SingleFastqReader(
                              VDJCAlignerSJFirstTest.class.getClassLoader()
-                                     .getResourceAsStream("sequences/sample_IGH_R1.fastq"))) {
+                                     .getResourceAsStream("sequences/sample_IGH_R1.fastq"), true)) {
             VDJCAlignerSJFirst aligner = new VDJCAlignerSJFirst(parameters);
             for (Allele allele : ll.getLocus(Species.HomoSapiens, Locus.IGH).getAllAlleles())
                 if (parameters.containsRequiredFeature(allele))
@@ -80,7 +80,7 @@ public void testSerialization1() throws Exception {
                 Assert.assertEquals(alignemntsList.get(i++), alignments);
         }
     }
-    
+
 //    @Test
 //    public void testSerializationAndFilter() throws Exception {
 //        Assume.assumeTrue(TestUtil.lt());

diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java
@@ -67,7 +67,7 @@ public void test1() throws Exception {
                              VDJCAlignerSJFirstTest.class.getClassLoader()
                                      .getResourceAsStream("sequences/sample_IGH_R1.fastq"),
                              VDJCAlignerSJFirstTest.class.getClassLoader()
-                                     .getResourceAsStream("sequences/sample_IGH_R2.fastq"))) {
+                                     .getResourceAsStream("sequences/sample_IGH_R2.fastq"), true)) {
 
             VDJCAlignerWithMerge aligner = new VDJCAlignerWithMerge(parameters);
 

diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java
@@ -1,6 +1,6 @@
 package com.milaboratory.mixcr.vdjaligners;
 
-import com.milaboratory.core.io.util.TestUtil;
+import com.milaboratory.core.io.util.IOTestUtil;
 import org.junit.Test;
 
 /**
@@ -9,6 +9,6 @@
 public class VDJCParametersPresetsTest {
     @Test
     public void test1() throws Exception {
-        TestUtil.assertJavaSerialization(VDJCParametersPresets.getByName("default"));
+        IOTestUtil.assertJavaSerialization(VDJCParametersPresets.getByName("default"));
     }
 }