Merge branch 'release/1.0.1'

pom.xml

@@ -19,7 +19,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mitools</artifactId>
-    <version>1.0</version>
+    <version>1.0.1</version>
     <packaging>jar</packaging>
     <name>MiTools</name>
     <url>http://milaboratory.com/</url>
@@ -94,12 +94,12 @@
         <dependency>
             <groupId>com.milaboratory</groupId>
             <artifactId>milib</artifactId>
-            <version>1.0</version>
+            <version>1.0.1</version>
         </dependency>
         <dependency>
             <groupId>com.milaboratory</groupId>
             <artifactId>milib</artifactId>
-            <version>1.0</version>
+            <version>1.0.1</version>
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>

src/main/java/com/milaboratory/mitools/merger/MergerParameters.java

@@ -27,7 +27,7 @@
 @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE,
         getterVisibility = JsonAutoDetect.Visibility.NONE)
 @Serializable(asJson = true)
-public final class MergerParameters {
+public final class MergerParameters implements java.io.Serializable{
     final int minimalOverlap;
     final double minimalIdentity;
 

src/main/java/com/milaboratory/mitools/merger/MismatchOnlyPairedReadMerger.java

@@ -29,7 +29,8 @@
 import static com.milaboratory.core.sequence.SequencesUtils.mismatchCount;
 import static java.lang.Math.*;
 
-public final class MismatchOnlyPairedReadMerger implements Processor<PairedRead, PairedReadMergingResult> {
+public final class MismatchOnlyPairedReadMerger implements Processor<PairedRead, PairedReadMergingResult>,
+        java.io.Serializable {
     public static final int DEFAULT_MAX_SCORE_VALUE = 45;
     final int minOverlap;
     final double maxMismatchesPart;

src/main/java/com/milaboratory/mitools/merger/PairedReadMergingResult.java

@@ -18,7 +18,7 @@
 import com.milaboratory.core.io.sequence.PairedRead;
 import com.milaboratory.core.sequence.NSequenceWithQuality;
 
-public class PairedReadMergingResult {
+public class PairedReadMergingResult implements java.io.Serializable {
     private static final int MATCH_SCORE = 2;
     private static final int MISMATCH_SCORE = -5;
 
@@ -78,4 +78,37 @@ public int getErrors() {
     int score() {
         return (overlap - errors) * MATCH_SCORE + errors * MISMATCH_SCORE;
     }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+
+        PairedReadMergingResult that = (PairedReadMergingResult) o;
+
+        if (overlap != that.overlap) return false;
+        if (errors != that.errors) return false;
+        if (!originalRead.equals(that.originalRead)) return false;
+        return overlappedSequence.equals(that.overlappedSequence);
+
+    }
+
+    @Override
+    public int hashCode() {
+        int result = originalRead.hashCode();
+        result = 31 * result + overlappedSequence.hashCode();
+        result = 31 * result + overlap;
+        result = 31 * result + errors;
+        return result;
+    }
+
+    @Override
+    public String toString() {
+        return "PairedReadMergingResult{" +
+                "originalRead=" + originalRead +
+                ", overlappedSequence=" + overlappedSequence +
+                ", overlap=" + overlap +
+                ", errors=" + errors +
+                '}';
+    }
 }

src/main/java/com/milaboratory/mitools/trimmer/ReadLengthFilter.java

@@ -18,7 +18,7 @@
 import cc.redberry.primitives.Filter;
 import com.milaboratory.core.io.sequence.SingleRead;
 
-public class ReadLengthFilter implements Filter<SingleRead> {
+public class ReadLengthFilter implements Filter<SingleRead>, java.io.Serializable {
     final int minLength;
 
     public ReadLengthFilter(int minLength) {

src/main/java/com/milaboratory/mitools/trimmer/SequenceTrimmer.java

@@ -22,7 +22,7 @@
 
 import java.util.concurrent.atomic.AtomicLong;
 
-public final class SequenceTrimmer implements Processor<SingleRead, SingleRead> {
+public final class SequenceTrimmer implements Processor<SingleRead, SingleRead>, java.io.Serializable {
     final int qualityToTrimm;
     final boolean trimmLeft, trimmRight;
     final AtomicLong trimmedNucleotidesLeft = new AtomicLong(),

src/test/java/com/milaboratory/mitools/merger/PairedReadMergingResultTest.java

@@ -0,0 +1,23 @@
+package com.milaboratory.mitools.merger;
+
+import com.milaboratory.core.io.sequence.PairedRead;
+import com.milaboratory.core.io.sequence.SingleReadImpl;
+import com.milaboratory.core.io.util.TestUtil;
+import com.milaboratory.core.sequence.NSequenceWithQuality;
+import com.milaboratory.core.sequence.NucleotideSequence;
+import com.milaboratory.core.sequence.SequenceQuality;
+import org.junit.Test;
+
+/**
+ * Created by poslavsky on 15/04/15.
+ */
+public class PairedReadMergingResultTest {
+    @Test
+    public void test1() throws Exception {
+        PairedReadMergingResult se = new PairedReadMergingResult(new PairedRead(
+                new SingleReadImpl(12, new NSequenceWithQuality(new NucleotideSequence("atgc"), new SequenceQuality("++++")), "x"),
+                new SingleReadImpl(12, new NSequenceWithQuality(new NucleotideSequence("atgc"), new SequenceQuality("++++")), "x")),
+                new NSequenceWithQuality(new NucleotideSequence("atgc"), new SequenceQuality("++++")), 12, 3);
+        TestUtil.assertJavaSerialization(se);
+    }
+}