Build update. Update mixcr parser. Fixes #107

Author: mikessh

.gitignore

@@ -7,3 +7,7 @@ dependency-reduced-pom.xml
 .RData
 
 .Rproj.user
+
+.gradle/
+build/
+out/

.travis.yml

@@ -1,24 +1,16 @@
 language: java
 sudo: required
 
-jdk: oraclejdk9
-
-addons:
-  apt:
-    packages:
-      - oracle-java9-installer
+jdk: openjdk10
 
 install:
-  - jdk_switcher use oraclejdk8
   - curl -OL https://raw.githubusercontent.com/metacran/r-builder/master/pkg-build.sh
   - chmod 755 pkg-build.sh
   - ./pkg-build.sh bootstrap
   - export PATH="$PATH:`./pkg-build.sh r_path`"
 
 script:
-  - jdk_switcher use oraclejdk8
   - mvn clean install -Dmaven.javadoc.skip=true -q
-  - jdk_switcher use oraclejdk9
   - java -jar target/vdjtools-*.jar RInstall
   - wget https://github.com/mikessh/vdjtools-examples/releases/download/1.1/aging_lite.zip
   - unzip aging_lite.zip

build.gradle

@@ -0,0 +1,49 @@
+apply plugin: 'groovy'
+apply plugin: 'application'
+
+sourceCompatibility = 10
+targetCompatibility = 10
+
+group = 'com.antigenomics'
+version = '1.2.0'
+
+mainClassName = 'com.antigenomics.vdjtools.VdjTools'
+
+repositories {
+    mavenCentral()
+    maven { url 'https://jitpack.io' }
+}
+
+jar {
+    baseName = 'vdjtools'
+    version = "$version"
+
+    manifest {
+        attributes("Main-Class": "$mainClassName", "Implementation-Version": version)
+    }
+
+    from {
+        configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
+    }
+}
+
+sourceSets {
+    main {
+        java { srcDirs = [] }    // no source dirs for the java compiler
+        groovy { srcDirs = ["src/main/java", "src/main/groovy"] }  // compile   everything in src/ with groovy
+    }
+    test {
+        java { srcDirs = [] }    // no source dirs for the java compiler
+        groovy { srcDirs = ["src/test/java", "src/test/groovy"] }  // compile   everything in src/ with groovy
+    }
+}
+
+dependencies {
+    compile 'org.codehaus.groovy:groovy-all:2.5.2'
+    compile 'org.codehaus.gpars:gpars:1.2.1'
+    compile 'junit:junit:4.12'
+    compile 'com.milaboratory:milib:1.8.3'
+    compile 'commons-io:commons-io:1.2'
+    compile 'commons-cli:commons-cli:1.3.1'
+    compile 'org.apache.commons:commons-lang3:3.4'
+}

jitpack.yaml

@@ -0,0 +1,2 @@
+jdk:
+  - openjdk10

pom.xml

@@ -199,7 +199,7 @@ public class SegmentUsage {
      * @return
      */
     public double[][] vjUsageMatrix(int sampleIndex) {
-        double sampleTotal = (double) jSegmentUsage.values().collect { it[sampleIndex] }.sum() ?: 0.0
+        double sampleTotal = (double) (jSegmentUsage.values().collect { it[sampleIndex] }.sum() ?: 0.0)
 
         def matrix = new double[jSegmentUsage.size()][vSegmentUsage.size()]
 

src/main/groovy/com/antigenomics/vdjtools/basic/SegmentUsage.groovy

@@ -33,7 +33,6 @@ import com.antigenomics.vdjtools.misc.AtomicDouble
 import com.antigenomics.vdjtools.misc.ExecUtil
 import com.antigenomics.vdjtools.misc.MathUtil
 import groovyx.gpars.GParsPool
-import sun.reflect.generics.reflectiveObjects.NotImplementedException
 
 import static com.antigenomics.vdjtools.diversity.RichnessEstimateType.*
 
@@ -113,7 +112,7 @@ class ChaoEstimator {
      */
     SpeciesRichness chaoI(long interpolateTo) {
         if (n > Integer.MAX_VALUE)
-            throw new NotImplementedException()
+            throw new UnsupportedOperationException()
 
         if (interpolateTo < 0 || interpolateTo > n)
             throw new IllegalArgumentException("Should interpolate within the size of sample")

src/main/groovy/com/antigenomics/vdjtools/diversity/ChaoEstimator.groovy

@@ -33,7 +33,6 @@ import com.antigenomics.vdjtools.overlap.OverlapType
 import com.antigenomics.vdjtools.preprocess.DownSampler
 import com.antigenomics.vdjtools.sample.Sample
 import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics
-import sun.reflect.generics.reflectiveObjects.NotImplementedException
 
 /**
  * Class that computes richness estimates and diversity indices. 
@@ -148,7 +147,7 @@ class ResamplingEstimator extends DiversityEstimator {
      */
     @Override
     DiversityIndex getDxxIndex(double fraction) {
-        throw new NotImplementedException()
+        throw new UnsupportedOperationException()
     }
 
     /**
@@ -196,7 +195,7 @@ class ResamplingEstimator extends DiversityEstimator {
      */
     @Override
     SpeciesRichness getEfronThisted(int maxDepth, double cvThreshold) {
-        throw new NotImplementedException()
+        throw new UnsupportedOperationException()
     }
 
     /**
@@ -225,6 +224,6 @@ class ResamplingEstimator extends DiversityEstimator {
 
     @Override
     FrequencyTable getFrequencyTable() {
-        throw new NotImplementedException()
+        throw new UnsupportedOperationException()
     }
 }

src/main/groovy/com/antigenomics/vdjtools/diversity/ResamplingEstimator.groovy

@@ -74,21 +74,35 @@ public class MiXcrParser extends ClonotypeStreamParser {
             it.equalsIgnoreCase("Clone fraction") || it.equalsIgnoreCase("cloneFraction")
         }
         cdr3ntColumn = splitHeaderLine.findIndexOf {
-            it.equalsIgnoreCase("N. Seq. CDR3") || it.equalsIgnoreCase("nSeqCDR3")
+            it.equalsIgnoreCase("N. Seq. CDR3") || it.equalsIgnoreCase("nSeqCDR3") || it.equalsIgnoreCase("nSeqImputedCDR3")
         }
         cdr3aaColumn = splitHeaderLine.findIndexOf {
-            it.equalsIgnoreCase("AA. Seq. CDR3") || it.equalsIgnoreCase("aaSeqCDR3")
+            it.equalsIgnoreCase("AA. Seq. CDR3") || it.equalsIgnoreCase("aaSeqCDR3") || it.equalsIgnoreCase("aaSeqImputedCDR3")
+        }
+        vAlignmentsColumn = splitHeaderLine.findIndexOf {
+            it =~ /(?i)V alignment/ || it =~ /(?i)VAlignment/ || it =~ /(?i)allVAlignments/
+        }
+        dAlignmentsColumn = splitHeaderLine.findIndexOf {
+            it =~ /(?i)D alignment/ || it =~ /(?i)DAlignment/ || it =~ /(?i)allDAlignments/
+        }
+        jAlignmentsColumn = splitHeaderLine.findIndexOf {
+            it =~ /(?i)J alignment/ || it =~ /(?i)JAlignment/ || it =~ /(?i)allJAlignments/
+        }
+        vHitsColumn = splitHeaderLine.findIndexOf {
+            it =~ /(?i)V hits/ || it =~ /(?i)VHits/ || it =~ /(?i)allVHitsWithScore/
+        }
+        dHitsColumn = splitHeaderLine.findIndexOf {
+            it =~ /(?i)D hits/ || it =~ /(?i)DHits/ || it =~ /(?i)allDHitsWithScore/
+        }
+        jHitsColumn = splitHeaderLine.findIndexOf {
+            it =~ /(?i)J hits/ || it =~ /(?i)JHits/ || it =~ /(?i)allJHitsWithScore/
         }
-        vAlignmentsColumn = splitHeaderLine.findIndexOf { it =~ /(?i)V alignment/ || it =~ /(?i)VAlignment/ }
-        dAlignmentsColumn = splitHeaderLine.findIndexOf { it =~ /(?i)D alignment/ || it =~ /(?i)DAlignment/ }
-        jAlignmentsColumn = splitHeaderLine.findIndexOf { it =~ /(?i)J alignment/ || it =~ /(?i)JAlignment/ }
-        vHitsColumn = splitHeaderLine.findIndexOf { it =~ /(?i)V hits/ || it =~ /(?i)VHits/ }
-        dHitsColumn = splitHeaderLine.findIndexOf { it =~ /(?i)D hits/ || it =~ /(?i)DHits/ }
-        jHitsColumn = splitHeaderLine.findIndexOf { it =~ /(?i)J hits/ || it =~ /(?i)JHits/ }
         if (countColumn == -1 || freqColumn == -1 || cdr3ntColumn == -1 || cdr3aaColumn == -1 ||
                 vAlignmentsColumn == -1 || dAlignmentsColumn == -1 || jAlignmentsColumn == -1)
             throw new RuntimeException("Some mandatory columns are absent in the input file.")
 
+        //println([countColumn, freqColumn,cdr3ntColumn,cdr3aaColumn,vAlignmentsColumn,dAlignmentsColumn,jAlignmentsColumn])
+
         numberOfColumns = splitHeaderLine.size()
 
         // Initialized
@@ -104,7 +118,7 @@ public class MiXcrParser extends ClonotypeStreamParser {
 
         def splitString = clonotypeString.split(software.delimiter, numberOfColumns)
 
-        def count = splitString[countColumn].toInteger()
+        def count = (int) (splitString[countColumn].toDouble())
         def freq = splitString[freqColumn].toDouble()
 
         def cdr3nt = splitString[cdr3ntColumn]

src/main/groovy/com/antigenomics/vdjtools/io/parser/MiXcrParser.groovy

@@ -37,7 +37,6 @@ import com.antigenomics.vdjtools.misc.ExecUtil
 import com.antigenomics.vdjtools.misc.MathUtil
 import org.apache.commons.math3.stat.correlation.PearsonsCorrelation
 import org.apache.commons.math3.stat.correlation.SpearmansCorrelation
-import sun.reflect.generics.reflectiveObjects.NotImplementedException
 
 import static com.antigenomics.vdjtools.overlap.OverlapMetric.*
 
@@ -228,7 +227,7 @@ class OverlapEvaluator {
                         getSpectratype(j).histogram)
 
             default:
-                throw new NotImplementedException()
+                throw new UnsupportedOperationException()
         }
     }
 

src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapEvaluator.groovy

@@ -34,7 +34,6 @@
 import com.antigenomics.vdjtools.join.key.*;
 import com.antigenomics.vdjtools.overlap.OverlapType;
 import com.antigenomics.vdjtools.sample.Clonotype;
-import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 
 import java.util.HashSet;
 import java.util.Set;
@@ -118,7 +117,7 @@ public ClonotypeKey generateKey(Clonotype clonotype) {
                 return new StrictKey(clonotype);
 
             default:
-                throw new NotImplementedException();
+                throw new UnsupportedOperationException();
         }
     }