Merge pull request #25 from bvdmitri/master

static testing

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

@@ -25,6 +25,7 @@ import com.antigenomics.vdjtools.util.ExecUtil
  * Class that represents Variable and Joining segment frequency (usage) vector and V-J pairing matrix
  */
 public class SegmentUsage {
+    //This static field public but not final, and could be changed by malicious code or by accident from another package. The field could be made final to avoid this vulnerability.
     public static boolean VERBOSE = true
 
     private final Map<String, double[]> vSegmentUsage = new HashMap<>(),

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

@@ -29,6 +29,7 @@ import com.antigenomics.vdjtools.util.ExecUtil
  * computes a set of overlap metrics
  */
 public class Overlap {
+    //This static field public but not final, and could be changed by malicious code or by accident from another package. The field could be made final to avoid this vulnerability.
     public static boolean VERBOSE = true
 
     private final SamplePair samplePair

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

@@ -31,6 +31,7 @@ import static com.antigenomics.vdjtools.overlap.OverlapMetric.*
  * A helper class to compute various overlap metrics for joint overlap
  */
 class OverlapEvaluator {
+    //This static field public but not final, and could be changed by malicious code or by accident from another package. The field could be made final to avoid this vulnerability.
     public static boolean VERBOSE = true
 
     private final JointSample jointSample

src/main/java/com/antigenomics/vdjtools/LinkedListExt.java

@@ -98,6 +98,7 @@
 public class LinkedListExt<E>
         extends AbstractSequentialList<E>
         implements List<E>, Deque<E>, Cloneable, java.io.Serializable {
+    private static final long serialVersionUID = 876323262645176354L;
     private transient Entry<E> header = new Entry<E>(null, null, null);
     private transient int size = 0;
 
@@ -971,8 +972,6 @@ public <T> T[] toArray(T[] a) {
         return a;
     }
 
-    private static final long serialVersionUID = 876323262645176354L;
-
     /**
      * Save the state of this <tt>LinkedList</tt> instance to a stream (that
      * is, serialize it).

src/main/java/com/antigenomics/vdjtools/group/VJLenSignature.java

@@ -44,6 +44,7 @@ public int hashCode() {
 
     @Override
     public boolean equals(Object o) {
+        if (o == null) return false;
         VJLenSignature key = (VJLenSignature) o;
         return getV().equals(key.getV()) &&
                 getJ().equals(key.getJ()) &&

src/main/java/com/antigenomics/vdjtools/join/JointClonotype.java

@@ -176,6 +176,6 @@ JointClonotype changeParent(JointSample newParent) {
 
     @Override
     public int compareTo(JointClonotype o) {
-        return -Double.compare(this.getBaseFreq(), o.getBaseFreq());
+        return Double.compare(o.getBaseFreq(), this.getBaseFreq());
     }
 }

src/main/java/com/antigenomics/vdjtools/join/key/ClonotypeKey.java

@@ -33,6 +33,6 @@ public ClonotypeKey(Clonotype clonotype) {
     @Override
     public boolean equals(Object o) {
         // no it shouldn't
-        return this.equals(((ClonotypeKey) o).clonotype);
+        return o != null && this.equals(((ClonotypeKey) o).clonotype);
     }
 }

src/main/java/com/antigenomics/vdjtools/pool/ClonotypeAggregator.java

@@ -19,9 +19,6 @@
 import com.antigenomics.vdjtools.Misc;
 import com.antigenomics.vdjtools.sample.Clonotype;
 
-import java.util.HashSet;
-import java.util.Set;
-
 public abstract class ClonotypeAggregator {
     private int sampleId;
     private int incidenceCount, count;

src/main/java/com/antigenomics/vdjtools/sample/BlankClonotypeFilter.java

@@ -17,12 +17,13 @@
 package com.antigenomics.vdjtools.sample;
 
 public class BlankClonotypeFilter extends ClonotypeFilter {
+    //This static field public but not final, and could be changed by malicious code or by accident from another package. The field could be made final to avoid this vulnerability.
+    public static BlankClonotypeFilter INSTANCE = new BlankClonotypeFilter();
+
     private BlankClonotypeFilter() {
         super(false);
     }
 
-    public static BlankClonotypeFilter INSTANCE = new BlankClonotypeFilter();
-
     @Override
     protected boolean checkPass(Clonotype clonotype) {
         return true;

src/main/java/com/antigenomics/vdjtools/sample/Clonotype.java

@@ -18,8 +18,6 @@
 
 import com.antigenomics.vdjtools.ClonotypeContainer;
 import com.antigenomics.vdjtools.Countable;
-import com.antigenomics.vdjtools.join.key.ClonotypeKey;
-import com.antigenomics.vdjtools.join.key.StrictKey;
 
 /**
  * A class holding comprehensive info on a T- or B-cell clonotype.