Some code grooming

Author: mikessh

src/main/groovy/com/antigenomics/vdjtools/VdjTools.groovy

@@ -166,17 +166,18 @@ else {
     } catch (Exception e) {
         println "[ERROR] $e.message, see _vdjtools_error.log for details"
         new File("_vdjtools_error.log").withWriterAppend { writer ->
-            writer.println("[${new Date()}]")
+            writer.println("[${new Date()} BEGIN]")
             writer.println("[Script]")
             writer.println(args[0])
             writer.println("[CommandLine]")
             writer.println("executing vdjtools-${version}.jar ${args.join(" ")}")
             writer.println("[Message]")
-            writer.println(e.message)
+            writer.println(e.toString())
             writer.println("[StackTrace-Short]")
             writer.println(e.stackTrace.findAll { it.toString().contains("com.antigenomics.vdjtools") }.join("\n"))
             writer.println("[StackTrace-Full]")
             e.printStackTrace(new PrintWriter(writer))
+            writer.println("[END]")
         }
         System.exit(-1)
     }

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

@@ -15,10 +15,8 @@
  */
 
 
-
 package com.antigenomics.vdjtools.basic
 
-import com.antigenomics.vdjtools.Software
 import com.antigenomics.vdjtools.sample.Sample
 import com.antigenomics.vdjtools.sample.SampleCollection
 import com.antigenomics.vdjtools.sample.metadata.MetadataTable

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

@@ -16,7 +16,6 @@
 
 package com.antigenomics.vdjtools.basic
 
-import com.antigenomics.vdjtools.Software
 import com.antigenomics.vdjtools.sample.SampleCollection
 import com.antigenomics.vdjtools.sample.metadata.MetadataTable
 import com.antigenomics.vdjtools.util.RUtil
@@ -84,8 +83,8 @@ println "[${new Date()} $scriptName] ${sampleCollection.size()} samples loaded"
 
 def segmentUsage = new SegmentUsage(sampleCollection, unweighted)
 
-def outputPathV = formOutputPath(outputFilePrefix, "segments", unweighted ? "unwt" : "wt" ,"V"),
-        outputPathJ = formOutputPath(outputFilePrefix, "segments", unweighted ? "unwt" : "wt" ,"J")
+def outputPathV = formOutputPath(outputFilePrefix, "segments", unweighted ? "unwt" : "wt", "V"),
+    outputPathJ = formOutputPath(outputFilePrefix, "segments", unweighted ? "unwt" : "wt", "J")
 new File(outputPathV).withPrintWriter { pwV ->
     new File(outputPathJ).withPrintWriter { pwJ ->
         def header = "#$MetadataTable.SAMPLE_ID_COLUMN\t" + sampleCollection.metadataTable.columnHeader

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

@@ -16,7 +16,6 @@
 
 package com.antigenomics.vdjtools.basic
 
-import com.antigenomics.vdjtools.Software
 import com.antigenomics.vdjtools.sample.Sample
 import com.antigenomics.vdjtools.sample.SampleCollection
 import com.antigenomics.vdjtools.sample.metadata.MetadataTable

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

@@ -25,7 +25,6 @@ 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/imgt/ImgtParser.groovy

@@ -1,17 +1,17 @@
-/**
- Copyright 2014 Mikhail Shugay (mikhail.shugay@gmail.com)
-
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
+/*
+ * Copyright 2013-2015 Mikhail Shugay (mikhail.shugay@gmail.com)
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  */
 
 

src/main/groovy/com/antigenomics/vdjtools/imgt/Test.groovy

@@ -1,17 +1,17 @@
-/**
- Copyright 2014 Mikhail Shugay (mikhail.shugay@gmail.com)
-
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
+/*
+ * Copyright 2013-2015 Mikhail Shugay (mikhail.shugay@gmail.com)
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  */
 
 package com.antigenomics.vdjtools.imgt

src/main/groovy/com/antigenomics/vdjtools/operate/PoolSamples.groovy

@@ -14,8 +14,6 @@
  * limitations under the License.
  */
 
-// todo: UNTESTED
-
 package com.antigenomics.vdjtools.operate
 
 import com.antigenomics.vdjtools.Software

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

@@ -29,7 +29,6 @@ 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

@@ -31,7 +31,6 @@ 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