minor code style fixes

heuermh · heuermh · commit 1dc60cd1e251 · 2022-01-10T14:53:50.000-06:00
diff --git a/HEADER.txt b/HEADER.txt
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadFastaDna.scala b/scripts/loadFastaDna.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadFastaProtein.scala b/scripts/loadFastaProtein.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadFastaRna.scala b/scripts/loadFastaRna.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadFastqReads.scala b/scripts/loadFastqReads.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadGenbankDna.scala b/scripts/loadGenbankDna.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadGenbankDnaFeatures.scala b/scripts/loadGenbankDnaFeatures.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadGenbankProtein.scala b/scripts/loadGenbankProtein.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadGenbankProteinFeatures.scala b/scripts/loadGenbankProteinFeatures.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadGenbankRna.scala b/scripts/loadGenbankRna.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/scripts/loadGenbankRnaFeatures.scala b/scripts/loadGenbankRnaFeatures.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -34,7 +34,7 @@ val bac = BiojavaAdamContext(sc)
 val inputPath = Option(System.getenv("INPUT"))
 val outputPath = Option(System.getenv("OUTPUT"))
 
-if (!inputPath.isDefined || !outputPath.isDefined) {
+if (inputPath.isEmpty || outputPath.isEmpty) {
   logger.error("INPUT and OUTPUT environment variables are required")
   System.exit(1)
 }
diff --git a/src/main/java/org/biojava/nbio/adam/BiojavaKryoRegistrator.java b/src/main/java/org/biojava/nbio/adam/BiojavaKryoRegistrator.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/UnmodifiableCollectionsSerializer.java b/src/main/java/org/biojava/nbio/adam/UnmodifiableCollectionsSerializer.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/BiojavaModule.java b/src/main/java/org/biojava/nbio/adam/convert/BiojavaModule.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -32,11 +32,8 @@
 import com.google.inject.Singleton;
 
 import org.bdgenomics.convert.Converter;
-import org.bdgenomics.convert.ConversionStringency;
 
-import org.bdgenomics.formats.avro.Dbxref;
 import org.bdgenomics.formats.avro.Feature;
-import org.bdgenomics.formats.avro.OntologyTerm;
 import org.bdgenomics.formats.avro.Read;
 import org.bdgenomics.formats.avro.Sequence;
 import org.bdgenomics.formats.avro.Strand;
diff --git a/src/main/java/org/biojava/nbio/adam/convert/BiojavaStrandToBdgenomicsStrand.java b/src/main/java/org/biojava/nbio/adam/convert/BiojavaStrandToBdgenomicsStrand.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/ConvertUtils.java b/src/main/java/org/biojava/nbio/adam/convert/ConvertUtils.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/DnaSequenceToFeatures.java b/src/main/java/org/biojava/nbio/adam/convert/DnaSequenceToFeatures.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/DnaSequenceToSequence.java b/src/main/java/org/biojava/nbio/adam/convert/DnaSequenceToSequence.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/FastqToRead.java b/src/main/java/org/biojava/nbio/adam/convert/FastqToRead.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -26,15 +26,13 @@
 import javax.annotation.concurrent.Immutable;
 
 import org.bdgenomics.convert.AbstractConverter;
-import org.bdgenomics.convert.Converter;
 import org.bdgenomics.convert.ConversionException;
 import org.bdgenomics.convert.ConversionStringency;
 
 import org.bdgenomics.formats.avro.Alphabet;
 import org.bdgenomics.formats.avro.Read;
 
 import org.biojava.nbio.genome.io.fastq.Fastq;
-import org.biojava.nbio.genome.io.fastq.FastqVariant;
 
 import org.slf4j.Logger;
 
@@ -68,7 +66,7 @@ public Read convert(final Fastq fastq,
             .setDescription(fastq.getDescription())
             .setAlphabet(Alphabet.DNA)
             .setSequence(fastq.getSequence().toUpperCase())
-            .setLength(Long.valueOf(fastq.getSequence().length()))
+            .setLength((long) fastq.getSequence().length())
             .setQualityScores(fastq.getQuality())
             .build();
     }
diff --git a/src/main/java/org/biojava/nbio/adam/convert/ProteinSequenceToFeatures.java b/src/main/java/org/biojava/nbio/adam/convert/ProteinSequenceToFeatures.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/ProteinSequenceToSequence.java b/src/main/java/org/biojava/nbio/adam/convert/ProteinSequenceToSequence.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/ReadToFastq.java b/src/main/java/org/biojava/nbio/adam/convert/ReadToFastq.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -26,7 +26,6 @@
 import javax.annotation.concurrent.Immutable;
 
 import org.bdgenomics.convert.AbstractConverter;
-import org.bdgenomics.convert.Converter;
 import org.bdgenomics.convert.ConversionException;
 import org.bdgenomics.convert.ConversionStringency;
 
@@ -72,12 +71,9 @@ public Fastq convert(final Read read,
                 .withVariant(FastqVariant.FASTQ_SANGER)
                 .build();
         }
-        catch (NullPointerException e) {
+        catch (NullPointerException | IllegalArgumentException e) {
             warnOrThrow(read, "could not convert read", e, stringency, logger); 
         }
-        catch (IllegalArgumentException e) {
-            warnOrThrow(read, "could not convert read", e, stringency, logger);
-        }
         return fastq;
     }
 
diff --git a/src/main/java/org/biojava/nbio/adam/convert/RnaSequenceToFeatures.java b/src/main/java/org/biojava/nbio/adam/convert/RnaSequenceToFeatures.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/RnaSequenceToSequence.java b/src/main/java/org/biojava/nbio/adam/convert/RnaSequenceToSequence.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/package-info.java b/src/main/java/org/biojava/nbio/adam/convert/package-info.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/package-info.java b/src/main/java/org/biojava/nbio/adam/package-info.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/scala/org/biojava/nbio/adam/BiojavaAdamContext.scala b/src/main/scala/org/biojava/nbio/adam/BiojavaAdamContext.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2021 held jointly by the individual authors.
+    Copyright (c) 2017-2022 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/scala/org/biojava/nbio/adam/TryWith.scala b/src/main/scala/org/biojava/nbio/adam/TryWith.scala
diff --git a/src/test/java/org/biojava/nbio/adam/convert/BiojavaModuleTest.java b/src/test/java/org/biojava/nbio/adam/convert/BiojavaModuleTest.java
diff --git a/src/test/java/org/biojava/nbio/adam/convert/BiojavaStrandToBdgenomicsStrandTest.java b/src/test/java/org/biojava/nbio/adam/convert/BiojavaStrandToBdgenomicsStrandTest.java
diff --git a/src/test/java/org/biojava/nbio/adam/convert/FastqToReadTest.java b/src/test/java/org/biojava/nbio/adam/convert/FastqToReadTest.java
diff --git a/src/test/java/org/biojava/nbio/adam/convert/ReadToFastqTest.java b/src/test/java/org/biojava/nbio/adam/convert/ReadToFastqTest.java
