JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index f4ffc0c..29b3004 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -20,26 +20,7 @@
  */
 package jalview.io.vcf;
 
-import jalview.analysis.Dna;
-import jalview.api.AlignViewControllerGuiI;
-import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.GeneLociI;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureAttributeType;
-import jalview.datamodel.features.FeatureSource;
-import jalview.datamodel.features.FeatureSources;
-import jalview.ext.ensembl.EnsemblMap;
-import jalview.ext.htsjdk.HtsContigDb;
-import jalview.ext.htsjdk.VCFReader;
-import jalview.io.gff.Gff3Helper;
-import jalview.io.gff.SequenceOntologyI;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-import jalview.util.StringUtils;
+import java.util.Locale;
 
 import java.io.File;
 import java.io.IOException;
@@ -67,6 +48,27 @@ import htsjdk.variant.vcf.VCFHeaderLine;
 import htsjdk.variant.vcf.VCFHeaderLineCount;
 import htsjdk.variant.vcf.VCFHeaderLineType;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
+import jalview.analysis.Dna;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureSource;
+import jalview.datamodel.features.FeatureSources;
+import jalview.ext.ensembl.EnsemblMap;
+import jalview.ext.htsjdk.HtsContigDb;
+import jalview.ext.htsjdk.VCFReader;
+import jalview.io.gff.Gff3Helper;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 
 /**
  * A class to read VCF data (using the htsjdk) and add variants as sequence
@@ -313,7 +315,7 @@ public class VCFLoader
     VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
     if (headerLine == null)
     {
-      Cache.log.error("VCF reference header not found");
+      Console.error("VCF reference header not found");
       return null;
     }
     String ref = headerLine.getValue();
@@ -335,7 +337,7 @@ public class VCFLoader
     }
     else
     {
-      Cache.log.error("VCF reference not found: " + ref);
+      Console.error("VCF reference not found: " + ref);
     }
 
     return seq;
@@ -428,11 +430,11 @@ public class VCFLoader
   {
     if (reference == null)
     {
-      Cache.log.error("No VCF ##reference found, defaulting to "
+      Console.error("No VCF ##reference found, defaulting to "
               + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
       reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
     }
-    reference = reference.toLowerCase();
+    reference = reference.toLowerCase(Locale.ROOT);
 
     /*
      * for a non-human species, or other assembly identifier,
@@ -447,7 +449,7 @@ public class VCFLoader
       String[] tokens = token.split("=");
       if (tokens.length == 2)
       {
-        if (reference.contains(tokens[0].trim().toLowerCase()))
+        if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
         {
           vcfAssembly = tokens[1].trim();
           break;
@@ -464,7 +466,7 @@ public class VCFLoader
         String[] tokens = token.split("=");
         if (tokens.length == 2)
         {
-          if (reference.contains(tokens[0].trim().toLowerCase()))
+          if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
           {
             vcfSpecies = tokens[1].trim();
             break;
@@ -569,7 +571,7 @@ public class VCFLoader
   {
     for (Pattern p : filters)
     {
-      if (p.matcher(id.toUpperCase()).matches())
+      if (p.matcher(id.toUpperCase(Locale.ROOT)).matches())
       {
         return true;
       }
@@ -663,7 +665,7 @@ public class VCFLoader
     {
       try
       {
-      patterns.add(Pattern.compile(token.toUpperCase()));
+      patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
       } catch (PatternSyntaxException e)
       {
         System.err.println("Invalid pattern ignored: " + token);
@@ -674,7 +676,6 @@ public class VCFLoader
 
   /**
    * Transfers VCF features to sequences to which this sequence has a mapping.
-   * If the mapping is 3:1, computes peptide variants from nucleotide variants.
    * 
    * @param seq
    */
@@ -775,7 +776,7 @@ public class VCFLoader
     GeneLociI seqCoords = seq.getGeneLoci();
     if (seqCoords == null)
     {
-      Cache.log.warn(String.format(
+      Console.warn(String.format(
               "Can't query VCF for %s as chromosome coordinates not known",
               seq.getName()));
       return null;
@@ -790,7 +791,7 @@ public class VCFLoader
     // returned with the Ensembl sequence; todo: support aliases?
     if (!vcfSpecies.equalsIgnoreCase(species))
     {
-      Cache.log.warn("No VCF loaded to " + seq.getName()
+      Console.warn("No VCF loaded to " + seq.getName()
               + " as species not matched");
       return null;
     }
@@ -820,7 +821,7 @@ public class VCFLoader
               vcfAssembly);
       if (newRange == null)
       {
-        Cache.log.error(
+        Console.error(
                 String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
                         chromosome, seqRef, range[0], range[1],
                         vcfAssembly));
@@ -897,12 +898,19 @@ public class VCFLoader
           int[] featureRange = map.map.locateInFrom(variant.getStart(),
                   variant.getEnd());
 
+          /*
+           * only take features whose range is fully mappable to sequence positions
+           */
           if (featureRange != null)
           {
             int featureStart = Math.min(featureRange[0], featureRange[1]);
             int featureEnd = Math.max(featureRange[0], featureRange[1]);
-            count += addAlleleFeatures(seq, variant, featureStart,
-                    featureEnd, forwardStrand);
+            if (featureEnd - featureStart == variant.getEnd()
+                    - variant.getStart())
+            {
+              count += addAlleleFeatures(seq, variant, featureStart,
+                      featureEnd, forwardStrand);
+            }
           }
         }
         variants.close();
@@ -913,7 +921,7 @@ public class VCFLoader
          */
         String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
                 map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
-        Cache.log.error(msg);
+        Console.error(msg);
       }
     }
 
@@ -1028,7 +1036,7 @@ public class VCFLoader
      */
     String consequence = getConsequenceForAlleleAndFeature(variant, CSQ_FIELD,
             altAlleleIndex, csqAlleleFieldIndex,
-            csqAlleleNumberFieldIndex, seq.getName().toLowerCase(),
+            csqAlleleNumberFieldIndex, seq.getName().toLowerCase(Locale.ROOT),
             csqFeatureFieldIndex);
 
     /*
@@ -1221,7 +1229,7 @@ public class VCFLoader
       {
         String featureIdentifier = csqFields[featureFieldIndex];
         if (featureIdentifier.length() > 4
-                && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
+                && seqName.indexOf(featureIdentifier.toLowerCase(Locale.ROOT)) > -1)
         {
           /*
            * feature (transcript) matched - now check for allele match
@@ -1375,7 +1383,7 @@ public class VCFLoader
     VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(infoId);
     if (infoHeader == null)
     {
-      Cache.log.error("Field " + infoId + " has no INFO header");
+      Console.error("Field " + infoId + " has no INFO header");
       return false;
     }
     VCFHeaderLineType infoType = infoHeader.getType();
@@ -1416,7 +1424,7 @@ public class VCFLoader
     if (!badData.contains(token))
     {
       badData.add(token);
-      Cache.log.error(String.format("Invalid VCF data at %s:%d %s=%s",
+      Console.error(String.format("Invalid VCF data at %s:%d %s=%s",
               variant.getContig(), variant.getStart(), infoId, value));
     }
   }