Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

[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 13d7ae8..1abe638 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -48,6 +48,7 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
@@ -256,9 +257,9 @@ public class VCFLoader
   private Set<String> badData;
 
   /**
-   * Constructor given a VCF file
+   * Constructor given a path to a VCF file
    * 
-   * @param alignment
+   * @param vcfFile
    */
   public VCFLoader(String vcfFile)
   {
@@ -569,7 +570,7 @@ 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 +664,7 @@ 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);
@@ -921,7 +922,11 @@ public class VCFLoader
   }
 
   /**
-   * A convenience method to get an attribute value for an alternate allele
+   * A convenience method to get an attribute value for an alternate allele.
+   * {@code alleleIndex} is the position in the list of values for the allele.
+   * If {@alleleIndex == -1} then all values are concatenated (comma-separated).
+   * This is the case for fields declared with "Number=." i.e. values are not
+   * related to specific alleles.
    * 
    * @param variant
    * @param attributeName
@@ -933,16 +938,25 @@ public class VCFLoader
   {
     Object att = variant.getAttribute(attributeName);
 
+    String result = null;
     if (att instanceof String)
     {
-      return (String) att;
+      result = (String) att;
     }
-    else if (att instanceof ArrayList)
+    else if (att instanceof List<?>)
     {
-      return ((List<String>) att).get(alleleIndex);
+      List<String> theList = (List<String>) att;
+      if (alleleIndex == -1)
+      {
+        result = StringUtils.listToDelimitedString(theList, ",");
+      }
+      else
+      {
+        result = theList.get(alleleIndex);
+      }
     }
 
-    return null;
+    return result;
   }
 
   /**
@@ -1331,6 +1345,10 @@ public class VCFLoader
          */
         index++;
       }
+      else if (number == VCFHeaderLineCount.UNBOUNDED) // .
+      {
+        index = -1;
+      }
       else if (number != VCFHeaderLineCount.A)
       {
         /*