JAL-3469 add "Number=." fields (all values) to all alleles in VCF record

[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 ac707d8..d3afc57 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -19,6 +19,7 @@ import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 
 import java.io.File;
 import java.io.IOException;
@@ -247,9 +248,9 @@ 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)
   {
@@ -912,7 +913,11 @@ 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
@@ -924,16 +929,25 @@ 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;
   }
 
   /**
@@ -1322,6 +1336,10 @@ public class VCFLoader
          */
         index++;
       }
+      else if (number == VCFHeaderLineCount.UNBOUNDED) // .
+      {
+        index = -1;
+      }
       else if (number != VCFHeaderLineCount.A)
       {
         /*