From dc91411856157cb32a4eb3cb8b3e61de2754475e Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 29 Mar 2022 23:20:21 +0100
Subject: [PATCH] JAL-3982 JAL-3860 encapsulate genomic coordinates
 mapping/liftover logic

---
 src/jalview/datamodel/GenomicAssemblies.java |   64 +++++++++++++++++++++++---
 src/jalview/io/vcf/VCFLoader.java            |   36 +--------------
 2 files changed, 59 insertions(+), 41 deletions(-)

diff --git a/src/jalview/datamodel/GenomicAssemblies.java b/src/jalview/datamodel/GenomicAssemblies.java
index 9754b90..13d9a61 100644
--- a/src/jalview/datamodel/GenomicAssemblies.java
+++ b/src/jalview/datamodel/GenomicAssemblies.java
@@ -1,13 +1,24 @@
 package jalview.datamodel;
 
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.bin.Console;
 import jalview.ext.ensembl.EnsemblMap;
 import jalview.io.vcf.VCFLoader;
+import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+/**
+ * Holds mappings between gemomic assemblies Lazily populated as required from
+ * Ensembl Liftover and other datasources
+ * 
+ * @author gmungoc
+ *
+ */
 public class GenomicAssemblies
 {
 
@@ -33,7 +44,7 @@ public class GenomicAssemblies
    * @param toRef
    * @return
    */
-  public static String makeRangesKey(String chromosome, String species,
+  private static String makeRangesKey(String chromosome, String species,
           String fromRef, String toRef)
   {
     return species + EXCL + chromosome + EXCL + fromRef + EXCL + toRef;
@@ -60,8 +71,8 @@ public class GenomicAssemblies
    *          assembly reference we wish to translate to
    * @return the start-end range in 'toRef' coordinates
    */
-  public static int[] mapReferenceRange(int[] queryRange, String chromosome,
-          String species, String fromRef, String toRef)
+  private static int[] mapReferenceRange(int[] queryRange,
+          String chromosome, String species, String fromRef, String toRef)
   {
     /*
      * first try shorcut of computing the mapping as a subregion of one
@@ -90,7 +101,8 @@ public class GenomicAssemblies
     /*
      * save mapping for possible future re-use
      */
-    String key = GenomicAssemblies.makeRangesKey(chromosome, species, fromRef, toRef);
+    String key = GenomicAssemblies.makeRangesKey(chromosome, species,
+            fromRef, toRef);
     if (!assemblyMappings.containsKey(key))
     {
       assemblyMappings.put(key, new HashMap<int[], int[]>());
@@ -122,10 +134,11 @@ public class GenomicAssemblies
    * @param toRef
    * @return
    */
-  protected static int[] findSubsumedRangeMapping(int[] queryRange,
+  private static int[] findSubsumedRangeMapping(int[] queryRange,
           String chromosome, String species, String fromRef, String toRef)
   {
-    String key = GenomicAssemblies.makeRangesKey(chromosome, species, fromRef, toRef);
+    String key = GenomicAssemblies.makeRangesKey(chromosome, species,
+            fromRef, toRef);
     if (assemblyMappings.containsKey(key))
     {
       Map<int[], int[]> mappedRanges = assemblyMappings.get(key);
@@ -155,4 +168,43 @@ public class GenomicAssemblies
     return null;
   }
 
+  /**
+   * query Ensembl to map chromosomal coordinates between different
+   * assemblies<br>
+   * <em>will most likely fail for species other than human</em>
+   */
+  public static MapList mapAssemblyFor(String seqRef, String species,
+          MapList map, String chromosome, String vcfAssembly)
+  {
+    List<int[]> toVcfRanges = new ArrayList<>();
+    List<int[]> fromSequenceRanges = new ArrayList<>();
+
+    for (int[] range : map.getToRanges())
+    {
+      int[] fromRange = map.locateInFrom(range[0], range[1]);
+      if (fromRange == null)
+      {
+        // corrupted map?!?
+        continue;
+      }
+
+      int[] newRange = mapReferenceRange(range, chromosome, species, seqRef,
+              vcfAssembly);
+      if (newRange == null)
+      {
+        Console.error(String.format("Failed to map %s:%s:%s:%d:%d to %s",
+                species, chromosome, seqRef, range[0], range[1],
+                vcfAssembly));
+        continue;
+      }
+      else
+      {
+        toVcfRanges.add(newRange);
+        fromSequenceRanges.add(fromRange);
+      }
+    }
+
+    return new MapList(fromSequenceRanges, toVcfRanges, 1, 1);
+  }
+
 }
diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index bd03448..f76c2ef 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -796,42 +796,8 @@ public class VCFLoader
       return new VCFMap(chromosome, map);
     }
 
-    /*
-     * VCF data has a different reference assembly to the sequence:
-     * query Ensembl to map chromosomal coordinates from sequence to VCF
-     */
-    List<int[]> toVcfRanges = new ArrayList<>();
-    List<int[]> fromSequenceRanges = new ArrayList<>();
-
-    for (int[] range : map.getToRanges())
-    {
-      int[] fromRange = map.locateInFrom(range[0], range[1]);
-      if (fromRange == null)
-      {
-        // corrupted map?!?
-        continue;
-      }
-
-      int[] newRange = GenomicAssemblies.mapReferenceRange(range, chromosome, "human", seqRef,
-              vcfAssembly);
-      if (newRange == null)
-      {
-        Console.error(String.format("Failed to map %s:%s:%s:%d:%d to %s",
-                species, chromosome, seqRef, range[0], range[1],
-                vcfAssembly));
-        continue;
-      }
-      else
-      {
-        toVcfRanges.add(newRange);
-        fromSequenceRanges.add(fromRange);
-      }
-    }
-
-    return new VCFMap(chromosome,
-            new MapList(fromSequenceRanges, toVcfRanges, 1, 1));
+    return new VCFMap(chromosome,GenomicAssemblies.mapAssemblyFor(seqRef,"human",map,chromosome,vcfAssembly));
   }
-
   /**
    * If the sequence id matches a contig declared in the VCF file, and the
    * sequence length matches the contig length, then returns a 1:1 map of the
-- 
1.7.10.2