JAL-1793 update spike build to latest incl stop and synonymous variants on peptides

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 35ceea3..9229379 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -49,8 +49,6 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
 
 /**
  * Base class for Ensembl sequence fetchers
@@ -60,10 +58,6 @@ import java.util.Map.Entry;
  */
 public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
-  protected static final String PARENT = "Parent";
-
-  protected static final String ID = "ID";
-
   protected static final String NAME = "Name";
 
   protected static final String DESCRIPTION = "description";
@@ -208,7 +202,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     try
     {
       /*
-       * get 'dummy' genomic sequence with exon, cds and variation features
+       * get 'dummy' genomic sequence with gene, transcript, 
+       * exon, cds and variation features
        */
       SequenceI genomicSequence = null;
       EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
@@ -224,7 +219,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         /*
          * transfer features to the query sequence
          */
-        SequenceI querySeq = alignment.findName(accId);
+        SequenceI querySeq = alignment.findName(accId, true);
         if (transferFeatures(accId, genomicSequence, querySeq))
         {
 
@@ -471,14 +466,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     urlstring.append("?type=").append(getSourceEnsemblType().getType());
     urlstring.append(("&Accept=text/x-fasta"));
 
-    Map<String, String> params = getAdditionalParameters();
-    if (params != null)
+    String objectType = getObjectType();
+    if (objectType != null)
     {
-      for (Entry<String, String> entry : params.entrySet())
-      {
-        urlstring.append("&").append(entry.getKey()).append("=")
-                .append(entry.getValue());
-      }
+      urlstring.append("&").append(OBJECT_TYPE).append("=")
+              .append(objectType);
     }
 
     URL url = new URL(urlstring.toString());
@@ -486,11 +478,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   }
 
   /**
-   * Override this method to add any additional x=y URL parameters needed
+   * Override this method to specify object_type request parameter
    * 
    * @return
    */
-  protected Map<String, String> getAdditionalParameters()
+  protected String getObjectType()
   {
     return null;
   }
@@ -559,7 +551,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
           String accId, int start)
   {
-    // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
     List<SequenceFeature> sfs = sourceSequence.getFeatures()
             .getPositionalFeatures();
     if (sfs.isEmpty())
@@ -571,7 +562,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
      * generously initial size for number of cds regions
      * (worst case titin Q8WZ42 has c. 313 exons)
      */
-    List<int[]> regions = new ArrayList<int[]>(100);
+    List<int[]> regions = new ArrayList<>(100);
     int mappedLength = 0;
     int direction = 1; // forward
     boolean directionSet = false;
@@ -871,7 +862,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   {
     String parent = (String) sf.getValue(PARENT);
     // using contains to allow for prefix "gene:", "transcript:" etc
-    if (parent != null && !parent.contains(identifier))
+    if (parent != null
+            && !parent.toUpperCase().contains(identifier.toUpperCase()))
     {
       // this genomic feature belongs to a different transcript
       return false;
@@ -899,14 +891,14 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   protected List<SequenceFeature> findFeatures(SequenceI sequence,
           String term, String parentId)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
     List<SequenceFeature> sfs = sequence.getFeatures()
             .getFeaturesByOntology(term);
     for (SequenceFeature sf : sfs)
     {
       String parent = (String) sf.getValue(PARENT);
-      if (parent != null && parent.equals(parentId))
+      if (parent != null && parent.equalsIgnoreCase(parentId))
       {
         result.add(sf);
       }