JAL-1705 regular expression updates, tests, other refactoring

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index f60125b..467fc6d 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -10,9 +10,13 @@ import com.stevesoft.pat.Regex;
 
 public class EnsemblCdna extends EnsemblSeqProxy
 {
-  // TODO modify to accept other species e.g. ENSMUSPnnn
+  /*
+   * accepts ENST or ENSTG with 11 digits
+   * or ENSMUST or similar for other species
+   * or CCDSnnnnn.nn with at least 3 digits
+   */
   private static final Regex ACCESSION_REGEX = new Regex(
-          "(ENST|ENSG|CCDS)[0-9.]{3,}$");
+          "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
   
   /*
    * fetch exon features on genomic sequence (to identify the cdna regions)

diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
index 29c7eda..fb79ccf 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -10,9 +10,13 @@ import com.stevesoft.pat.Regex;
 
 public class EnsemblProtein extends EnsemblSeqProxy
 {
-  // TODO modify to accept other species e.g. ENSMUSPnnn
+  /*
+   * accepts ENSP with 11 digits
+   * or ENSMUSP or similar for other species
+   * or CCDSnnnnn.nn with at least 3 digits
+   */
   private static final Regex ACCESSION_REGEX = new Regex(
-          "(ENSP|CCDS)[0-9.]{3,}$");
+          "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
 
   private static final List<String> CROSSREFS = Arrays.asList(new String[] {
       "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 215eb7a..297f71b 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -14,6 +14,8 @@ import java.util.List;
 
 import javax.ws.rs.HttpMethod;
 
+import com.stevesoft.pat.Regex;
+
 /**
  * Base class for Ensembl REST service clients
  * 
@@ -31,12 +33,28 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   private final static long RETEST_INTERVAL = 10000L; // 10 seconds
 
+  private static final Regex TRANSCRIPT_REGEX = new Regex(
+            "(ENS)([A-Z]{3}|)T[0-9]{11}$");
+
+  private static final Regex GENE_REGEX = new Regex(
+            "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+
   private static boolean ensemblRestAvailable = false;
 
   private static long lastCheck = -1;
 
   protected volatile boolean inProgress = false;
 
+  public static boolean isTranscriptIdentifier(String query)
+  {
+    return query == null ? false : TRANSCRIPT_REGEX.search(query);
+  }
+
+  public static boolean isGeneIdentifier(String query)
+  {
+    return query == null ? false : GENE_REGEX.search(query);
+  }
+
   @Override
   public boolean queryInProgress()
   {

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index a2be17b..77263ff 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -30,8 +30,6 @@ import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map.Entry;
 
-import com.stevesoft.pat.Regex;
-
 /**
  * Base class for Ensembl sequence fetchers
  * 
@@ -39,12 +37,8 @@ import com.stevesoft.pat.Regex;
  */
 public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
-  // TODO modify to accept other species e.g. ENSMUSTnnn
-  private static final Regex TRANSCRIPT_REGEX = new Regex(
-          "(ENST)[0-9]{11}$");
-
   private static final List<String> CROSS_REFERENCES = Arrays
-          .asList(new String[] { "CCDS" });
+          .asList(new String[] { "CCDS", "Uniprot/SWISSPROT" });
 
   protected static final String CONSEQUENCE_TYPE = "consequence_type";
 
@@ -163,6 +157,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       }
     }
 
+    if (alignment == null)
+    {
+      return null;
+    }
+
     /*
      * fetch and transfer genomic sequence features,
      * fetch protein product and add as cross-reference
@@ -344,7 +343,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     int mappedDnaLength = getCdsRanges(dnaSeq, ranges);
 
     int proteinLength = proteinSeq.getLength();
-    List<int[]> proteinRange = new ArrayList<int[]>();
     int proteinStart = 1;
 
     /*
@@ -356,15 +354,20 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       proteinStart = 2;
       proteinLength--;
     }
-    proteinRange.add(new int[] { proteinStart, proteinLength });
+    List<int[]> proteinRange = new ArrayList<int[]>();
 
     /*
      * dna length should map to protein (or protein plus stop codon)
      */
     int codesForResidues = mappedDnaLength / 3;
-    if (codesForResidues == proteinLength
-            || codesForResidues == (proteinLength + 1))
+    if (codesForResidues == (proteinLength + 1))
+    {
+      MappingUtils.unmapStopCodon(ranges, mappedDnaLength);
+      codesForResidues--;
+    }
+    if (codesForResidues == proteinLength)
     {
+      proteinRange.add(new int[] { proteinStart, proteinLength });
       return new MapList(ranges, proteinRange, 3, 1);
     }
     return null;
@@ -389,14 +392,14 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     {
       return 0;
     }
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
     int mappedDnaLength = 0;
     for (SequenceFeature sf : sfs)
     {
       /*
        * process a CDS feature (or a sub-type of CDS)
        */
-      if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
-              SequenceOntologyI.CDS))
+      if (so.isA(sf.getType(), SequenceOntologyI.CDS))
       {
         int phase = 0;
         try {
@@ -411,7 +414,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
          */
         int begin = sf.getBegin();
         int end = sf.getEnd();
-        if (ranges.isEmpty() && phase > 0)
+        if (ranges.isEmpty())
         {
           begin += phase;
           if (begin > end)
@@ -1129,9 +1132,4 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
             || SequenceOntologyFactory.getInstance().isA(featureType,
                     SequenceOntologyI.TRANSCRIPT);
   }
-
-  public static boolean isTranscriptIdentifier(String query)
-  {
-    return query == null ? false : TRANSCRIPT_REGEX.search(query);
-  }
 }

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index 67c5e63..9a4952e 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -12,9 +12,13 @@ import com.stevesoft.pat.Regex;
  */
 abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 {
-  // TODO modify to accept other species e.g. ENSMUSTnnn
+  /*
+   * accepts ENSG/T/E/P with 11 digits
+   * or ENSMUSP or similar for other species
+   * or CCDSnnnnn.nn with at least 3 digits
+   */
   private static final Regex ACCESSION_REGEX = new Regex(
-          "(ENSP|ENST|ENSG|CCDS)[0-9.]{3,}$");
+          "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
 
   /*
    * possible values for the 'feature' parameter of the /overlap REST service

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index d4c5b18..514e44a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -22,7 +22,7 @@ import org.json.simple.parser.ParseException;
  * service
  * 
  * @author gmcarstairs
- *
+ * @see http://rest.ensembl.org/documentation/info/xref_id
  */
 class EnsemblXref extends EnsemblRestClient
 {
@@ -42,8 +42,7 @@ class EnsemblXref extends EnsemblRestClient
   @Override
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getUrl(ids.get(0));
   }
 
   @Override

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index 2d99a52..90c38d4 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -14,6 +14,7 @@ import jalview.util.MapList;
 
 import java.util.List;
 
+import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -234,4 +235,17 @@ public class EnsemblCdnaTest
     sf.setType("CDS");
     assertFalse(testee.identifiesSequence(sf, accId));
   }
+
+  @Test(groups = "Functional")
+  public void testIsValidReference() throws Exception
+  {
+    EnsemblSequenceFetcher esq = new EnsemblCdna();
+    Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
+    Assert.assertTrue(esq.isValidReference("ENST00000288602"));
+    Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
+    Assert.assertFalse(esq.isValidReference("ENSP00000288602"));
+    Assert.assertFalse(esq.isValidReference("ENST0000288602"));
+    // non-human species having a 3 character identifier included:
+    Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
+  }
 }

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index fb17845..183f933 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdsTest.java
@@ -13,6 +13,7 @@ import jalview.util.MapList;
 
 import java.util.List;
 
+import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -151,4 +152,17 @@ public class EnsemblCdsTest
     assertFalse(testee.identifiesSequence(sf, accId));
   }
 
+  @Test(groups = "Functional")
+  public void testIsValidReference() throws Exception
+  {
+    EnsemblSequenceFetcher esq = new EnsemblCds();
+    Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
+    Assert.assertTrue(esq.isValidReference("ENST00000288602"));
+    Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
+    Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
+    Assert.assertFalse(esq.isValidReference("ENST0000288602"));
+    // non-human species have a 3 character identifier included:
+    Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
+  }
+
 }

diff --git a/test/jalview/ext/ensembl/EnsemblProteinTest.java b/test/jalview/ext/ensembl/EnsemblProteinTest.java
index c5db0a8..e6f6683 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblProteinTest.java
+++ b/test/jalview/ext/ensembl/EnsemblProteinTest.java
@@ -16,6 +16,8 @@ public class EnsemblProteinTest
     Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
     Assert.assertFalse(esq.isValidReference("ENST00000288602"));
     Assert.assertFalse(esq.isValidReference("ENSG00000288602"));
+    // non-human species having a 3 character identifier included:
+    Assert.assertTrue(esq.isValidReference("ENSMUSP00000099398"));
   }
 
   @Test(groups = "Functional")

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 73d2858..7ef8dd7 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -368,8 +368,22 @@ public class EnsemblSeqProxyTest
     assertFalse(EnsemblSeqProxy.isTranscriptIdentifier(""));
     assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENSG00000012345"));
     assertTrue(EnsemblSeqProxy.isTranscriptIdentifier("ENST00000012345"));
+    assertTrue(EnsemblSeqProxy.isTranscriptIdentifier("ENSMUST00000012345"));
     assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("enst00000012345"));
     assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENST000000123456"));
     assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENST0000001234"));
   }
+
+  @Test(groups = "Functional")
+  public void testIsGeneIdentifier()
+  {
+    assertFalse(EnsemblSeqProxy.isGeneIdentifier(null));
+    assertFalse(EnsemblSeqProxy.isGeneIdentifier(""));
+    assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENST00000012345"));
+    assertTrue(EnsemblSeqProxy.isGeneIdentifier("ENSG00000012345"));
+    assertTrue(EnsemblSeqProxy.isGeneIdentifier("ENSMUSG00000012345"));
+    assertFalse(EnsemblSeqProxy.isGeneIdentifier("ensg00000012345"));
+    assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENSG000000123456"));
+    assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENSG0000001234"));
+  }
 }
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