X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=69ee379c6a0b5144884860703d962a2520662757;hb=9bfda76754fb426a471e1c12c9f0ca0c4c1784bc;hp=371eb50bc227365a4e74ae147aa73ea94a0d6261;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 371eb50..69ee379 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -20,9 +20,26 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Locale;
+import java.util.Vector;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -41,23 +58,6 @@ import jalview.xml.binding.uniprot.LocationType;
 import jalview.xml.binding.uniprot.PositionType;
 import jalview.xml.binding.uniprot.PropertyType;
 
-import java.io.InputStream;
-import java.net.HttpURLConnection;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * This class queries the Uniprot database for sequence data, unmarshals the
  * returned XML, and converts it to Jalview Sequence records (including attached
@@ -194,7 +194,7 @@ public class Uniprot extends DbSourceProxyImpl
 
     SequenceI sequence = new Sequence(id, seqString);
     sequence.setDescription(getUniprotEntryDescription(entry));
-
+    final String uniprotRecordVersion = "" + entry.getVersion();
     /*
      * add a 'self' DBRefEntry for each accession
      */
@@ -203,8 +203,8 @@ public class Uniprot extends DbSourceProxyImpl
     boolean canonical = true;
     for (String accessionId : entry.getAccession())
     {
-      DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
-              accessionId, null, canonical);
+      DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT,
+              uniprotRecordVersion, accessionId, null, canonical);
       canonical = false;
       dbRefs.add(dbRef);
     }
@@ -242,13 +242,23 @@ public class Uniprot extends DbSourceProxyImpl
           // remove version
           String[] vrs = cdsId.split("\\.");
           String version = vrs.length > 1 ? vrs[1]
-                  : DBRefSource.UNIPROT + ":" + dbVersion;
+                  : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
           dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
+          // TODO: process VARIANT features to allow EMBLCDS record's product to
+          // match Uniprot
+          dbr.setCanonical(true);
           dbRefs.add(dbr);
         }
       }
-      if ("Ensembl".equals(type))
+      if (type != null
+              && type.toLowerCase(Locale.ROOT).startsWith("ensembl"))
       {
+        // remove version
+        String[] vrs = dbref.getId().split("\\.");
+        String version = vrs.length > 1 ? vrs[1]
+                : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
+        dbr.setAccessionId(vrs[0]);
+        dbr.setVersion(version);
         /*
          * e.g. Uniprot accession Q9BXM7 has
          * <dbReference type="Ensembl" id="ENST00000321556">
@@ -261,8 +271,12 @@ public class Uniprot extends DbSourceProxyImpl
                 "protein sequence ID");
         if (cdsId != null && cdsId.trim().length() > 0)
         {
+          // remove version
+          String[] cdsVrs = cdsId.split("\\.");
+          String cdsVersion = cdsVrs.length > 1 ? cdsVrs[1]
+                  : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
           dbr = new DBRefEntry(DBRefSource.ENSEMBL,
-                  DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
+                  DBRefSource.UNIPROT + ":" + cdsVersion, cdsVrs[0]);
           dbRefs.add(dbr);
         }
       }
@@ -279,19 +293,68 @@ public class Uniprot extends DbSourceProxyImpl
         LocationType location = uf.getLocation();
         int start = 0;
         int end = 0;
+        String uncertain_start = null, uncertain_end = null,
+                uncertain_pos = null;
         if (location.getPosition() != null)
         {
-          start = location.getPosition().getPosition().intValue();
-          end = start;
+          if (location.getPosition().getPosition() == null
+                  || "unknown".equals(location.getPosition().getStatus()))
+          {
+            Console.warn(
+                    "Ignoring single position feature with uncertain location "
+                            + uf.getType() + ":" + getDescription(uf));
+            uncertain_pos = location.getPosition().getStatus() == null
+                    ? "unknown"
+                    : location.getPosition().getStatus();
+          }
+          else
+          {
+            start = location.getPosition().getPosition().intValue();
+            end = start;
+          }
         }
         else
         {
-          start = location.getBegin().getPosition().intValue();
-          end = location.getEnd().getPosition().intValue();
+          if (location.getBegin().getPosition() == null)
+          {
+            Console.warn(
+                    "Setting start position of feature with uncertain start to 1: "
+                            + uf.getType() + ":" + getDescription(uf));
+            start = sequence.getStart();
+            uncertain_start = location.getBegin().getStatus();
+          }
+          else
+          {
+            start = location.getBegin().getPosition().intValue();
+          }
+          if (location.getEnd().getPosition() == null)
+          {
+            Console.warn(
+                    "Setting start position of feature with uncertain start to 1: "
+                            + uf.getType() + ":" + getDescription(uf));
+            end = sequence.getEnd();
+            uncertain_end = location.getEnd().getStatus();
+          }
+          else
+          {
+            end = location.getEnd().getPosition().intValue();
+          }
         }
         SequenceFeature sf = new SequenceFeature(uf.getType(),
                 getDescription(uf), start, end, "Uniprot");
         sf.setStatus(uf.getStatus());
+        if (uncertain_end != null)
+        {
+          sf.setValue("end_status", uncertain_end);
+        }
+        if (uncertain_start != null)
+        {
+          sf.setValue("start_status", uncertain_start);
+        }
+        if (uncertain_pos != null)
+        {
+          sf.setValue("pos_status", uncertain_pos);
+        }
         sequence.addSequenceFeature(sf);
       }
     }