X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSequenceSource.java;h=eeaccf4cd2befe6376f49f13b56cbb2d7ebf534f;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=a63727ffd199cfd4dd8d72feaf7d0c8a1fcaebf3;hpb=a7f34b0d86a0ebc79dcb26d36e73fc7a64581fee;p=jalview.git

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index a63727f..eeaccf4 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -67,7 +67,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   protected String dbname = "DASCS";
 
   protected String dbrefname = "das:source";
-  protected MultipleConnectionPropertyProviderI connprops=null;
+
+  protected MultipleConnectionPropertyProviderI connprops = null;
+
   /**
    * create a new DbSource proxy for a DAS 1 source
    * 
@@ -84,20 +86,23 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
    *           if source is not capable of the 'sequence' command
    */
   public DasSequenceSource(String dbname, String dbrefname, SOURCE source,
-          VERSION version, COORDINATES coordsys, MultipleConnectionPropertyProviderI connprops) throws Exception
+          VERSION version, COORDINATES coordsys,
+          MultipleConnectionPropertyProviderI connprops) throws Exception
   {
-    if (!(jsrc = new JalviewSource(source, connprops, false)).isSequenceSource())
+    if (!(jsrc = new JalviewSource(source, connprops, false))
+            .isSequenceSource())
     {
       throw new Exception("Source " + source.getTitle()
               + " does not support the sequence command.");
     }
     this.source = source;
     this.dbname = dbname;
-    this.dbrefname = dbrefname;
-    if (coordsys!=null ) {
+    this.dbrefname = dbrefname.toUpperCase();
+    if (coordsys != null)
+    {
       this.coordsys = coordsys;
     }
-    this.connprops=connprops;
+    this.connprops = connprops;
   }
 
   public String getAccessionSeparator()
@@ -108,7 +113,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   public Regex getAccessionValidator()
   {
     /** ? * */
-    return Regex.perlCode("\\S+");
+    return Regex.perlCode("m/([^:]+)(:\\d+,\\d+)?/");
   }
 
   public String getDbName()
@@ -124,7 +129,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 
   public String getDbVersion()
   {
-    return coordsys!=null ? coordsys.getVersion() : "";
+    return coordsys != null ? coordsys.getVersion() : "";
   }
 
   public AlignmentI getSequenceRecords(String queries) throws Exception
@@ -140,7 +145,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     src.add(jsrc.getSourceURL());
     Map<String, Map<List<String>, DasSequenceAdapter>> resultset = new HashMap<String, Map<List<String>, DasSequenceAdapter>>();
     Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();
-    
+
     // First try multiple sources
     boolean multiple = true, retry = false;
     do
@@ -154,7 +159,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
           System.err
                   .println("Retrieving IDs individually from das source: "
                           + sr);
-          org.biodas.jdas.client.SequenceClient sq = new SequenceClient(connprops.getConnectionPropertyProviderFor(sr));
+          org.biodas.jdas.client.SequenceClient sq = new SequenceClient(
+                  connprops.getConnectionPropertyProviderFor(sr));
           for (String q : toks)
           {
             List<String> qset = Arrays.asList(new String[]
@@ -253,6 +259,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
               // in the XML
               Sequence sq = new Sequence(lbl, e.getContent().replaceAll(
                       "\\s+", ""));
+              sq.setStart(e.getStart().intValue());
               sq.addDBRef(new DBRefEntry(getDbSource(), getDbVersion()
                       + ":" + e.getVersion(), lbl));
               seqs.addElement(sq);
@@ -275,18 +282,19 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
         srcs.addElement(jsrc);
         try
         {
-          jalview.ws.DasSequenceFeatureFetcher dssf=new jalview.ws.DasSequenceFeatureFetcher(sqs, null, srcs, false,
-                  false, multiple);
+          jalview.ws.DasSequenceFeatureFetcher dssf = new jalview.ws.DasSequenceFeatureFetcher(
+                  sqs, null, srcs, false, false, multiple);
           while (dssf.isRunning())
           {
-            try {
+            try
+            {
               Thread.sleep(200);
             } catch (InterruptedException x)
             {
-              
+
             }
           }
-          
+
         } catch (Exception x)
         {
           Cache.log
@@ -301,7 +309,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 
   public String getTestQuery()
   {
-    return coordsys==null ? "" : coordsys.getTestRange();
+    return coordsys == null ? "" : coordsys.getTestRange();
   }
 
   public boolean isValidReference(String accession)