X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=00bd074d66f11feb62e9767b98247cb4cea35973;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=942046596ce3bdbc8c9d8986910de170a035ab08;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 9420465..00bd074 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -31,10 +31,13 @@ import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -230,7 +233,7 @@ public class DBRefFetcher implements Runnable
     }
     else
     {
-      new Thread(this).start();
+      new Thread(this,"FetchDBRef").start();
     }
   }
 
@@ -303,8 +306,7 @@ public class DBRefFetcher implements Runnable
       e.printStackTrace();
     }
 
-    Vector<SequenceI> sdataset = new Vector<>(
-            Arrays.asList(dataset));
+    Vector<SequenceI> sdataset = new Vector<>(Arrays.asList(dataset));
     List<String> warningMessages = new ArrayList<>();
 
     // clear any old feature display settings recorded from past sessions
@@ -360,10 +362,10 @@ public class DBRefFetcher implements Runnable
           AlignmentI retrieved = null;
           try
           {
-            if (Cache.log.isDebugEnabled())
+            if (Console.isDebugEnabled())
             {
-              Cache.log.debug("Querying " + dbsource.getDbName()
-                      + " with : '" + queryString.toString() + "'");
+              Console.debug("Querying " + dbsource.getDbName() + " with : '"
+                      + queryString.toString() + "'");
             }
             retrieved = dbsource.getSequenceRecords(queryString.toString());
           } catch (Exception ex)
@@ -376,8 +378,8 @@ public class DBRefFetcher implements Runnable
           }
           if (retrieved != null)
           {
-            transferReferences(sdataset, dbsource, retrieved,
-                    trimDsSeqs, warningMessages);
+            transferReferences(sdataset, dbsource, retrieved, trimDsSeqs,
+                    warningMessages);
           }
         }
         else
@@ -396,7 +398,7 @@ public class DBRefFetcher implements Runnable
             {
               for (int j = 0, n = uprefs.size(); j < n; j++)
               {
-            	DBRefEntry upref = uprefs.get(j);
+                DBRefEntry upref = uprefs.get(j);
                 addSeqId(sequence, upref.getAccessionId());
                 queries.addElement(
                         upref.getAccessionId().toUpperCase(Locale.ROOT));
@@ -404,12 +406,14 @@ public class DBRefFetcher implements Runnable
             }
             else
             {
+              Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
               // generate queries from sequence ID string
-              StringTokenizer st = new StringTokenizer(sequence.getName(),
-                      "|");
-              while (st.hasMoreTokens())
+              Matcher tokens = possibleIds.matcher(sequence.getName());
+              int p = 0;
+              while (tokens.find(p))
               {
-                String token = st.nextToken();
+                String token = tokens.group();
+                p = tokens.end();
                 UPEntry[] presp = null;
                 if (picrClient != null)
                 {
@@ -505,9 +509,8 @@ public class DBRefFetcher implements Runnable
    *          a list of messages to add to
    */
   boolean transferReferences(Vector<SequenceI> sdataset,
-          DbSourceProxy dbSourceProxy,
-          AlignmentI retrievedAl, boolean trimDatasetSeqs,
-          List<String> warningMessages)
+          DbSourceProxy dbSourceProxy, AlignmentI retrievedAl,
+          boolean trimDatasetSeqs, List<String> warningMessages)
   {
     // System.out.println("trimming ? " + trimDatasetSeqs);
     if (retrievedAl == null || retrievedAl.getHeight() == 0)
@@ -539,7 +542,7 @@ public class DBRefFetcher implements Runnable
       }
       for (int j = 0, n = entryRefs.size(); j < n; j++)
       {
-    	DBRefEntry ref = entryRefs.get(j);
+        DBRefEntry ref = entryRefs.get(j);
         String accessionId = ref.getAccessionId();
         // match up on accessionId
         if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
@@ -736,7 +739,8 @@ public class DBRefFetcher implements Runnable
                       .toUpperCase(Locale.ROOT);
               int oldstrt = alseqs[alsq].getStart();
               alseqs[alsq].setStart(sequence.getSequenceAsString()
-                      .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
+                      .toUpperCase(Locale.ROOT).indexOf(ngAlsq)
+                      + sequence.getStart());
               if (oldstrt != alseqs[alsq].getStart())
               {
                 alseqs[alsq].setEnd(
@@ -777,15 +781,17 @@ public class DBRefFetcher implements Runnable
 
   /**
    * 
-   * @return any feature settings associated with sources that have provided sequences
+   * @return any feature settings associated with sources that have provided
+   *         sequences
    */
-  public List<FeatureSettingsModelI>getFeatureSettingsModels()
+  public List<FeatureSettingsModelI> getFeatureSettingsModels()
   {
     return featureDisplaySettings == null
             ? Arrays.asList(new FeatureSettingsModelI[0])
             : Arrays.asList(featureDisplaySettings.values()
                     .toArray(new FeatureSettingsModelI[1]));
   }
+
   /**
    * Adds the message to the list unless it already contains it
    * 
@@ -808,11 +814,13 @@ public class DBRefFetcher implements Runnable
    */
   private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
   {
-	int n;
-	if (sequencesArray == null || (n = sequencesArray.length) == 0)
-	  return sequencesArray;
+    int n;
+    if (sequencesArray == null || (n = sequencesArray.length) == 0)
+    {
+      return sequencesArray;
+    }
     ArrayList<SequenceI> nseq = new ArrayList<>();
-    for (int i = 0;i < n; i++)
+    for (int i = 0; i < n; i++)
     {
       nseq.add(sequencesArray[i]);
       List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
@@ -827,11 +835,12 @@ public class DBRefFetcher implements Runnable
             {
               nseq.add(map.getTo());
             }
-          }  
+          }
         }
       }
     }
-    // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found?
+    // BH 2019.01.25 question here if this is the right logic. Return the
+    // original if nothing found?
     if (nseq.size() > 0)
     {
       return nseq.toArray(new SequenceI[nseq.size()]);