Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 7daa7b4..4705fe5 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws;
 
+import java.util.Locale;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Enumeration;
@@ -29,10 +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;
@@ -243,7 +248,7 @@ public class DBRefFetcher implements Runnable
    */
   void addSeqId(SequenceI seq, String key)
   {
-    key = key.toUpperCase();
+    key = key.toUpperCase(Locale.ROOT);
 
     Vector<SequenceI> seqs;
     if (seqRefs.containsKey(key))
@@ -358,9 +363,9 @@ public class DBRefFetcher implements Runnable
           AlignmentI retrieved = null;
           try
           {
-            if (Cache.log.isDebugEnabled())
+            if (Console.isDebugEnabled())
             {
-              Cache.log.debug("Querying " + dbsource.getDbName()
+              Console.debug("Querying " + dbsource.getDbName()
                       + " with : '" + queryString.toString() + "'");
             }
             retrieved = dbsource.getSequenceRecords(queryString.toString());
@@ -397,17 +402,19 @@ public class DBRefFetcher implements Runnable
                DBRefEntry upref = uprefs.get(j);
                 addSeqId(sequence, upref.getAccessionId());
                 queries.addElement(
-                        upref.getAccessionId().toUpperCase());
+                        upref.getAccessionId().toUpperCase(Locale.ROOT));
               }
             }
             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)
                 {
@@ -436,7 +443,7 @@ public class DBRefFetcher implements Runnable
                           "Validated ID against PICR... (for what its worth):"
                                   + token);
                   addSeqId(sequence, token);
-                  queries.addElement(token.toUpperCase());
+                  queries.addElement(token.toUpperCase(Locale.ROOT));
                 }
                 else
                 {
@@ -444,7 +451,7 @@ public class DBRefFetcher implements Runnable
                   // System.out.println("Not querying source with
                   // token="+token+"\n");
                   addSeqId(sequence, token);
-                  queries.addElement(token.toUpperCase());
+                  queries.addElement(token.toUpperCase(Locale.ROOT));
                 }
               }
             }
@@ -540,7 +547,7 @@ public class DBRefFetcher implements Runnable
        DBRefEntry ref = entryRefs.get(j);
         String accessionId = ref.getAccessionId();
         // match up on accessionId
-        if (seqRefs.containsKey(accessionId.toUpperCase()))
+        if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
         {
           Vector<SequenceI> seqs = seqRefs.get(accessionId);
           for (int jj = 0; jj < seqs.size(); jj++)
@@ -592,7 +599,7 @@ public class DBRefFetcher implements Runnable
       // sequenceMatches now contains the set of all sequences associated with
       // the returned db record
       final String retrievedSeqString = retrievedSeq.getSequenceAsString();
-      String entrySeq = retrievedSeqString.toUpperCase();
+      String entrySeq = retrievedSeqString.toUpperCase(Locale.ROOT);
       for (int m = 0; m < sequenceMatches.size(); m++)
       {
         sequence = sequenceMatches.elementAt(m);
@@ -611,7 +618,7 @@ public class DBRefFetcher implements Runnable
         boolean remoteEnclosesLocal = false;
         String nonGapped = AlignSeq
                 .extractGaps("-. ", sequence.getSequenceAsString())
-                .toUpperCase();
+                .toUpperCase(Locale.ROOT);
         int absStart = entrySeq.indexOf(nonGapped);
         if (absStart == -1)
         {
@@ -731,10 +738,10 @@ public class DBRefFetcher implements Runnable
               String ngAlsq = AlignSeq
                       .extractGaps("-. ",
                               alseqs[alsq].getSequenceAsString())
-                      .toUpperCase();
+                      .toUpperCase(Locale.ROOT);
               int oldstrt = alseqs[alsq].getStart();
               alseqs[alsq].setStart(sequence.getSequenceAsString()
-                      .toUpperCase().indexOf(ngAlsq) + sequence.getStart());
+                      .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
               if (oldstrt != alseqs[alsq].getStart())
               {
                 alseqs[alsq].setEnd(