X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;fp=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=d8858a928da000aee0c8ceeaccd31d02a581bf04;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=67b44d73b220edbda12416ae7900cc676c6f0303;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 67b44d7..d8858a9 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -37,6 +37,7 @@ 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;
@@ -305,8 +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
@@ -362,10 +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)
@@ -378,8 +378,8 @@ public class DBRefFetcher implements Runnable
           }
           if (retrieved != null)
           {
-            transferReferences(sdataset, dbsource, retrieved,
-                    trimDsSeqs, warningMessages);
+            transferReferences(sdataset, dbsource, retrieved, trimDsSeqs,
+                    warningMessages);
           }
         }
         else
@@ -398,7 +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));
@@ -406,10 +406,10 @@ public class DBRefFetcher implements Runnable
             }
             else
             {
-              Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+"); 
+              Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
               // generate queries from sequence ID string
               Matcher tokens = possibleIds.matcher(sequence.getName());
-              int p=0;
+              int p = 0;
               while (tokens.find(p))
               {
                 String token = tokens.group();
@@ -509,9 +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)
@@ -543,7 +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)))
@@ -740,7 +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(
@@ -781,15 +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
    * 
@@ -812,11 +814,11 @@ 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();
@@ -831,11 +833,12 @@ 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()]);