Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 4705fe5..0ebd3c3 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -302,12 +302,11 @@ public class DBRefFetcher implements Runnable
       }
     } catch (Exception e)
     {
-      System.err.println("Couldn't locate PICR service instance.\n");
+      jalview.bin.Console.errPrintln("Couldn't locate PICR service instance.\n");
       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
@@ -317,7 +316,7 @@ public class DBRefFetcher implements Runnable
     while (sdataset.size() > 0 && db < dbSources.length)
     {
       int maxqlen = 1; // default number of queries made at one time
-      System.out.println("Verifying against " + dbSources[db].getDbName());
+      jalview.bin.Console.outPrintln("Verifying against " + dbSources[db].getDbName());
 
       // iterate through db for each remaining un-verified sequence
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];
@@ -365,8 +364,8 @@ public class DBRefFetcher implements Runnable
           {
             if (Console.isDebugEnabled())
             {
-              Console.debug("Querying " + dbsource.getDbName()
-                      + " with : '" + queryString.toString() + "'");
+              Console.debug("Querying " + dbsource.getDbName() + " with : '"
+                      + queryString.toString() + "'");
             }
             retrieved = dbsource.getSequenceRecords(queryString.toString());
           } catch (Exception ex)
@@ -379,8 +378,8 @@ public class DBRefFetcher implements Runnable
           }
           if (retrieved != null)
           {
-            transferReferences(sdataset, dbsource, retrieved,
-                    trimDsSeqs, warningMessages);
+            transferReferences(sdataset, dbsource, retrieved, trimDsSeqs,
+                    warningMessages);
           }
         }
         else
@@ -399,7 +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));
@@ -407,10 +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();
@@ -426,7 +425,7 @@ public class DBRefFetcher implements Runnable
                             true);
                   } catch (Exception e)
                   {
-                    System.err.println(
+                    jalview.bin.Console.errPrintln(
                             "Exception with Picr for '" + token + "'\n");
                     e.printStackTrace();
                   }
@@ -439,7 +438,7 @@ public class DBRefFetcher implements Runnable
                     // present, and do a transferReferences
                     // otherwise transfer non sequence x-references directly.
                   }
-                  System.out.println(
+                  jalview.bin.Console.outPrintln(
                           "Validated ID against PICR... (for what its worth):"
                                   + token);
                   addSeqId(sequence, token);
@@ -448,7 +447,7 @@ public class DBRefFetcher implements Runnable
                 else
                 {
                   // if ()
-                  // System.out.println("Not querying source with
+                  // jalview.bin.Console.outPrintln("Not querying source with
                   // token="+token+"\n");
                   addSeqId(sequence, token);
                   queries.addElement(token.toUpperCase(Locale.ROOT));
@@ -510,11 +509,10 @@ 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);
+    // jalview.bin.Console.outPrintln("trimming ? " + trimDatasetSeqs);
     if (retrievedAl == null || retrievedAl.getHeight() == 0)
     {
       return false;
@@ -544,7 +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)))
@@ -680,7 +678,7 @@ public class DBRefFetcher implements Runnable
           }
         }
 
-        System.out.println("Adding dbrefs to " + sequence.getName()
+        jalview.bin.Console.outPrintln("Adding dbrefs to " + sequence.getName()
                 + " from " + dbSource + " sequence : "
                 + retrievedSeq.getName());
         sequence.transferAnnotation(retrievedSeq, mp);
@@ -741,7 +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(
@@ -782,15 +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
    * 
@@ -813,11 +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();
@@ -832,11 +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()]);