Merge branch 'develop' into releases/Release_2_10_2_Branch

[jalview.git] / src / jalview / ws / dbsources / das / datamodel / DasSequenceSource.java

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 32e4f3e..84f6d4d 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -57,8 +57,8 @@ import com.stevesoft.pat.Regex;
  * @author JimP
  * 
  */
-public class DasSequenceSource extends DbSourceProxyImpl implements
-        DbSourceProxy
+public class DasSequenceSource extends DbSourceProxyImpl
+        implements DbSourceProxy
 {
   private jalviewSourceI jsrc;
 
@@ -104,7 +104,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     {
       throw new Exception(MessageManager.formatMessage(
               "exception.das_source_doesnt_support_sequence_command",
-              new String[] { source.getTitle() }));
+              new String[]
+              { source.getTitle() }));
     }
     this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
     this.source = source;
@@ -147,7 +148,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     StringTokenizer st = new StringTokenizer(queries, "\t");
-    List<String> toks = new ArrayList<String>(), src = new ArrayList<String>(), acIds = new ArrayList<String>();
+    List<String> toks = new ArrayList<String>(),
+            src = new ArrayList<String>(), acIds = new ArrayList<String>();
     while (st.hasMoreTokens())
     {
       String t;
@@ -168,9 +170,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
         // slow, fetch one at a time.
         for (String sr : src)
         {
-          System.err
-                  .println("Retrieving IDs individually from das source: "
-                          + sr);
+          System.err.println(
+                  "Retrieving IDs individually from das source: " + sr);
           org.biodas.jdas.client.SequenceClient sq = new SequenceClient(
                   connprops.getConnectionPropertyProviderFor(sr));
           for (String q : toks)
@@ -182,9 +183,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
               Map<List<String>, DasSequenceAdapter> dss = resultset.get(sr);
               if (dss == null)
               {
-                resultset
-                        .put(sr,
-                                dss = new HashMap<List<String>, DasSequenceAdapter>());
+                resultset.put(sr,
+                        dss = new HashMap<List<String>, DasSequenceAdapter>());
               }
               dss.put(qset, s);
             } catch (Exception x)
@@ -192,7 +192,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
               Map<List<String>, Exception> ers = errors.get(sr);
               if (ers == null)
               {
-                errors.put(sr, ers = new HashMap<List<String>, Exception>());
+                errors.put(sr,
+                        ers = new HashMap<List<String>, Exception>());
               }
               ers.put(qset, x);
             }
@@ -246,8 +247,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 
             if (acIds.indexOf(lbl) == -1)
             {
-              System.err
-                      .println("Warning - received sequence event for strange accession code ("
+              System.err.println(
+                      "Warning - received sequence event for strange accession code ("
                               + lbl + ")");
             }
             else
@@ -256,11 +257,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
               {
                 if (e.getContent().length() == 0)
                 {
-                  System.err
-                          .println("Empty sequence returned for accession code ("
-                                  + lbl
-                                  + ") from "
-                                  + resset.getKey()
+                  System.err.println(
+                          "Empty sequence returned for accession code ("
+                                  + lbl + ") from " + resset.getKey()
                                   + " (source is " + getDbName());
                   continue;
                 }
@@ -268,11 +267,11 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
               seqs = new java.util.Vector<SequenceI>();
               // JDAS returns a sequence complete with any newlines and spaces
               // in the XML
-              Sequence sq = new Sequence(lbl, e.getContent().replaceAll(
-                      "\\s+", ""));
+              Sequence sq = new Sequence(lbl,
+                      e.getContent().replaceAll("\\s+", ""));
               sq.setStart(e.getStart().intValue());
-              sq.addDBRef(new DBRefEntry(getDbSource(), getDbVersion()
-                      + ":" + e.getVersion(), lbl));
+              sq.addDBRef(new DBRefEntry(getDbSource(),
+                      getDbVersion() + ":" + e.getVersion(), lbl));
               seqs.addElement(sq);
             }
           }
@@ -308,9 +307,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 
         } catch (Exception x)
         {
-          Cache.log
-                  .error("Couldn't retrieve features for sequence from its source.",
-                          x);
+          Cache.log.error(
+                  "Couldn't retrieve features for sequence from its source.",
+                  x);
         }
       }