X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSequenceSource.java;h=84f6d4da05261611adecb02f8da8dda0787adbcf;hb=9b8a7cae41e5d0e2dfcd806319ca2d301dd133c5;hp=3ad35733f71ae781499e286324c089fd75cd95ee;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 3ad3573..84f6d4d 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,17 @@
  */
 package jalview.ws.dbsources.das.datamodel;
 
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -39,16 +50,6 @@ import org.biodas.jdas.schema.sources.VERSION;
 
 import com.stevesoft.pat.Regex;
 
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.*;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
 /**
  * an instance of this class is created for each unique DAS Sequence source (ie
  * one capable of handling the 'sequence' for a particular MapMaster)
@@ -56,8 +57,8 @@ import jalview.datamodel.SequenceI;
  * @author JimP
  * 
  */
-public class DasSequenceSource extends DbSourceProxyImpl implements
-        DbSourceProxy
+public class DasSequenceSource extends DbSourceProxyImpl
+        implements DbSourceProxy
 {
   private jalviewSourceI jsrc;
 
@@ -101,7 +102,10 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     if (!(jsrc = new JalviewSource(source, connprops, false))
             .isSequenceSource())
     {
-      throw new Exception(MessageManager.formatMessage("exception.das_source_doesnt_support_sequence_command", new String[]{source.getTitle()}));
+      throw new Exception(MessageManager.formatMessage(
+              "exception.das_source_doesnt_support_sequence_command",
+              new String[]
+              { source.getTitle() }));
     }
     this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
     this.source = source;
@@ -144,7 +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;
@@ -165,24 +170,21 @@ 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)
           {
-            List<String> qset = Arrays.asList(new String[]
-            { q });
+            List<String> qset = Arrays.asList(new String[] { q });
             try
             {
               DasSequenceAdapter s = sq.fetchData(sr, qset);
               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)
@@ -190,7 +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);
             }
@@ -244,8 +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
@@ -254,11 +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;
                 }
@@ -266,11 +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);
             }
           }
@@ -306,9 +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);
         }
       }