formatting

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

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 5413a30..bbf3143 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -106,7 +106,8 @@ public class DBRefFetcher implements Runnable
    * @param sources\r
    *          array of database source strings to query references from\r
    */\r
-  public DBRefFetcher(SequenceI[] seqs, AlignFrame af, DbSourceProxy[] sources)\r
+  public DBRefFetcher(SequenceI[] seqs, AlignFrame af,\r
+          DbSourceProxy[] sources)\r
   {\r
     this.af = af;\r
     alseqs = new SequenceI[seqs.length];\r
@@ -135,11 +136,11 @@ public class DBRefFetcher implements Runnable
       while (en.hasMoreElements())\r
       {\r
         jalviewSourceI src = en.nextElement();\r
-        List<DbSourceProxy> sp=src.getSequenceSourceProxies();\r
+        List<DbSourceProxy> sp = src.getSequenceSourceProxies();\r
         selsources.addAll(sp);\r
-        if (sp.size()>1)\r
+        if (sp.size() > 1)\r
         {\r
-          Cache.log.debug("Added many Db Sources for :"+src.getTitle());\r
+          Cache.log.debug("Added many Db Sources for :" + src.getTitle());\r
         }\r
       }\r
       // select appropriate databases based on alignFrame context.\r
@@ -151,14 +152,16 @@ public class DBRefFetcher implements Runnable
       {\r
         defdb = DBRefSource.PROTEINDBS;\r
       }\r
-      List<DbSourceProxy> srces=new ArrayList<DbSourceProxy>();\r
-      for (String ddb:defdb) {\r
-        List<DbSourceProxy> srcesfordb=sfetcher.getSourceProxy(ddb);\r
-        if (srcesfordb!=null) {\r
+      List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();\r
+      for (String ddb : defdb)\r
+      {\r
+        List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);\r
+        if (srcesfordb != null)\r
+        {\r
           srces.addAll(srcesfordb);\r
         }\r
       }\r
-      \r
+\r
       // append the selected sequence sources to the default dbs\r
       srces.addAll(selsources);\r
       dbSources = srces.toArray(new DbSourceProxy[0]);\r
@@ -182,11 +185,12 @@ public class DBRefFetcher implements Runnable
       dbSources = new DbSourceProxy[0];\r
     }\r
     // append additional sources\r
-    DbSourceProxy[] otherdb=sfetcher\r
+    DbSourceProxy[] otherdb = sfetcher\r
             .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);\r
     if (otherdb != null && otherdb.length > 0)\r
     {\r
-      DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length + otherdb.length];\r
+      DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length\r
+              + otherdb.length];\r
       System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);\r
       System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);\r
       dbSources = newsrc;\r
@@ -304,8 +308,11 @@ public class DBRefFetcher implements Runnable
 \r
       jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];\r
       {\r
-        // for moment, we dumbly iterate over all retrieval sources for a particular database\r
-        // TODO: introduce multithread multisource queries and logic to remove a query from other sources if any source for a database returns a record\r
+        // for moment, we dumbly iterate over all retrieval sources for a\r
+        // particular database\r
+        // TODO: introduce multithread multisource queries and logic to remove a\r
+        // query from other sources if any source for a database returns a\r
+        // record\r
         if (dbsource.getDbSourceProperties().containsKey(\r
                 DBRefSource.MULTIACC))\r
         {\r
@@ -360,7 +367,8 @@ public class DBRefFetcher implements Runnable
             }\r
             if (retrieved != null)\r
             {\r
-              transferReferences(sdataset, dbsource.getDbSource(), retrieved);\r
+              transferReferences(sdataset, dbsource.getDbSource(),\r
+                      retrieved);\r
             }\r
           }\r
           else\r