formatting

[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 269baf1..eeaccf4 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -67,7 +67,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   protected String dbname = "DASCS";\r
 \r
   protected String dbrefname = "das:source";\r
-  protected MultipleConnectionPropertyProviderI connprops=null;\r
+\r
+  protected MultipleConnectionPropertyProviderI connprops = null;\r
+\r
   /**\r
    * create a new DbSource proxy for a DAS 1 source\r
    * \r
@@ -84,9 +86,11 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
    *           if source is not capable of the 'sequence' command\r
    */\r
   public DasSequenceSource(String dbname, String dbrefname, SOURCE source,\r
-          VERSION version, COORDINATES coordsys, MultipleConnectionPropertyProviderI connprops) throws Exception\r
+          VERSION version, COORDINATES coordsys,\r
+          MultipleConnectionPropertyProviderI connprops) throws Exception\r
   {\r
-    if (!(jsrc = new JalviewSource(source, connprops, false)).isSequenceSource())\r
+    if (!(jsrc = new JalviewSource(source, connprops, false))\r
+            .isSequenceSource())\r
     {\r
       throw new Exception("Source " + source.getTitle()\r
               + " does not support the sequence command.");\r
@@ -94,10 +98,11 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     this.source = source;\r
     this.dbname = dbname;\r
     this.dbrefname = dbrefname.toUpperCase();\r
-    if (coordsys!=null ) {\r
+    if (coordsys != null)\r
+    {\r
       this.coordsys = coordsys;\r
     }\r
-    this.connprops=connprops;\r
+    this.connprops = connprops;\r
   }\r
 \r
   public String getAccessionSeparator()\r
@@ -124,7 +129,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 \r
   public String getDbVersion()\r
   {\r
-    return coordsys!=null ? coordsys.getVersion() : "";\r
+    return coordsys != null ? coordsys.getVersion() : "";\r
   }\r
 \r
   public AlignmentI getSequenceRecords(String queries) throws Exception\r
@@ -140,7 +145,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     src.add(jsrc.getSourceURL());\r
     Map<String, Map<List<String>, DasSequenceAdapter>> resultset = new HashMap<String, Map<List<String>, DasSequenceAdapter>>();\r
     Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();\r
-    \r
+\r
     // First try multiple sources\r
     boolean multiple = true, retry = false;\r
     do\r
@@ -154,7 +159,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
           System.err\r
                   .println("Retrieving IDs individually from das source: "\r
                           + sr);\r
-          org.biodas.jdas.client.SequenceClient sq = new SequenceClient(connprops.getConnectionPropertyProviderFor(sr));\r
+          org.biodas.jdas.client.SequenceClient sq = new SequenceClient(\r
+                  connprops.getConnectionPropertyProviderFor(sr));\r
           for (String q : toks)\r
           {\r
             List<String> qset = Arrays.asList(new String[]\r
@@ -276,18 +282,19 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
         srcs.addElement(jsrc);\r
         try\r
         {\r
-          jalview.ws.DasSequenceFeatureFetcher dssf=new jalview.ws.DasSequenceFeatureFetcher(sqs, null, srcs, false,\r
-                  false, multiple);\r
+          jalview.ws.DasSequenceFeatureFetcher dssf = new jalview.ws.DasSequenceFeatureFetcher(\r
+                  sqs, null, srcs, false, false, multiple);\r
           while (dssf.isRunning())\r
           {\r
-            try {\r
+            try\r
+            {\r
               Thread.sleep(200);\r
             } catch (InterruptedException x)\r
             {\r
-              \r
+\r
             }\r
           }\r
-          \r
+\r
         } catch (Exception x)\r
         {\r
           Cache.log\r
@@ -302,7 +309,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 \r
   public String getTestQuery()\r
   {\r
-    return coordsys==null ? "" : coordsys.getTestRange();\r
+    return coordsys == null ? "" : coordsys.getTestRange();\r
   }\r
 \r
   public boolean isValidReference(String accession)\r