apply jalview code style

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

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index ad8c0f0..c1fe276 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -126,8 +126,8 @@ public class DBRefFetcher implements Runnable
       String[] defdb = null, otherdb = sfetcher\r
               .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
       Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings\r
-              .getSelectedSources()\r
-              : new jalview.gui.DasSourceBrowser().getSelectedSources();\r
+              .getSelectedSources() : new jalview.gui.DasSourceBrowser()\r
+              .getSelectedSources();\r
       Enumeration en = dasselsrc.elements();\r
       while (en.hasMoreElements())\r
       {\r
@@ -193,9 +193,7 @@ public class DBRefFetcher implements Runnable
     {\r
       String[] newsrc = new String[dbSources.length + otherdb.length];\r
       System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);\r
-      System\r
-              .arraycopy(otherdb, 0, newsrc, dbSources.length,\r
-                      otherdb.length);\r
+      System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);\r
       dbSources = newsrc;\r
     }\r
   }\r
@@ -387,9 +385,7 @@ public class DBRefFetcher implements Runnable
               for (int j = 0; j < uprefs.length; j++)\r
               {\r
                 addSeqId(sequence, uprefs[j].getAccessionId());\r
-                queries\r
-                        .addElement(uprefs[j].getAccessionId()\r
-                                .toUpperCase());\r
+                queries.addElement(uprefs[j].getAccessionId().toUpperCase());\r
               }\r
             }\r
             else\r
@@ -407,8 +403,9 @@ public class DBRefFetcher implements Runnable
                   try\r
                   {\r
                     presp = picrClient\r
-                            .getUPIForAccession(token, null, picrClient\r
-                                    .getMappedDatabaseNames(), null, true);\r
+                            .getUPIForAccession(token, null,\r
+                                    picrClient.getMappedDatabaseNames(),\r
+                                    null, true);\r
                   } catch (Exception e)\r
                   {\r
                     System.err.println("Exception with Picr for '" + token\r
@@ -447,11 +444,10 @@ public class DBRefFetcher implements Runnable
     } // all databases have been queries.\r
     if (sbuffer.length() > 0)\r
     {\r
-      output\r
-              .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"\r
-                      + "altered, most likely the start/end residue will have been updated.\n"\r
-                      + "Save your alignment to maintain the updated id.\n\n"\r
-                      + sbuffer.toString());\r
+      output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"\r
+              + "altered, most likely the start/end residue will have been updated.\n"\r
+              + "Save your alignment to maintain the updated id.\n\n"\r
+              + sbuffer.toString());\r
       Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
       // The above is the dataset, we must now find out the index\r
       // of the viewed sequence\r
@@ -496,9 +492,9 @@ public class DBRefFetcher implements Runnable
       // taking into account all accessionIds and names in the file\r
       Vector sequenceMatches = new Vector();\r
       // look for corresponding accession ids\r
-      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry\r
-              .getDBRef(), new String[]\r
-      { dbSource });\r
+      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(\r
+              entry.getDBRef(), new String[]\r
+              { dbSource });\r
       if (entryRefs == null)\r
       {\r
         System.err\r