formatting

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index bf522ef..f9779ad 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -61,7 +61,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   /**
    * Blocking method that initialises and returns the shared instance of the
    * SequenceFetcher client
-   *
+   * 
    * @param guiWindow
    *          - where the initialisation delay message should be shown
    * @return the singleton instance of the sequence fetcher client
@@ -182,7 +182,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   /**
    * called by thread spawned by constructor
-   *
+   * 
    * @param guiWindow
    */
   private void initGui(IProgressIndicator guiWindow)
@@ -305,8 +305,9 @@ public class SequenceFetcher extends JPanel implements Runnable
                           + " others)" : ""));
           String eq = database.getExampleQueries();
           dbeg.setText("Example query: " + eq);
-          boolean enablePunct=!(eq != null && eq.indexOf(",") > -1);
-          for (DbSourceProxy dbs:database.getSelectedSources()) {
+          boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+          for (DbSourceProxy dbs : database.getSelectedSources())
+          {
             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
             {
               enablePunct = false;
@@ -457,7 +458,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       return;
     }
     // indicate if successive sources should be merged into one alignment.
-    boolean addToLast=false;
+    boolean addToLast = false;
     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
@@ -573,15 +574,21 @@ public class SequenceFetcher extends JPanel implements Runnable
                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
                 dbr.setSource(proxy.getDbSource());
                 dbr.setVersion(null);
-                if (proxy.getAccessionValidator()!=null) {
-                  Regex vgr=proxy.getAccessionValidator();
+                if (proxy.getAccessionValidator() != null)
+                {
+                  Regex vgr = proxy.getAccessionValidator();
                   vgr.search(q);
-                  if (vgr.numSubs()>0) {
+                  if (vgr.numSubs() > 0)
+                  {
                     dbr.setAccessionId(vgr.stringMatched(1));
-                  } else {
+                  }
+                  else
+                  {
                     dbr.setAccessionId(vgr.stringMatched());
                   }
-                } else {
+                }
+                else
+                {
                   dbr.setAccessionId(q);
                 }
                 boolean rfound = false;
@@ -641,7 +648,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         AlignmentI ar = null;
         if (isAliSource)
         {
-          addToLast=false;
+          addToLast = false;
           // new window for each result
           while (aresult.size() > 0)
           {
@@ -652,11 +659,11 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         else
         {
-          String titl=null;
-          if (addToLast && presult.size()>0)
+          String titl = null;
+          if (addToLast && presult.size() > 0)
           {
-            ar=presult.remove(presult.size()-1);
-            titl=presultTitle.remove(presultTitle.size()-1);
+            ar = presult.remove(presult.size() - 1);
+            titl = presultTitle.remove(presultTitle.size() - 1);
           }
           // concatenate all results in one window
           while (aresult.size() > 0)
@@ -671,14 +678,16 @@ public class SequenceFetcher extends JPanel implements Runnable
             }
             ;
           }
-          addToLast=true;
+          addToLast = true;
           presult.add(ar);
           presultTitle.add(titl);
         }
       }
-      guiWindow.setProgressBar("Finished querying", Thread.currentThread().hashCode());
+      guiWindow.setProgressBar("Finished querying", Thread.currentThread()
+              .hashCode());
     }
-    guiWindow.setProgressBar((presult.size()>0) ? "Parsing results.":"Processing ..", Thread.currentThread().hashCode());
+    guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
+            : "Processing ..", Thread.currentThread().hashCode());
     // process results
     while (presult.size() > 0)
     {
@@ -692,14 +701,14 @@ public class SequenceFetcher extends JPanel implements Runnable
       sb.append("Didn't retrieve the following "
               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
                       + " queries") + ": \n");
-      int l = sb.length(),lr=0;
+      int l = sb.length(), lr = 0;
       for (String s : nextfetch)
       {
         if (l != sb.length())
         {
           sb.append("; ");
         }
-        if (lr-sb.length()>40)
+        if (lr - sb.length() > 40)
         {
           sb.append("\n");
         }
@@ -740,7 +749,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   }
 
   /**
-   *
+   * 
    * @return a standard title for any results retrieved using the currently
    *         selected source and settings
    */