X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=e05230bdb71f1e223acf5d7b80e05f9c73cee643;hb=refs%2Fheads%2Ffeatures%2FJAL-2446NCList;hp=da026b50b1d832a4495558d5231f39c8b3c9d146;hpb=d1bb7a31fc091606aedbc255a5766ac79e36fa91;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index da026b5..e05230b 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -136,11 +136,10 @@ public class SequenceFetcher extends JPanel implements Runnable
     {
       if (guiWindow != null)
       {
-        guiWindow
-                .setProgressBar(
-                        MessageManager
-                                .getString("status.waiting_sequence_database_fetchers_init"),
-                        Thread.currentThread().hashCode());
+        guiWindow.setProgressBar(
+                MessageManager.getString(
+                        "status.waiting_sequence_database_fetchers_init"),
+                Thread.currentThread().hashCode());
       }
       // initting happening on another thread - so wait around to see if it
       // finishes.
@@ -157,18 +156,17 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
       if (guiWindow != null)
       {
-        guiWindow
-                .setProgressBar(
-                        MessageManager
-                                .getString("status.waiting_sequence_database_fetchers_init"),
-                        Thread.currentThread().hashCode());
+        guiWindow.setProgressBar(
+                MessageManager.getString(
+                        "status.waiting_sequence_database_fetchers_init"),
+                Thread.currentThread().hashCode());
       }
     }
-    if (sfetch == null
-            || dasRegistry != Cache.getDasSourceRegistry()
+    if (sfetch == null || dasRegistry != Cache.getDasSourceRegistry()
             || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
-                    .getDasRegistryURL() + Cache.getDasSourceRegistry()
-                    .getLocalSourceString()).hashCode())
+                    .getDasRegistryURL()
+                    + Cache.getDasSourceRegistry().getLocalSourceString())
+                            .hashCode())
     {
       _initingFetcher = true;
       initingThread = Thread.currentThread();
@@ -177,8 +175,9 @@ public class SequenceFetcher extends JPanel implements Runnable
        */
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(MessageManager
-                .getString("status.init_sequence_database_fetchers"),
+        guiWindow.setProgressBar(
+                MessageManager.getString(
+                        "status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
       dasRegistry = Cache.getDasSourceRegistry();
@@ -189,8 +188,8 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
       }
-      lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
-              .getLocalSourceString()).hashCode();
+      lastDasSourceRegistry = (dasRegistry.getDasRegistryURL()
+              + dasRegistry.getLocalSourceString()).hashCode();
       sfetch = sf;
       _initingFetcher = false;
       initingThread = null;
@@ -234,14 +233,12 @@ public class SequenceFetcher extends JPanel implements Runnable
             @Override
             public void run()
             {
-              JvOptionPane
-                      .showInternalMessageDialog(
-                              Desktop.desktop,
-                              MessageManager
-                                      .getString("warn.couldnt_create_sequence_fetcher_client"),
-                              MessageManager
-                                      .getString("label.couldnt_create_sequence_fetcher"),
-                              JvOptionPane.ERROR_MESSAGE);
+              JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                      MessageManager.getString(
+                              "warn.couldnt_create_sequence_fetcher_client"),
+                      MessageManager.getString(
+                              "label.couldnt_create_sequence_fetcher"),
+                      JvOptionPane.ERROR_MESSAGE);
             }
           });
 
@@ -311,14 +308,15 @@ public class SequenceFetcher extends JPanel implements Runnable
         if (sourcep.getTier() == 0)
         {
           database.selection = Arrays
-                  .asList(new DbSourceProxy[] { sourcep });
+                  .asList(new DbSourceProxy[]
+                  { sourcep });
           break;
         }
       }
       if (database.selection == null || database.selection.size() == 0)
       {
-        System.err.println("Ignoring fetch parameter db='" + selectedDb
-                + "'");
+        System.err.println(
+                "Ignoring fetch parameter db='" + selectedDb + "'");
         return false;
       }
       textArea.setText(queryString);
@@ -379,9 +377,10 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private String getFrameTitle()
   {
-    return ((alignFrame == null) ? MessageManager
-            .getString("label.new_sequence_fetcher") : MessageManager
-            .getString("label.additional_sequence_fetcher"));
+    return ((alignFrame == null)
+            ? MessageManager.getString("label.new_sequence_fetcher")
+            : MessageManager
+                    .getString("label.additional_sequence_fetcher"));
   }
 
   private void jbInit() throws Exception
@@ -398,8 +397,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
     replacePunctuation
             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
-    replacePunctuation.setText(MessageManager
-            .getString("label.replace_commas_semicolons"));
+    replacePunctuation.setText(
+            MessageManager.getString("label.replace_commas_semicolons"));
     ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
@@ -538,8 +537,9 @@ public class SequenceFetcher extends JPanel implements Runnable
                       + database.getSelectedSources().size() + " others)"
                       : ""));
       String eq = database.getExampleQueries();
-      dbeg.setText(MessageManager.formatMessage(
-              "label.example_query_param", new String[] { eq }));
+      dbeg.setText(MessageManager.formatMessage("label.example_query_param",
+              new String[]
+              { eq }));
       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
       for (DbSourceProxy dbs : database.getSelectedSources())
       {
@@ -621,7 +621,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
     {
       empty = new com.stevesoft.pat.Regex(
-      // replace commas and spaces with a semicolon
+              // replace commas and spaces with a semicolon
               "(\\s|[,; ])+", ";");
     }
     else
@@ -631,8 +631,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     }
     textArea.setText(empty.replaceAll(textArea.getText()));
     // see if there's anthing to search with
-    if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
-            .getText()))
+    if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]")
+            .search(textArea.getText()))
     {
       error += "Please enter a (semi-colon separated list of) database id(s)";
     }
@@ -652,8 +652,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
             .iterator();
     String[] qries;
-    List<String> nextFetch = Arrays.asList(qries = textArea.getText()
-            .split(";"));
+    List<String> nextFetch = Arrays
+            .asList(qries = textArea.getText().split(";"));
     Iterator<String> en = Arrays.asList(new String[0]).iterator();
     int nqueries = qries.length;
 
@@ -673,13 +673,11 @@ public class SequenceFetcher extends JPanel implements Runnable
       try
       {
         // update status
-        guiWindow
-                .setProgressBar(MessageManager.formatMessage(
-                        "status.fetching_sequence_queries_from",
-                        new String[] {
-                            Integer.valueOf(nqueries).toString(),
-                            proxy.getDbName() }), Thread.currentThread()
-                        .hashCode());
+        guiWindow.setProgressBar(MessageManager.formatMessage(
+                "status.fetching_sequence_queries_from", new String[]
+                { Integer.valueOf(nqueries).toString(),
+                    proxy.getDbName() }),
+                Thread.currentThread().hashCode());
         if (proxy.getMaximumQueryCount() == 1)
         {
           /*
@@ -703,8 +701,8 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
       } catch (Exception e)
       {
-        showErrorMessage("Error retrieving " + textArea.getText()
-                + " from " + database.getSelectedItem());
+        showErrorMessage("Error retrieving " + textArea.getText() + " from "
+                + database.getSelectedItem());
         // error
         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
         System.err.println("Retrieval failed for source ='"
@@ -714,9 +712,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       } catch (OutOfMemoryError e)
       {
         showErrorMessage("Out of Memory when retrieving "
-                + textArea.getText()
-                + " from "
-                + database.getSelectedItem()
+                + textArea.getText() + " from " + database.getSelectedItem()
                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
         e.printStackTrace();
       } catch (Error e)
@@ -744,8 +740,8 @@ public class SequenceFetcher extends JPanel implements Runnable
           while (aresult.size() > 0)
           {
             presult.add(aresult.remove(0));
-            presultTitle.add(aresultq.remove(0) + " "
-                    + getDefaultRetrievalTitle());
+            presultTitle.add(
+                    aresultq.remove(0) + " " + getDefaultRetrievalTitle());
           }
         }
         else
@@ -773,15 +769,17 @@ public class SequenceFetcher extends JPanel implements Runnable
           presultTitle.add(titl);
         }
       }
-      guiWindow.setProgressBar(MessageManager
-              .getString("status.finshed_querying"), Thread.currentThread()
-              .hashCode());
+      guiWindow.setProgressBar(
+              MessageManager.getString("status.finshed_querying"),
+              Thread.currentThread().hashCode());
     }
-    guiWindow.setProgressBar(
-            (presult.size() > 0) ? MessageManager
-                    .getString("status.parsing_results") : MessageManager
-                    .getString("status.processing"), Thread.currentThread()
-                    .hashCode());
+    guiWindow
+            .setProgressBar(
+                    (presult.size() > 0)
+                            ? MessageManager
+                                    .getString("status.parsing_results")
+                            : MessageManager.getString("status.processing"),
+                    Thread.currentThread().hashCode());
     // process results
     while (presult.size() > 0)
     {
@@ -794,8 +792,9 @@ public class SequenceFetcher extends JPanel implements Runnable
     {
       StringBuffer sb = new StringBuffer();
       sb.append("Didn't retrieve the following "
-              + (nextFetch.size() == 1 ? "query" : nextFetch.size()
-                      + " queries") + ": \n");
+              + (nextFetch.size() == 1 ? "query"
+                      : nextFetch.size() + " queries")
+              + ": \n");
       int l = sb.length(), lr = 0;
       for (String s : nextFetch)
       {
@@ -830,8 +829,7 @@ public class SequenceFetcher extends JPanel implements Runnable
    */
   void fetchMultipleAccessions(DbSourceProxy proxy,
           Iterator<String> accessions, List<String> aresultq,
-          List<AlignmentI> aresult, List<String> nextFetch)
-          throws Exception
+          List<AlignmentI> aresult, List<String> nextFetch) throws Exception
   {
     StringBuilder multiacc = new StringBuilder();
     List<String> tosend = new ArrayList<String>();
@@ -906,8 +904,9 @@ public class SequenceFetcher extends JPanel implements Runnable
         indres = proxy.getSequenceRecords(accession);
       } catch (OutOfMemoryError oome)
       {
-        new OOMWarning("fetching " + accession + " from "
-                + proxy.getDbName(), oome, this);
+        new OOMWarning(
+                "fetching " + accession + " from " + proxy.getDbName(),
+                oome, this);
       }
       if (indres != null)
       {
@@ -917,9 +916,8 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
     } catch (Exception e)
     {
-      Cache.log.info(
-              "Error retrieving " + accession + " from "
-                      + proxy.getDbName(), e);
+      Cache.log.info("Error retrieving " + accession + " from "
+              + proxy.getDbName(), e);
     }
     return success;
   }