JAL-1807 explicit imports (jalview.gui)

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index c330a92..1561ecc 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -29,7 +30,9 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -155,9 +158,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
     }
     if (sfetch == null
-            || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
-            || lastDasSourceRegistry != (jalview.bin.Cache
-                    .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+            || dasRegistry != Cache.getDasSourceRegistry()
+            || lastDasSourceRegistry != (Cache
+                    .getDasSourceRegistry().getDasRegistryURL() + Cache
                     .getDasSourceRegistry().getLocalSourceString())
                     .hashCode())
     {
@@ -171,7 +174,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
-      dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+      dasRegistry = Cache.getDasSourceRegistry();
       dasRegistry.refreshSources();
 
       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
@@ -260,7 +263,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
     }
@@ -408,7 +411,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
       for (DbSourceProxy dbs : database.getSelectedSources())
       {
-        if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+        if (dbs instanceof DasSequenceSource)
         {
           enablePunct = false;
           break;
@@ -484,21 +487,21 @@ public class SequenceFetcher extends JPanel implements Runnable
       error += "Please select the source database\n";
     }
     // TODO: make this transformation more configurable
-    com.stevesoft.pat.Regex empty;
+    Regex empty;
     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
     {
-      empty = new com.stevesoft.pat.Regex(
+      empty = new Regex(
       // replace commas and spaces with a semicolon
               "(\\s|[,; ])+", ";");
     }
     else
     {
       // just turn spaces and semicolons into single semicolons
-      empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+      empty = new Regex("(\\s|[; ])+", ";");
     }
     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
+    if (!new Regex("[A-Za-z0-9_.]").search(textArea
             .getText()))
     {
       error += "Please enter a (semi-colon separated list of) database id(s)";
@@ -579,7 +582,7 @@ public class SequenceFetcher extends JPanel implements Runnable
               }
             } catch (Exception e)
             {
-              jalview.bin.Cache.log.info("Error retrieving " + item
+              Cache.log.info("Error retrieving " + item
                       + " from " + proxy.getDbName(), e);
               nextfetch.add(item);
             }
@@ -856,7 +859,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         try
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+          af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
                   false));
         } catch (Exception ex)
         {