Merge branch 'develop' into improvement/JAL-3594_BG_and_UoD_logos_added

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8deff01..07baa2e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -93,6 +93,7 @@ import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -368,7 +369,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+    String sortby = Cache.getDefault("SORT_ALIGNMENT",
             "No sort");
 
     if (sortby.equals("Id"))
@@ -411,7 +412,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       wrapMenuItem_actionPerformed(null);
     }
 
-    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+    if (Cache.getDefault("SHOW_OVERVIEW", false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
@@ -1014,7 +1015,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public String getVersion()
   {
-    return jalview.bin.Cache.getProperty("VERSION");
+    return Cache.getProperty("VERSION");
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -1216,7 +1217,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       else
       {
-        Cache.log.error(MessageManager
+        Console.error(MessageManager
                 .formatMessage("label.couldnt_save_file", new Object[]
                 { lastFilenameSaved }));
       }
@@ -1299,7 +1300,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           BackupFiles backupfiles = null;
           if (doBackup)
           {
-            Cache.log.trace(
+            Console.trace(
                     "ALIGNFRAME making backupfiles object for " + file);
             backupfiles = new BackupFiles(file);
           }
@@ -1307,19 +1308,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             String tempFilePath = doBackup ? backupfiles.getTempFilePath()
                     : file;
-            Cache.log.trace("ALIGNFRAME setting PrintWriter");
+            Console.trace("ALIGNFRAME setting PrintWriter");
             PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
 
             if (backupfiles != null)
             {
-              Cache.log.trace("ALIGNFRAME about to write to temp file "
+              Console.trace("ALIGNFRAME about to write to temp file "
                       + backupfiles.getTempFilePath());
             }
 
             out.print(output);
-            Cache.log.trace("ALIGNFRAME about to close file");
+            Console.trace("ALIGNFRAME about to close file");
             out.close();
-            Cache.log.trace("ALIGNFRAME closed file");
+            Console.trace("ALIGNFRAME closed file");
             AlignFrame.this.setTitle(file);
             statusBar.setText(MessageManager.formatMessage(
                     "label.successfully_saved_to_file_in_format",
@@ -1329,29 +1330,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           } catch (IOException e)
           {
             lastSaveSuccessful = false;
-            Cache.log.error(
+            Console.error(
                     "ALIGNFRAME Something happened writing the temp file");
-            Cache.log.error(e.getMessage());
-            Cache.log.debug(Cache.getStackTraceString(e));
+            Console.error(e.getMessage());
+            Console.debug(Cache.getStackTraceString(e));
           } catch (Exception ex)
           {
             lastSaveSuccessful = false;
-            Cache.log.error(
+            Console.error(
                     "ALIGNFRAME Something unexpected happened writing the temp file");
-            Cache.log.error(ex.getMessage());
-            Cache.log.debug(Cache.getStackTraceString(ex));
+            Console.error(ex.getMessage());
+            Console.debug(Cache.getStackTraceString(ex));
           }
 
           if (doBackup)
           {
             backupfiles.setWriteSuccess(lastSaveSuccessful);
-            Cache.log.debug("ALIGNFRAME writing temp file was "
+            Console.debug("ALIGNFRAME writing temp file was "
                     + (lastSaveSuccessful ? "" : "NOT ") + "successful");
             // do the backup file roll and rename the temp file to actual file
-            Cache.log.trace(
+            Console.trace(
                     "ALIGNFRAME about to rollBackupsAndRenameTempFile");
             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
-            Cache.log.debug(
+            Console.debug(
                     "ALIGNFRAME performed rollBackupsAndRenameTempFile "
                             + (lastSaveSuccessful ? "" : "un")
                             + "successfully");
@@ -1534,7 +1535,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void associatedData_actionPerformed(ActionEvent e)
   {
     final JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     String tooltip = MessageManager
             .getString("label.load_jalview_annotations");
@@ -1546,7 +1547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void run()
       {
         String choice = chooser.getSelectedFile().getPath();
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+        Cache.setProperty("LAST_DIRECTORY", choice);
         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
       }
     });
@@ -1733,7 +1734,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (originalSource != viewport)
       {
-        Cache.log.warn(
+        Console.warn(
                 "Implementation worry: mismatch of viewport origin for undo");
       }
       originalSource.updateHiddenColumns();
@@ -1773,7 +1774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (originalSource != viewport)
       {
-        Cache.log.warn(
+        Console.warn(
                 "Implementation worry: mismatch of viewport origin for redo");
       }
       originalSource.updateHiddenColumns();
@@ -4069,7 +4070,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.select_newick_like_tree_file"));
@@ -4333,7 +4334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               } catch (Exception e)
               {
-                Cache.log.debug(
+                Console.debug(
                         "Exception during web service menu building process.",
                         e);
               }
@@ -4430,7 +4431,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showProducts.setEnabled(showp);
     } catch (Exception e)
     {
-      Cache.log.warn(
+      Console.warn(
               "canShowProducts threw an exception - please report to help@jalview.org",
               e);
       return false;
@@ -4471,7 +4472,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       al = dna.translateCdna(codeTable);
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error(
+      Console.error(
               "Exception during translation. Please report this !", ex);
       final String msg = MessageManager.getString(
               "label.error_when_translating_sequences_submit_bug_report");
@@ -4834,7 +4835,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         } catch (Exception x)
         {
-          Cache.log.debug(
+          Console.debug(
                   "Exception when processing data source as T-COFFEE score file",
                   x);
           tcf = null;