X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileLoader.java;h=bf79fa4c0c0c4fcc4e49db3663f672d18af6dee4;hb=81d1b5ee333dee61382971eca41792d6a64a29fc;hp=3b4cc3127b3b4aa7d644d0e74e703b3c6c94df84;hpb=2e59bc7938c0f10bde61fd30d1841bedb3d8319e;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3b4cc31..bf79fa4 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -74,6 +74,8 @@ public class FileLoader implements Runnable
 
   private File selectedFile;
 
+  private static boolean useDefaultFileFormat = false;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -288,8 +290,6 @@ public class FileLoader implements Runnable
   @Override
   public void run()
   {
-    System.out.println("######## Starting FileLoader.run()");
-    System.out.println("######## loading file " + file);
     String title = protocol == DataSourceType.PASTE
             ? "Copied From Clipboard"
             : file;
@@ -323,7 +323,7 @@ public class FileLoader implements Runnable
       if (format == null)
       {
         Desktop.instance.stopLoading();
-        System.err.println("The input file \"" + file
+        jalview.bin.Console.errPrintln("The input file \"" + file
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
@@ -334,7 +334,8 @@ public class FileLoader implements Runnable
                   MessageManager.getString("label.couldnt_read_data"),
                   JvOptionPane.WARNING_MESSAGE);
         }
-        this.setShouldBeSaved();
+        // don't set shouldBeSaved if didn't load anything
+        // this.setShouldBeSaved();
         return;
       }
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
@@ -355,7 +356,7 @@ public class FileLoader implements Runnable
         if (source != null)
         {
           // Tell the user (developer?) that this is going to cause a problem
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
           // We read the data anyway - it might make sense.
         }
@@ -553,7 +554,7 @@ public class FileLoader implements Runnable
           }
           else
           {
-            System.err.println(errorMessage);
+            jalview.bin.Console.errPrintln(errorMessage);
           }
         }
       }
@@ -562,7 +563,7 @@ public class FileLoader implements Runnable
 
     } catch (Exception er)
     {
-      System.err.println("Exception whilst opening file '" + file);
+      jalview.bin.Console.errPrintln("Exception whilst opening file '" + file);
       er.printStackTrace();
       if (raiseGUI)
       {
@@ -602,7 +603,7 @@ public class FileLoader implements Runnable
           }
         });
       }
-      System.err.println("Out of memory loading file " + file + "!!");
+      jalview.bin.Console.errPrintln("Out of memory loading file " + file + "!!");
 
     }
     loadtime += System.currentTimeMillis();
@@ -621,7 +622,7 @@ public class FileLoader implements Runnable
       {
         AlignmentI al = alignFrame.getViewport().getAlignment();
 
-        System.out.println("Loaded '" + title + "' in "
+        jalview.bin.Console.outPrintln("Loaded '" + title + "' in "
                 + (loadtime / 1000.0) + "s, took an additional "
                 + (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
                 + al.getHeight() + " seqs by " + al.getWidth() + " cols)");
@@ -630,7 +631,7 @@ public class FileLoader implements Runnable
       {
         // report that we didn't load anything probably due to an out of memory
         // error
-        System.out.println("Failed to load '" + title + "' in "
+        jalview.bin.Console.outPrintln("Failed to load '" + title + "' in "
                 + (loadtime / 1000.0) + "s, took an additional "
                 + (1.0 * memused / (1024.0 * 1024.0))
                 + " MB (alignment is null)");
@@ -643,6 +644,8 @@ public class FileLoader implements Runnable
     }
 
     this.setShouldBeSaved();
+    // after first file loaded we revert to assuming a default file format
+    useDefaultFileFormat = true;
   }
 
   /**
@@ -685,4 +688,9 @@ public class FileLoader implements Runnable
             QuitHandler.Message.UNSAVED_ALIGNMENTS);
   }
 
+  public static boolean getUseDefaultFileFormat()
+  {
+    return useDefaultFileFormat;
+  }
+
 }