X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=b16c37f83ce16b5e3088d9443e3a865d3d133947;hb=373ea2f39547c5432fc2922e5d958e1955de14e8;hp=9ede0f55d69b2d3e54d49167bcb6d988aaafa64e;hpb=3bf2b5ea57b1d77d6e2e7adc11a50387e5376dc0;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9ede0f5..b16c37f 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -323,9 +323,9 @@ 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())
+        if (!Jalview.isHeadlessMode() && !Jalview.isBatchMode())
         {
           JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                   MessageManager.getString("label.couldnt_read_data")
@@ -356,13 +356,14 @@ 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.
         }
         // BH 2018 switch to File object here instead of filename
-        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(
-                selectedFile == null ? file : selectedFile);
+        alignFrame = new Jalview2XML(raiseGUI && !Jalview.isBatchMode())
+                .loadJalviewAlign(
+                        selectedFile == null ? file : selectedFile);
       }
       else
       {
@@ -537,7 +538,7 @@ public class FileLoader implements Runnable
                   "label.couldnt_load_file") + " " + title + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
-          if (raiseGUI && Desktop.desktop != null)
+          if (raiseGUI && !Jalview.isBatchMode() && Desktop.desktop != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
@@ -554,7 +555,7 @@ public class FileLoader implements Runnable
           }
           else
           {
-            System.err.println(errorMessage);
+            jalview.bin.Console.errPrintln(errorMessage);
           }
         }
       }
@@ -563,9 +564,10 @@ 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)
+      if (raiseGUI && !Jalview.isBatchMode())
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
@@ -587,7 +589,7 @@ public class FileLoader implements Runnable
 
       er.printStackTrace();
       alignFrame = null;
-      if (raiseGUI)
+      if (raiseGUI && !Jalview.isBatchMode())
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
@@ -603,7 +605,8 @@ 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();
@@ -622,7 +625,7 @@ 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)");
@@ -631,7 +634,7 @@ 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)");
@@ -684,10 +687,18 @@ public class FileLoader implements Runnable
     AlignViewport avp = af.getViewport();
     if (avp == null)
       return;
-    avp.setSavedUpToDate(!protocol.isDynamic(),
-            QuitHandler.Message.UNSAVED_ALIGNMENTS);
+    boolean upToDate = !protocol.isDynamic();
+    if (protocol.isUrl() && !Cache
+            .getDefault(PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS, true))
+    {
+      upToDate = true;
+    }
+    avp.setSavedUpToDate(upToDate,
+            upToDate ? null : QuitHandler.Message.UNSAVED_ALIGNMENTS);
   }
 
+  public static final String PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS = "PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS";
+
   public static boolean getUseDefaultFileFormat()
   {
     return useDefaultFileFormat;