Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux' into...

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 5211fa7..63247a7 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -677,7 +677,7 @@ public class Commands
       AlignFrame af = afMap.get(id);
       if (af != null)
       {
-        af.setWrapFormat(wrap);
+        af.setWrapFormat(wrap, true);
       }
     }
 
@@ -854,6 +854,7 @@ public class Commands
         String val = av.getValue();
         SubVals subVals = av.getSubVals();
         String fileName = subVals.getContent();
+        boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
         File file = new File(fileName);
         boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
                 Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
@@ -866,7 +867,7 @@ public class Commands
                 !Platform.isHeadless());
 
         // if backups is not true then --overwrite must be specified
-        if (file.exists() && !(overwrite || backups))
+        if (file.exists() && !(overwrite || backups || stdout))
         {
           Console.error("Won't overwrite file '" + fileName + "' without "
                   + Arg.OVERWRITE.argString() + " or "
@@ -904,23 +905,30 @@ public class Commands
         }
         if (ff == null)
         {
-          StringBuilder validSB = new StringBuilder();
-          for (String f : validFormats)
-          {
-            if (validSB.length() > 0)
-              validSB.append(", ");
-            validSB.append(f);
-            FileFormatI tff = ffs.forName(f);
-            validSB.append(" (");
-            validSB.append(tff.getExtensions());
-            validSB.append(")");
+          if (stdout)
+          {
+            ff = FileFormat.Fasta;
           }
+          else
+          {
+            StringBuilder validSB = new StringBuilder();
+            for (String f : validFormats)
+            {
+              if (validSB.length() > 0)
+                validSB.append(", ");
+              validSB.append(f);
+              FileFormatI tff = ffs.forName(f);
+              validSB.append(" (");
+              validSB.append(tff.getExtensions());
+              validSB.append(")");
+            }
 
-          Jalview.exit("No valid format specified for "
-                  + Arg.OUTPUT.argString() + ". Valid formats are "
-                  + validSB.toString() + ".", 1);
-          // this return really shouldn't happen
-          return false;
+            Jalview.exit("No valid format specified for "
+                    + Arg.OUTPUT.argString() + ". Valid formats are "
+                    + validSB.toString() + ".", 1);
+            // this return really shouldn't happen
+            return false;
+          }
         }
 
         String savedBackupsPreference = Cache
@@ -931,7 +939,7 @@ public class Commands
 
         Console.info("Writing " + fileName);
 
-        af.saveAlignment(fileName, ff);
+        af.saveAlignment(fileName, ff, stdout);
         Console.debug("Returning backups to " + savedBackupsPreference);
         if (savedBackupsPreference != null)
           Cache.applicationProperties.put(BackupFiles.ENABLED,