From: Ben Soares Date: Wed, 23 Aug 2023 07:58:11 +0000 (+0100) Subject: Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into... X-Git-Tag: Release_2_11_3_0~8^2~41 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1ef93cb2817f75699773f049b8d25e5b509c2830;hp=03bc8848382795bda548083f0bc3202dfe6a9b8b;p=jalview.git Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0 --- diff --git a/build.gradle b/build.gradle index 7ad6f99..c4ed582 100644 --- a/build.gradle +++ b/build.gradle @@ -1834,6 +1834,10 @@ tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { te info.events = [ TestLogEvent.FAILED ] } + if (OperatingSystem.current().isMacOsX()) { + testTask.systemProperty "apple.awt.UIElement", "true" + testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true" + } ignoreFailures = true // Always try to run all tests for all modules diff --git a/examples/argfiles/test_fab41.txt b/examples/argfiles/test_fab41.txt index e6f7627..b7f0d45 100644 --- a/examples/argfiles/test_fab41.txt +++ b/examples/argfiles/test_fab41.txt @@ -10,4 +10,4 @@ --paematrix=[label=pAE R4-M5]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json --structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1.pdb --paematrix=[label=pAE R5-M1]./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json ---image=output1.html +--image=[textrenderer=text]output1.html diff --git a/examples/argfiles/test_fab41_nostructureviewers.txt b/examples/argfiles/test_fab41_nostructureviewers.txt new file mode 100644 index 0000000..ab52cdf --- /dev/null +++ b/examples/argfiles/test_fab41_nostructureviewers.txt @@ -0,0 +1,14 @@ +--open=./examples/test_fab41.result/sample.a2m +--colour=gecos:flower +--gui +--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb +--paematrix=[label=pAE R1-M3]./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json +--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb +--paematrix=[label=pAE R2-M4]./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4_scores.json +--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb +--paematrix=[label=pAE R3-M2]./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2_scores.json +--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5.pdb +--paematrix=[label=pAE R4-M5]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json +--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1.pdb +--paematrix=[label=pAE R5-M1]./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json +--image=[textrenderer=text]output1.html diff --git a/getdown/lib/FJVL_VERSION b/getdown/lib/FJVL_VERSION index 35bd812..25d39f4 100644 --- a/getdown/lib/FJVL_VERSION +++ b/getdown/lib/FJVL_VERSION @@ -1 +1 @@ -1.8.3-1.2.14_FJVL +1.8.3-1.3.0_FJVL diff --git a/getdown/lib/JVL_VERSION b/getdown/lib/JVL_VERSION index 0a14c3b..12110b2 100644 --- a/getdown/lib/JVL_VERSION +++ b/getdown/lib/JVL_VERSION @@ -1 +1 @@ -1.8.3-1.2.14_JVL +1.8.3-1.3.0_JVL diff --git a/getdown/lib/getdown-core.jar b/getdown/lib/getdown-core.jar index 7c99c93..fb8f1bc 100644 Binary files a/getdown/lib/getdown-core.jar and b/getdown/lib/getdown-core.jar differ diff --git a/getdown/lib/getdown-launcher-local.jar b/getdown/lib/getdown-launcher-local.jar index c6901ae..c74dcc5 100644 Binary files a/getdown/lib/getdown-launcher-local.jar and b/getdown/lib/getdown-launcher-local.jar differ diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar index 24e3eb2..e1f1726 100644 Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ diff --git a/getdown/src/getdown/ant/pom.xml b/getdown/src/getdown/ant/pom.xml index b0c54e2..d8bb7e9 100644 --- a/getdown/src/getdown/ant/pom.xml +++ b/getdown/src/getdown/ant/pom.xml @@ -4,7 +4,7 @@ com.threerings.getdown getdown - 1.8.3-1.2.14_FJVL + 1.8.3-1.3.0_FJVL getdown-ant diff --git a/getdown/src/getdown/core/pom.xml b/getdown/src/getdown/core/pom.xml index 5dd429d..6126686 100644 --- a/getdown/src/getdown/core/pom.xml +++ b/getdown/src/getdown/core/pom.xml @@ -4,7 +4,7 @@ com.threerings.getdown getdown - 1.8.3-1.2.14_FJVL + 1.8.3-1.3.0_FJVL getdown-core diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java index 0781a11..1faaa28 100644 --- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java +++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java @@ -17,6 +17,8 @@ import javax.xml.bind.DatatypeConverter; import java.security.MessageDigest; +import jalview.util.LaunchUtils; + import static com.threerings.getdown.Log.log; /** @@ -88,6 +90,7 @@ public class LaunchUtil return getJVMPath(appdir, false); } + private static String jvmPath = null; /** * Reconstructs the path to the JVM used to launch this process. * @@ -95,22 +98,27 @@ public class LaunchUtil */ public static String getJVMPath (File appdir, boolean windebug) { - // first look in our application directory for an installed VM - String vmpath = checkJVMPath(new File(appdir, LOCAL_JAVA_DIR).getAbsolutePath(), windebug); - if (vmpath == null && isMacOS()) { - vmpath = checkJVMPath(new File(appdir, LOCAL_JAVA_DIR + "/Contents/Home").getAbsolutePath(), windebug); + if (jvmPath != null) { + return jvmPath; } + + // first look in our application directory for an installed VM + final String appDir = isMacOS() ? + (new File(appdir, LOCAL_JAVA_DIR).getAbsolutePath()) + "/Contents/Home" + : new File(appdir, LOCAL_JAVA_DIR).getAbsolutePath(); + + String javaBin = LaunchUtils.findJavaBin(appDir, windebug, false); // then fall back to the VM in which we're already running - if (vmpath == null) { - vmpath = checkJVMPath(System.getProperty("java.home"), windebug); + if (javaBin == null) { + javaBin = LaunchUtils.findJavaBin(System.getProperty("java.home"), windebug, false); } // then throw up our hands and hope for the best - if (vmpath == null) { + if (javaBin == null) { + javaBin = LaunchUtils.findJavaBin(null, windebug, true); log.warning("Unable to find java [appdir=" + appdir + ", java.home=" + System.getProperty("java.home") + "]!"); - vmpath = "java"; } // Oddly, the Mac OS X specific java flag -Xdock:name will only work if java is launched @@ -120,15 +128,16 @@ public class LaunchUtil if (isMacOS()) { try { File localVM = new File("/usr/bin/java").getCanonicalFile(); - if (localVM.equals(new File(vmpath).getCanonicalFile())) { - vmpath = "/usr/bin/java"; + if (localVM.equals(new File(javaBin).getCanonicalFile())) { + javaBin = "/usr/bin/java"; } } catch (IOException ioe) { log.warning("Failed to check Mac OS canonical VM path.", ioe); } } - return vmpath; + jvmPath = javaBin; + return jvmPath; } private static String _getMD5FileChecksum (File file) { diff --git a/getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java b/getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java index ee3b2c6..784eb5a 100644 --- a/getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java +++ b/getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java @@ -32,6 +32,16 @@ import java.util.Properties; public class LaunchUtils { + // setting these is LaunchUtils so don't need to import Platform + public final static boolean isMac = System.getProperty("os.name") + .indexOf("Mac") > -1; + + public final static boolean isWindows = System.getProperty("os.name") + .indexOf("Win") > -1; + + private static boolean isJS = /** @j2sNative true || */ + false; + public static void loadChannelProps(File dir) { ChannelProperties.loadProps(dir); @@ -81,7 +91,11 @@ public class LaunchUtils public static int getJavaCompileVersion() { - if (JAVA_COMPILE_VERSION > 0) + if (LaunchUtils.isJS) + { + return -1; + } + else if (JAVA_COMPILE_VERSION > 0) { return JAVA_COMPILE_VERSION; } @@ -125,7 +139,11 @@ public class LaunchUtils public static int getJavaVersion() { - if (JAVA_VERSION > 0) + if (LaunchUtils.isJS) + { + return -1; + } + else if (JAVA_VERSION > 0) { return JAVA_VERSION; } @@ -153,6 +171,10 @@ public class LaunchUtils public static boolean checkJavaVersion() { + if (LaunchUtils.isJS) + { + return true; + } String buildDetails = "jar:".concat(LaunchUtils.class .getProtectionDomain().getCodeSource().getLocation().toString() .concat("!" + "/.build_properties")); @@ -174,4 +196,88 @@ public class LaunchUtils return true; } + + public static String findJavaBin(boolean winConsole) + { + return findJavaBin(System.getProperty("java.home"), winConsole, true); + } + + /* + * Returns a string path to the most likely java binary wanted to run this + * installation of Jalview. + * + * @param winConsole whether to use java.exe (console) in preference to javaw.exe + * (only affects Windows). + * @param javaHome Try this javaHome dir (defaults to the running java.home). + * @param generic Return a generic java command if not found. + */ + public static String findJavaBin(String javaHome, boolean winConsole, + boolean generic) + { + String javaBin = null; + final String javaExe = winConsole ? "java.exe" : "javaw.exe"; + final String java = "java"; + + if (javaHome != null) + { + // property "channel.app_name" is set by install4j when launching getdown + String propertyAppName = System.getProperty("channel.app_name"); + final String appName = (propertyAppName != null + && propertyAppName.length() > 0) ? propertyAppName + : ChannelProperties.getProperty("app_name"); + + final String javaBinDir = javaHome + File.separator + "bin" + + File.separator; + + // appName and "Jalview" will not point to javaw.exe or java.exe but in + // this case that's okay because the taskbar display name problem doesn't + // manifest in Windows. See JAL-3820, JAL-4189. + for (String name : new String[] { appName, "Jalview", java, javaExe }) + { + if (LaunchUtils.checkJVMSymlink(javaBinDir + name, winConsole)) + { + javaBin = javaBinDir + name; + break; + } + } + } + + if (javaBin == null && generic) + { + javaBin = LaunchUtils.isWindows ? javaExe : java; + } + + return javaBin; + } + + /* + * checkJVMSymlink returns true if the path in testBin *is* a java binary, or + * points to a java binary. + * @param testBin The binary or symbolic link to check + * @param winConsole whether we are in/want a Windows console (only relevant for Windows, + * determines whether we use java.exe or javaw.exe) + */ + private static boolean checkJVMSymlink(String testBin, boolean winConsole) + { + File testBinFile = new File(testBin); + if (!testBinFile.exists()) + { + return false; + } + File targetFile = null; + try + { + targetFile = testBinFile.getCanonicalFile(); + } catch (IOException e) + { + return false; + } + final String javaExe = winConsole ? "java.exe" : "javaw.exe"; + if (targetFile != null && ("java".equals(targetFile.getName()) + || javaExe.equals(targetFile.getName()))) + { + return true; + } + return false; + } } diff --git a/getdown/src/getdown/launcher/pom.xml b/getdown/src/getdown/launcher/pom.xml index ea3b6ef..4374899 100644 --- a/getdown/src/getdown/launcher/pom.xml +++ b/getdown/src/getdown/launcher/pom.xml @@ -4,7 +4,7 @@ com.threerings.getdown getdown - 1.8.3-1.2.14_FJVL + 1.8.3-1.3.0_FJVL getdown-launcher diff --git a/getdown/src/getdown/mvn_cmd b/getdown/src/getdown/mvn_cmd index b30194f..ba092a7 100755 --- a/getdown/src/getdown/mvn_cmd +++ b/getdown/src/getdown/mvn_cmd @@ -3,7 +3,7 @@ if [ x$JVLVERSION != x ]; then export VERSION=$JVLVERSION else - export VERSION=1.8.3-1.2.14_JVL + export VERSION=1.8.3-1.3.0_JVL fi if [ x${VERSION%_JVL} = x$VERSION ]; then diff --git a/getdown/src/getdown/pom.xml b/getdown/src/getdown/pom.xml index ef8c811..51e9514 100644 --- a/getdown/src/getdown/pom.xml +++ b/getdown/src/getdown/pom.xml @@ -10,7 +10,7 @@ com.threerings.getdown getdown pom - 1.8.3-1.2.14_FJVL + 1.8.3-1.3.0_FJVL getdown An application installer and updater. diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html index 7a87602..7eb2294 100644 --- a/help/help/html/features/clarguments-basic.html +++ b/help/help/html/features/clarguments-basic.html @@ -393,6 +393,7 @@ phylip (phy),
jalview (jvp, jar). +

For example, to open a FASTA file, append another FASTA file and then save the concatenation as a Stockholm file, do 

@@ -409,7 +410,21 @@
   

 
   

-  Important! If you use --output or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified --headless).  To use Jalview with --output and not assume headless mode, use the --gui or --noheadless argument (the order doesn't matter).
+  Important! If you use --output or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified --headless).  To use Jalview with --output and not assume headless mode, use the --gui argument (the order doesn't matter).
+  

+
+  

+  If you would like to output an alignment file directly to standard output (often referred to as STDOUT), then use the filename - (a single hyphen).  In this case any messages that would normally appear on STDOUT will be diverted to STDERR to avoid invalidating the output file.
+  

+  

+  For example, to open a Stockholm file and pipe it to another command as a Block file, do
+  
+  jalview --open alignment1.stk --output - --format blc | another_command
+  

+  or equivalently
+  
+  jalview alignment1.stk --output=[format=blc]- | another_command
+  

   

 
   
--format

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index dd0bd52..60951d8 100644
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -65,10 +65,10 @@
     ‑‑help‑allHelp for all arguments
 
     
-    ‑‑headless / ‑‑noheadless
-    Run Jalview in headless (/ or not in headless) mode.  In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
+    ‑‑headless
+    Run Jalview in headless mode.  In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
     

-    If you use a command line argument to specify an output file of some kind (--output, --image or --structureimage) then headless mode will be assumed.  If you don't want this behaviour use --noheadless or --gui.
+    If you use a command line argument to specify an output file of some kind (--output, --image or --structureimage) then headless mode will be assumed.  If you don't want this behaviour use --gui.
     
     
 
@@ -521,6 +521,8 @@
     phylip (phy),
     

     jalview (jvp, jar).
+    

+    To output directly to STDOUT (console output) use the filename - (a single hyphen).  In this case all STDOUT messages will instead go to STDERR.  If no format is supplied then Fasta will be assumed.
     
     format=name
     ✓
diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index b763a81..7c2e9d5 100644
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -163,7 +163,7 @@
   If you specify an argument for an output file (one or more of --output, --image or --structureimage) then it will be assumed that you wish to run in headless mode.
   

   

-  You can force Jalview to run in graphical mode using the --gui or --noheadless arguments.
+  You can force Jalview to run in graphical mode using the --gui argument.
   

 
   

diff --git a/help/help/icons/jalview_docs_logo.png b/help/help/icons/jalview_docs_logo.png
new file mode 100644
index 0000000..21f5386
Binary files /dev/null and b/help/help/icons/jalview_docs_logo.png differ
diff --git a/j11lib/flatlaf-3.0.jar b/j11lib/flatlaf-3.0.jar
deleted file mode 100644
index 75d90d3..0000000
Binary files a/j11lib/flatlaf-3.0.jar and /dev/null differ
diff --git a/j11lib/flatlaf-3.1.1.jar b/j11lib/flatlaf-3.1.1.jar
deleted file mode 100644
index 2b13cdd..0000000
Binary files a/j11lib/flatlaf-3.1.1.jar and /dev/null differ
diff --git a/j11lib/flatlaf-3.2.jar b/j11lib/flatlaf-3.2.jar
new file mode 100644
index 0000000..450c1e8
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diff --git a/j11lib/flatlaf-extras-3.0.jar b/j11lib/flatlaf-extras-3.0.jar
deleted file mode 100644
index 1f6bbc3..0000000
Binary files a/j11lib/flatlaf-extras-3.0.jar and /dev/null differ
diff --git a/j8lib/flatlaf-extras-3.1.1.jar b/j11lib/flatlaf-extras-3.2.jar
similarity index 52%
rename from j8lib/flatlaf-extras-3.1.1.jar
rename to j11lib/flatlaf-extras-3.2.jar
index 9d91bd0..ccdbf94 100644
Binary files a/j8lib/flatlaf-extras-3.1.1.jar and b/j11lib/flatlaf-extras-3.2.jar differ
diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar
index 7c99c93..fb8f1bc 100644
Binary files a/j11lib/getdown-core.jar and b/j11lib/getdown-core.jar differ
diff --git a/j8lib/flatlaf-3.1.1.jar b/j8lib/flatlaf-3.1.1.jar
deleted file mode 100644
index 2b13cdd..0000000
Binary files a/j8lib/flatlaf-3.1.1.jar and /dev/null differ
diff --git a/j8lib/flatlaf-3.2.jar b/j8lib/flatlaf-3.2.jar
new file mode 100644
index 0000000..450c1e8
Binary files /dev/null and b/j8lib/flatlaf-3.2.jar differ
diff --git a/j11lib/flatlaf-extras-3.1.1.jar b/j8lib/flatlaf-extras-3.2.jar
similarity index 52%
rename from j11lib/flatlaf-extras-3.1.1.jar
rename to j8lib/flatlaf-extras-3.2.jar
index 9d91bd0..ccdbf94 100644
Binary files a/j11lib/flatlaf-extras-3.1.1.jar and b/j8lib/flatlaf-extras-3.2.jar differ
diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar
index 7c99c93..fb8f1bc 100644
Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 924b9cb..0c4f165 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -363,6 +363,7 @@ label.sequences_from = Sequences from {0}
 label.successfully_loaded_file  = Successfully loaded file {0}
 label.successfully_loaded_matrix  = Successfully loaded score matrix {0}
 label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.
+label.successfully_printed_to_stdout_in_format = Successfully printed to STDOUT in {0} format.
 label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.
 label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.
 label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file
@@ -1462,4 +1463,4 @@ action.show_tree_for_matrix_tooltip = Opens a tree viewer to display the average
 action.cluster_matrix = Cluster matrix
 action.clustering_matrix_for = Calculating tree for matrix {0} and clustering at {1}
 action.cluster_matrix_tooltip = Computes an average distance tree for the matrix and displays it
-
+label.all_known_alignment_files = All known alignment files
diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 150a407..1f256cb 100644
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -326,6 +326,7 @@ label.sequences_from = Secuencias de {0}
 label.successfully_loaded_file  = Fichero cargado exitosamente {0}
 label.successfully_loaded_matrix  = Matriz cargada exitosamente {0}
 label.successfully_saved_to_file_in_format = Guardado exitosamente en el fichero: {0} en formato {1}.
+label.successfully_printed_to_stdout_in_format = Impresso exitosamente al STDOUT en formato {0}.
 label.copied_sequences_to_clipboard = Copiadas {0} secuencias en el portapapeles.
 label.check_file_matches_sequence_ids_alignment = Comprobar que el fichero coincide con el ID de la secuencia en el alineamiento.
 label.problem_reading_tcoffee_score_file = Problema de lectura del fichero de puntuaciones T-COFFEE
@@ -1436,3 +1437,4 @@ label.add_pae_matrix_file = A
 label.nothing_selected = Nada seleccionado
 prompt.analytics_title = Jalview Estadísticas de Uso
 prompt.analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con análisis Plausible?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
+label.all_known_alignment_files = Todos los archivos de alineación conocidos
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index b1505d6..6967885 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -147,7 +147,7 @@ public class AAFrequency
       {
         if (sequences[row] == null)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "WARNING: Consensus skipping null sequence - possible race condition.");
           continue;
         }
@@ -188,7 +188,7 @@ public class AAFrequency
     }
     return new Profiles(result);
     // long elapsed = System.currentTimeMillis() - now;
-    // System.out.println(elapsed);
+    // jalview.bin.Console.outPrintln(elapsed);
   }
 
   /**
@@ -285,7 +285,7 @@ public class AAFrequency
               ' ', value);
     }
     // long elapsed = System.currentTimeMillis() - now;
-    // System.out.println(-elapsed);
+    // jalview.bin.Console.outPrintln(-elapsed);
   }
 
   /**
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 02b3f41..e1d5669 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -826,7 +826,7 @@ public class AlignSeq
       }
     }
 
-    System.out.println(max + " " + min);
+    jalview.bin.Console.outPrintln(max + " " + min);
 
     for (int i = 0; i < n; i++)
     {
@@ -835,12 +835,12 @@ public class AlignSeq
         int x = psize * i;
         int y = psize * j;
 
-        // System.out.println(mat[i][j]);
+        // jalview.bin.Console.outPrintln(mat[i][j]);
         float score = (float) (mat[i][j] - min) / (float) (max - min);
         g.setColor(new Color(score, 0, 0));
         g.fillRect(x, y, psize, psize);
 
-        // System.out.println(x + " " + y + " " + score);
+        // jalview.bin.Console.outPrintln(x + " " + y + " " + score);
       }
     }
   }
@@ -983,7 +983,7 @@ public class AlignSeq
             bestm = msq;
           }
         }
-        // System.out.println("Best Score for " + (matches.size() + 1) + " :"
+        // jalview.bin.Console.outPrintln("Best Score for " + (matches.size() + 1) + " :"
         // + bestscore);
         matches.add(bestm);
         aligns.add(bestaseq);
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index b02d49c..b037336 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -453,7 +453,7 @@ public class AlignmentSorter
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+        jalview.bin.Console.errPrintln("WARNING: tmp.size()=" + tmp.size() + " != nseq="
                 + nSeq
                 + " in getOrderByTree - tree contains sequences not in alignment");
       }
@@ -714,7 +714,7 @@ public class AlignmentSorter
       String msg = String.format(
               "Implementation Error - sortByFeature method must be either '%s' or '%s'",
               FEATURE_SCORE, FEATURE_DENSITY);
-      System.err.println(msg);
+      jalview.bin.Console.errPrintln(msg);
       return;
     }
 
@@ -832,7 +832,7 @@ public class AlignmentSorter
           {
             // int nf = (feats[i] == null) ? 0
             // : ((SequenceFeature[]) feats[i]).length;
-            // // System.err.println("Sorting on Score: seq " +
+            // // jalview.bin.Console.errPrintln("Sorting on Score: seq " +
             // seqs[i].getName()
             // + " Feats: " + nf + " Score : " + scores[i]);
           }
@@ -847,7 +847,7 @@ public class AlignmentSorter
         int featureCount = feats[i] == null ? 0
                 : ((SequenceFeature[]) feats[i]).length;
         scores[i] = featureCount;
-        // System.err.println("Sorting on Density: seq "+seqs[i].getName()+
+        // jalview.bin.Console.errPrintln("Sorting on Density: seq "+seqs[i].getName()+
         // " Feats: "+featureCount+" Score : "+scores[i]);
       }
       QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 6ab49b2..f470dc6 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -547,7 +547,7 @@ public class AlignmentUtils
       if (translated == null || !(aaRes == translated.charAt(0)))
       {
         // debug
-        // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
+        // jalview.bin.Console.outPrintln(("Mismatch at " + i + "/" + aaResidue + ": "
         // + codon + "(" + translated + ") != " + aaRes));
         return false;
       }
@@ -698,7 +698,7 @@ public class AlignmentUtils
          * unmapped position; treat like a gap
          */
         sourceGapMappedLength += ratio;
-        // System.err.println("Can't align: no codon mapping to residue "
+        // jalview.bin.Console.errPrintln("Can't align: no codon mapping to residue "
         // + sourceDsPos + "(" + sourceChar + ")");
         // return;
         continue;
@@ -883,7 +883,7 @@ public class AlignmentUtils
   {
     if (protein.isNucleotide() || !dna.isNucleotide())
     {
-      System.err.println("Wrong alignment type in alignProteinAsDna");
+      jalview.bin.Console.errPrintln("Wrong alignment type in alignProteinAsDna");
       return 0;
     }
     List unmappedProtein = new ArrayList<>();
@@ -908,7 +908,7 @@ public class AlignmentUtils
   {
     if (protein.isNucleotide() || !dna.isNucleotide())
     {
-      System.err.println("Wrong alignment type in alignProteinAsDna");
+      jalview.bin.Console.errPrintln("Wrong alignment type in alignProteinAsDna");
       return 0;
     }
     // todo: implement this
@@ -988,7 +988,7 @@ public class AlignmentUtils
                           .getLength() == mappedFromLength - 1);
           if (cdsLength != mappedToLength && !addStopCodon)
           {
-            System.err.println(String.format(
+            jalview.bin.Console.errPrintln(String.format(
                     "Can't align cds as protein (length mismatch %d/%d): %s",
                     cdsLength, mappedToLength, cdsSeq.getName()));
           }
@@ -1162,7 +1162,7 @@ public class AlignmentUtils
         AlignedCodon codon = sequenceCodon.getValue();
         if (codon.peptideCol > 1)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Problem mapping protein with >1 unmapped start positions: "
                           + seq.getName());
         }
@@ -2770,7 +2770,7 @@ public class AlignmentUtils
                 fromRange[i + 1]);
         if (range == null)
         {
-          System.err.println("Error in mapping " + seqMap + " from "
+          jalview.bin.Console.errPrintln("Error in mapping " + seqMap + " from "
                   + fromSeq.getName());
           return false;
         }
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index cbc4dca..5bb0b09 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -243,13 +243,13 @@ public class Conservation
       }
       else
       {
-        System.out.println("SEQUENCE HAS BEEN DELETED!!!");
+        jalview.bin.Console.outPrintln("SEQUENCE HAS BEEN DELETED!!!");
       }
     }
     else
     {
       // JBPNote INFO level debug
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
     }
   }
@@ -711,7 +711,7 @@ public class Conservation
       // tmp = ((max - tmp) * (size - cons2[j][23])) / size;
       tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
 
-      // System.out.println(tmp+ " " + j);
+      // jalview.bin.Console.outPrintln(tmp+ " " + j);
       quality.setElementAt(Double.valueOf(tmp), j);
 
       if (tmp > newmax)
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 9b90ca5..41582b4 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -293,7 +293,7 @@ public class CrossRef
             if (matchInDataset != null && xref.getMap().getTo() != null
                     && matchInDataset != xref.getMap().getTo())
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
                               + "Found:" + matchInDataset + "\nExpected:"
                               + xref.getMap().getTo() + "\nFor xref:"
@@ -424,7 +424,7 @@ public class CrossRef
       retrieved = sftch.getSequences(sourceRefs, !fromDna);
     } catch (Exception e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Problem whilst retrieving cross references for Sequence : "
                       + seq.getName());
       e.printStackTrace();
@@ -607,7 +607,7 @@ public class CrossRef
                 String msg = "Mapping updated from " + ms.getName()
                         + " to retrieved crossreference "
                         + matched.getName();
-                System.out.println(msg);
+                jalview.bin.Console.outPrintln(msg);
 
                 List toRefs = map.getTo().getDBRefs();
                 if (toRefs != null)
@@ -662,7 +662,7 @@ public class CrossRef
               cf.addMap(retrievedSequence, map.getTo(), map.getMap());
             } catch (Exception e)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Exception when consolidating Mapped sequence set...");
               e.printStackTrace(System.err);
             }
@@ -1029,7 +1029,7 @@ public class CrossRef
     }
     if (dataset.getSequences() == null)
     {
-      System.err.println("Empty dataset sequence set - NO VECTOR");
+      jalview.bin.Console.errPrintln("Empty dataset sequence set - NO VECTOR");
       return false;
     }
     List ds = dataset.getSequences();
@@ -1041,7 +1041,7 @@ public class CrossRef
         {
           if (nxt.getDatasetSequence() != null)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! ("
                             + nxt.getDisplayId(true) + " has ds reference "
                             + nxt.getDatasetSequence().getDisplayId(true)
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 5dcf212..aa71eb7 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -653,7 +653,7 @@ public class Dna
       if (rf != 0)
       {
         final String errMsg = "trimming contigs for incomplete terminal codon.";
-        System.err.println(errMsg);
+        jalview.bin.Console.errPrintln(errMsg);
         // map and trim contigs to ORF region
         vc = scontigs.length - 1;
         lastnpos = vismapping.shift(lastnpos); // place npos in context of
diff --git a/src/jalview/analysis/GeneticCodes.java b/src/jalview/analysis/GeneticCodes.java
index 133cb3a..4c826b2 100644
--- a/src/jalview/analysis/GeneticCodes.java
+++ b/src/jalview/analysis/GeneticCodes.java
@@ -140,7 +140,7 @@ public final class GeneticCodes
       InputStream is = getClass().getResourceAsStream(fileName);
       if (is == null)
       {
-        System.err.println("Resource file not found: " + fileName);
+        jalview.bin.Console.errPrintln("Resource file not found: " + fileName);
         return;
       }
       BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
@@ -166,7 +166,7 @@ public final class GeneticCodes
     }
     if (codeTables.isEmpty())
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "No genetic code tables loaded, check format of file "
                       + fileName);
     }
@@ -190,7 +190,7 @@ public final class GeneticCodes
       InputStream is = getClass().getResourceAsStream(fileName);
       if (is == null)
       {
-        System.err.println("Resource file not found: " + fileName);
+        jalview.bin.Console.errPrintln("Resource file not found: " + fileName);
         return;
       }
       BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
@@ -208,7 +208,7 @@ public final class GeneticCodes
           }
           else
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Unexpected data in " + fileName + ": " + line);
           }
         }
diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 066814e..def5d5a 100644
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -269,7 +269,7 @@ public class Grouping
      * seqs.length) { for (int i = 0; i < seqs.length; i++) { if (!hasScore[i])
      * { scores[i] = (max + i); } else { int nf=(feats[i]==null) ? 0
      * :((SequenceFeature[]) feats[i]).length;
-     * System.err.println("Sorting on Score: seq "+seqs[i].getName()+
+     * jalview.bin.Console.errPrintln("Sorting on Score: seq "+seqs[i].getName()+
      * " Feats: "+nf+" Score : "+scores[i]); } } }
      * 
      * jalview.util.QuickSort.sort(scores, seqs); } else if
@@ -280,7 +280,7 @@ public class Grouping
      * (int i=0;i 0) ? "_" + reps : ""),
                   ScoreDescriptions[cols], null);
           an.setScore(score);
-          System.out.println(seqs[i].getName() + " score: '"
+          jalview.bin.Console.outPrintln(seqs[i].getName() + " score: '"
                   + ScoreNames[cols] + "' = " + score); // DEBUG
           an.setSequenceRef(seqs[i]);
           seqs[i].addAlignmentAnnotation(an);
diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 9649240..911ee04 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -421,8 +421,8 @@ public class Rna
       final int open = basePair.getBP5();
       final int close = basePair.getBP3();
 
-      // System.out.println("open " + open + " close " + close);
-      // System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
+      // jalview.bin.Console.outPrintln("open " + open + " close " + close);
+      // jalview.bin.Console.outPrintln("lastclose " + lastclose + " lastopen " + lastopen);
 
       // we're moving from right to left based on closing pair
       /*
@@ -441,7 +441,7 @@ public class Rna
       {
         int popen = bps.get(j).getBP5();
 
-        // System.out.println("j " + j + " popen " + popen + " lastopen "
+        // jalview.bin.Console.outPrintln("j " + j + " popen " + popen + " lastopen "
         // +lastopen + " open " + open);
         if ((popen < lastopen) && (popen > open))
         {
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index fdca89d..837462f 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -129,7 +129,7 @@ public class SeqsetUtils
     {
       if (sfeatures != null)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
       }
       sq.setDatasetSequence(seqds);
@@ -244,7 +244,7 @@ public class SeqsetUtils
         {
           if (!quiet)
           {
-            System.err.println("Can't find '" + ((String) key)
+            jalview.bin.Console.errPrintln("Can't find '" + ((String) key)
                     + "' in uniquified alignment");
           }
         }
@@ -252,7 +252,7 @@ public class SeqsetUtils
     }
     if (unmatched.size() > 0 && !quiet)
     {
-      System.err.println("Did not find matches for :");
+      jalview.bin.Console.errPrintln("Did not find matches for :");
       for (Enumeration i = unmatched.elements(); i
               .hasMoreElements(); System.out
                       .println(((SequenceI) i.nextElement()).getName()))
diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index c04df6c..3f5099b 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -148,7 +148,7 @@ public class StructureFrequency
           {
             if (sequences[j] == null)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "WARNING: Consensus skipping null sequence - possible race condition.");
               continue;
             }
diff --git a/src/jalview/analysis/TreeEngine.java b/src/jalview/analysis/TreeEngine.java
index daf7836..a7cbc25 100644
--- a/src/jalview/analysis/TreeEngine.java
+++ b/src/jalview/analysis/TreeEngine.java
@@ -214,7 +214,7 @@ public abstract class TreeEngine
   {
     // if (_lycount<_lylimit)
     // {
-    // System.err.println("Warning: depth of _recount greater than number of
+    // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than number of
     // nodes.");
     // }
     if (nd == null)
diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 0e57a58..90fe089 100644
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -353,13 +353,13 @@ public class TreeModel
 
     if ((nd.left() == null) && (nd.right() == null))
     {
-      System.out.println("Leaf = " + ((SequenceI) nd.element()).getName());
-      System.out.println("Dist " + nd.dist);
-      System.out.println("Boot " + nd.getBootstrap());
+      jalview.bin.Console.outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
+      jalview.bin.Console.outPrintln("Dist " + nd.dist);
+      jalview.bin.Console.outPrintln("Boot " + nd.getBootstrap());
     }
     else
     {
-      System.out.println("Dist " + nd.dist);
+      jalview.bin.Console.outPrintln("Dist " + nd.dist);
       printNode((BinaryNode) nd.left());
       printNode((BinaryNode) nd.right());
     }
@@ -480,10 +480,10 @@ public class TreeModel
     }
     else
     {
-      System.out.println(" name = " + ((SequenceI) nd.element()).getName());
+      jalview.bin.Console.outPrintln(" name = " + ((SequenceI) nd.element()).getName());
     }
 
-    System.out.println(
+    jalview.bin.Console.outPrintln(
             " dist = " + nd.dist + " " + nd.count + " " + nd.height);
   }
 
@@ -513,7 +513,7 @@ public class TreeModel
   {
     // if (_lycount<_lylimit)
     // {
-    // System.err.println("Warning: depth of _recount greater than number of
+    // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than number of
     // nodes.");
     // }
     if (nd == null)
diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index 9c2f6d1..bcc0855 100644
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -63,7 +63,7 @@ public class FeatureDistanceModel extends DistanceScoreModel
       return instance;
     } catch (InstantiationException | IllegalAccessException e)
     {
-      System.err.println("Error in " + getClass().getName()
+      jalview.bin.Console.errPrintln("Error in " + getClass().getName()
               + ".getInstance(): " + e.getMessage());
       return null;
     } catch (ReflectiveOperationException roe)
diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index b206339..aa841ac 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -331,12 +331,12 @@ public class ScoreMatrix extends SimilarityScoreModel
   {
     if (c >= symbolIndex.length)
     {
-      System.err.println(String.format(BAD_ASCII_ERROR, c));
+      jalview.bin.Console.errPrintln(String.format(BAD_ASCII_ERROR, c));
       return 0;
     }
     if (d >= symbolIndex.length)
     {
-      System.err.println(String.format(BAD_ASCII_ERROR, d));
+      jalview.bin.Console.errPrintln(String.format(BAD_ASCII_ERROR, d));
       return 0;
     }
 
diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index ebc9a26..d0f21bd 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -105,7 +105,7 @@ public class ScoreModels
       return sm;
     } catch (IOException e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error reading " + resourcePath + ": " + e.getMessage());
     }
     return null;
@@ -143,7 +143,7 @@ public class ScoreModels
     ScoreModelI sm2 = models.get(sm.getName());
     if (sm2 != null)
     {
-      System.err.println("Warning: replacing score model " + sm2.getName());
+      jalview.bin.Console.errPrintln("Warning: replacing score model " + sm2.getName());
     }
     models.put(sm.getName(), sm);
   }
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b860a36..413b0d4 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -393,14 +393,14 @@ public class APopupMenu extends java.awt.PopupMenu
         urlLink = new UrlLink(link);
       } catch (Exception foo)
       {
-        System.err.println("Exception for URLLink '" + link + "': "
+        jalview.bin.Console.errPrintln("Exception for URLLink '" + link + "': "
                 + foo.getMessage());
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        System.err.println(urlLink.getInvalidMessage());
+        jalview.bin.Console.errPrintln(urlLink.getInvalidMessage());
         continue;
       }
 
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0159bc7..4b858e1 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1577,7 +1577,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     /*
      * When we finally deprecate 1.1 compatibility, we can start to use
      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
-     * (UnsupportedEncodingException ex) { System.err.println("WARNING -
+     * (UnsupportedEncodingException ex) { jalview.bin.Console.errPrintln("WARNING -
      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
      * ex.printStackTrace(); }
      */
@@ -1586,7 +1586,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       url = viewport.applet.getCodeBase() + url;
     } catch (UnsupportedEncodingException ex)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
                       + url);
       ex.printStackTrace();
@@ -2975,7 +2975,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     if (viewport.applet.debug)
     {
-      System.err.println("Sorting " + alorder.getOrder().size()
+      jalview.bin.Console.errPrintln("Sorting " + alorder.getOrder().size()
               + " in alignment '" + getTitle() + "'");
     }
     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
@@ -3061,7 +3061,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     if (viewport.applet == null)
     {
-      System.out.println("Not running as applet - no browser available.");
+      jalview.bin.Console.outPrintln("Not running as applet - no browser available.");
     }
     else
     {
@@ -3977,12 +3977,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewer = (Viewer) jmolviewer;
     } catch (ClassCastException ex)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Unsupported viewer object :" + jmolviewer.getClass());
     }
     if (viewer == null)
     {
-      System.err.println("Can't use this object as a structure viewer:"
+      jalview.bin.Console.errPrintln("Can't use this object as a structure viewer:"
               + jmolviewer.getClass());
       return null;
     }
@@ -4127,7 +4127,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     chains = (String[]) sqch[1];
     if (seqs == null || seqs.length == 0)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
     }
     if (protocol == null)
@@ -4142,7 +4142,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       if (protocol == null)
       {
-        System.err.println("Couldn't work out protocol to open structure: "
+        jalview.bin.Console.errPrintln("Couldn't work out protocol to open structure: "
                 + pdb.getId());
         return;
       }
@@ -4154,7 +4154,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               .setMapping(seqs, chains, pdb.getFile(), protocol,
                       null) == null)
       {
-        System.err.println("Failed to map " + pdb.getFile() + " ("
+        jalview.bin.Console.errPrintln("Failed to map " + pdb.getFile() + " ("
                 + protocol + ") to any sequences");
       }
       return;
@@ -4176,7 +4176,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       if (ajm != null)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
         // try and add the pdb structure
         // ajm.addS
@@ -4201,7 +4201,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           SequenceI[][] seqs, String[][] chains, String[] protocols)
   {
     // TODO Auto-generated method stub
-    System.err.println("Aligned Structure View: Not yet implemented.");
+    jalview.bin.Console.errPrintln("Aligned Structure View: Not yet implemented.");
   }
 
   /**
@@ -4258,9 +4258,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (!file.isValid())
     {
       // TODO: raise dialog for gui
-      System.err.println("Problems parsing T-Coffee scores: "
+      jalview.bin.Console.errPrintln("Problems parsing T-Coffee scores: "
               + file.getWarningMessage());
-      System.err.println("Origin was:\n" + source);
+      jalview.bin.Console.errPrintln("Origin was:\n" + source);
       return false;
     }
 
@@ -4273,7 +4273,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                     || aln.getWidth() != file.getWidth()))
     {
       // TODO: raise a dialog box here rather than bomb out.
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "The scores matrix does not match the alignment dimensions");
 
     }
@@ -4289,10 +4289,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else
     {
-      System.err.println("Problems resolving T-Coffee scores:");
+      jalview.bin.Console.errPrintln("Problems resolving T-Coffee scores:");
       if (file.getWarningMessage() != null)
       {
-        System.err.println(file.getWarningMessage());
+        jalview.bin.Console.errPrintln(file.getWarningMessage());
       }
     }
     return false;
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index d64cd75..c1de259 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -77,14 +77,14 @@ public class AlignViewport extends AlignmentViewport
         }
         if (widthScale <= 1.0)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Invalid alignment character width scaling factor ("
                           + widthScale + "). Ignoring.");
           widthScale = 1;
         }
         if (JalviewLite.debug)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Alignment character width scaling factor is now "
                           + widthScale);
         }
@@ -100,14 +100,14 @@ public class AlignViewport extends AlignmentViewport
         }
         if (heightScale <= 1.0)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Invalid alignment character height scaling factor ("
                           + heightScale + "). Ignoring.");
           heightScale = 1;
         }
         if (JalviewLite.debug)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Alignment character height scaling factor is now "
                           + heightScale);
         }
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index fd75296..71ddcef 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -363,7 +363,7 @@ public class AlignmentPanel extends Panel
       {
         if (JalviewLite.debug)
         {// DEBUG
-          System.out.println(
+          jalview.bin.Console.outPrintln(
                   "DEBUG: scroll didn't happen - results not within alignment : "
                           + seq.getStart() + "," + seq.getEnd());
         }
@@ -373,7 +373,7 @@ public class AlignmentPanel extends Panel
       {
         // DEBUG
         /*
-         * System.out.println("DEBUG: scroll: start=" + r[0] +
+         * jalview.bin.Console.outPrintln("DEBUG: scroll: start=" + r[0] +
          * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
          * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
          * " hextent=" + hextent);
@@ -555,7 +555,7 @@ public class AlignmentPanel extends Panel
     // this is called after loading new annotation onto alignment
     if (alignFrame.getSize().height == 0)
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "adjustAnnotationHeight frame size zero NEEDS FIXING");
     }
     fontChanged();
@@ -693,7 +693,7 @@ public class AlignmentPanel extends Panel
 
       if ((hextent + x) > width)
       {
-        System.err.println("hextent was " + hextent + " and x was " + x);
+        jalview.bin.Console.errPrintln("hextent was " + hextent + " and x was " + x);
 
         x = width - hextent;
       }
@@ -710,7 +710,7 @@ public class AlignmentPanel extends Panel
 
       if (x < 0)
       {
-        System.err.println("x was " + x);
+        jalview.bin.Console.errPrintln("x was " + x);
         x = 0;
       }
 
@@ -1111,7 +1111,7 @@ public class AlignmentPanel extends Panel
   public void raiseOOMWarning(String string, OutOfMemoryError error)
   {
     // TODO: JAL-960
-    System.err.println("Out of memory whilst '" + string + "'");
+    jalview.bin.Console.errPrintln("Out of memory whilst '" + string + "'");
     error.printStackTrace();
   }
 
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index b0722c0..cca9aff 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -275,7 +275,7 @@ public class AppletJmol extends EmbmenuFrame implements
               "-applet", scriptWindow, null);
     } catch (Exception e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
                       + ap.av.applet.getDocumentBase() + "\nCodebase="
                       + ap.av.applet.getCodeBase());
@@ -320,7 +320,7 @@ public class AppletJmol extends EmbmenuFrame implements
           {
             if (jalview.bin.JalviewLite.debug)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "AppletJmol:Trying to reuse existing PDBfile IO parser.");
             }
             // re-use the one we opened earlier
@@ -330,7 +330,7 @@ public class AppletJmol extends EmbmenuFrame implements
           {
             if (jalview.bin.JalviewLite.debug)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "AppletJmol:Creating new PDBfile IO parser.");
             }
             FileParse fp = new FileParse(pdbentry.getFile(), protocol);
@@ -355,7 +355,7 @@ public class AppletJmol extends EmbmenuFrame implements
         } catch (Exception e)
         {
           // give up!
-          System.err.println("Couldn't access pdbentry id="
+          jalview.bin.Console.errPrintln("Couldn't access pdbentry id="
                   + pdbentry.getId() + " and file=" + pdbentry.getFile()
                   + " using protocol=" + protocol);
           e.printStackTrace();
@@ -433,7 +433,7 @@ public class AppletJmol extends EmbmenuFrame implements
       } catch (OutOfMemoryError ex)
       {
         frame.dispose();
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Out of memory when trying to create dialog box with sequence-structure mapping.");
         return;
       }
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 47f9df0..e2b8f23 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -154,7 +154,7 @@ public class ExtJmol extends JalviewJmolBinding
   {
     // This never gets called because we haven't overriden the associated Jmol's
     // console
-    System.err.println(
+    jalview.bin.Console.errPrintln(
             "WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
                     + show);
   }
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 7c0dfa9..7730210 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -145,7 +145,7 @@ public class PCAPanel extends EmbmenuFrame
       top = pcaModel.getTop();
     } catch (OutOfMemoryError x)
     {
-      System.err.println("Out of memory when calculating PCA.");
+      jalview.bin.Console.errPrintln("Out of memory when calculating PCA.");
       return;
     }
     calcSettings.setEnabled(true);
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index bc775c6..566aad9 100644
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -102,7 +102,7 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
 
     if (count > 2)
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "Pairwise alignment scaled similarity score matrix\n");
 
       for (int i = 0; i < count; i++)
@@ -111,7 +111,7 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
                 ("" + i) + " " + seqs[i].getName());
       }
 
-      System.out.println("\n");
+      jalview.bin.Console.outPrintln("\n");
 
       for (int i = 0; i < count; i++)
       {
@@ -122,7 +122,7 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
         }
       }
 
-      System.out.println("\n");
+      jalview.bin.Console.outPrintln("\n");
     }
   }
 
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index bd36b0d..a5b652f 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -148,7 +148,7 @@ public class RedundancyPanel extends SliderPanel
 
     validate();
     sliderValueChanged();
-    // System.out.println("blob done "+ (System.currentTimeMillis()-start));
+    // jalview.bin.Console.outPrintln("blob done "+ (System.currentTimeMillis()-start));
   }
 
   void sliderValueChanged()
diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index a870ca4..87266b4 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -145,7 +145,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
     scale = findScale();
 
-    // System.out.println("Scale factor = " + scale);
+    // jalview.bin.Console.outPrintln("Scale factor = " + scale);
 
     addMouseListener(this);
     addKeyListener(this);
@@ -301,7 +301,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
         scale = findScale();
 
-        // System.out.println("New scale = " + scale);
+        // jalview.bin.Console.outPrintln("New scale = " + scale);
         img = createImage(getSize().width, getSize().height);
         ig = img.getGraphics();
 
@@ -427,7 +427,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     }
     else if (evt.getKeyChar() == 's')
     {
-      System.err.println("DEBUG: Rectangle selection"); // log.debug
+      jalview.bin.Console.errPrintln("DEBUG: Rectangle selection"); // log.debug
       if (rectx2 != -1 && recty2 != -1)
       {
         rectSelect(rectx1, recty1, rectx2, recty2);
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 70366e4..c573612 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -772,7 +772,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   @Override
   public void updateColours(SequenceI seq, int index)
   {
-    System.out.println("update the seqPanel colours");
+    jalview.bin.Console.outPrintln("update the seqPanel colours");
     // repaint();
   }
 
@@ -1817,7 +1817,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       {
         if (av.getAlignment() == null)
         {
-          System.out.println("Selection message: alignviewport av SeqSetId="
+          jalview.bin.Console.outPrintln("Selection message: alignviewport av SeqSetId="
                   + av.getSequenceSetId() + " ViewId=" + av.getViewId()
                   + " 's alignment is NULL! returning immediatly.");
           return;
@@ -1869,7 +1869,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (copycolsel && av.hasHiddenColumns()
             && (av.getColumnSelection() == null))
     {
-      System.err.println("Bad things");
+      jalview.bin.Console.errPrintln("Bad things");
     }
     if (repaint)
     {
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 671fee1..0316e0b 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -166,7 +166,7 @@ public class TreePanel extends EmbmenuFrame
     }
     else
     {
-      System.out.println("Original Tree Data not available");
+      jalview.bin.Console.outPrintln("Original Tree Data not available");
     }
   }
 
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 5741908..3750d9d 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -407,9 +407,9 @@ public class Cache
           fis = new URL(propertiesFile).openStream();
           if (!Jalview.quiet())
           {
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "Loading jalview properties from : " + propertiesFile);
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "Disabling Jalview writing to user's local properties file.");
           }
           propsAreReadOnly = true;
@@ -440,7 +440,8 @@ public class Cache
       } catch (Exception ex)
       {
         if (!Jalview.quiet())
-          System.out.println("Error reading properties file: " + ex);
+          jalview.bin.Console
+                  .outPrintln("Error reading properties file: " + ex);
       }
     }
 
@@ -497,7 +498,8 @@ public class Cache
     } catch (Exception ex)
     {
       if (!Jalview.quiet())
-        System.out.println("Error reading author details: " + ex);
+        jalview.bin.Console
+                .outPrintln("Error reading author details: " + ex);
       authorDetails = null;
     }
     if (authorDetails == null)
@@ -583,10 +585,10 @@ public class Cache
             {
               if (!Jalview.quiet())
               {
-                System.out.println(
+                jalview.bin.Console.outPrintln(
                         "Non-fatal exception when checking version at "
                                 + remoteBuildPropertiesUrl + ":");
-                System.out.println(ex);
+                jalview.bin.Console.printStackTrace(ex);
               }
               remoteVersion = getProperty("VERSION");
             }
@@ -636,7 +638,7 @@ public class Cache
         url = Cache.class.getResource(resourcePath).toString();
       } catch (Exception ex)
       {
-        System.err.println("Failed to resolve resource " + resourcePath
+        jalview.bin.Console.errPrintln("Failed to resolve resource " + resourcePath
                 + ": " + ex.getMessage());
       }
     }
@@ -687,7 +689,8 @@ public class Cache
     } catch (Exception ex)
     {
       if (!Jalview.quiet())
-        System.out.println("Error reading build details: " + ex);
+        jalview.bin.Console
+                .outPrintln("Error reading build details: " + ex);
       applicationProperties.remove("VERSION");
     }
     String codeVersion = getProperty("VERSION");
@@ -707,8 +710,9 @@ public class Cache
     new BuildDetails(codeVersion, null, codeInstallation);
     if (printVersion && reportVersion)
     {
-      System.out.println(ChannelProperties.getProperty("app_name")
-              + " version: " + codeVersion + codeInstallation);
+      jalview.bin.Console
+              .outPrintln(ChannelProperties.getProperty("app_name")
+                      + " version: " + codeVersion + codeInstallation);
     }
   }
 
@@ -784,8 +788,8 @@ public class Cache
       } catch (NumberFormatException e)
       {
         if (!Jalview.quiet())
-          System.out.println("Error parsing int property '" + property
-                  + "' with value '" + string + "'");
+          jalview.bin.Console.outPrintln("Error parsing int property '"
+                  + property + "' with value '" + string + "'");
       }
     }
 
@@ -835,7 +839,7 @@ public class Cache
     } catch (Exception ex)
     {
       if (!Jalview.quiet())
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "Error setting property: " + key + " " + obj + "\n" + ex);
     }
     return oldValue;
@@ -867,7 +871,7 @@ public class Cache
       } catch (Exception ex)
       {
         if (!Jalview.quiet())
-          System.out.println("Error saving properties: " + ex);
+          jalview.bin.Console.outPrintln("Error saving properties: " + ex);
       }
     }
   }
@@ -1057,7 +1061,7 @@ public class Cache
         return date_format.parse(val);
       } catch (Exception ex)
       {
-        System.err.println("Invalid or corrupt date in property '"
+        jalview.bin.Console.errPrintln("Invalid or corrupt date in property '"
                 + propertyName + "' : value was '" + val + "'");
       }
     }
@@ -1081,7 +1085,7 @@ public class Cache
         return Integer.valueOf(val);
       } catch (NumberFormatException x)
       {
-        System.err.println("Invalid integer in property '" + property
+        jalview.bin.Console.errPrintln("Invalid integer in property '" + property
                 + "' (value was '" + val + "')");
       }
     }
@@ -1146,7 +1150,8 @@ public class Cache
       } catch (Exception ex)
       {
         if (!Jalview.quiet())
-          System.out.println("Error loading User ColourFile\n" + ex);
+          jalview.bin.Console
+                  .outPrintln("Error loading User ColourFile\n" + ex);
       }
     }
     if (!files.equals(coloursFound.toString()))
@@ -1652,7 +1657,7 @@ public class Cache
       return null;
     if (!file.exists())
     {
-      System.err.println("Could not load bootstrap preferences file '"
+      jalview.bin.Console.errPrintln("Could not load bootstrap preferences file '"
               + filename + "'");
       return null;
     }
@@ -1669,11 +1674,11 @@ public class Cache
       }
     } catch (FileNotFoundException e)
     {
-      System.err.println("Could not find bootstrap preferences file '"
+      jalview.bin.Console.errPrintln("Could not find bootstrap preferences file '"
               + file.getAbsolutePath() + "'");
     } catch (IOException e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "IOException when loading bootstrap preferences file '"
                       + file.getAbsolutePath() + "'");
     }
diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index d7d1ea3..63247a7 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -6,7 +6,6 @@ import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
@@ -103,16 +102,20 @@ public class Commands
         theseArgsWereParsed &= processLinked(id);
         processGroovyScript(id);
         boolean processLinkedOkay = theseArgsWereParsed;
-        
+
         // wait around until alignFrame isn't busy
-        AlignFrame af=afMap.get(id);
-        while (af!=null && af.getViewport().isCalcInProgress())
+        AlignFrame af = afMap.get(id);
+        while (af != null && af.getViewport().isCalcInProgress())
         {
-          try {
+          try
+          {
             Thread.sleep(25);
-          } catch (Exception q) {};
+          } catch (Exception q)
+          {
+          }
+          ;
         }
-        
+
         theseArgsWereParsed &= processImages(id);
         if (processLinkedOkay)
           theseArgsWereParsed &= processOutput(id);
@@ -162,13 +165,9 @@ public class Commands
     if (avm == null)
       return true;
 
-    /*
-     * // script to execute after all loading is completed one way or another String
-     * groovyscript = m.get(Arg.GROOVY) == null ? null :
-     * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
-     * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
-     * DataSourceType protocol = null;
-     */
+    // set wrap scope here so it can be applied after structures are opened
+    boolean wrap = false;
+
     if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
     {
       commandArgsProvided = true;
@@ -252,23 +251,22 @@ public class Commands
           af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
                   format);
 
-          // wrap alignment?
-          boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
-                  null, "WRAP_ALIGNMENT", false);
-          af.getCurrentView().setWrapAlignment(wrap);
-
           // colour alignment?
           String colour = ArgParser.getFromSubValArgOrPref(avm, av,
                   Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
           if ("" != colour)
           {
             ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
-                    af.getViewport(), af.getViewport().getAlignment(), colour);
-            
-            if (cs==null && !"None".equals(colour))
+                    af.getViewport(), af.getViewport().getAlignment(),
+                    colour);
+
+            if (cs == null && !"None".equals(colour))
+            {
+              Console.warn(
+                      "Couldn't parse '" + colour + "' as a colourscheme.");
+            }
+            else
             {
-              Console.warn("Couldn't parse '"+colour+"' as a colourscheme.");
-            } else {
               af.changeColour(cs);
             }
             Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
@@ -357,6 +355,12 @@ public class Commands
                     false, false);
           }
 
+          // wrap alignment? do this last for formatting reasons
+          wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null,
+                  "WRAP_ALIGNMENT", false);
+          // af.setWrapFormat(wrap) is applied after structures are opened for
+          // annotation reasons
+
           // store the AlignFrame for this id
           afMap.put(id, af);
 
@@ -548,20 +552,7 @@ public class Commands
           String sViewer = ArgParser.getFromSubValArgOrPref(avm,
                   Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
                   null, "jmol");
-          ViewerType viewerType = null;
-          if (!"none".equals(sViewer))
-          {
-            for (ViewerType v : EnumSet.allOf(ViewerType.class))
-            {
-              String name = v.name().toLowerCase(Locale.ROOT)
-                      .replaceAll(" ", "");
-              if (sViewer.equals(name))
-              {
-                viewerType = v;
-                break;
-              }
-            }
-          }
+          ViewerType viewerType = ViewerType.getFromString(sViewer);
 
           // TODO use ssFromStructure
           StructureViewer sv = StructureChooser
@@ -569,15 +560,15 @@ public class Commands
                           structureFilepath, tft, paeFilepath, false,
                           ssFromStructure, false, viewerType);
 
-          if (sv==null)
+          if (sv == null)
           {
             Console.error("Failed to import and open structure view.");
             continue;
           }
           try
           {
-            long tries=1000;
-            while (sv.isBusy() && tries>0)
+            long tries = 1000;
+            while (sv.isBusy() && tries > 0)
             {
               Thread.sleep(25);
               if (sv.isBusy())
@@ -587,15 +578,18 @@ public class Commands
                         "Waiting for viewer for " + structureFilepath);
               }
             }
-            if (tries==0 && sv.isBusy())
+            if (tries == 0 && sv.isBusy())
             {
-              Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong.");
+              Console.warn(
+                      "Gave up waiting for structure viewer to load. Something may have gone wrong.");
             }
           } catch (Exception x)
           {
-            Console.warn("Exception whilst waiting for structure viewer "+structureFilepath,x);
+            Console.warn("Exception whilst waiting for structure viewer "
+                    + structureFilepath, x);
           }
-          Console.debug("Successfully opened viewer for "+structureFilepath);
+          Console.debug(
+                  "Successfully opened viewer for " + structureFilepath);
           String structureImageFilename = ArgParser.getValueFromSubValOrArg(
                   avm, av, Arg.STRUCTUREIMAGE, subVals);
           if (sv != null && structureImageFilename != null)
@@ -652,16 +646,18 @@ public class Commands
               if (sview instanceof AppJmol)
               {
                 AppJmol jmol = (AppJmol) sview;
-                try { 
-                  Console.debug("Rendering image to "+structureImageFile);
+                try
+                {
+                  Console.debug("Rendering image to " + structureImageFile);
                   jmol.makePDBImage(structureImageFile, imageType, renderer,
-                        userBis);
-                  Console.debug("Finished Rendering image to "+structureImageFile);
+                          userBis);
+                  Console.debug("Finished Rendering image to "
+                          + structureImageFile);
 
-                }
-                catch (ImageOutputException ioexc)
+                } catch (ImageOutputException ioexc)
                 {
-                  Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc);
+                  Console.warn("Unexpected error whilst exporting image to "
+                          + structureImageFile, ioexc);
                 }
 
               }
@@ -676,6 +672,15 @@ public class Commands
       }
     }
 
+    if (wrap)
+    {
+      AlignFrame af = afMap.get(id);
+      if (af != null)
+      {
+        af.setWrapFormat(wrap, true);
+      }
+    }
+
     /*
     boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
     if (doShading)
@@ -771,57 +776,60 @@ public class Commands
         Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
 
         Console.info("Writing " + file);
-        try {
-        switch (type)
+        try
         {
-
-        case "svg":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          af.createSVG(file, renderer);
-          break;
-
-        case "png":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          af.createPNG(file, null, userBis);
-          break;
-
-        case "html":
-          Console.debug("Outputting type '" + type + "' to " + fileName);
-          HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-          htmlSVG.exportHTML(fileName, renderer);
-          break;
-
-        case "biojs":
-          Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
-          try
-          {
-            BioJsHTMLOutput.refreshVersionInfo(
-                    BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
-          } catch (URISyntaxException e)
+          switch (type)
           {
-            e.printStackTrace();
+
+          case "svg":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            af.createSVG(file, renderer);
+            break;
+
+          case "png":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            af.createPNG(file, null, userBis);
+            break;
+
+          case "html":
+            Console.debug("Outputting type '" + type + "' to " + fileName);
+            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+            htmlSVG.exportHTML(fileName, renderer);
+            break;
+
+          case "biojs":
+            Console.debug(
+                    "Creating BioJS MSA Viwer HTML file: " + fileName);
+            try
+            {
+              BioJsHTMLOutput.refreshVersionInfo(
+                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+            } catch (URISyntaxException e)
+            {
+              e.printStackTrace();
+            }
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+            bjs.exportHTML(fileName);
+            break;
+
+          case "eps":
+            Console.debug("Creating EPS file: " + fileName);
+            af.createEPS(file, name);
+            break;
+
+          case "imagemap":
+            Console.debug("Creating ImageMap file: " + fileName);
+            af.createImageMap(file, name);
+            break;
+
+          default:
+            Console.warn(Arg.IMAGE.argString() + " type '" + type
+                    + "' not known. Ignoring");
+            break;
           }
-          BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
-          bjs.exportHTML(fileName);
-          break;
-
-        case "eps":
-          Console.debug("Creating EPS file: " + fileName);
-          af.createEPS(file, name);
-          break;
-
-        case "imagemap":
-          Console.debug("Creating ImageMap file: " + fileName);
-          af.createImageMap(file, name);
-          break;
-
-        default:
-          Console.warn(Arg.IMAGE.argString() + " type '" + type
-                  + "' not known. Ignoring");
-          break;
-        }
-        } catch (Exception ioex) {
-          Console.warn("Unexpected error during export",ioex);
+        } catch (Exception ioex)
+        {
+          Console.warn("Unexpected error during export", ioex);
         }
       }
     }
@@ -846,6 +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);
@@ -858,7 +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 "
@@ -896,23 +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
@@ -923,7 +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,
diff --git a/src/jalview/bin/Console.java b/src/jalview/bin/Console.java
index 30fd530..c42d519 100644
--- a/src/jalview/bin/Console.java
+++ b/src/jalview/bin/Console.java
@@ -20,6 +20,7 @@
  */
 package jalview.bin;
 
+import java.io.PrintStream;
 import java.util.Locale;
 
 import jalview.log.JLogger;
@@ -43,8 +44,8 @@ public class Console
     }
     else
     {
-      System.out.println(message);
-      t.printStackTrace();
+      outPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -57,7 +58,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outPrintln(message);
     }
 
   }
@@ -70,8 +71,8 @@ public class Console
     }
     else
     {
-      System.out.println(message);
-      t.printStackTrace();
+      outPrintln(message);
+      Console.printStackTrace(t);
     }
   }
 
@@ -83,7 +84,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outPrintln(message);
     }
 
   }
@@ -96,8 +97,8 @@ public class Console
     }
     else
     {
-      System.out.println(message);
-      t.printStackTrace();
+      outPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -110,7 +111,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outPrintln(message);
     }
 
   }
@@ -123,7 +124,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outPrintln(message);
     }
   }
 
@@ -135,8 +136,8 @@ public class Console
     }
     else
     {
-      System.out.println(message);
-      t.printStackTrace();
+      outPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -149,7 +150,7 @@ public class Console
     }
     else
     {
-      System.err.println(message);
+      jalview.bin.Console.errPrintln(message);
     }
 
   }
@@ -162,8 +163,8 @@ public class Console
     }
     else
     {
-      System.err.println(message);
-      t.printStackTrace(System.err);
+      jalview.bin.Console.errPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -176,7 +177,7 @@ public class Console
     }
     else
     {
-      System.err.println(message);
+      jalview.bin.Console.errPrintln(message);
     }
 
   }
@@ -189,8 +190,8 @@ public class Console
     }
     else
     {
-      System.err.println(message);
-      t.printStackTrace(System.err);
+      jalview.bin.Console.errPrintln(message);
+      Console.printStackTrace(t);
     }
 
   }
@@ -253,7 +254,7 @@ public class Console
       {
         if (!Jalview.quiet())
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Setting initial log level to " + logLevel.name());
         }
         Log4j.init(logLevel);
@@ -267,8 +268,9 @@ public class Console
       log = JLoggerLog4j.getLogger(Cache.JALVIEW_LOGGER_NAME, logLevel);
     } catch (NoClassDefFoundError e)
     {
-      System.err.println("Could not initialise the logger framework");
-      e.printStackTrace();
+      jalview.bin.Console
+              .errPrintln("Could not initialise the logger framework");
+      Console.printStackTrace(e);
     }
 
     // Test message
@@ -306,6 +308,86 @@ public class Console
     }
   }
 
+  public static void outPrint()
+  {
+    outPrint("");
+  }
+
+  public static void outPrintln()
+  {
+    outPrintln("");
+  }
+
+  public static void outPrint(Object message)
+  {
+    outPrintMessage(message, false, false);
+  }
+
+  public static void outPrint(Object message, boolean forceStdout)
+  {
+    outPrintMessage(message, false, forceStdout);
+  }
+
+  public static void outPrintln(Object message)
+  {
+    outPrintMessage(message, true, false);
+  }
+
+  public static PrintStream outputStream(boolean forceStdout)
+  {
+    // send message to stderr if an output file to stdout is expected
+    if (!forceStdout && Jalview.getInstance() != null
+            && Jalview.getInstance().bootstrapArgs != null
+            && Jalview.getInstance().bootstrapArgs.outputToStdout())
+    {
+      return System.err;
+    }
+    else
+    {
+      return System.out;
+    }
+  }
+
+  public static void outPrintMessage(Object message, boolean newline,
+          boolean forceStdout)
+  {
+    PrintStream ps = outputStream(forceStdout);
+    if (newline)
+    {
+      ps.println(message);
+    }
+    else
+    {
+      ps.print(message);
+    }
+  }
+
+  public static void errPrint()
+  {
+    errPrint("");
+  }
+
+  public static void errPrintln()
+  {
+    errPrintln("");
+  }
+
+  public static void errPrint(Object message)
+  {
+    System.err.print(message);
+  }
+
+  public static void errPrintln(Object message)
+  {
+    System.err.println(message);
+  }
+
+  public static void printStackTrace(Throwable t)
+  {
+    // send message to stderr if output to stdout is expected
+    t.printStackTrace(System.err);
+  }
+
   public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
 
-}
+}
\ No newline at end of file
diff --git a/src/jalview/bin/GetMemory.java b/src/jalview/bin/GetMemory.java
index b01dfb8..5332704 100644
--- a/src/jalview/bin/GetMemory.java
+++ b/src/jalview/bin/GetMemory.java
@@ -61,7 +61,7 @@ class GetMemory
     } catch (NoClassDefFoundError e)
     {
       // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "No com.sun.management.OperatingSystemMXBean: cannot get total physical memory size");
     }
 
diff --git a/src/jalview/bin/HiDPISetting.java b/src/jalview/bin/HiDPISetting.java
index 2bce673..e14c032 100644
--- a/src/jalview/bin/HiDPISetting.java
+++ b/src/jalview/bin/HiDPISetting.java
@@ -20,9 +20,8 @@
  */
 package jalview.bin;
 
-import java.util.Locale;
-
 import java.awt.HeadlessException;
+import java.util.Locale;
 
 public class HiDPISetting
 {
@@ -117,8 +116,9 @@ public class HiDPISetting
         }
       } catch (NumberFormatException e)
       {
-        System.err.println(setHiDPIScalePropertyName + " property give ("
-                + setHiDPIScaleProperty + ") but not parseable as integer");
+        jalview.bin.Console.errPrintln(setHiDPIScalePropertyName
+                + " property give (" + setHiDPIScaleProperty
+                + ") but not parseable as integer");
       }
     }
     if (setHiDPI && setHiDPIScale > 0)
@@ -135,8 +135,8 @@ public class HiDPISetting
       try
       {
         int existingPropertyVal = Integer.parseInt(existingProperty);
-        System.out.println("Existing " + scalePropertyName + " is "
-                + existingPropertyVal);
+        jalview.bin.Console.outPrintln("Existing " + scalePropertyName
+                + " is " + existingPropertyVal);
         if (existingPropertyVal > 1)
         {
           setHiDPIScale(existingPropertyVal);
@@ -144,8 +144,9 @@ public class HiDPISetting
         }
       } catch (NumberFormatException e)
       {
-        System.out.println("Could not convert property " + scalePropertyName
-                + " vale '" + existingProperty + "' to number");
+        jalview.bin.Console.outPrintln(
+                "Could not convert property " + scalePropertyName
+                        + " vale '" + existingProperty + "' to number");
       }
     }
 
@@ -159,7 +160,11 @@ public class HiDPISetting
       dpi = screenInfo.getScreenResolution();
     } catch (HeadlessException e)
     {
-      System.err.println("Cannot get screen resolution: " + e.getMessage());
+      if (isLinux)
+      {
+        jalview.bin.Console.errPrintln(
+                "Cannot get screen resolution: " + e.getMessage());
+      }
     }
 
     // try and get screen size height and width
@@ -171,8 +176,12 @@ public class HiDPISetting
       mindimension = Math.min(height, width);
     } catch (HeadlessException e)
     {
-      System.err.println(
-              "Cannot get screen size height and width:" + e.getMessage());
+      if (isLinux)
+      {
+        jalview.bin.Console
+                .errPrintln("Cannot get screen size height and width:"
+                        + e.getMessage());
+      }
     }
 
     // attempt at a formula for scaling based on screen dpi and mindimension.
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 57f2575..810d835 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -274,7 +274,7 @@ public class Jalview
      * 
      */
     {
-      System.out.println("not in js");
+      Console.outPrintln("not in js");
     }
 
     // BH - for event debugging in JavaScript (Java mode only)
@@ -383,29 +383,30 @@ public class Jalview
       }.start();
     }
 
-    if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
+    if (!quiet() || !bootstrapArgs.outputToStdout()
+            || bootstrapArgs.contains(Arg.VERSION))
     {
-      System.out.println(
+      Console.outPrintln(
               "Java version: " + System.getProperty("java.version"));
-      System.out.println("Java home: " + System.getProperty("java.home"));
-      System.out.println("Java arch: " + System.getProperty("os.arch") + " "
+      Console.outPrintln("Java home: " + System.getProperty("java.home"));
+      Console.outPrintln("Java arch: " + System.getProperty("os.arch") + " "
               + System.getProperty("os.name") + " "
               + System.getProperty("os.version"));
 
       String val = System.getProperty("sys.install4jVersion");
       if (val != null)
       {
-        System.out.println("Install4j version: " + val);
+        Console.outPrintln("Install4j version: " + val);
       }
       val = System.getProperty("installer_template_version");
       if (val != null)
       {
-        System.out.println("Install4j template version: " + val);
+        Console.outPrintln("Install4j template version: " + val);
       }
       val = System.getProperty("launcher_version");
       if (val != null)
       {
-        System.out.println("Launcher version: " + val);
+        Console.outPrintln("Launcher version: " + val);
       }
     }
 
@@ -463,6 +464,7 @@ public class Jalview
     // register SIGTERM listener
     Runtime.getRuntime().addShutdownHook(new Thread()
     {
+      @Override
       public void run()
       {
         Console.debug("Running shutdown hook");
@@ -509,7 +511,7 @@ public class Jalview
     Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
     {
-      System.out.println(
+      Console.outPrintln(
               "CMD [-props " + usrPropsFile + "] executed successfully!");
       testoutput(bootstrapArgs, Arg.PROPS,
               "test/jalview/bin/testProps.jvprops", usrPropsFile);
@@ -541,7 +543,7 @@ public class Jalview
       {
         List> helpArgs = bootstrapArgs
                 .getList(Arg.HELP);
-        System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
+        Console.outPrintln(Arg.usage(helpArgs.stream().map(e -> e.getKey())
                 .collect(Collectors.toList())));
         Jalview.exit(null, 0);
       }
@@ -551,7 +553,7 @@ public class Jalview
          * Now using new usage statement.
         showUsage();
         */
-        System.out.println(Arg.usage());
+        Console.outPrintln(Arg.usage());
         Jalview.exit(null, 0);
       }
 
@@ -581,13 +583,13 @@ public class Jalview
         try
         {
           Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
-          System.out.println(
+          Console.outPrintln(
                   "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
           testoutput(bootstrapArgs, Arg.JABAWS,
                   "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
         } catch (MalformedURLException e)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Invalid jabaws parameter: " + jabawsUrl + " ignored");
         }
       }
@@ -617,7 +619,8 @@ public class Jalview
       }
       else
       {
-        System.out.println("Executing setprop argument: " + setprop);
+        jalview.bin.Console
+                .errPrintln("Executing setprop argument: " + setprop);
         if (Platform.isJS())
         {
           Cache.setProperty(setprop.substring(0, p),
@@ -749,7 +752,7 @@ public class Jalview
         }
         else
         {
-          System.out.println("CMD [-nousagestats] executed successfully!");
+          Console.outPrintln("CMD [-nousagestats] executed successfully!");
           testoutput(argparser, Arg.NOUSAGESTATS);
         }
 
@@ -765,7 +768,7 @@ public class Jalview
             // questionnaire
             Console.debug("Starting questionnaire url at " + url);
             desktop.checkForQuestionnaire(url);
-            System.out.println("CMD questionnaire[-" + url
+            Console.outPrintln("CMD questionnaire[-" + url
                     + "] executed successfully!");
           }
           else
@@ -786,8 +789,8 @@ public class Jalview
         }
         else
         {
-          System.out
-                  .println("CMD [-noquestionnaire] executed successfully!");
+          Console.outPrintln(
+                  "CMD [-noquestionnaire] executed successfully!");
           testoutput(argparser, Arg.QUESTIONNAIRE);
         }
 
@@ -877,7 +880,7 @@ public class Jalview
                         .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
-      System.out.println("CMD [-open " + file + "] executed successfully!");
+      Console.outPrintln("CMD [-open " + file + "] executed successfully!");
 
       if (!Platform.isJS())
       /**
@@ -914,7 +917,7 @@ public class Jalview
               format);
       if (af == null)
       {
-        System.out.println("error");
+        Console.outPrintln("error");
       }
       else
       {
@@ -929,7 +932,7 @@ public class Jalview
 
           if (cs != null)
           {
-            System.out.println(
+            Console.outPrintln(
                     "CMD [-colour " + data + "] executed successfully!");
           }
           af.changeColour(cs);
@@ -941,8 +944,8 @@ public class Jalview
         {
           af.parseFeaturesFile(data,
                   AppletFormatAdapter.checkProtocol(data));
-          // System.out.println("Added " + data);
-          System.out.println(
+          // Console.outPrintln("Added " + data);
+          Console.outPrintln(
                   "CMD groups[-" + data + "]  executed successfully!");
         }
         data = aparser.getValue("features", true);
@@ -950,8 +953,8 @@ public class Jalview
         {
           af.parseFeaturesFile(data,
                   AppletFormatAdapter.checkProtocol(data));
-          // System.out.println("Added " + data);
-          System.out.println(
+          // Console.outPrintln("Added " + data);
+          Console.outPrintln(
                   "CMD [-features " + data + "]  executed successfully!");
         }
 
@@ -959,8 +962,8 @@ public class Jalview
         if (data != null)
         {
           af.loadJalviewDataFile(data, null, null, null);
-          // System.out.println("Added " + data);
-          System.out.println(
+          // Console.outPrintln("Added " + data);
+          Console.outPrintln(
                   "CMD [-annotations " + data + "] executed successfully!");
         }
         // set or clear the sortbytree flag.
@@ -969,7 +972,7 @@ public class Jalview
           af.getViewport().setSortByTree(true);
           if (af.getViewport().getSortByTree())
           {
-            System.out.println("CMD [-sortbytree] executed successfully!");
+            Console.outPrintln("CMD [-sortbytree] executed successfully!");
           }
         }
         if (aparser.contains("no-annotation"))
@@ -977,7 +980,7 @@ public class Jalview
           af.getViewport().setShowAnnotation(false);
           if (!af.getViewport().isShowAnnotation())
           {
-            System.out.println("CMD no-annotation executed successfully!");
+            Console.outPrintln("CMD no-annotation executed successfully!");
           }
         }
         if (aparser.contains("nosortbytree"))
@@ -985,8 +988,8 @@ public class Jalview
           af.getViewport().setSortByTree(false);
           if (!af.getViewport().getSortByTree())
           {
-            System.out
-                    .println("CMD [-nosortbytree] executed successfully!");
+            Console.outPrintln(
+                    "CMD [-nosortbytree] executed successfully!");
           }
         }
         data = aparser.getValue("tree", true);
@@ -994,7 +997,7 @@ public class Jalview
         {
           try
           {
-            System.out.println(
+            Console.outPrintln(
                     "CMD [-tree " + data + "] executed successfully!");
             NewickFile nf = new NewickFile(data,
                     AppletFormatAdapter.checkProtocol(data));
@@ -1002,7 +1005,7 @@ public class Jalview
                     .setCurrentTree(af.showNewickTree(nf, data).getTree());
           } catch (IOException ex)
           {
-            System.err.println("Couldn't add tree " + data);
+            jalview.bin.Console.errPrintln("Couldn't add tree " + data);
             ex.printStackTrace(System.err);
           }
         }
@@ -1011,9 +1014,9 @@ public class Jalview
         {
           // Execute the groovy script after we've done all the rendering stuff
           // and before any images or figures are generated.
-          System.out.println("Executing script " + groovyscript);
+          Console.outPrintln("Executing script " + groovyscript);
           executeGroovyScript(groovyscript, af);
-          System.out.println("CMD groovy[" + groovyscript
+          Console.outPrintln("CMD groovy[" + groovyscript
                   + "] executed successfully!");
           groovyscript = null;
         }
@@ -1027,14 +1030,14 @@ public class Jalview
 
             if (outputFormat.equalsIgnoreCase("png"))
             {
-              System.out.println("Creating PNG image: " + file);
+              Console.outPrintln("Creating PNG image: " + file);
               af.createPNG(new File(file));
               imageName = (new File(file)).getName();
               continue;
             }
             else if (outputFormat.equalsIgnoreCase("svg"))
             {
-              System.out.println("Creating SVG image: " + file);
+              Console.outPrintln("Creating SVG image: " + file);
               File imageFile = new File(file);
               imageName = imageFile.getName();
               af.createSVG(imageFile);
@@ -1046,7 +1049,7 @@ public class Jalview
               imageName = imageFile.getName();
               HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
 
-              System.out.println("Creating HTML image: " + file);
+              Console.outPrintln("Creating HTML image: " + file);
               htmlSVG.exportHTML(file);
               continue;
             }
@@ -1054,7 +1057,8 @@ public class Jalview
             {
               if (file == null)
               {
-                System.err.println("The output html file must not be null");
+                jalview.bin.Console.errPrintln(
+                        "The output html file must not be null");
                 return;
               }
               try
@@ -1066,21 +1070,21 @@ public class Jalview
                 e.printStackTrace();
               }
               BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
-              System.out.println(
+              Console.outPrintln(
                       "Creating BioJS MSA Viwer HTML file: " + file);
               bjs.exportHTML(file);
               continue;
             }
             else if (outputFormat.equalsIgnoreCase("imgMap"))
             {
-              System.out.println("Creating image map: " + file);
+              Console.outPrintln("Creating image map: " + file);
               af.createImageMap(new File(file), imageName);
               continue;
             }
             else if (outputFormat.equalsIgnoreCase("eps"))
             {
               File outputFile = new File(file);
-              System.out.println(
+              Console.outPrintln(
                       "Creating EPS file: " + outputFile.getAbsolutePath());
               af.createEPS(outputFile);
               continue;
@@ -1092,14 +1096,14 @@ public class Jalview
               outFormat = FileFormats.getInstance().forName(outputFormat);
             } catch (Exception formatP)
             {
-              System.out.println("Couldn't parse " + outFormat
+              Console.outPrintln("Couldn't parse " + outFormat
                       + " as a valid Jalview format string.");
             }
             if (outFormat != null)
             {
               if (!outFormat.isWritable())
               {
-                System.out.println(
+                Console.outPrintln(
                         "This version of Jalview does not support alignment export as "
                                 + outputFormat);
               }
@@ -1108,19 +1112,19 @@ public class Jalview
                 af.saveAlignment(file, outFormat);
                 if (af.isSaveAlignmentSuccessful())
                 {
-                  System.out.println("Written alignment in "
+                  Console.outPrintln("Written alignment in "
                           + outFormat.getName() + " format to " + file);
                 }
                 else
                 {
-                  System.out.println("Error writing file " + file + " in "
+                  Console.outPrintln("Error writing file " + file + " in "
                           + outFormat.getName() + " format!!");
                 }
               }
             }
           } catch (ImageOutputException ioexc)
           {
-            System.out.println(
+            Console.outPrintln(
                     "Unexpected error whilst exporting image to " + file);
             ioexc.printStackTrace();
           }
@@ -1129,7 +1133,7 @@ public class Jalview
 
         while (aparser.getSize() > 0)
         {
-          System.out.println("Unknown arg: " + aparser.nextValue());
+          Console.outPrintln("Unknown arg: " + aparser.nextValue());
         }
       }
     }
@@ -1197,12 +1201,12 @@ public class Jalview
     {
       if (Cache.groovyJarsPresent())
       {
-        System.out.println("Executing script " + groovyscript);
+        Console.outPrintln("Executing script " + groovyscript);
         executeGroovyScript(groovyscript, startUpAlframe);
       }
       else
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
                         + groovyscript);
       }
@@ -1497,7 +1501,7 @@ public class Jalview
       UIManager.put("TabbedPane.tabType", "card");
       UIManager.put("TabbedPane.showTabSeparators", true);
       UIManager.put("TabbedPane.showContentSeparator", true);
-      UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
+      // UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
       UIManager.put("TabbedPane.tabsOverlapBorder", true);
       UIManager.put("TabbedPane.hasFullBorder", true);
       UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
@@ -1547,7 +1551,7 @@ public class Jalview
   /*
   private static void showUsage()
   {
-    System.out.println(
+    jalview.bin.Console.outPrintln(
             "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
                     + "-nodisplay\tRun Jalview without User Interface.\n"
                     + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
@@ -1658,9 +1662,10 @@ public class Jalview
 
       } catch (Exception ex)
       {
-        System.err.println("Failed to read from STDIN into tempfile "
-                + ((tfile == null) ? "(tempfile wasn't created)"
-                        : tfile.toString()));
+        jalview.bin.Console
+                .errPrintln("Failed to read from STDIN into tempfile "
+                        + ((tfile == null) ? "(tempfile wasn't created)"
+                                : tfile.toString()));
         ex.printStackTrace();
         return;
       }
@@ -1669,7 +1674,7 @@ public class Jalview
         sfile = tfile.toURI().toURL();
       } catch (Exception x)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
                         + tfile.toURI());
         x.printStackTrace();
@@ -1686,17 +1691,20 @@ public class Jalview
         tfile = new File(groovyscript);
         if (!tfile.exists())
         {
-          System.err.println("File '" + groovyscript + "' does not exist.");
+          jalview.bin.Console.errPrintln(
+                  "File '" + groovyscript + "' does not exist.");
           return;
         }
         if (!tfile.canRead())
         {
-          System.err.println("File '" + groovyscript + "' cannot be read.");
+          jalview.bin.Console.errPrintln(
+                  "File '" + groovyscript + "' cannot be read.");
           return;
         }
         if (tfile.length() < 1)
         {
-          System.err.println("File '" + groovyscript + "' is empty.");
+          jalview.bin.Console
+                  .errPrintln("File '" + groovyscript + "' is empty.");
           return;
         }
         try
@@ -1704,7 +1712,7 @@ public class Jalview
           sfile = tfile.getAbsoluteFile().toURI().toURL();
         } catch (Exception ex)
         {
-          System.err.println("Failed to create a file URL for "
+          jalview.bin.Console.errPrintln("Failed to create a file URL for "
                   + tfile.getAbsoluteFile());
           return;
         }
@@ -1729,8 +1737,9 @@ public class Jalview
       }
     } catch (Exception e)
     {
-      System.err.println("Exception Whilst trying to execute file " + sfile
-              + " as a groovy script.");
+      jalview.bin.Console
+              .errPrintln("Exception Whilst trying to execute file " + sfile
+                      + " as a groovy script.");
       e.printStackTrace(System.err);
 
     }
@@ -1786,11 +1795,11 @@ public class Jalview
       {
         if (exitcode == 0)
         {
-          System.out.println(message);
+          Console.outPrintln(message);
         }
         else
         {
-          System.err.println(message);
+          jalview.bin.Console.errPrintln(message);
         }
       }
     }
@@ -1882,7 +1891,7 @@ public class Jalview
     if (yes && ((s1 == null && s2 == null)
             || (s1 != null && s1.equals(s2))))
     {
-      System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+      Console.outPrintln("[TESTOUTPUT] arg " + a.argString() + "='" + s1
               + "' was set");
     }
   }
@@ -1940,6 +1949,6 @@ public class Jalview
     {
       message = a.argString() + (yes ? " was set" : " was not set");
     }
-    System.out.println("[TESTOUTPUT] arg " + message);
+    Console.outPrintln("[TESTOUTPUT] arg " + message);
   }
 }
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 7d66f6d..e8be95f 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -292,7 +292,7 @@ public class JalviewLite extends Applet
     {
       if (debug)
       {
-        System.err.println("Selecting region using separator string '"
+        jalview.bin.Console.errPrintln("Selecting region using separator string '"
                 + separator + "'");
       }
     }
@@ -344,7 +344,7 @@ public class JalviewLite extends Applet
             from--;
           } catch (NumberFormatException ex)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "ERROR: Couldn't parse first integer in range element column selection string '"
                             + cl + "' - format is 'from-to'");
             return;
@@ -355,7 +355,7 @@ public class JalviewLite extends Applet
             to--;
           } catch (NumberFormatException ex)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "ERROR: Couldn't parse second integer in range element column selection string '"
                             + cl + "' - format is 'from-to'");
             return;
@@ -396,13 +396,13 @@ public class JalviewLite extends Applet
             }
             if (debug)
             {
-              System.err.println("Range '" + cl + "' deparsed as [" + from
+              jalview.bin.Console.errPrintln("Range '" + cl + "' deparsed as [" + from
                       + "," + to + "]");
             }
           }
           else
           {
-            System.err.println("ERROR: Invalid Range '" + cl
+            jalview.bin.Console.errPrintln("ERROR: Invalid Range '" + cl
                     + "' deparsed as [" + from + "," + to + "]");
           }
         }
@@ -422,7 +422,7 @@ public class JalviewLite extends Applet
             }
             else
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "ERROR: Couldn't parse integer from point selection element of column selection string '"
                               + cl + "'");
               return;
@@ -451,13 +451,13 @@ public class JalviewLite extends Applet
             csel.addElement(r);
             if (debug)
             {
-              System.err.println("Point selection '" + cl
+              jalview.bin.Console.errPrintln("Point selection '" + cl
                       + "' deparsed as [" + r + "]");
             }
           }
           else
           {
-            System.err.println("ERROR: Invalid Point selection '" + cl
+            jalview.bin.Console.errPrintln("ERROR: Invalid Point selection '" + cl
                     + "' deparsed as [" + r + "]");
           }
         }
@@ -940,7 +940,7 @@ public class JalviewLite extends Applet
       listener = listener.trim();
       if (listener.length() == 0)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "jalview Javascript error: Ignoring empty function for mouseover listener.");
         return;
       }
@@ -952,11 +952,11 @@ public class JalviewLite extends Applet
             .addStructureViewerListener(mol);
     if (debug)
     {
-      System.err.println("Added a mouseover listener for "
+      jalview.bin.Console.errPrintln("Added a mouseover listener for "
               + ((af == null) ? "All frames"
                       : "Just views for "
                               + af.getAlignViewport().getSequenceSetId()));
-      System.err.println("There are now " + javascriptListeners.size()
+      jalview.bin.Console.errPrintln("There are now " + javascriptListeners.size()
               + " listeners in total.");
     }
   }
@@ -987,7 +987,7 @@ public class JalviewLite extends Applet
       listener = listener.trim();
       if (listener.length() == 0)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "jalview Javascript error: Ignoring empty function for selection listener.");
         return;
       }
@@ -999,11 +999,11 @@ public class JalviewLite extends Applet
             .addSelectionListener(mol);
     if (debug)
     {
-      System.err.println("Added a selection listener for "
+      jalview.bin.Console.errPrintln("Added a selection listener for "
               + ((af == null) ? "All frames"
                       : "Just views for "
                               + af.getAlignViewport().getSequenceSetId()));
-      System.err.println("There are now " + javascriptListeners.size()
+      jalview.bin.Console.errPrintln("There are now " + javascriptListeners.size()
               + " listeners in total.");
     }
   }
@@ -1027,7 +1027,7 @@ public class JalviewLite extends Applet
       listener = listener.trim();
       if (listener.length() == 0)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "jalview Javascript error: Ignoring empty function for selection listener.");
         return;
       }
@@ -1039,9 +1039,9 @@ public class JalviewLite extends Applet
             .addStructureViewerListener(mol);
     if (debug)
     {
-      System.err.println("Added a javascript structure viewer listener '"
+      jalview.bin.Console.errPrintln("Added a javascript structure viewer listener '"
               + listener + "'");
-      System.err.println("There are now " + javascriptListeners.size()
+      jalview.bin.Console.errPrintln("There are now " + javascriptListeners.size()
               + " listeners in total.");
     }
   }
@@ -1087,7 +1087,7 @@ public class JalviewLite extends Applet
         rprt = debug;
         if (debug)
         {
-          System.err.println("Removed listener '" + listener + "'");
+          jalview.bin.Console.errPrintln("Removed listener '" + listener + "'");
         }
       }
       else
@@ -1097,7 +1097,7 @@ public class JalviewLite extends Applet
     }
     if (rprt)
     {
-      System.err.println("There are now " + javascriptListeners.size()
+      jalview.bin.Console.errPrintln("There are now " + javascriptListeners.size()
               + " listeners in total.");
     }
   }
@@ -1105,14 +1105,14 @@ public class JalviewLite extends Applet
   @Override
   public void stop()
   {
-    System.err.println("Applet " + getName() + " stop().");
+    jalview.bin.Console.errPrintln("Applet " + getName() + " stop().");
     tidyUp();
   }
 
   @Override
   public void destroy()
   {
-    System.err.println("Applet " + getName() + " destroy().");
+    jalview.bin.Console.errPrintln("Applet " + getName() + " destroy().");
     tidyUp();
   }
 
@@ -1189,7 +1189,7 @@ public class JalviewLite extends Applet
           }
         } catch (NumberFormatException e)
         {
-          System.err.println("Ignoring invalid residue number string '"
+          jalview.bin.Console.errPrintln("Ignoring invalid residue number string '"
                   + pdbResNum + "'");
         }
 
@@ -1220,7 +1220,7 @@ public class JalviewLite extends Applet
 
         } catch (Exception ex)
         {
-          System.err.println("Couldn't parse integer arguments (topRow='"
+          jalview.bin.Console.errPrintln("Couldn't parse integer arguments (topRow='"
                   + topRow + "' and leftHandColumn='" + leftHandColumn
                   + "')");
           ex.printStackTrace();
@@ -1251,7 +1251,7 @@ public class JalviewLite extends Applet
 
         } catch (Exception ex)
         {
-          System.err.println("Couldn't parse integer arguments (topRow='"
+          jalview.bin.Console.errPrintln("Couldn't parse integer arguments (topRow='"
                   + topRow + "')");
           ex.printStackTrace();
         }
@@ -1283,7 +1283,7 @@ public class JalviewLite extends Applet
 
         } catch (Exception ex)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Couldn't parse integer arguments (leftHandColumn='"
                           + leftHandColumn + "')");
           ex.printStackTrace();
@@ -1415,18 +1415,18 @@ public class JalviewLite extends Applet
     {
       if (debug)
       {
-        System.err.println("Applet context is '"
+        jalview.bin.Console.errPrintln("Applet context is '"
                 + getAppletContext().getClass().toString() + "'");
       }
       JSObject scriptObject = JSObject.getWindow(this);
       if (debug && scriptObject != null)
       {
-        System.err.println("Applet has Javascript callback support.");
+        jalview.bin.Console.errPrintln("Applet has Javascript callback support.");
       }
 
     } catch (Exception ex)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Warning: No JalviewLite javascript callbacks available.");
       if (debug)
       {
@@ -1436,9 +1436,9 @@ public class JalviewLite extends Applet
 
     if (debug)
     {
-      System.err.println("JalviewLite Version " + getVersion());
-      System.err.println("Build Date : " + getBuildDate());
-      System.err.println("Installation : " + getInstallation());
+      jalview.bin.Console.errPrintln("JalviewLite Version " + getVersion());
+      jalview.bin.Console.errPrintln("Build Date : " + getBuildDate());
+      jalview.bin.Console.errPrintln("Installation : " + getInstallation());
     }
     String externalsviewer = getParameter("externalstructureviewer");
     if (externalsviewer != null)
@@ -1465,7 +1465,7 @@ public class JalviewLite extends Applet
         separator = sep;
         if (debug)
         {
-          System.err.println("Separator set to '" + separator + "'");
+          jalview.bin.Console.errPrintln("Separator set to '" + separator + "'");
         }
       }
       else
@@ -1573,7 +1573,7 @@ public class JalviewLite extends Applet
     {
       if (tries > 0)
       {
-        System.err.println("LiveConnect request thread going to sleep.");
+        jalview.bin.Console.errPrintln("LiveConnect request thread going to sleep.");
       }
       try
       {
@@ -1584,7 +1584,7 @@ public class JalviewLite extends Applet
       ;
       if (tries++ > 0)
       {
-        System.err.println("LiveConnect request thread woken up.");
+        jalview.bin.Console.errPrintln("LiveConnect request thread woken up.");
       }
       try
       {
@@ -1595,7 +1595,7 @@ public class JalviewLite extends Applet
         }
       } catch (Exception jsex)
       {
-        System.err.println("Attempt " + tries
+        jalview.bin.Console.errPrintln("Attempt " + tries
                 + " to access LiveConnect javascript failed.");
       }
     }
@@ -1632,14 +1632,14 @@ public class JalviewLite extends Applet
                   "Calling oninit callback '" + initjscallback + "'.");
         } catch (Exception e)
         {
-          System.err.println("Exception when executing _oninit callback '"
+          jalview.bin.Console.errPrintln("Exception when executing _oninit callback '"
                   + initjscallback + "'.");
           e.printStackTrace();
         }
       }
       else
       {
-        System.err.println("Not executing _oninit callback '"
+        jalview.bin.Console.errPrintln("Not executing _oninit callback '"
                 + initjscallback + "' - no scripting allowed.");
       }
     }
@@ -1700,7 +1700,7 @@ public class JalviewLite extends Applet
           ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
           if (debug)
           {
-            System.err.println("Activated window " + frame);
+            jalview.bin.Console.errPrintln("Activated window " + frame);
           }
         }
         // be good.
@@ -1715,7 +1715,7 @@ public class JalviewLite extends Applet
        * 
        * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
        * frame) { currentAlignFrame = null; if (debug) {
-       * System.err.println("Deactivated window "+frame); } }
+       * jalview.bin.Console.errPrintln("Deactivated window "+frame); } }
        * super.windowDeactivated(e); }
        */
     });
@@ -1801,7 +1801,7 @@ public class JalviewLite extends Applet
           }
           if (!jmolAvailable)
           {
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "Jmol not available - Using mc_view for structures");
           }
         } catch (java.lang.ClassNotFoundException ex)
@@ -1813,7 +1813,7 @@ public class JalviewLite extends Applet
         jmolAvailable = false;
         if (debug)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Skipping Jmol check. Will use mc_view (probably)");
         }
       }
@@ -1844,7 +1844,7 @@ public class JalviewLite extends Applet
     {
       if (JalviewLite.debug)
       {
-        System.err.println(msg);
+        jalview.bin.Console.errPrintln(msg);
       }
     }
 
@@ -1884,7 +1884,7 @@ public class JalviewLite extends Applet
       {
         if (debug)
         {
-          System.err.println("Prepended document base '" + documentBase
+          jalview.bin.Console.errPrintln("Prepended document base '" + documentBase
                   + "' to make: '" + withDocBase + "'");
         }
         protocol = DataSourceType.URL;
@@ -1903,7 +1903,7 @@ public class JalviewLite extends Applet
         protocol = DataSourceType.URL;
         if (debug)
         {
-          System.err.println("Prepended codebase '" + codeBase
+          jalview.bin.Console.errPrintln("Prepended codebase '" + codeBase
                   + "' to make: '" + withCodeBase + "'");
         }
         return withCodeBase;
@@ -2010,7 +2010,7 @@ public class JalviewLite extends Applet
                   + " as "
                   + (al1.isNucleotide() ? "protein product" : "cDNA")
                   + " for " + af.getTitle();
-          System.err.println(msg);
+          jalview.bin.Console.errPrintln(msg);
         }
       }
 
@@ -2084,7 +2084,7 @@ public class JalviewLite extends Applet
             dbgMsg(">>>Dump finished.");
           } catch (Exception e)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Exception when trying to dump the content of the file parameter.");
             e.printStackTrace();
           }
@@ -2214,7 +2214,7 @@ public class JalviewLite extends Applet
                 {
                   // this may not really be a problem but we give a warning
                   // anyway
-                  System.err.println(
+                  jalview.bin.Console.errPrintln(
                           "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
                                   + i + ")");
                 }
@@ -2320,7 +2320,7 @@ public class JalviewLite extends Applet
         }
         else
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Annotations were not added from annotation file '"
                           + param + "'");
         }
@@ -2392,13 +2392,13 @@ public class JalviewLite extends Applet
         {
           if (debug)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Attempting to load T-COFFEE score file from the scoreFile parameter");
           }
           result = alignFrame.loadScoreFile(sScoreFile);
           if (!result)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Failed to parse T-COFFEE parameter as a valid score file ('"
                             + sScoreFile + "')");
           }
@@ -2469,13 +2469,13 @@ public class JalviewLite extends Applet
         boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
         if (debug)
         {
-          System.err.println("Resource '" + f + "' was "
+          jalview.bin.Console.errPrintln("Resource '" + f + "' was "
                   + (rtn ? "" : "not ") + "located by classloader.");
         }
         return rtn;
       } catch (Exception ex)
       {
-        System.out.println("Exception checking resources: " + f + " " + ex);
+        jalview.bin.Console.outPrintln("Exception checking resources: " + f + " " + ex);
         return false;
       }
     }
@@ -2496,7 +2496,7 @@ public class JalviewLite extends Applet
     {
       return initialAlignFrame;
     }
-    System.err.println(
+    jalview.bin.Console.errPrintln(
             "Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
     return null;
   }
@@ -2564,18 +2564,18 @@ public class JalviewLite extends Applet
       jv.removeAllElements();
       if (debug)
       {
-        System.err.println("Array from '" + separator
+        jalview.bin.Console.errPrintln("Array from '" + separator
                 + "' separated List:\n" + v.length);
         for (int i = 0; i < v.length; i++)
         {
-          System.err.println("item " + i + " '" + v[i] + "'");
+          jalview.bin.Console.errPrintln("item " + i + " '" + v[i] + "'");
         }
       }
       return v;
     }
     if (debug)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Empty Array from '" + separator + "' separated List");
     }
     return null;
@@ -2620,13 +2620,13 @@ public class JalviewLite extends Applet
       {
         System.err
                 .println("Returning '" + separator + "' separated List:\n");
-        System.err.println(v);
+        jalview.bin.Console.errPrintln(v);
       }
       return v.toString();
     }
     if (debug)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Returning empty '" + separator + "' separated List\n");
     }
     return "" + separator;
@@ -2745,7 +2745,7 @@ public class JalviewLite extends Applet
     this.separator = separator;
     if (debug)
     {
-      System.err.println("Default Separator now: '" + separator + "'");
+      jalview.bin.Console.errPrintln("Default Separator now: '" + separator + "'");
     }
   }
 
@@ -2901,7 +2901,7 @@ public class JalviewLite extends Applet
     Color col = ColorUtils.parseColourString(colprop);
     if (col == null)
     {
-      System.err.println("Couldn't parse '" + colprop + "' as a colour for "
+      jalview.bin.Console.errPrintln("Couldn't parse '" + colprop + "' as a colour for "
               + colparam);
     }
     return (col == null) ? defcolour : col;
@@ -2971,7 +2971,7 @@ public class JalviewLite extends Applet
     }
     if (debug)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
     }
     return resolvedPath;
@@ -3000,7 +3000,7 @@ public class JalviewLite extends Applet
                         : getDocumentBase());
         if (debug)
         {
-          System.err.println("Show url (prepended " + prepend
+          jalview.bin.Console.errPrintln("Show url (prepended " + prepend
                   + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
                   + url);
         }
@@ -3009,7 +3009,7 @@ public class JalviewLite extends Applet
       {
         if (debug)
         {
-          System.err.println("Show url: " + url);
+          jalview.bin.Console.errPrintln("Show url: " + url);
         }
       }
       if (url.indexOf("javascript:") == 0)
diff --git a/src/jalview/bin/JalviewLiteURLRetrieve.java b/src/jalview/bin/JalviewLiteURLRetrieve.java
index f2ffda5..d38892a 100644
--- a/src/jalview/bin/JalviewLiteURLRetrieve.java
+++ b/src/jalview/bin/JalviewLiteURLRetrieve.java
@@ -64,7 +64,7 @@ public class JalviewLiteURLRetrieve extends Applet
     DataSourceType protocol = null;
     try
     {
-      System.out.println("Loading thread started with:\n>>file\n" + file
+      jalview.bin.Console.outPrintln("Loading thread started with:\n>>file\n" + file
               + ">>endfile");
       // This might throw a security exception in certain browsers
       // Netscape Communicator for instance.
@@ -77,7 +77,7 @@ public class JalviewLiteURLRetrieve extends Applet
           rtn = true;
           is.close();
         }
-        System.err.println("Resource '" + file + "' was "
+        jalview.bin.Console.errPrintln("Resource '" + file + "' was "
                 + (rtn ? "" : "not") + " located by classloader.");
         if (rtn)
         {
@@ -86,7 +86,7 @@ public class JalviewLiteURLRetrieve extends Applet
 
       } catch (Exception ex)
       {
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "Exception checking resources: " + file + " " + ex);
       }
       if (file.indexOf("://") > -1)
@@ -99,7 +99,7 @@ public class JalviewLiteURLRetrieve extends Applet
         protocol = DataSourceType.FILE;
       }
 
-      System.out.println("Trying to get contents of resource:");
+      jalview.bin.Console.outPrintln("Trying to get contents of resource:");
       FileParse fp = new FileParse(file, protocol);
       if (fp.isValid())
       {
@@ -112,7 +112,7 @@ public class JalviewLiteURLRetrieve extends Applet
       }
       else
       {
-        System.out.println("Resource at " + file
+        jalview.bin.Console.outPrintln("Resource at " + file
                 + " cannot be read with protocol==" + protocol);
         return;
       }
@@ -121,11 +121,11 @@ public class JalviewLiteURLRetrieve extends Applet
       if (format == null)
       {
         format = new IdentifyFile().identify(file, protocol);
-        System.out.println("Format is " + format);
+        jalview.bin.Console.outPrintln("Format is " + format);
       }
       else
       {
-        System.out.println("User specified Format is " + format);
+        jalview.bin.Console.outPrintln("User specified Format is " + format);
       }
       AlignmentI al = null;
       try
@@ -133,17 +133,17 @@ public class JalviewLiteURLRetrieve extends Applet
         al = new AppletFormatAdapter().readFile(file, protocol, format);
       } catch (java.io.IOException ex)
       {
-        System.err.println("Failed to open the file.");
+        jalview.bin.Console.errPrintln("Failed to open the file.");
         ex.printStackTrace();
       }
       if (al != null)
       {
-        System.out.println(new AppletFormatAdapter()
+        jalview.bin.Console.outPrintln(new AppletFormatAdapter()
                 .formatSequences(FileFormat.Fasta, al, false));
       }
     } catch (Exception e)
     {
-      System.err.println("bailing out : Unexpected exception:");
+      jalview.bin.Console.errPrintln("bailing out : Unexpected exception:");
       e.printStackTrace();
     }
   }
diff --git a/src/jalview/bin/JalviewTaskbar.java b/src/jalview/bin/JalviewTaskbar.java
index c7ababa..e04c04f 100644
--- a/src/jalview/bin/JalviewTaskbar.java
+++ b/src/jalview/bin/JalviewTaskbar.java
@@ -46,7 +46,7 @@ public class JalviewTaskbar
         }
         else
         {
-          System.out.println("Unable to setIconImage()");
+          Console.outPrintln("Unable to setIconImage()");
         }
       }
     }
diff --git a/src/jalview/bin/Launcher.java b/src/jalview/bin/Launcher.java
index a87d322..e1415be 100644
--- a/src/jalview/bin/Launcher.java
+++ b/src/jalview/bin/Launcher.java
@@ -50,28 +50,7 @@ public class Launcher
 {
   private final static String startClass = "jalview.bin.Jalview";
 
-  private static boolean checkJVMSymlink(String testBin)
-  {
-    File testBinFile = new File(testBin);
-    if (!testBinFile.exists())
-    {
-      return false;
-    }
-    File targetFile = null;
-    try
-    {
-      targetFile = testBinFile.getCanonicalFile();
-    } catch (IOException e)
-    {
-      return false;
-    }
-    if (targetFile != null && ("java".equals(targetFile.getName())
-            || "java.exe".equals(targetFile.getName())))
-    {
-      return true;
-    }
-    return false;
-  }
+  private final static String headlessProperty = "java.awt.headless";
 
   /**
    * main method for jalview.bin.Launcher. This restarts the same JRE's JVM with
@@ -85,53 +64,27 @@ public class Launcher
   {
     if (!LaunchUtils.checkJavaVersion())
     {
-      System.err.println("WARNING - The Java version being used (Java "
-              + LaunchUtils.getJavaVersion()
-              + ") may lead to problems. This installation of Jalview should be used with Java "
-              + LaunchUtils.getJavaCompileVersion() + ".");
-    }
-    final String appName = ChannelProperties.getProperty("app_name");
-    final String javaBinDir = System.getProperty("java.home")
-            + File.separator + "bin" + File.separator;
-    String javaBin = null;
-    if (javaBin == null && checkJVMSymlink(javaBinDir + appName))
-    {
-      javaBin = javaBinDir + appName;
-    }
-    if (javaBin == null && checkJVMSymlink(javaBinDir + "Jalview"))
-    {
-      javaBin = javaBinDir + "Jalview";
-    }
-    if (javaBin == null)
-    {
-      javaBin = "java";
-    }
-
-    List command = new ArrayList<>();
-    command.add(javaBin);
-
-    String memSetting = null;
-
-    boolean isAMac = System.getProperty("os.name").indexOf("Mac") > -1;
-
-    for (String jvmArg : ManagementFactory.getRuntimeMXBean()
-            .getInputArguments())
-    {
-      command.add(jvmArg);
+      jalview.bin.Console
+              .errPrintln("WARNING - The Java version being used (Java "
+                      + LaunchUtils.getJavaVersion()
+                      + ") may lead to problems. This installation of Jalview should be used with Java "
+                      + LaunchUtils.getJavaCompileVersion() + ".");
     }
-    command.add("-cp");
-    command.add(ManagementFactory.getRuntimeMXBean().getClassPath());
 
     String jvmmempc = null;
     String jvmmemmax = null;
     boolean debug = false;
     boolean wait = true;
     boolean quiet = false;
+    boolean headless = false;
+    boolean gui = false;
+    boolean stdout = false;
     // must set --debug before --launcher...
     boolean launcherstop = false;
     boolean launcherprint = false;
     boolean launcherwait = false;
     ArrayList arguments = new ArrayList<>();
+    String previousArg = null;
     for (String arg : args)
     {
       if (arg.equals("--debug"))
@@ -142,6 +95,19 @@ public class Launcher
       {
         quiet = true;
       }
+      if (arg.equals("--headless"))
+      {
+        headless = true;
+      }
+      if (arg.equals("--gui"))
+      {
+        gui = true;
+      }
+      if (arg.equals("--output=-")
+              || (arg.equals("-") && "--output".equals(previousArg)))
+      {
+        stdout = true;
+      }
       if (debug && arg.equals("--launcherprint"))
       {
         launcherprint = true;
@@ -159,6 +125,7 @@ public class Launcher
       {
         wait = false;
       }
+      previousArg = arg;
       // Don't add the --launcher... args to Jalview launch
       if (arg.startsWith("--launcher"))
       {
@@ -199,6 +166,29 @@ public class Launcher
         arguments.add(arg);
       }
     }
+    if (gui)
+    {
+      // --gui takes precedence over --headless
+      headless = false;
+    }
+
+    final String appName = ChannelProperties.getProperty("app_name");
+
+    // if we're using jalview.bin.Launcher we always assume a console is in use
+    final String javaBin = LaunchUtils.findJavaBin(true);
+
+    List command = new ArrayList<>();
+    command.add(javaBin);
+
+    String memSetting = null;
+
+    for (String jvmArg : ManagementFactory.getRuntimeMXBean()
+            .getInputArguments())
+    {
+      command.add(jvmArg);
+    }
+    command.add("-cp");
+    command.add(ManagementFactory.getRuntimeMXBean().getClassPath());
 
     // use saved preferences if no cmdline args
     boolean useCustomisedSettings = LaunchUtils
@@ -221,6 +211,7 @@ public class Launcher
     boolean memSet = false;
     boolean dockIcon = false;
     boolean dockName = false;
+    boolean headlessProp = false;
     for (int i = 0; i < command.size(); i++)
     {
       String arg = command.get(i);
@@ -241,6 +232,10 @@ public class Launcher
       {
         dockName = true;
       }
+      else if (arg.startsWith("-D" + headlessProperty + "="))
+      {
+        headlessProp = true;
+      }
     }
 
     if (!memSet)
@@ -255,7 +250,7 @@ public class Launcher
       }
     }
 
-    if (isAMac)
+    if (LaunchUtils.isMac)
     {
       if (!dockIcon)
       {
@@ -276,11 +271,16 @@ public class Launcher
                 + appName);
       }
     }
+    if (headless && !headlessProp)
+    {
+      System.setProperty(headlessProperty, "true");
+      command.add("-D" + headlessProperty + "=true");
+    }
 
     String scalePropertyArg = HiDPISetting.getScalePropertyArg();
     if (scalePropertyArg != null)
     {
-      sysout(debug, quiet, "Running " + startClass + " with scale setting "
+      syserr(debug, quiet, "Running " + startClass + " with scale setting "
               + scalePropertyArg);
       command.add(scalePropertyArg);
     }
@@ -293,10 +293,10 @@ public class Launcher
     if ((Boolean.parseBoolean(System.getProperty("launcherprint", "false"))
             || launcherprint))
     {
-      sysout(debug, quiet,
+      syserr(debug, quiet,
               "LAUNCHER COMMAND: " + String.join(" ", builder.command()));
     }
-    sysout(debug, quiet,
+    syserr(debug, quiet,
             "Running " + startClass + " with "
                     + (memSetting == null ? "no memory setting"
                             : ("memory setting " + memSetting)));
@@ -304,7 +304,7 @@ public class Launcher
     if (Boolean.parseBoolean(System.getProperty("launcherstop", "false"))
             || (debug && launcherstop))
     {
-      sysout(debug, quiet,
+      syserr(debug, quiet,
               "System property 'launcherstop' is set and not 'false'. Exiting.");
       System.exit(0);
     }
@@ -314,22 +314,23 @@ public class Launcher
       Process process = builder.start();
       if (wait || launcherwait)
       {
-        sysout(debug, quiet, "Launching application process");
+        syserr(debug, quiet, "Launching application process");
         process.waitFor();
       }
       else
       {
         int waitInt = 0;
-        sysout(debug, quiet,
+        syserr(debug, quiet,
                 "Wait time for application process is " + waitInt + "ms");
         process.waitFor(waitInt, TimeUnit.MILLISECONDS);
       }
-      sysout(debug, quiet, "Launcher process ending");
+      syserr(debug, quiet, "Launcher process ending");
     } catch (IOException e)
     {
       if (e.getMessage().toLowerCase(Locale.ROOT).contains("memory"))
       {
-        System.err.println("Caught a memory exception: " + e.getMessage());
+        jalview.bin.Console
+                .errPrintln("Caught a memory exception: " + e.getMessage());
         // Probably the "Cannot allocate memory" error, try without the memory
         // setting
         ArrayList commandNoMem = new ArrayList<>();
@@ -342,7 +343,7 @@ public class Launcher
         }
         final ProcessBuilder builderNoMem = new ProcessBuilder(
                 commandNoMem);
-        System.err.println("Command without memory setting: "
+        jalview.bin.Console.errPrintln("Command without memory setting: "
                 + String.join(" ", builderNoMem.command()));
         try
         {
@@ -364,11 +365,11 @@ public class Launcher
     }
   }
 
-  private static void sysout(boolean debug, boolean quiet, String message)
+  private static void syserr(boolean debug, boolean quiet, String message)
   {
     if (debug && !quiet)
     {
-      System.out.println("LAUNCHERDEBUG - " + message);
+      jalview.bin.Console.errPrintln("LAUNCHERDEBUG - " + message);
     }
   }
 
diff --git a/src/jalview/bin/MemorySetting.java b/src/jalview/bin/MemorySetting.java
index bb545cb..7458d55 100644
--- a/src/jalview/bin/MemorySetting.java
+++ b/src/jalview/bin/MemorySetting.java
@@ -354,7 +354,7 @@ public class MemorySetting
     else
     {
       // number too big for a Long. Limit to Long.MAX_VALUE
-      System.out.println("Memory parsing of '" + memString
+      jalview.bin.Console.outPrintln("Memory parsing of '" + memString
               + "' produces number too big.  Limiting to Long.MAX_VALUE="
               + Long.MAX_VALUE);
       return Long.MAX_VALUE;
@@ -395,7 +395,7 @@ public class MemorySetting
     ADJUSTMENT_MESSAGE = reason;
     if (!quiet)
     {
-      System.out.println(reason);
+      jalview.bin.Console.outPrintln(reason);
     }
   }
 
diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 2f25978..7882d7b 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -29,8 +29,8 @@ public enum Arg
           Opt.UNARY, Opt.BOOTSTRAP),
   HEADLESS(Type.CONFIG,
           "Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed. "
-                  + "Headless mode is assumed if an output file is to be generated, this can be overridden with --noheadless or --gui.",
-          Opt.BOOLEAN, Opt.BOOTSTRAP),
+                  + "Headless mode is assumed if an output file is to be generated, this can be overridden with --gui.",
+          Opt.UNARY, Opt.BOOTSTRAP),
   GUI(Type.CONFIG,
           "Do not run Jalview in headless mode.  This overrides the assumption of headless mode when an output file is to be generated.",
           Opt.UNARY, Opt.BOOTSTRAP),
@@ -93,11 +93,10 @@ public enum Arg
                   + "turn-propensity,\n" + "buried-index,\n"
                   + "nucleotide,\n" + "nucleotide-ambiguity,\n"
                   + "purine-pyrimidine,\n" + "rna-helices,\n"
-                  + "t-coffee-scores,\n" + "sequence-id.\n"
-                  +"\n"
+                  + "t-coffee-scores,\n" + "sequence-id.\n" + "\n"
                   + "Names of user defined colourschemes will also work,\n"
-                 +"and jalview colourscheme specifications like\n"
-                  +"--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
+                  + "and jalview colourscheme specifications like\n"
+                  + "--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.",
           Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
@@ -200,7 +199,7 @@ public enum Arg
                   + "clustal (aln),\n" + "phylip (phy),\n"
                   + "jalview (jvp, jar).",
           Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
-          Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
+          Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.STDOUT, Opt.PRIMARY),
   FORMAT(Type.OUTPUT,
           "Sets the format for the preceding --output file. Valid formats are:\n"
                   + "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n"
@@ -384,6 +383,11 @@ public enum Arg
      */
     OUTPUTFILE("output file --headless will be assumed unless --gui used"),
     /*
+     * A STDOUT Arg can take an output filename that can be '-' to mean print to STDOUT.
+     */
+    STDOUT("allows the output filename '" + ArgParser.STDOUTFILENAME
+            + "' to mean output to STDOUT"),
+    /*
      * A STORED Arg resets and creates a new set of "opened" linkedIds
      */
     STORED(null),
diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 907b1fa..3862375 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -50,6 +50,8 @@ public class ArgParser
 
   public static final char EQUALS = '=';
 
+  public static final String STDOUTFILENAME = "-";
+
   protected static final String NEGATESTRING = "no";
 
   /**
@@ -209,12 +211,15 @@ public class ArgParser
   public ArgParser(String[] args, boolean initsubstitutions,
           BootstrapArgs bsa)
   {
-    // Make a mutable new ArrayList so that shell globbing parser works.
-    // (When shell file globbing is used, there are a sequence of non-Arg
-    // arguments (which are the expanded globbed filenames) that need to be
-    // consumed by the --append/--argfile/etc Arg which is most easily done by
-    // removing these filenames from the list one at a time. This can't be done
-    // with an ArrayList made with only Arrays.asList(String[] args). )
+    /*
+     *  Make a mutable new ArrayList so that shell globbing parser works.
+     * (When shell file globbing is used, there are a sequence of non-Arg
+     * arguments (which are the expanded globbed filenames) that need to be
+     * consumed by the --append/--argfile/etc Arg which is most easily done
+     * by removing these filenames from the list one at a time. This can't be
+     * done with an ArrayList made with only Arrays.asList(String[] args) as
+     * that is not mutable. )
+     */
     this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
             bsa);
   }
@@ -260,27 +265,30 @@ public class ArgParser
           boolean allowPrivate)
   {
     this.substitutions = initsubstitutions;
-    boolean openEachInitialFilenames = true;
-    for (int i = 0; i < args.size(); i++)
-    {
-      String arg = args.get(i);
 
-      // If the first arguments do not start with "--" or "-" or is not "open"
-      // and` is a filename that exists it is probably a file/list of files to
-      // open so we fake an Arg.OPEN argument and when adding files only add the
-      // single arg[i] and increment the defaultLinkedIdCounter so that each of
-      // these files is opened separately.
-      if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
-              && !arg.startsWith("-") && !arg.equals("open")
-              && (new File(arg).exists()
-                      || HttpUtils.startsWithHttpOrHttps(arg)))
-      {
-        arg = Arg.OPEN.argString();
-      }
-      else
+    /*
+     *  If the first argument does not start with "--" or "-" or is not "open",
+     *  and is a filename that exists or a URL, it is probably a file/list of
+     *  files to open so we insert an Arg.OPEN argument before it. This will
+     *  mean the list of files at the start of the arguments are all opened
+     *  separately.
+     */
+    if (args.size() > 0)
+    {
+      String arg0 = args.get(0);
+      if (arg0 != null
+              && (!arg0.startsWith(DOUBLEDASH) && !arg0.startsWith("-")
+                      && !arg0.equals("open") && (new File(arg0).exists()
+                              || HttpUtils.startsWithHttpOrHttps(arg0))))
       {
-        openEachInitialFilenames = false;
+        // insert "--open" at the start
+        args.add(0, Arg.OPEN.argString());
       }
+    }
+
+    for (int i = 0; i < args.size(); i++)
+    {
+      String arg = args.get(i);
 
       // look for double-dash, e.g. --arg
       if (arg.startsWith(DOUBLEDASH))
@@ -431,7 +439,7 @@ public class ArgParser
           {
             // There is no "=" so value is next arg or args (possibly shell
             // glob-expanded)
-            if ((openEachInitialFilenames ? i : i + 1) >= args.size())
+            if (i + 1 >= args.size())
             {
               // no value to take for arg, which wants a value
               Console.error("Argument '" + a.getName()
@@ -446,8 +454,7 @@ public class ArgParser
             {
               // if this is the first argument with a file list at the start of
               // the args we add filenames from index i instead of i+1
-              globVals = getShellGlobbedFilenameValues(a, args,
-                      openEachInitialFilenames ? i : i + 1);
+              globVals = getShellGlobbedFilenameValues(a, args, i + 1);
             }
             else
             {
diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index 4b7b180..ec62bcd 100644
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -28,6 +28,8 @@ public class BootstrapArgs
 
   private Set argsTypes = new HashSet<>();
 
+  private boolean outputToStdout = false;
+
   public static BootstrapArgs getBootstrapArgs(String[] args)
   {
     List argList = new ArrayList<>(Arrays.asList(args));
@@ -53,7 +55,7 @@ public class BootstrapArgs
     {
       if (argFiles.contains(inArgFile))
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Looped argfiles detected: '" + inArgFile.getPath() + "'");
         return;
       }
@@ -127,11 +129,6 @@ public class BootstrapArgs
           }
         }
 
-        if (ArgParser.argMap.containsKey(argName) && val == null)
-        {
-          val = "true";
-        }
-
         Arg a = ArgParser.argMap.get(argName);
 
         if (a != null)
@@ -152,7 +149,27 @@ public class BootstrapArgs
 
         if (a == null || !a.hasOption(Opt.BOOTSTRAP))
         {
-          // not a valid bootstrap arg
+          // not a bootstrap arg
+
+          // make a check for an output going to stdout
+          if (a != null && a.hasOption(Opt.OUTPUTFILE)
+                  && a.hasOption(Opt.STDOUT))
+          {
+            if (val == null && i + 1 < args.size())
+            {
+              val = args.get(i + 1);
+            }
+            if (val.startsWith("[") && val.indexOf(']') > 0)
+            {
+              val = val.substring(val.indexOf(']') + 1);
+            }
+
+            if (ArgParser.STDOUTFILENAME.equals(val))
+            {
+              this.outputToStdout = true;
+            }
+          }
+
           continue;
         }
 
@@ -188,6 +205,11 @@ public class BootstrapArgs
         }
         else
         {
+          if (val == null)
+          {
+            val = "true";
+          }
+
           add(a, type, val);
         }
       }
@@ -362,7 +384,7 @@ public class BootstrapArgs
     }
     else if (this.contains(Arg.HEADLESS))
     {
-      // --headless, --noheadless specified => use value
+      // --headless has been specified on the command line => headless
       isHeadless = this.getBoolean(Arg.HEADLESS);
     }
     else if (this.argsHaveOption(Opt.OUTPUTFILE))
@@ -373,4 +395,9 @@ public class BootstrapArgs
     }
     return isHeadless;
   }
+
+  public boolean outputToStdout()
+  {
+    return this.outputToStdout;
+  }
 }
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 62ef660..c15bbf8 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -473,7 +473,7 @@ public class EditCommand implements CommandI
     {
       command.seqs[s].insertCharAt(command.position, command.number,
               command.gapChar);
-      // System.out.println("pos: "+command.position+" number:
+      // jalview.bin.Console.outPrintln("pos: "+command.position+" number:
       // "+command.number);
     }
 
@@ -486,7 +486,7 @@ public class EditCommand implements CommandI
   //
   // for (int s = 0; s < command.seqs.length; s++)
   // {
-  // System.out.println("pos: "+command.position+" number: "+command.number);
+  // jalview.bin.Console.outPrintln("pos: "+command.position+" number: "+command.number);
   // command.seqs[s].insertCharAt(command.position, command.number,'A');
   // }
   //
@@ -1433,7 +1433,7 @@ public class EditCommand implements CommandI
           }
           else
           {
-            System.err.println("Can't undo edit action " + action);
+            jalview.bin.Console.errPrintln("Can't undo edit action " + action);
             // throw new IllegalStateException("Can't undo edit action " +
             // action);
           }
diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index f5154ec..cb74a66 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -707,7 +707,7 @@ public class AlignedCodonFrame
             ds.setSequenceFeatures(dna.getSequenceFeatures());
             // dnaSeqs[i] = ds;
             ssm.fromSeq = ds;
-            System.out.println("Realised mapped sequence " + ds.getName());
+            jalview.bin.Console.outPrintln("Realised mapped sequence " + ds.getName());
           }
         }
       }
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index de98c64..7e6b904 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -126,7 +126,7 @@ public class AlignmentAnnotation
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
-      // DEBUG System.out.println(px);
+      // DEBUG jalview.bin.Console.outPrintln(px);
       invalidrnastruc = px.getProblemPos();
     }
     if (invalidrnastruc > -1)
@@ -142,7 +142,7 @@ public class AlignmentAnnotation
       scaleColLabel = true;
       _markRnaHelices();
     }
-    // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+    // jalview.bin.Console.outPrintln("featuregroup " + _rnasecstr[0].getFeatureGroup());
 
   }
 
@@ -156,10 +156,10 @@ public class AlignmentAnnotation
     {
 
       /*
-       * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+       * jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
        * this.annotation._rnasecstr[x].getBegin());
        */
-      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+      // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
       int val = 0;
       try
       {
@@ -386,7 +386,7 @@ public class AlignmentAnnotation
     char firstChar = 0;
     for (int i = 0; i < annotations.length; i++)
     {
-      // DEBUG System.out.println(i + ": " + annotations[i]);
+      // DEBUG jalview.bin.Console.outPrintln(i + ": " + annotations[i]);
       if (annotations[i] == null)
       {
         continue;
@@ -394,14 +394,14 @@ public class AlignmentAnnotation
       if (annotations[i].secondaryStructure == 'H'
               || annotations[i].secondaryStructure == 'E')
       {
-        // DEBUG System.out.println( "/H|E/ '" +
+        // DEBUG jalview.bin.Console.outPrintln( "/H|E/ '" +
         // annotations[i].secondaryStructure + "'");
         hasIcons |= true;
       }
       else
       // Check for RNA secondary structure
       {
-        // DEBUG System.out.println( "/else/ '" +
+        // DEBUG jalview.bin.Console.outPrintln( "/else/ '" +
         // annotations[i].secondaryStructure + "'");
         // TODO: 2.8.2 should this ss symbol validation check be a function in
         // RNA/ResidueProperties ?
@@ -446,7 +446,7 @@ public class AlignmentAnnotation
         }
       }
 
-      // System.out.println("displaychar " + annotations[i].displayCharacter);
+      // jalview.bin.Console.outPrintln("displaychar " + annotations[i].displayCharacter);
 
       if (annotations[i].displayCharacter == null
               || annotations[i].displayCharacter.length() == 0)
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index e6604d1..6ab71c7 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1128,11 +1128,11 @@ public class AlignmentView
   public static void testSelectionViews(AlignmentI alignment,
           HiddenColumns hidden, SequenceGroup selection)
   {
-    System.out.println("Testing standard view creation:\n");
+    jalview.bin.Console.outPrintln("Testing standard view creation:\n");
     AlignmentView view = null;
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, no limit to selection, no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, false,
               false);
@@ -1141,12 +1141,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, no limit to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, false,
               true);
@@ -1154,12 +1154,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection marked but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, limited to selection and no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, true,
               false);
@@ -1167,12 +1167,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, limited to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, true,
               true);
@@ -1180,12 +1180,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted and groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, no limit to selection, no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, false,
               false);
@@ -1193,12 +1193,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, no limit to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, false,
               true);
@@ -1206,12 +1206,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection marked but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, limited to selection and no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, true,
               false);
@@ -1219,12 +1219,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, limited to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, true,
               true);
@@ -1232,7 +1232,7 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted and groups marked.");
     }
 
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index b5efeb4..e2ef318 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -159,7 +159,7 @@ public class HiddenSequences
 
     if (alignmentIndex < 0 || hiddenSequences[alignmentIndex] != null)
     {
-      System.out.println("ERROR!!!!!!!!!!!");
+      jalview.bin.Console.outPrintln("ERROR!!!!!!!!!!!");
       return;
     }
 
@@ -239,7 +239,7 @@ public class HiddenSequences
           }
           else
           {
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     seq.getName() + " has been deleted whilst hidden");
           }
         }
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 909a0fe..8d6cbb1 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -269,7 +269,7 @@ public class SearchResults implements SearchResultsI
         else
         {
           // debug
-          // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+          // jalview.bin.Console.errPrintln("Outwith bounds!" + matchStart+">"+end +" or "
           // + matchEnd+"<"+start);
         }
       }
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 5bb55e5..7a5d5bc 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -174,7 +174,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (name == null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
       name = "";
     }
@@ -387,7 +387,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sf.getType() == null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "SequenceFeature type may not be null: " + sf.toString());
       return false;
     }
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 326793d..9837104 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -644,7 +644,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
-      System.out.println("Out of memory loading groups: " + err);
+      jalview.bin.Console.outPrintln("Out of memory loading groups: " + err);
     }
     return upd;
   }
diff --git a/src/jalview/datamodel/features/FeatureMatcher.java b/src/jalview/datamodel/features/FeatureMatcher.java
index 65cba0d..124909c 100644
--- a/src/jalview/datamodel/features/FeatureMatcher.java
+++ b/src/jalview/datamodel/features/FeatureMatcher.java
@@ -147,7 +147,7 @@ public class FeatureMatcher implements FeatureMatcherI
       int nextQuotePos = descriptor.indexOf(QUOTE, 1);
       if (nextQuotePos == -1)
       {
-        System.err.println(invalidFormat);
+        jalview.bin.Console.errPrintln(invalidFormat);
         return null;
       }
       firstField = descriptor.substring(1, nextQuotePos);
@@ -159,7 +159,7 @@ public class FeatureMatcher implements FeatureMatcherI
       int nextSpacePos = descriptor.indexOf(SPACE);
       if (nextSpacePos == -1)
       {
-        System.err.println(invalidFormat);
+        jalview.bin.Console.errPrintln(invalidFormat);
         return null;
       }
       firstField = descriptor.substring(0, nextSpacePos);
@@ -193,7 +193,7 @@ public class FeatureMatcher implements FeatureMatcherI
       cond = Condition.fromString(leftToParse);
       if (cond == null || cond.needsAPattern())
       {
-        System.err.println(invalidFormat);
+        jalview.bin.Console.errPrintln(invalidFormat);
         return null;
       }
     }
@@ -214,7 +214,7 @@ public class FeatureMatcher implements FeatureMatcherI
         else
         {
           // unbalanced quote
-          System.err.println(invalidFormat);
+          jalview.bin.Console.errPrintln(invalidFormat);
           return null;
         }
       }
diff --git a/src/jalview/datamodel/features/FeatureMatcherSet.java b/src/jalview/datamodel/features/FeatureMatcherSet.java
index a5efe5d..eae3664 100644
--- a/src/jalview/datamodel/features/FeatureMatcherSet.java
+++ b/src/jalview/datamodel/features/FeatureMatcherSet.java
@@ -93,7 +93,7 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
         if (spacePos == -1)
         {
           // trailing junk after a match condition
-          System.err.println(invalid);
+          jalview.bin.Console.errPrintln(invalid);
           return null;
         }
         String conjunction = leftToParse.substring(0, spacePos);
@@ -109,7 +109,7 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
         else
         {
           // not an AND or an OR - invalid
-          System.err.println(invalid);
+          jalview.bin.Console.errPrintln(invalid);
           return null;
         }
       }
@@ -123,7 +123,7 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
         int closePos = leftToParse.indexOf(CLOSE_BRACKET);
         if (closePos == -1)
         {
-          System.err.println(invalid);
+          jalview.bin.Console.errPrintln(invalid);
           return null;
         }
         nextCondition = leftToParse.substring(1, closePos);
@@ -137,7 +137,7 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
       FeatureMatcher fm = FeatureMatcher.fromString(nextCondition);
       if (fm == null)
       {
-        System.err.println(invalid);
+        jalview.bin.Console.errPrintln(invalid);
         return null;
       }
       try
@@ -154,7 +154,7 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
       } catch (IllegalStateException e)
       {
         // thrown if OR and AND are mixed
-        System.err.println(invalid);
+        jalview.bin.Console.errPrintln(invalid);
         return null;
       }
 
diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index eb5688c..c19d782 100644
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -401,7 +401,7 @@ public class FeatureStore
       SequenceFeature sf = contactFeatureEnds.get(index);
       if (!sf.isContactFeature())
       {
-        System.err.println("Error! non-contact feature type " + sf.getType()
+        jalview.bin.Console.errPrintln("Error! non-contact feature type " + sf.getType()
                 + " in contact features list");
         index++;
         continue;
@@ -454,7 +454,7 @@ public class FeatureStore
       SequenceFeature sf = contactFeatureStarts.get(index);
       if (!sf.isContactFeature())
       {
-        System.err.println("Error! non-contact feature " + sf.toString()
+        jalview.bin.Console.errPrintln("Error! non-contact feature " + sf.toString()
                 + " in contact features list");
         index++;
         continue;
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 905fd8b..ed4474e 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -88,7 +88,7 @@ public class SequenceFeatures implements SequenceFeaturesI
     String type = sf.getType();
     if (type == null)
     {
-      System.err.println("Feature type may not be null: " + sf.toString());
+      jalview.bin.Console.errPrintln("Feature type may not be null: " + sf.toString());
       return false;
     }
 
diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 75a7154..391fd6f 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -226,7 +226,7 @@ public class EnsemblGene extends EnsemblSeqProxy
         return true;
       } catch (NumberFormatException e)
       {
-        System.err.println("Bad integers in description " + description);
+        jalview.bin.Console.errPrintln("Bad integers in description " + description);
       }
     }
     return false;
diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 0813ba8..e188986 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -222,7 +222,7 @@ public class EnsemblLookup extends EnsemblRestClient
               ids, -1, MODE_MAP, null);
     } catch (IOException | ParseException e)
     {
-      System.err.println("Error parsing " + identifier + " lookup response "
+      jalview.bin.Console.errPrintln("Error parsing " + identifier + " lookup response "
               + e.getMessage());
       return null;
     }
diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
index f2ab195..1fd9a23 100644
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -157,7 +157,7 @@ public class EnsemblMap extends EnsemblRestClient
       return (parseAssemblyMappingResponse(url));
     } catch (Throwable t)
     {
-      System.out.println("Error calling " + url + ": " + t.getMessage());
+      jalview.bin.Console.outPrintln("Error calling " + url + ": " + t.getMessage());
       return null;
     }
   }
@@ -265,7 +265,7 @@ public class EnsemblMap extends EnsemblRestClient
       return null;
     } catch (Throwable t)
     {
-      System.out.println("Error calling " + url + ": " + t.getMessage());
+      jalview.bin.Console.outPrintln("Error calling " + url + ": " + t.getMessage());
       return null;
     }
   }
@@ -342,7 +342,7 @@ public class EnsemblMap extends EnsemblRestClient
         String ass = mapped.get("assembly_name").toString();
         if (assembly != null && !assembly.equals(ass))
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "EnsemblMap found multiple assemblies - can't resolve");
           return null;
         }
@@ -350,7 +350,7 @@ public class EnsemblMap extends EnsemblRestClient
         String chr = mapped.get("seq_region_name").toString();
         if (chromosome != null && !chromosome.equals(chr))
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "EnsemblMap found multiple chromosomes - can't resolve");
           return null;
         }
diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 4a5544e..540fc98 100644
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -211,7 +211,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       return pingString != null;
     } catch (Throwable t)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error connecting to " + pingUrl + ": " + t.getMessage());
     } finally
     {
@@ -313,7 +313,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
        * note: a GET request for an invalid id returns an error code e.g. 415
        * but POST request returns 200 and an empty Fasta response 
        */
-      System.err.println("Response code " + responseCode);// + " for " + url);
+      jalview.bin.Console.errPrintln("Response code " + responseCode);// + " for " + url);
       return null;
     }
 
@@ -338,7 +338,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected HttpURLConnection tryConnection(URL url, List ids,
           int readTimeout) throws IOException, ProtocolException
   {
-    // System.out.println(System.currentTimeMillis() + " " + url);
+    // jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
 
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
 
@@ -387,14 +387,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
         int retrySecs = Integer.valueOf(retryDelay);
         if (retrySecs > 0 && retrySecs < 10)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Ensembl REST service rate limit exceeded, waiting "
                           + retryDelay + " seconds before retrying");
           Thread.sleep(1000 * retrySecs);
         }
       } catch (NumberFormatException | InterruptedException e)
       {
-        System.err.println("Error handling Retry-After: " + e.getMessage());
+        jalview.bin.Console.errPrintln("Error handling Retry-After: " + e.getMessage());
       }
     }
   }
@@ -566,7 +566,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
         }
       } catch (NumberFormatException e)
       {
-        System.err.println("Error in REST version: " + e.toString());
+        jalview.bin.Console.errPrintln("Error in REST version: " + e.toString());
       }
 
       /*
@@ -578,14 +578,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
               expected) == 1;
       if (laterVersion)
       {
-        System.err.println(String.format(
+        jalview.bin.Console.errPrintln(String.format(
                 "EnsemblRestClient expected %s REST version %s but found %s, see %s",
                 getDbSource(), expected, version, REST_CHANGE_LOG));
       }
       info.restVersion = version;
     } catch (Throwable t)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error checking Ensembl REST version: " + t.getMessage());
     }
   }
@@ -617,7 +617,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       domainData.get(getDomain()).dataVersion = versions.get(0).toString();
     } catch (Throwable e)
     {// could be IOException | ParseException e) {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error checking Ensembl data version: " + e.getMessage());
     }
   }
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 56eda5e..949c52e 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -155,7 +155,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         String msg = "Aborting ID retrieval after " + v
                 + " chunks. Unexpected problem (" + r.getLocalizedMessage()
                 + ")";
-        System.err.println(msg);
+        jalview.bin.Console.errPrintln(msg);
         r.printStackTrace();
         break;
       }
@@ -240,7 +240,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       }
     } catch (IOException e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error transferring Ensembl features: " + e.getMessage());
     }
     // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
@@ -265,12 +265,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String accId = querySeq.getName();
     try
     {
-      System.out.println("Adding protein product for " + accId);
+      jalview.bin.Console.outPrintln("Adding protein product for " + accId);
       AlignmentI protein = new EnsemblProtein(getDomain())
               .getSequenceRecords(accId);
       if (protein == null || protein.getHeight() == 0)
       {
-        System.out.println("No protein product found for " + accId);
+        jalview.bin.Console.outPrintln("No protein product found for " + accId);
         return;
       }
       SequenceI proteinSeq = protein.getSequenceAt(0);
@@ -382,7 +382,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       seq.addDBRef(xrefs.get(i));
     }
 
-    // System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
+    // jalview.bin.Console.outPrintln("primaries are " + seq.getPrimaryDBRefs().toString());
     /*
      * and add a reference to itself
      */
@@ -430,7 +430,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (seqs.size() != ids.size())
     {
-      System.out.println(String.format(
+      jalview.bin.Console.outPrintln(String.format(
               "Only retrieved %d sequences for %d query strings",
               seqs.size(), ids.size()));
     }
@@ -508,7 +508,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       result.add(sequence);
     } catch (ParseException | IOException e)
     {
-      System.err.println("Error processing JSON response: " + e.toString());
+      jalview.bin.Console.errPrintln("Error processing JSON response: " + e.toString());
       // ignore
     }
     // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
@@ -659,7 +659,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (regions.isEmpty())
     {
-      System.out.println("Failed to identify target sequence for " + accId
+      jalview.bin.Console.outPrintln("Failed to identify target sequence for " + accId
               + " from genomic features");
       return null;
     }
@@ -829,7 +829,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     boolean result = transferFeatures(sfs, targetSequence, mapping,
             accessionId);
-    // System.out.println("transferFeatures (" + (sfs.size()) + " --> "
+    // jalview.bin.Console.outPrintln("transferFeatures (" + (sfs.size()) + " --> "
     // + targetSequence.getFeatures().getFeatureCount(true) + ") to "
     // + targetSequence.getName() + " took "
     // + (System.currentTimeMillis() - start) + "ms");
diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index 9a985b6..8cce87a 100644
--- a/src/jalview/ext/htsjdk/HtsContigDb.java
+++ b/src/jalview/ext/htsjdk/HtsContigDb.java
@@ -261,7 +261,7 @@ public class HtsContigDb
   {
     if (!isValid() || !refFile.isIndexed())
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Cannot read contig as file is invalid or not indexed");
       return null;
     }
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 21a19ae..870db65 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -163,21 +163,21 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   public void createImage(String file, String type, int quality)
   {
-    System.out.println("JMOL CREATE IMAGE");
+    jalview.bin.Console.outPrintln("JMOL CREATE IMAGE");
   }
 
   @Override
   public String createImage(String fileName, String type,
           Object textOrBytes, int quality)
   {
-    System.out.println("JMOL CREATE IMAGE");
+    jalview.bin.Console.outPrintln("JMOL CREATE IMAGE");
     return null;
   }
 
   @Override
   public String eval(String strEval)
   {
-    // System.out.println(strEval);
+    // jalview.bin.Console.outPrintln(strEval);
     // "# 'eval' is implemented only for the applet.";
     return null;
   }
@@ -476,7 +476,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastMessage = strInfo;
     if (data != null)
     {
-      System.err.println("Ignoring additional hover info: " + data
+      jalview.bin.Console.errPrintln("Ignoring additional hover info: " + data
               + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
     }
     mouseOverStructure(atomIndex, strInfo);
@@ -497,7 +497,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
      */
     if (strData != null)
     {
-      System.err.println("Ignoring additional pick data string " + strData);
+      jalview.bin.Console.errPrintln("Ignoring additional pick data string " + strData);
     }
     int chainSeparator = strInfo.indexOf(":");
     int p = 0;
@@ -599,7 +599,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
                 (data == null) ? ((String) null) : (String) data[1]);
         break;
       case ERROR:
-        // System.err.println("Ignoring error callback.");
+        // jalview.bin.Console.errPrintln("Ignoring error callback.");
         break;
       case SYNC:
       case RESIZE:
@@ -609,13 +609,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
       case CLICK:
       default:
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Unhandled callback " + type + " " + data[1].toString());
         break;
       }
     } catch (Exception e)
     {
-      System.err.println("Squashed Jmol callback handler error:");
+      jalview.bin.Console.errPrintln("Squashed Jmol callback handler error:");
       e.printStackTrace();
     }
   }
@@ -864,7 +864,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void setCallbackFunction(String callbackType,
           String callbackFunction)
   {
-    System.err.println("Ignoring set-callback request to associate "
+    jalview.bin.Console.errPrintln("Ignoring set-callback request to associate "
             + callbackType + " with function " + callbackFunction);
 
   }
@@ -938,7 +938,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           String buttonsToShow)
   {
 
-    System.err.println("Allocating Jmol Viewer: " + commandOptions);
+    jalview.bin.Console.errPrintln("Allocating Jmol Viewer: " + commandOptions);
 
     if (commandOptions == null)
     {
@@ -956,7 +956,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       console = createJmolConsole(consolePanel, buttonsToShow);
     } catch (Throwable e)
     {
-      System.err.println("Could not create Jmol application console. "
+      jalview.bin.Console.errPrintln("Could not create Jmol application console. "
               + e.getMessage());
       e.printStackTrace();
     }
diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 57b406e..0ca2ba8 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -338,7 +338,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       }
     } catch (OutOfMemoryError er)
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
       throw new IOException(MessageManager
               .getString("exception.outofmemory_loading_mmcif_file"));
@@ -391,7 +391,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           org.jmol.modelset.Atom prevAtom,
           HashMap chainTerMap)
   {
-    // System.out.println("Atom: " + curAtom.getAtomNumber()
+    // jalview.bin.Console.outPrintln("Atom: " + curAtom.getAtomNumber()
     // + " Last atom index " + curAtom.group.lastAtomIndex);
     if (chainTerMap == null || prevAtom == null)
     {
diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index de1d90c..3817ee9 100644
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -229,7 +229,7 @@ class RvalsIterator implements Iterator, AutoCloseable
 
     if (sval == null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
                       + val.toString());
 
diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index 7dfdb0c..ddc8d84 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -158,7 +158,7 @@ public class PymolManager
           boolean getReply)
   {
     String postBody = getPostRequest(command);
-    // System.out.println(postBody);// debug
+    // jalview.bin.Console.outPrintln(postBody);// debug
     String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
     PrintWriter out = null;
     BufferedReader in = null;
diff --git a/src/jalview/ext/rbvi/chimera/ChimeraListener.java b/src/jalview/ext/rbvi/chimera/ChimeraListener.java
index 40b0ff0..af31b78 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraListener.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraListener.java
@@ -126,12 +126,12 @@ public class ChimeraListener extends AbstractRequestHandler
       }
       else if (message.startsWith(MODEL_CHANGED))
       {
-        System.err.println(message);
+        jalview.bin.Console.errPrintln(message);
         processModelChanged(message.substring(MODEL_CHANGED.length()));
       }
       else
       {
-        System.err.println("Unexpected chimeraNotification: " + message);
+        jalview.bin.Console.errPrintln("Unexpected chimeraNotification: " + message);
       }
     }
   }
@@ -143,7 +143,7 @@ public class ChimeraListener extends AbstractRequestHandler
    */
   protected void processModelChanged(String message)
   {
-    // System.out.println(message + " (not implemented in Jalview)");
+    // jalview.bin.Console.outPrintln(message + " (not implemented in Jalview)");
   }
 
   /**
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index aebfede..a292e88 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -207,7 +207,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       startListening(chimeraListener.getUri());
     } catch (BindException e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to start Chimera listener: " + e.getMessage());
     }
   }
@@ -568,7 +568,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private void log(String message)
   {
-    System.err.println("## Chimera log: " + message);
+    jalview.bin.Console.errPrintln("## Chimera log: " + message);
   }
 
   /**
@@ -627,7 +627,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       executeCommand(false, null, command);
     } catch (IOException e)
     {
-      System.err.println("Sending commands to Chimera via file failed with "
+      jalview.bin.Console.errPrintln("Sending commands to Chimera via file failed with "
               + e.getMessage());
     }
   }
diff --git a/src/jalview/fts/core/FTSDataColumnPreferences.java b/src/jalview/fts/core/FTSDataColumnPreferences.java
index 0971235..86b8c7d 100644
--- a/src/jalview/fts/core/FTSDataColumnPreferences.java
+++ b/src/jalview/fts/core/FTSDataColumnPreferences.java
@@ -94,7 +94,7 @@ public class FTSDataColumnPreferences extends JScrollPane
     int x = 0;
     for (FTSDataColumnI field : allFTSDataColumns)
     {
-      // System.out.println("allFTSDataColumns==" + allFTSDataColumns);
+      // jalview.bin.Console.outPrintln("allFTSDataColumns==" + allFTSDataColumns);
       if (field.getName().equalsIgnoreCase("all"))
       {
         continue;
@@ -106,7 +106,7 @@ public class FTSDataColumnPreferences extends JScrollPane
         data[x++] = new Object[] { ftsRestClient
                 .getAllDefaultDisplayedFTSDataColumns().contains(field),
             field.getName(), field.getGroup() };
-        // System.out.println(" PUIS " + field.getName() + " ET AUSSI " +
+        // jalview.bin.Console.outPrintln(" PUIS " + field.getName() + " ET AUSSI " +
         // field.getGroup() + "X = " + x);
         break;
       case STRUCTURE_CHOOSER:
diff --git a/src/jalview/fts/service/alphafold/AlphafoldRestClient.java b/src/jalview/fts/service/alphafold/AlphafoldRestClient.java
index 7e95dd2..a631902 100644
--- a/src/jalview/fts/service/alphafold/AlphafoldRestClient.java
+++ b/src/jalview/fts/service/alphafold/AlphafoldRestClient.java
@@ -118,7 +118,7 @@ public class AlphafoldRestClient
           } catch (Exception e)
           {
             e.printStackTrace();
-            System.out.println("offending value:" + fieldData);
+            jalview.bin.Console.outPrintln("offending value:" + fieldData);
           }
         }
       }
diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index 796bc0e..5619075 100644
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -175,7 +175,7 @@ public class PDBFTSRestClient extends FTSRestClient
 
       URI uri = webResource.getURI();
 
-      System.out.println(uri);
+      jalview.bin.Console.outPrintln(uri);
       ClientResponse clientResponse = null;
       int responseStatus = -1;
       // Get the JSON string from the response object or directly from the
@@ -183,7 +183,7 @@ public class PDBFTSRestClient extends FTSRestClient
       Map jsonObj = null;
       String responseString = null;
 
-      System.out.println("query >>>>>>> " + pdbRestRequest.toString());
+      jalview.bin.Console.outPrintln("query >>>>>>> " + pdbRestRequest.toString());
 
       if (!isMocked())
       {
@@ -413,10 +413,10 @@ public class PDBFTSRestClient extends FTSRestClient
 
     for (FTSDataColumnI field : diplayFields)
     {
-      // System.out.println("Field " + field);
+      // jalview.bin.Console.outPrintln("Field " + field);
       String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
               : pdbJsonDoc.get(field.getCode()).toString();
-      // System.out.println("Field Data : " + fieldData);
+      // jalview.bin.Console.outPrintln("Field Data : " + fieldData);
       if (field.isPrimaryKeyColumn())
       {
         primaryKey = fieldData;
@@ -440,7 +440,7 @@ public class PDBFTSRestClient extends FTSRestClient
         } catch (Exception e)
         {
           e.printStackTrace();
-          System.out.println("offending value:" + fieldData);
+          jalview.bin.Console.outPrintln("offending value:" + fieldData);
         }
       }
     }
diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
index 253de42..dfb39cb 100644
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
@@ -277,7 +277,7 @@ public class TDBeaconsFTSPanel extends GFTSPanel
   @Override
   protected void showHelp()
   {
-    System.out.println("No help implemented yet.");
+    jalview.bin.Console.outPrintln("No help implemented yet.");
 
   }
 
diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index d7f534e..c275bda 100644
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -101,7 +101,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query);
 
       URI uri = webResource.getURI();
-      System.out.println(uri.toString());
+      jalview.bin.Console.outPrintln(uri.toString());
 
       // Execute the REST request
       ClientResponse clientResponse;
@@ -269,7 +269,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
               ? " "
               : tdbJsonStructure.get(field.getCode()).toString();
-      // System.out.println("Field : " + field + " Data : " + fieldData);
+      // jalview.bin.Console.outPrintln("Field : " + field + " Data : " + fieldData);
       if (field.isPrimaryKeyColumn())
       {
         primaryKey = fieldData;
@@ -293,7 +293,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
         } catch (Exception e)
         {
           // e.printStackTrace();
-          System.out.println("offending value:" + fieldData + fieldData);
+          jalview.bin.Console.outPrintln("offending value:" + fieldData + fieldData);
         }
       }
     }
diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 1827293..df48c0d 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -219,7 +219,7 @@ public class UniProtFTSRestClient extends FTSRestClient
               .getEntity(String.class);
       // Make redundant objects eligible for garbage collection to conserve
       // memory
-      // System.out.println(">>>>> response : "
+      // jalview.bin.Console.outPrintln(">>>>> response : "
       // + uniProtTabDelimittedResponseString);
       if (clientResponse.getStatus() != 200)
       {
@@ -307,7 +307,7 @@ public class UniProtFTSRestClient extends FTSRestClient
           firstRow = false;
           continue;
         }
-        // System.out.println(dataRow);
+        // jalview.bin.Console.outPrintln(dataRow);
         result.add(getFTSData(dataRow, uniprotRestRequest));
       }
       searchResult.setNumberOfItemsFound(xTotalResults);
@@ -389,7 +389,7 @@ public class UniProtFTSRestClient extends FTSRestClient
           } catch (Exception e)
           {
             e.printStackTrace();
-            System.out.println("offending value:" + fieldData);
+            jalview.bin.Console.outPrintln("offending value:" + fieldData);
           }
         }
       } catch (Exception e)
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 49bd4e9..25376af 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -49,6 +49,7 @@ import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.net.URL;
 import java.util.ArrayList;
@@ -157,7 +158,6 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
-import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -624,12 +624,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // if (viewport.cursorMode)
         // {
         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
-        // //System.out.println("A");
+        // //jalview.bin.Console.outPrintln("A");
         // }
         // break;
         /*
          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
-         * System.out.println("closing bracket"); } break;
+         * jalview.bin.Console.outPrintln("closing bracket"); } break;
          */
         case KeyEvent.VK_DELETE:
         case KeyEvent.VK_BACK_SPACE:
@@ -830,7 +830,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
-                // // System.out.println("Discoverer property change.");
+                // // jalview.bin.Console.outPrintln("Discoverer property
+                // change.");
                 // if (evt.getPropertyName().equals("services"))
                 {
                   SwingUtilities.invokeLater(new Runnable()
@@ -839,7 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     @Override
                     public void run()
                     {
-                      System.err.println(
+                      jalview.bin.Console.errPrintln(
                               "Rebuild WS Menu for service change");
                       BuildWebServiceMenu();
                     }
@@ -854,7 +855,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
-        // System.out.println("deregistering discoverer listener");
+        // jalview.bin.Console.outPrintln("deregistering discoverer listener");
         Desktop.instance.removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
@@ -1251,8 +1252,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void saveAlignment(String file, FileFormatI format)
   {
+    saveAlignment(file, format, false);
+  }
+
+  public void saveAlignment(String file, FileFormatI format, boolean stdout)
+  {
     lastSaveSuccessful = true;
-    lastFilenameSaved = file;
+    if (!stdout)
+    {
+      lastFilenameSaved = file;
+    }
     lastFormatSaved = format;
 
     if (FileFormat.Jalview.equals(format))
@@ -1263,6 +1272,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         shortName = shortName
                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
       }
+      // TODO deal with stdout=true
       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
               shortName);
 
@@ -1298,7 +1308,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // create backupfiles object and get new temp filename destination
-        boolean doBackup = BackupFiles.getEnabled();
+        boolean doBackup = BackupFiles.getEnabled() && !stdout;
         BackupFiles backupfiles = null;
         if (doBackup)
         {
@@ -1310,7 +1320,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           String tempFilePath = doBackup ? backupfiles.getTempFilePath()
                   : file;
           Console.trace("ALIGNFRAME setting PrintWriter");
-          PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+          PrintWriter out = stdout
+                  ? new PrintWriter(new OutputStreamWriter(System.out))
+                  : new PrintWriter(new FileWriter(tempFilePath));
 
           if (backupfiles != null)
           {
@@ -1319,13 +1331,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
 
           out.print(output);
-          Console.trace("ALIGNFRAME about to close file");
-          out.close();
-          Console.trace("ALIGNFRAME closed file");
-          AlignFrame.this.setTitle(file);
-          statusBar.setText(MessageManager.formatMessage(
-                  "label.successfully_saved_to_file_in_format", new Object[]
-                  { fileName, format.getName() }));
+          out.flush();
+          if (!stdout)
+          {
+            Console.trace("ALIGNFRAME about to close file");
+            out.close();
+            Console.trace("ALIGNFRAME closed file");
+          }
+          AlignFrame.this.setTitle(stdout ? "STDOUT" : file);
+          if (stdout)
+          {
+            statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_printed_to_stdout_in_format",
+                    new Object[]
+                    { format.getName() }));
+          }
+          else
+          {
+            statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_saved_to_file_in_format",
+                    new Object[]
+                    { fileName, format.getName() }));
+          }
           lastSaveSuccessful = true;
         } catch (IOException e)
         {
@@ -1456,9 +1483,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
-    try {
+    try
+    {
       htmlSVG.exportHTML(null);
-    } catch (ImageOutputException x) {
+    } catch (ImageOutputException x)
+    {
       // report problem to console and raise dialog
     }
   }
@@ -1467,51 +1496,64 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
-    try {
-    bjs.exportHTML(null);
-  } catch (ImageOutputException x) {
-    // report problem to console and raise dialog
-  }
+    try
+    {
+      bjs.exportHTML(null);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
   }
 
   public void createImageMap(File file, String image)
   {
-    try {
-    alignPanel.makePNGImageMap(file, image);
-    } catch (ImageOutputException x) {
+    try
+    {
+      alignPanel.makePNGImageMap(file, image);
+    } catch (ImageOutputException x)
+    {
       // report problem to console and raise dialog
     }
   }
 
   @Override
-  public void createPNG_actionPerformed(ActionEvent e) {
-    try{
+  public void createPNG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createPNG(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
   }
+
   @Override
-  public void createEPS_actionPerformed(ActionEvent e) {
-    try{
+  public void createEPS_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createEPS(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
-    
+
   }
+
   @Override
-  public void createSVG_actionPerformed(ActionEvent e) {
-    try{
+  public void createSVG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createSVG(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
-    
+
   }
+
   /**
    * Creates a PNG image of the alignment and writes it to the given file. If
    * the file is null, the user is prompted to choose a file.
@@ -1523,7 +1565,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
   }
 
-  public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException
+  public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+          throws ImageOutputException
   {
     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
   }
@@ -1534,7 +1577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  public void createEPS(File f)  throws ImageOutputException
+  public void createEPS(File f) throws ImageOutputException
   {
     createEPS(f, null);
   }
@@ -1550,7 +1593,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  public void createSVG(File f)  throws ImageOutputException
+  public void createSVG(File f) throws ImageOutputException
   {
     createSVG(f, null);
   }
@@ -2341,12 +2384,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // annotation was duplicated earlier
             alignment.addAnnotation(sequences[i].getAnnotation()[a]);
             // take care of contact matrix too
-            ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]);
-            if (cm!=null)
+            ContactMatrixI cm = sequences[i]
+                    .getContactMatrixFor(sequences[i].getAnnotation()[a]);
+            if (cm != null)
             {
-              alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+              alignment.addContactListFor(sequences[i].getAnnotation()[a],
+                      cm);
             }
-            
+
             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
                     a);
           }
@@ -2454,7 +2499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Exception whilst pasting: " + ex);
+      jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
       // could be anything being pasted in here
     }
 
@@ -2502,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Exception whilst pasting: " + ex);
+      jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
       // could be anything being pasted in here
     } catch (OutOfMemoryError oom)
     {
@@ -3138,11 +3183,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    scaleAbove.setVisible(wrapMenuItem.isSelected());
-    scaleLeft.setVisible(wrapMenuItem.isSelected());
-    scaleRight.setVisible(wrapMenuItem.isSelected());
-    viewport.setWrapAlignment(wrapMenuItem.isSelected());
+    setWrapFormat(wrapMenuItem.isSelected(), false);
+  }
+
+  public void setWrapFormat(boolean b, boolean setMenuItem)
+  {
+    scaleAbove.setVisible(b);
+    scaleLeft.setVisible(b);
+    scaleRight.setVisible(b);
+    viewport.setWrapAlignment(b);
     alignPanel.updateLayout();
+    if (setMenuItem)
+    {
+      wrapMenuItem.setSelected(b);
+    }
   }
 
   @Override
@@ -3480,7 +3534,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     JInternalFrame frame = new JInternalFrame();
-
+    frame.setFrameIcon(null);
     frame.getContentPane().add(new JScrollPane(pane));
 
     Desktop.addInternalFrame(frame, MessageManager
@@ -3508,12 +3562,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return alignPanel.overviewPanel;
     }
     JInternalFrame frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
             showHidden);
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
             frame.getHeight(), true, true);
-    frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     final AlignmentPanel thePanel = this.alignPanel;
@@ -3787,6 +3841,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       JInternalFrame frame = new JInternalFrame();
+      frame.setFrameIcon(null);
       frame.setContentPane(new PairwiseAlignPanel(viewport));
       Desktop.addInternalFrame(frame,
               MessageManager.getString("action.pairwise_alignment"), 600,
@@ -4239,8 +4294,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
-  public void showContactMapTree(AlignmentAnnotation aa,
-          ContactMatrixI cm)
+  public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
   {
     int x = 4, y = 5;
     int w = 400, h = 500;
@@ -4249,8 +4303,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       NewickFile fin = new NewickFile(
               new FileParse(cm.getNewick(), DataSourceType.PASTE));
-      String title = aa.label + " "
-              + cm.getTreeMethod() + " tree" + (aa.sequenceRef != null
+      String title = aa.label + " " + cm.getTreeMethod() + " tree"
+              + (aa.sequenceRef != null
                       ? (" for " + aa.sequenceRef.getDisplayId(false))
                       : "");
 
@@ -4303,7 +4357,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       try
       {
-        System.err.println("Waiting for building menu to finish.");
+        jalview.bin.Console
+                .errPrintln("Waiting for building menu to finish.");
         Thread.sleep(10);
       } catch (Exception e)
       {
@@ -4319,7 +4374,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         final List legacyItems = new ArrayList<>();
         try
         {
-          // System.err.println("Building ws menu again "
+          // jalview.bin.Console.errPrintln("Building ws menu again "
           // + Thread.currentThread());
           // TODO: add support for context dependent disabling of services based
           // on
@@ -4857,7 +4912,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                     Desktop.instance);
                     if (pe != null)
                     {
-                      System.err.println("Associated file : "
+                      jalview.bin.Console.errPrintln("Associated file : "
                               + (fm[0].toString()) + " with "
                               + toassoc.getDisplayId(true));
                       assocfiles++;
@@ -5890,7 +5945,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               viewport.getAlignment()));
     } catch (Exception ex)
     {
-      System.err.println(ex.getMessage());
+      jalview.bin.Console.errPrintln(ex.getMessage());
       return;
     }
   }
@@ -5912,7 +5967,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         console.runScript();
       } catch (Exception ex)
       {
-        System.err.println((ex.toString()));
+        jalview.bin.Console.errPrintln((ex.toString()));
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.couldnt_run_groovy_script"),
                 MessageManager.getString("label.groovy_support_failed"),
@@ -5921,7 +5976,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      System.err.println("Can't run Groovy script as console not found");
+      jalview.bin.Console
+              .errPrintln("Can't run Groovy script as console not found");
     }
   }
 
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5613f16..ef9e575 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -45,7 +45,6 @@ import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactMatrixI;
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index aa28a8c..ee71483 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -50,6 +50,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
@@ -269,10 +270,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Dimension r = null;
     if (av.getIdWidth() < 0)
     {
-      int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
-      int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
-      int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
-      r = calculateIdWidth(maxwidth);
+      r = calculateDefaultAlignmentIdWidth();
       av.setIdWidth(r.width);
     }
     else
@@ -294,6 +292,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return r;
   }
 
+  public Dimension calculateDefaultAlignmentIdWidth()
+  {
+    int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+    int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
+    int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
+    return calculateIdWidth(-1, false, false);
+  }
+
   /**
    * Calculate the width of the alignment labels based on the displayed names
    * and any bounds on label width set in preferences.
@@ -305,6 +311,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected Dimension calculateIdWidth(int maxwidth)
   {
+    return calculateIdWidth(maxwidth, true, false);
+  }
+
+  public Dimension calculateIdWidth(int maxwidth,
+          boolean includeAnnotations, boolean visibleOnly)
+  {
     Container c = new Container();
 
     FontMetrics fm = c.getFontMetrics(
@@ -324,18 +336,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
 
     // Also check annotation label widths
-    i = 0;
-
-    if (al.getAlignmentAnnotation() != null)
+    if (includeAnnotations && al.getAlignmentAnnotation() != null)
     {
-      fm = c.getFontMetrics(getAlabels().getFont());
-
-      while (i < al.getAlignmentAnnotation().length)
+      if (Jalview.isHeadlessMode())
       {
-        String label = al.getAlignmentAnnotation()[i].label;
-        int stringWidth = fm.stringWidth(label);
+        AnnotationLabels aal = this.getAlabels();
+        int stringWidth = aal.drawLabels(null, false, idWidth, false, fm);
         idWidth = Math.max(idWidth, stringWidth);
-        i++;
+      }
+      else
+      {
+        fm = c.getFontMetrics(getAlabels().getFont());
+
+        for (i = 0; i < al.getAlignmentAnnotation().length; i++)
+        {
+          AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+          if (visibleOnly && !aa.visible)
+          {
+            continue;
+          }
+          String label = aa.label;
+          int stringWidth = fm.stringWidth(label);
+          idWidth = Math.max(idWidth, stringWidth);
+        }
       }
     }
 
@@ -543,7 +566,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // this is called after loading new annotation onto alignment
     if (alignFrame.getHeight() == 0)
     {
-      System.out.println("NEEDS FIXING");
+      jalview.bin.Console.outPrintln("NEEDS FIXING");
     }
     validateAnnotationDimensions(true);
     addNotify();
@@ -567,21 +590,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // not be called directly by programs.
     // I note that addNotify() is called in several areas of Jalview.
 
-    int annotationHeight = getAnnotationPanel().adjustPanelHeight();
-    annotationHeight = getAnnotationPanel()
-            .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
+    AnnotationPanel ap = getAnnotationPanel();
+    int annotationHeight = ap.adjustPanelHeight();
+    annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight,
+            annotationHeight);
 
     hscroll.addNotify();
-    annotationScroller.setPreferredSize(
-            new Dimension(annotationScroller.getWidth(), annotationHeight));
-
     Dimension e = idPanel.getSize();
-    alabels.setSize(new Dimension(e.width, annotationHeight));
+    int idWidth = e.width;
+    boolean manuallyAdjusted = this.getIdPanel().getIdCanvas()
+            .manuallyAdjusted();
+    annotationScroller.setPreferredSize(new Dimension(
+            manuallyAdjusted ? idWidth : annotationScroller.getWidth(),
+            annotationHeight));
+
+    alabels.setPreferredSize(new Dimension(idWidth, annotationHeight));
 
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-            annotationSpaceFillerHolder.getWidth(), annotationHeight));
+            manuallyAdjusted ? idWidth
+                    : annotationSpaceFillerHolder.getWidth(),
+            annotationHeight));
     annotationScroller.validate();
     annotationScroller.addNotify();
+    ap.validate();
   }
 
   /**
@@ -597,9 +628,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     boolean wrap = av.getWrapAlignment();
     ViewportRanges ranges = av.getRanges();
     ranges.setStartSeq(0);
-    scalePanelHolder.setVisible(!wrap);
+    // scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
-    idwidthAdjuster.setVisible(!wrap);
+    // Allow idPanel width adjustment in wrap mode
+    idwidthAdjuster.setVisible(true);
 
     if (wrap)
     {
@@ -633,7 +665,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     }
 
-    idSpaceFillerPanel1.setVisible(!wrap);
+    // idSpaceFillerPanel1.setVisible(!wrap);
 
     repaint();
   }
@@ -854,10 +886,27 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void paintComponent(Graphics g)
   {
     invalidate(); // needed so that the id width adjuster works correctly
-
     Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
-    idPanelHolder.setPreferredSize(d);
-    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+    int idWidth = d.width;
+
+    // check wrapped alignment as at least 1 residue width
+    if (av.getWrapAlignment())
+    {
+      SeqCanvas sc = this.getSeqPanel().seqCanvas;
+      if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth())
+      {
+        // need to make some adjustments
+        idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth());
+        av.setIdWidth(idWidth);
+        av.getAlignPanel().getIdPanel().getIdCanvas()
+                .setManuallyAdjusted(true);
+
+        validateAnnotationDimensions(false);
+      }
+    }
+
+    idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height));
+    hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
 
     validate(); // needed so that the id width adjuster works correctly
 
@@ -1172,6 +1221,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
 
     int w = getIdPanel().getWidth();
+    w = this.calculateIdWidth(-1, true, true).width;
     return (w > 0 ? w : calculateIdWidth().width);
   }
 
@@ -1197,6 +1247,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     final int borderBottomOffset = 5;
 
     AlignmentDimension aDimension = getAlignmentDimension();
+
     // todo use a lambda function in place of callback here?
     ImageWriterI writer = new ImageWriterI()
     {
@@ -1410,8 +1461,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
 
-    if (System.getProperty("java.awt.headless") != null
-            && System.getProperty("java.awt.headless").equals("true"))
+    if (Jalview.isHeadlessMode())
     {
       seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
               - vscroll.getPreferredSize().width
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 28065c3..20e1b1b 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import java.awt.Canvas;
 import java.awt.Color;
 import java.awt.Cursor;
 import java.awt.Dimension;
@@ -50,6 +51,8 @@ import javax.swing.ToolTipManager;
 
 import jalview.analysis.AlignSeq;
 import jalview.analysis.AlignmentUtils;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -85,7 +88,7 @@ public class AnnotationLabels extends JPanel
   /**
    * height in pixels for allowing height adjuster to be active
    */
-  private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+  public static int HEIGHT_ADJUSTER_HEIGHT = 10;
 
   private static final Font font = new Font("Arial", Font.PLAIN, 11);
 
@@ -113,6 +116,8 @@ public class AnnotationLabels extends JPanel
   private static final String COPYCONS_SEQ = MessageManager
           .getString("label.copy_consensus_sequence");
 
+  private static final String ADJUST_ANNOTATION_LABELS_WIDTH_PREF = "ADJUST_ANNOTATION_LABELS_WIDTH";
+
   private final boolean debugRedraw = false;
 
   private AlignmentPanel ap;
@@ -131,6 +136,10 @@ public class AnnotationLabels extends JPanel
 
   private boolean resizePanel = false;
 
+  private int annotationIdWidth = -1;
+
+  public static final String RESIZE_MARGINS_MARK_PREF = "RESIZE_MARGINS_MARK";
+
   /**
    * Creates a new AnnotationLabels object
    * 
@@ -138,7 +147,6 @@ public class AnnotationLabels extends JPanel
    */
   public AnnotationLabels(AlignmentPanel ap)
   {
-
     this.ap = ap;
     av = ap.av;
     ToolTipManager.sharedInstance().registerComponent(this);
@@ -418,65 +426,74 @@ public class AnnotationLabels extends JPanel
         pop.add(consclipbrd);
       }
 
-      addColourOrFilterByOptions(ap,aa[selectedRow],pop);
-      
+      addColourOrFilterByOptions(ap, aa[selectedRow], pop);
+
       if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
       {
-        addContactMatrixOptions(ap,aa[selectedRow],pop);
-          // Set/adjust threshold for grouping ?
-          // colour alignment by this [type]
-          // select/hide columns by this row
-          
-        }
+        addContactMatrixOptions(ap, aa[selectedRow], pop);
+        // Set/adjust threshold for grouping ?
+        // colour alignment by this [type]
+        // select/hide columns by this row
+
       }
-    
+    }
+
     pop.show(this, evt.getX(), evt.getY());
   }
 
   static void addColourOrFilterByOptions(final AlignmentPanel ap,
-          final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+          final AlignmentAnnotation alignmentAnnotation,
+          final JPopupMenu pop)
   {
     JMenuItem item;
-    item = new JMenuItem(MessageManager.getString("label.colour_by_annotation"));
+    item = new JMenuItem(
+            MessageManager.getString("label.colour_by_annotation"));
     item.addActionListener(new ActionListener()
     {
-      
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false);
+        AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation,
+                false);
       };
     });
     pop.add(item);
-    if (alignmentAnnotation.sequenceRef!=null)
+    if (alignmentAnnotation.sequenceRef != null)
     {
-      item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")");
+      item = new JMenuItem(
+              MessageManager.getString("label.colour_by_annotation") + " ("
+                      + MessageManager.getString("label.per_seq") + ")");
       item.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,true);
+          AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation,
+                  true);
         };
       });
       pop.add(item);
     }
-    item = new JMenuItem(MessageManager.getString("action.select_by_annotation"));
+    item = new JMenuItem(
+            MessageManager.getString("action.select_by_annotation"));
     item.addActionListener(new ActionListener()
     {
-      
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        AnnotationColumnChooser.displayFor(ap.av,ap,alignmentAnnotation);
+        AnnotationColumnChooser.displayFor(ap.av, ap, alignmentAnnotation);
       };
     });
     pop.add(item);
   }
+
   static void addContactMatrixOptions(final AlignmentPanel ap,
-          final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+          final AlignmentAnnotation alignmentAnnotation,
+          final JPopupMenu pop)
   {
-    
+
     final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation);
     JMenuItem item;
     if (cm != null)
@@ -485,10 +502,13 @@ public class AnnotationLabels extends JPanel
 
       if (cm.hasGroups())
       {
-        JCheckBoxMenuItem chitem = new JCheckBoxMenuItem(MessageManager.getString("action.show_groups_on_matrix"));
-        chitem.setToolTipText(MessageManager.getString("action.show_groups_on_matrix_tooltip"));
-        boolean showGroups = alignmentAnnotation.isShowGroupsForContactMatrix();
-        final AlignmentAnnotation sel_row=alignmentAnnotation;
+        JCheckBoxMenuItem chitem = new JCheckBoxMenuItem(
+                MessageManager.getString("action.show_groups_on_matrix"));
+        chitem.setToolTipText(MessageManager
+                .getString("action.show_groups_on_matrix_tooltip"));
+        boolean showGroups = alignmentAnnotation
+                .isShowGroupsForContactMatrix();
+        final AlignmentAnnotation sel_row = alignmentAnnotation;
         chitem.setState(showGroups);
         chitem.addActionListener(new ActionListener()
         {
@@ -507,8 +527,10 @@ public class AnnotationLabels extends JPanel
       }
       if (cm.hasTree())
       {
-        item = new JMenuItem(MessageManager.getString("action.show_tree_for_matrix"));
-        item.setToolTipText(MessageManager.getString("action.show_tree_for_matrix_tooltip"));
+        item = new JMenuItem(
+                MessageManager.getString("action.show_tree_for_matrix"));
+        item.setToolTipText(MessageManager
+                .getString("action.show_tree_for_matrix_tooltip"));
         item.addActionListener(new ActionListener()
         {
 
@@ -524,8 +546,10 @@ public class AnnotationLabels extends JPanel
       }
       else
       {
-        item = new JMenuItem(MessageManager.getString("action.cluster_matrix"));
-        item.setToolTipText(MessageManager.getString("action.cluster_matrix_tooltip"));
+        item = new JMenuItem(
+                MessageManager.getString("action.cluster_matrix"));
+        item.setToolTipText(
+                MessageManager.getString("action.cluster_matrix_tooltip"));
         item.addActionListener(new ActionListener()
         {
           @Override
@@ -537,7 +561,11 @@ public class AnnotationLabels extends JPanel
               public void run()
               {
                 final long progBar;
-                ap.alignFrame.setProgressBar(MessageManager.formatMessage("action.clustering_matrix_for",cm.getAnnotDescr(),5f), progBar = System.currentTimeMillis());
+                ap.alignFrame.setProgressBar(
+                        MessageManager.formatMessage(
+                                "action.clustering_matrix_for",
+                                cm.getAnnotDescr(), 5f),
+                        progBar = System.currentTimeMillis());
                 cm.setGroupSet(GroupSet.makeGroups(cm, true));
                 cm.randomlyReColourGroups();
                 cm.transferGroupColorsTo(alignmentAnnotation);
@@ -1141,7 +1169,6 @@ public class AnnotationLabels extends JPanel
     }
 
     drawComponent(g2, true, width);
-
   }
 
   /**
@@ -1171,32 +1198,146 @@ public class AnnotationLabels extends JPanel
    * @param width
    *          Width for scaling labels
    */
-  public void drawComponent(Graphics g, boolean clip, int width)
+  public void drawComponent(Graphics g, boolean clip, int givenWidth)
   {
-    if (av.getFont().getSize() < 10)
+    int width = givenWidth;
+    IdwidthAdjuster iwa = null;
+    if (ap != null)
     {
-      g.setFont(font);
+      iwa = ap.idwidthAdjuster;
+      if ((Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true)
+              || Jalview.isHeadlessMode()))
+      {
+        Graphics2D g2d = (Graphics2D) g;
+        Graphics dummy = g2d.create();
+        int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
+                null);
+        dummy.dispose();
+        Dimension d = ap.calculateDefaultAlignmentIdWidth();
+        int alignmentIdWidth = d.width;
+        if (iwa != null && !iwa.manuallyAdjusted())
+        {
+          // If no manual adjustment to ID column with has been made then adjust
+          // width match widest of alignment or annotation id widths
+          boolean allowShrink = Cache.getDefault("ALLOW_SHRINK_ID_WIDTH",
+                  false);
+          width = Math.max(alignmentIdWidth, newAnnotationIdWidth);
+          if (clip && width < givenWidth && !allowShrink)
+          {
+            width = givenWidth;
+          }
+        }
+        else if (newAnnotationIdWidth != annotationIdWidth
+                && newAnnotationIdWidth > givenWidth
+                && newAnnotationIdWidth > alignmentIdWidth)
+        {
+          // otherwise if the annotation id width has become larger than the
+          // current id width, increase
+          width = newAnnotationIdWidth;
+          annotationIdWidth = newAnnotationIdWidth;
+        }
+        // set the width if it's changed
+        if (width != ap.av.getIdWidth())
+        {
+          iwa.setWidth(width);
+        }
+      }
     }
     else
     {
-      g.setFont(av.getFont());
+      int newAnnotationIdWidth = drawLabels(g, clip, width, false, null);
+      width = Math.max(newAnnotationIdWidth, givenWidth);
+    }
+    drawLabels(g, clip, width, true, null);
+  }
+
+  /**
+   * Render the full set of annotation Labels for the alignment at the given
+   * cursor. If actuallyDraw is false or g is null then no actual drawing will
+   * occur, but the widest label width will be returned. If g is null then
+   * fmetrics must be supplied.
+   * 
+   * Returns the width of the annotation labels.
+   * 
+   * @param g
+   *          Graphics2D instance (needed for font scaling)
+   * @param clip
+   *          - true indicates that only current visible area needs to be
+   *          rendered
+   * @param width
+   *          Width for scaling labels
+   * @param fmetrics
+   *          FontMetrics if Graphics object g is null
+   */
+  public int drawLabels(Graphics g0, boolean clip, int width,
+          boolean actuallyDraw, FontMetrics fmetrics)
+  {
+    if (clip)
+    {
+      clip = Cache.getDefault("MOVE_SEQUENCE_ID_WITH_VISIBLE_ANNOTATIONS",
+              true);
+    }
+    Graphics g = null;
+    // create a dummy Graphics object if not drawing and one is supplied
+    if (g0 != null)
+    {
+      if (!actuallyDraw)
+      {
+        Graphics2D g2d = (Graphics2D) g0;
+        g = g2d.create();
+      }
+      else
+      {
+        g = g0;
+      }
     }
+    int actualWidth = 0;
+    if (g != null)
+    {
+      if (av.getFont().getSize() < 10)
+      {
+        g.setFont(font);
+      }
+      else
+      {
+        g.setFont(av.getFont());
+      }
+    }
+
+    FontMetrics fm = fmetrics == null ? g.getFontMetrics(g.getFont())
+            : fmetrics;
+    if (actuallyDraw)
+    {
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getWidth(), getHeight());
+
+      if (!Cache.getDefault(RESIZE_MARGINS_MARK_PREF, false)
+              && !av.getWrapAlignment())
+      {
+        g.setColor(Color.LIGHT_GRAY);
+        g.drawLine(0, HEIGHT_ADJUSTER_HEIGHT / 4, HEIGHT_ADJUSTER_WIDTH / 4,
+                HEIGHT_ADJUSTER_HEIGHT / 4);
+        g.drawLine(0, 3 * HEIGHT_ADJUSTER_HEIGHT / 4,
+                HEIGHT_ADJUSTER_WIDTH / 4, 3 * HEIGHT_ADJUSTER_HEIGHT / 4);
 
-    FontMetrics fm = g.getFontMetrics(g.getFont());
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+      }
+    }
 
-    g.translate(0, getScrollOffset());
-    g.setColor(Color.black);
+    if (actuallyDraw)
+    {
+      g.translate(0, getScrollOffset());
+      g.setColor(Color.black);
+    }
     SequenceI lastSeqRef = null;
     String lastLabel = null;
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-    int fontHeight = g.getFont().getSize();
+    int fontHeight = g != null ? g.getFont().getSize()
+            : fm.getFont().getSize();
     int y = 0;
     int x = 0;
     int graphExtras = 0;
     int offset = 0;
-    Font baseFont = g.getFont();
+    Font baseFont = g != null ? g.getFont() : fm.getFont();
     FontMetrics baseMetrics = fm;
     int ofontH = fontHeight;
     int sOffset = 0;
@@ -1237,7 +1378,7 @@ public class AnnotationLabels extends JPanel
             {
               if (debugRedraw)
               {
-                System.out.println("before vis: " + i);
+                jalview.bin.Console.outPrintln("before vis: " + i);
               }
               before = true;
             }
@@ -1251,7 +1392,7 @@ public class AnnotationLabels extends JPanel
             {
               if (debugRedraw)
               {
-                System.out.println(
+                jalview.bin.Console.outPrintln(
                         "Scroll offset: " + sOffset + " after vis: " + i);
               }
               after = true;
@@ -1260,8 +1401,10 @@ public class AnnotationLabels extends JPanel
             continue;
           }
         }
-        g.setColor(Color.black);
-
+        if (actuallyDraw && g != null)
+        {
+          g.setColor(Color.black);
+        }
         offset = -aa[i].height / 2;
 
         if (aa[i].hasText)
@@ -1306,7 +1449,9 @@ public class AnnotationLabels extends JPanel
             vertBar = true;
           }
         }
-        x = width - fm.stringWidth(label) - 3;
+
+        int labelWidth = fm.stringWidth(label) + 3;
+        x = width - labelWidth;
 
         if (aa[i].graphGroup > -1)
         {
@@ -1339,10 +1484,15 @@ public class AnnotationLabels extends JPanel
               s = ((float) fontHeight) / (float) ofontH;
               Font f = baseFont
                       .deriveFont(AffineTransform.getScaleInstance(s, s));
-              g.setFont(f);
-              fm = g.getFontMetrics();
-              graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
-                      / 2;
+              Canvas c = new Canvas();
+              fm = c.getFontMetrics(f);
+              if (actuallyDraw && g != null)
+              {
+                g.setFont(f);
+                // fm = g.getFontMetrics();
+                graphExtras = (aa[i].height
+                        - (groupSize * (fontHeight + 8))) / 2;
+              }
             }
           }
           if (visible)
@@ -1351,58 +1501,81 @@ public class AnnotationLabels extends JPanel
             {
               if (aa[gg].graphGroup == aa[i].graphGroup)
               {
-                x = width - fm.stringWidth(aa[gg].label) - 3;
-                g.drawString(aa[gg].label, x, y - graphExtras);
-
-                if (aa[gg]._linecolour != null)
+                labelWidth = fm.stringWidth(aa[gg].label) + 3;
+                x = width - labelWidth;
+                if (actuallyDraw && g != null)
                 {
+                  g.drawString(aa[gg].label, x, y - graphExtras);
 
-                  g.setColor(aa[gg]._linecolour);
-                  g.drawLine(x, y - graphExtras + 3,
-                          x + fm.stringWidth(aa[gg].label),
-                          y - graphExtras + 3);
-                }
+                  if (aa[gg]._linecolour != null)
+                  {
+
+                    g.setColor(aa[gg]._linecolour);
+                    g.drawLine(x, y - graphExtras + 3,
+                            x + fm.stringWidth(aa[gg].label),
+                            y - graphExtras + 3);
+                  }
 
-                g.setColor(Color.black);
+                  g.setColor(Color.black);
+                }
                 graphExtras += fontHeight + 8;
               }
             }
           }
-          g.setFont(baseFont);
+          if (actuallyDraw && g != null)
+          {
+            g.setFont(baseFont);
+          }
           fm = baseMetrics;
           fontHeight = ofontH;
         }
         else
         {
-          if (vertBar)
+          if (actuallyDraw && g != null)
           {
-            g.drawLine(width - 3, y + offset - fontHeight, width - 3,
-                    (int) (y - 1.5 * aa[i].height - offset - fontHeight));
-            // g.drawLine(20, y + offset, x - 20, y + offset);
+            if (vertBar)
+            {
+              g.drawLine(width - 3, y + offset - fontHeight, width - 3,
+                      (int) (y - 1.5 * aa[i].height - offset - fontHeight));
+              // g.drawLine(20, y + offset, x - 20, y + offset);
 
+            }
+            g.drawString(label, x, y + offset);
           }
-          g.drawString(label, x, y + offset);
         }
         lastSeqRef = aa[i].sequenceRef;
+
+        if (labelWidth > actualWidth)
+        {
+          actualWidth = labelWidth;
+        }
       }
     }
 
     if (!resizePanel && dragEvent != null && aa != null)
     {
-      g.setColor(Color.lightGray);
-      g.drawString(
-              (aa[selectedRow].sequenceRef == null ? ""
-                      : aa[selectedRow].sequenceRef.getName())
-                      + aa[selectedRow].label,
-              dragEvent.getX(), dragEvent.getY() - getScrollOffset());
+      if (actuallyDraw && g != null)
+      {
+        g.setColor(Color.lightGray);
+        g.drawString(
+                (aa[selectedRow].sequenceRef == null ? ""
+                        : aa[selectedRow].sequenceRef.getName())
+                        + aa[selectedRow].label,
+                dragEvent.getX(), dragEvent.getY() - getScrollOffset());
+      }
     }
 
     if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
     {
-      g.drawString(MessageManager.getString("label.right_click"), 2, 8);
-      g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
-              18);
+      if (actuallyDraw && g != null)
+      {
+        g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+        g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+                18);
+      }
     }
+
+    return actualWidth;
   }
 
   public int getScrollOffset()
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 8321741..8a957bc 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1507,7 +1507,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           tried = true;
         } catch (IllegalArgumentException exc)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Serious issue with viewport geometry imgWidth requested was "
                           + imgWidth);
           return;
@@ -1650,7 +1650,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               && (fadedImage == null || fadedImage.getWidth() != imgWidth
                       || fadedImage.getHeight() != image.getHeight()))
       {
-        // System.err.println("redraw faded image ("+(fadedImage==null ?
+        // jalview.bin.Console.errPrintln("redraw faded image ("+(fadedImage==null ?
         // "null image" : "") + " lastGood="+lastImageGood+")");
         fadedImage = new BufferedImage(imgWidth, image.getHeight(),
                 BufferedImage.TYPE_INT_RGB);
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 49eae98..950f129 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -371,9 +371,9 @@ public class AppJmol extends StructureViewerBase
       }
       if (waitTotal > waitMax)
       {
-        System.err.println("Timed out waiting for Jmol to load files after "
+        jalview.bin.Console.errPrintln("Timed out waiting for Jmol to load files after "
                 + waitTotal + "ms");
-        // System.err.println("finished: " + jmb.isFinishedInit()
+        // jalview.bin.Console.errPrintln("finished: " + jmb.isFinishedInit()
         // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
         // + "; files: " + files.toString());
         jmb.getStructureFiles();
@@ -532,7 +532,7 @@ public class AppJmol extends StructureViewerBase
               .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/");
     } catch (Exception ex)
     {
-      System.err.println("Show Jmol help failed with: " + ex.getMessage());
+      jalview.bin.Console.errPrintln("Show Jmol help failed with: " + ex.getMessage());
     }
   }
 
diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 6fac8fc..eb2368d 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -476,7 +476,7 @@ public class AppVarna extends JInternalFrame
       if (shift != null)
       {
         int i = shift.shift(newBase.getIndex());
-        // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+        // jalview.bin.Console.errPrintln("shifted "+(arg1.getIndex())+" to "+i);
         ssm.mouseOverVamsasSequence(seq, i, this);
       }
       else
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 5cfe72a..8951df0 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -574,7 +574,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
     } catch (ExceptionNAViewAlgorithm e)
     {
       // only throwable for draw mode = 3 NAView
-      System.err.println("Error drawing RNA: " + e.getMessage());
+      jalview.bin.Console.errPrintln("Error drawing RNA: " + e.getMessage());
     }
   }
 }
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index af59ca7..c120a1b 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -772,7 +772,7 @@ public class BlogReader extends JPanel
       String formattedDate = Cache.setDateProperty(
               "JALVIEW_NEWS_RSS_LASTMODIFIED", lastread.getTime());
       BlogReader me = new BlogReader();
-      System.out.println("Set last date to " + formattedDate);
+      jalview.bin.Console.outPrintln("Set last date to " + formattedDate);
       if (me.isNewsNew())
       {
         Console.debug("There is news to read.");
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index cc6a785..f13e151 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -343,7 +343,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       boolean opened = jmb.openSession(chimeraSessionFile);
       if (!opened)
       {
-        System.err.println("An error occurred opening Chimera session file "
+        jalview.bin.Console.errPrintln("An error occurred opening Chimera session file "
                 + chimeraSessionFile);
       }
     }
diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java
index c1c75f1..574ba28 100644
--- a/src/jalview/gui/ColourMenuHelper.java
+++ b/src/jalview/gui/ColourMenuHelper.java
@@ -304,7 +304,7 @@ public class ColourMenuHelper
         }
       } catch (Exception ex)
       {
-        System.out.println("Error loading User ColourFile\n" + ex);
+        jalview.bin.Console.outPrintln("Error loading User ColourFile\n" + ex);
       }
     }
 
diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java
index 5a23048..6a6cb56 100644
--- a/src/jalview/gui/Console.java
+++ b/src/jalview/gui/Console.java
@@ -433,20 +433,20 @@ public class Console extends WindowAdapter
     // you may omit this part for your application
     //
 
-    System.out.println("Hello World 2");
-    System.out.println("All fonts available to Graphic2D:\n");
+    jalview.bin.Console.outPrintln("Hello World 2");
+    jalview.bin.Console.outPrintln("All fonts available to Graphic2D:\n");
     GraphicsEnvironment ge = GraphicsEnvironment
             .getLocalGraphicsEnvironment();
     String[] fontNames = ge.getAvailableFontFamilyNames();
     for (int n = 0; n < fontNames.length; n++)
     {
-      System.out.println(fontNames[n]);
+      jalview.bin.Console.outPrintln(fontNames[n]);
     }
     // Testing part: simple an error thrown anywhere in this JVM will be printed
     // on the Console
     // We do it with a seperate Thread becasue we don't wan't to break a Thread
     // used by the Console.
-    System.out.println("\nLets throw an error on this console");
+    jalview.bin.Console.outPrintln("\nLets throw an error on this console");
     errorThrower = new Thread(this);
     errorThrower.setDaemon(true);
     errorThrower.start();
diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index c15cf2d..6cb59c3 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -432,7 +432,7 @@ public class CrossRefAction implements Runnable
                 MessageManager.getString("label.cant_map_cds"),
                 MessageManager.getString("label.operation_failed"),
                 JvOptionPane.OK_OPTION);
-        System.err.println("Failed to make CDS alignment");
+        jalview.bin.Console.errPrintln("Failed to make CDS alignment");
         return null;
       }
 
@@ -466,7 +466,7 @@ public class CrossRefAction implements Runnable
 
     if (copyAlignment.getHeight() <= 0)
     {
-      System.err.println("No Sequences generated for xRef type " + source);
+      jalview.bin.Console.errPrintln("No Sequences generated for xRef type " + source);
       return null;
     }
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 12ff20b..66055a4 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -439,7 +439,7 @@ public class Desktop extends jalview.jbgui.GDesktop
          * Send this message to stderr as the warning that follows (due to
          * reflection) also goes to stderr.
          */
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that.");
       }
       final String awtAppClassName = "awtAppClassName";
@@ -572,15 +572,16 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
 
       // Thread off a new instance of the file chooser - this reduces the time
-      // it
-      // takes to open it later on.
+      // it takes to open it later on.
       new Thread(new Runnable()
       {
         @Override
         public void run()
         {
           jalview.bin.Console.debug("Filechooser init thread started.");
-          String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+          String fileFormat = FileLoader.getUseDefaultFileFormat()
+                  ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+                  : null;
           JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
                   fileFormat);
           jalview.bin.Console.debug("Filechooser init thread finished.");
@@ -873,7 +874,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
       } catch (Exception ex)
       {
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "Unable to paste alignment from system clipboard:\n" + ex);
       }
     }
@@ -1267,7 +1268,9 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
-    String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+    String fileFormat = FileLoader.getUseDefaultFileFormat()
+            ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+            : null;
     JalviewFileChooser chooser = JalviewFileChooser.forRead(
             Cache.getProperty("LAST_DIRECTORY"), fileFormat,
             BackupFiles.getEnabled());
@@ -1630,7 +1633,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
     } catch (Exception ex)
     {
-      System.err.println("Error opening help: " + ex.getMessage());
+      jalview.bin.Console.errPrintln("Error opening help: " + ex.getMessage());
     }
   }
 
@@ -1861,7 +1864,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     boolean autoSave = projectFile != null && !saveAs
             && BackupFiles.getEnabled();
 
-    // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+    // jalview.bin.Console.outPrintln("autoSave="+autoSave+", projectFile='"+projectFile+"',
     // saveAs="+saveAs+", Backups
     // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
 
@@ -3410,7 +3413,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
           if (Platform.isAMacAndNotJS())
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Please ignore plist error - occurs due to problem with java 8 on OSX");
           }
         }
diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java
index 4b8a1fd..6d5cb46 100644
--- a/src/jalview/gui/EditNameDialog.java
+++ b/src/jalview/gui/EditNameDialog.java
@@ -129,6 +129,6 @@ public class EditNameDialog
     
     JvOptionPane.frameDialog(panel, title, JvOptionPane.PLAIN_MESSAGE,
             options, ok, actions, false);
-            */
+    */
   }
 }
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 2e9731d..184fdc5 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1019,7 +1019,7 @@ public class FeatureSettings extends JPanel
       }
     } catch (Exception ex)
     {
-      System.out.println("Error loading User Colour File\n" + ex);
+      jalview.bin.Console.outPrintln("Error loading User Colour File\n" + ex);
     }
   }
 
@@ -1608,7 +1608,7 @@ public class FeatureSettings extends JPanel
     {
       Color newColor = gcol.getMaxColour();
       comp.setBackground(newColor);
-      // System.err.println("Width is " + w / 2);
+      // jalview.bin.Console.errPrintln("Width is " + w / 2);
       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
       comp.setIcon(ficon);
       // tt+="RGB value: Max (" + newColor.getRed() + ", "
diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index 09bb2a3..327f6ca 100644
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -1096,7 +1096,7 @@ public class FeatureTypeSettings extends JalviewDialog
   {
     if (featureSettings != null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
     }
     featureSettings = listener;
diff --git a/src/jalview/gui/Help.java b/src/jalview/gui/Help.java
index 658b34f..8829be9 100644
--- a/src/jalview/gui/Help.java
+++ b/src/jalview/gui/Help.java
@@ -133,7 +133,7 @@ public class Help
         hb.setCurrentID(id.getId());
       } catch (BadIDException bad)
       {
-        System.out.println("Bad help link: " + id.getId()
+        jalview.bin.Console.outPrintln("Bad help link: " + id.getId()
                 + ": must match a target in help.jhm");
         throw bad;
       }
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index c94dee0..eb0715a 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
@@ -382,6 +383,12 @@ public class IdCanvas extends JPanel implements ViewportListenerI
   void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
           int startSeq, int pageHeight)
   {
+    drawIdsWrapped(g, alignViewport, startSeq, pageHeight, -1);
+  }
+
+  void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
+          int startSeq, int pageHeight, int idWidth)
+  {
     int alignmentWidth = alignViewport.getAlignment().getWidth();
     final int alheight = alignViewport.getAlignment().getHeight();
 
@@ -428,8 +435,23 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
       if (labels != null && alignViewport.isShowAnnotation())
       {
+        int getWidth = getWidth();
+        int thisIdWidth = getWidth;
         g.translate(0, ypos + (alheight * charHeight));
-        labels.drawComponent(g, getWidth());
+        if (!manuallyAdjusted())
+        {
+          int getAnnotationsIdWidth = labels.drawLabels(g, false, -1, false,
+                  null);
+          thisIdWidth = idWidth < 0 ? getAnnotationsIdWidth : idWidth;
+          if (thisIdWidth > getWidth)
+          {
+            this.setPreferredSize(
+                    new Dimension(thisIdWidth, this.getHeight()));
+            this.repaint();
+            alignViewport.setIdWidth(thisIdWidth);
+          }
+        }
+        labels.drawComponent(g, false, thisIdWidth);
         g.translate(0, -ypos - (alheight * charHeight));
       }
 
@@ -585,4 +607,16 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       repaint();
     }
   }
+
+  private boolean manuallyAdjusted = false;
+
+  public boolean manuallyAdjusted()
+  {
+    return manuallyAdjusted;
+  }
+
+  public void setManuallyAdjusted(boolean b)
+  {
+    manuallyAdjusted = b;
+  }
 }
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 4ba0699..4596e1f 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -20,8 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.AlignViewportI;
-
 import java.awt.Color;
 import java.awt.Cursor;
 import java.awt.Graphics;
@@ -31,6 +29,9 @@ import java.awt.event.MouseMotionListener;
 
 import javax.swing.JPanel;
 
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+
 /**
  * DOCUMENT ME!
  * 
@@ -136,6 +137,18 @@ public class IdwidthAdjuster extends JPanel
       return;
     }
 
+    /*
+     * don't allow residue width to be < 1 in wrapped format
+     */
+    if (viewport.getWrapAlignment())
+    {
+      SeqCanvas sc = ap.getSeqPanel().seqCanvas;
+      if (sc != null && sc.getWrappedCanvasWidth(sc.getWidth() - dif) < 1)
+      {
+        return;
+      }
+    }
+
     oldX = evt.getX();
 
     /*
@@ -146,9 +159,29 @@ public class IdwidthAdjuster extends JPanel
       return;
     }
     viewport.setIdWidth(newWidth);
+    ap.validateAnnotationDimensions(false);
+    ap.paintAlignment(true, false);
+
+    ap.getIdPanel().getIdCanvas().setManuallyAdjusted(true);
+  }
+
+  public void setWidth(int newWidth)
+  {
+    if (newWidth < MIN_ID_WIDTH
+            || ap.getIdPanel().getIdCanvas().manuallyAdjusted())
+    {
+      return;
+    }
+    final AlignViewportI viewport = ap.getAlignViewport();
+    viewport.setIdWidth(newWidth);
     ap.paintAlignment(true, false);
   }
 
+  public boolean manuallyAdjusted()
+  {
+    return ap.getIdPanel().getIdCanvas().manuallyAdjusted();
+  }
+
   @Override
   public void mouseMoved(MouseEvent evt)
   {
@@ -167,8 +200,21 @@ public class IdwidthAdjuster extends JPanel
   @Override
   public void paintComponent(Graphics g)
   {
+    int width = getWidth();
+    int height = getHeight();
     g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+    g.fillRect(0, 0, width, height);
+
+    if (!Cache.getDefault(AnnotationLabels.RESIZE_MARGINS_MARK_PREF, false))
+    // && !ap.getAlignViewport().getWrapAlignment()) // now allowing adjustment
+    // in wrap mode
+    {
+      int spacer = Math.max(2, AnnotationLabels.HEIGHT_ADJUSTER_HEIGHT / 4);
+      g.setColor(Color.LIGHT_GRAY);
+      g.drawLine(width - 3 * spacer, 0, width - 3 * spacer, height / 2);
+      g.drawLine(width - spacer, 0, width - spacer, height / 2);
+    }
+
     setCursor(Cursor.getPredefinedCursor(Cursor.W_RESIZE_CURSOR));
   }
 }
diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java
index 327eade..9ae764e 100644
--- a/src/jalview/gui/JDatabaseTree.java
+++ b/src/jalview/gui/JDatabaseTree.java
@@ -122,7 +122,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
         }
         else
         {
-          System.err.println("dupe ig for : " + dbs[i] + " \t"
+          jalview.bin.Console.errPrintln("dupe ig for : " + dbs[i] + " \t"
                   + dbp.getDbName() + " (" + dbp.getDbSource() + ")");
           source.remove(tn);
         }
@@ -552,7 +552,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
   @Override
   public void setVisible(boolean arg0)
   {
-    System.out.println("setVisible: " + arg0);
+    jalview.bin.Console.outPrintln("setVisible: " + arg0);
     super.setVisible(arg0);
   }
 }
diff --git a/src/jalview/gui/JvOptionPane.java b/src/jalview/gui/JvOptionPane.java
index c0efd4a..eaaa2a1 100644
--- a/src/jalview/gui/JvOptionPane.java
+++ b/src/jalview/gui/JvOptionPane.java
@@ -36,6 +36,7 @@ import java.awt.event.MouseAdapter;
 import java.awt.event.MouseMotionAdapter;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -717,7 +718,7 @@ public class JvOptionPane extends JOptionPane
 
   private static void outputMessage(Object message)
   {
-    System.out.println(">>> JOption Message : " + message.toString());
+    jalview.bin.Console.outPrintln(">>> JOption Message : " + message.toString());
   }
 
   public static Object getMockResponse()
@@ -1080,37 +1081,44 @@ public class JvOptionPane extends JOptionPane
         @Override
         public void internalFrameActivated(InternalFrameEvent arg0)
         {
+          System.err.println("##### internalFrameActivated");
         }
 
         @Override
         public void internalFrameClosed(InternalFrameEvent arg0)
         {
+          System.err.println("##### internalFrameClosed");
           JvOptionPane.this.internalDialogHandleResponse();
         }
 
         @Override
         public void internalFrameClosing(InternalFrameEvent arg0)
         {
+          System.err.println("##### internalFrameClosing");
         }
 
         @Override
         public void internalFrameDeactivated(InternalFrameEvent arg0)
         {
+          System.err.println("##### internalFrameDeactivated");
         }
 
         @Override
         public void internalFrameDeiconified(InternalFrameEvent arg0)
         {
+          System.err.println("##### internalFrameDeiconified");
         }
 
         @Override
         public void internalFrameIconified(InternalFrameEvent arg0)
         {
+          System.err.println("##### internalFrameIconified");
         }
 
         @Override
         public void internalFrameOpened(InternalFrameEvent arg0)
         {
+          System.err.println("##### internalFrameOpened");
         }
       });
       jif.setVisible(true);
@@ -1129,7 +1137,13 @@ public class JvOptionPane extends JOptionPane
 
   private void internalDialogHandleResponse()
   {
-    String responseString = (String) this.getValue();
+    Object value = this.getValue();
+    if (value == null
+            || (value instanceof Integer && (Integer) value == -1))
+    {
+      return;
+    }
+    String responseString = value.toString();
     int response = ourOptions.indexOf(responseString);
 
     if (!Platform.isJS())
@@ -1504,7 +1518,8 @@ public class JvOptionPane extends JOptionPane
     EventQueue queue = Toolkit.getDefaultToolkit().getSystemEventQueue();
     try
     {
-      while (!f.isClosed())
+      boolean stillModal = true;
+      while (!f.isClosed() && stillModal)
       {
         if (EventQueue.isDispatchThread())
         {
@@ -1514,34 +1529,68 @@ public class JvOptionPane extends JOptionPane
           // This mimics EventQueue.dispatchEvent(). We can't use
           // EventQueue.dispatchEvent() directly, because it is
           // protected, unfortunately.
+          System.out.println(
+                  "##### ev source=" + ev.getSource().getClass() + "");
           if (ev instanceof ActiveEvent)
+          {
+            System.err.println("##### 1");
             ((ActiveEvent) ev).dispatch();
-          else if (ev.getSource() instanceof Component)
-            ((Component) ev.getSource()).dispatchEvent(ev);
+          }
           else if (ev.getSource() instanceof MenuComponent)
+          {
+            System.err.println("##### 2");
             ((MenuComponent) ev.getSource()).dispatchEvent(ev);
+          }
+          else if (ev.getSource() instanceof Component)
+          {
+            System.err.println("##### 3");
+            if (ev.getSource().equals(Desktop.getDesktop().getRootPane()))
+            {
+              stillModal = false;
+            }
+            else
+            {
+              ((Component) ev.getSource()).dispatchEvent(ev);
+            }
+          }
           // Other events are ignored as per spec in
           // EventQueue.dispatchEvent
+          System.err.println("##### 4");
         }
         else
         {
           // Give other threads a chance to become active.
+          System.err.println("##### 5");
           Thread.yield();
         }
       }
     } catch (InterruptedException ex)
     {
       // If we get interrupted, then leave the modal state.
+      System.err.println("##### 6");
     } finally
     {
+      System.err.println("##### 7");
       // Clean up the modal interceptor.
       lp.remove(modalInterceptor);
 
+      f.setVisible(false);
+
+      try
+      {
+        f.setClosed(true);
+      } catch (PropertyVetoException e)
+      {
+        f.doDefaultCloseAction();
+      }
+
       // Remove the internal frame from its parent, so it is no longer
       // lurking around and clogging memory.
       Container parent = f.getParent();
       if (parent != null)
+      {
         parent.remove(f);
+      }
     }
   }
 
diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index e0427cc..f05110f 100644
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -713,7 +713,7 @@ public class OptsAndParamsPage
             }
           } catch (NumberFormatException e)
           {
-            System.err.println(e.toString());
+            jalview.bin.Console.errPrintln(e.toString());
           }
           if (minValue != null || maxValue != null)
           {
@@ -750,7 +750,7 @@ public class OptsAndParamsPage
             }
           } catch (NumberFormatException e)
           {
-            System.err.println(e.toString());
+            jalview.bin.Console.errPrintln(e.toString());
           }
           if (minValue != null && maxValue != null)
           {
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 953fdc5..36849b0 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -194,7 +194,7 @@ public class PaintRefresher
           {
             // raise an implementation warning here - not sure if this situation
             // will ever occur
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
           }
           List alsq = comp.getSequences();
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index c4b5367..b5b6ffc 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -104,7 +104,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
         if (!first)
         {
-          System.out.println(DASHES);
+          jalview.bin.Console.outPrintln(DASHES);
           textarea.append(DASHES);
         }
         first = false;
@@ -139,7 +139,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
     for (int i = 0; i < seqs.length; i++)
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
     }
 
@@ -151,7 +151,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     {
       System.out.print(String.format("%7d", i + 1));
     }
-    System.out.println();
+    jalview.bin.Console.outPrintln();
 
     for (int i = 0; i < seqs.length; i++)
     {
@@ -163,10 +163,10 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
          */
         System.out.print(String.format("%7.3f", scores[i][j] / totscore));
       }
-      System.out.println();
+      jalview.bin.Console.outPrintln();
     }
 
-    System.out.println("\n");
+    jalview.bin.Console.outPrintln("\n");
   }
 
   /**
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 88c1292..109c140 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -906,6 +906,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     if (Platform.isJS())
     {
       details = new JInternalFrame();
+      details.setFrameIcon(null);
       JPanel panel = new JPanel(new BorderLayout());
       panel.setOpaque(true);
       panel.setBackground(Color.white);
@@ -1834,6 +1835,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       pane.setBackground(Color.WHITE);
       pane.add(textLabel, BorderLayout.NORTH);
       frame = new JInternalFrame();
+      frame.setFrameIcon(null);
       frame.getContentPane().add(new JScrollPane(pane));
     }
     else
@@ -2189,7 +2191,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     String[] omitHidden = null;
 
-    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+    jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a prompt happens
     // or we simply trust the user wants
     // wysiwig behaviour
 
diff --git a/src/jalview/gui/ProgressBar.java b/src/jalview/gui/ProgressBar.java
index 011d810..d68d95f 100644
--- a/src/jalview/gui/ProgressBar.java
+++ b/src/jalview/gui/ProgressBar.java
@@ -231,7 +231,7 @@ public class ProgressBar implements IProgressIndicator
         final JPanel progressPanel = progressBars.get(id);
         if (progressPanel == null)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "call setProgressBar before registering the progress bar's handler.");
           return;
         }
diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 705102a..62dce24 100644
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.java
@@ -121,7 +121,7 @@ public class PymolBindingModel extends AAStructureBindingModel
   protected List executeCommand(StructureCommandI command,
           boolean getReply)
   {
-    // System.out.println(command.toString()); // debug
+    // jalview.bin.Console.outPrintln(command.toString()); // debug
     return pymolManager.sendCommand(command, getReply);
   }
 
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 8d66a44..f487011 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -184,7 +184,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     validate();
     sliderValueChanged();
-    // System.out.println((System.currentTimeMillis()-start));
+    // jalview.bin.Console.outPrintln((System.currentTimeMillis()-start));
   }
 
   void sliderValueChanged()
diff --git a/src/jalview/gui/RestInputParamEditDialog.java b/src/jalview/gui/RestInputParamEditDialog.java
index 8ae5408..9b199fd 100644
--- a/src/jalview/gui/RestInputParamEditDialog.java
+++ b/src/jalview/gui/RestInputParamEditDialog.java
@@ -53,7 +53,7 @@ public class RestInputParamEditDialog extends GRestInputParamEditDialog
               .newInstance());
     } catch (Throwable x)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Unexpected exception when instantiating rest input type.");
       x.printStackTrace();
     }
@@ -166,7 +166,7 @@ public class RestInputParamEditDialog extends GRestInputParamEditDialog
           updated = true;
         } catch (InvalidArgumentException ex)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "IMPLEMENTATION ERROR: Invalid argument for type : "
                           + typeList.getSelectedValue() + "\n");
           ex.printStackTrace();
@@ -215,7 +215,7 @@ public class RestInputParamEditDialog extends GRestInputParamEditDialog
         types.add(jtype.getURLtokenPrefix());
       } catch (Throwable x)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Unexpected exception when instantiating rest input type.");
         x.printStackTrace();
       }
diff --git a/src/jalview/gui/RestServiceEditorPane.java b/src/jalview/gui/RestServiceEditorPane.java
index cda76d9..8953626 100644
--- a/src/jalview/gui/RestServiceEditorPane.java
+++ b/src/jalview/gui/RestServiceEditorPane.java
@@ -363,7 +363,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
                 mtch.group(2) + ":" + mtch.group(3), mtch.group(1),
                 mtch.group(2), mtch.group(3), inputTypes, warnings))
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "IMPLEMENTATION PROBLEM: Cannot parse RestService input parameter string '"
                           + its + "'" + "\n" + warnings);
         }
@@ -389,7 +389,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
         } catch (Throwable x)
         {
 
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "IMPLEMENTATION PROBLEM: Cannot parse RestService output parameter string '"
                           + its + "'" + "\n" + warnings);
         }
@@ -399,7 +399,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
     }
     else
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "IMPLEMENTATION PROBLEM: Restservice generated from GUI is invalid\n"
                       + warnings);
 
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d15cdcf..0faedb0 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -343,7 +343,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
         }
       }
 
-      // System.err.println(">>> FastPaint to " + transX + " " + transY + " "
+      // jalview.bin.Console.errPrintln(">>> FastPaint to " + transX + " " + transY + " "
       // + horizontal + " " + vertical + " " + startRes + " " + endRes
       // + " " + startSeq + " " + endSeq);
 
@@ -362,7 +362,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       // Call repaint on alignment panel so that repaints from other alignment
       // panel components can be aggregated. Otherwise performance of the
       // overview window and others may be adversely affected.
-      // System.out.println("SeqCanvas fastPaint() repaint() request...");
+      // jalview.bin.Console.outPrintln("SeqCanvas fastPaint() repaint() request...");
       av.getAlignPanel().repaint();
     } finally
     {
@@ -550,6 +550,20 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
   }
 
+  public int getMinimumWrappedCanvasWidth()
+  {
+    int charWidth = av.getCharWidth();
+    FontMetrics fm = getFontMetrics(av.getFont());
+    int labelWidth = 0;
+    if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
+    {
+      labelWidth = getLabelWidth(fm);
+    }
+    labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+    labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
+    return labelWidthEast + labelWidthWest + charWidth;
+  }
+
   /**
    * Returns a pixel width sufficient to show the largest sequence coordinate
    * (end position) in the alignment, calculated as the FontMetrics width of
@@ -1665,7 +1679,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
   public void propertyChange(PropertyChangeEvent evt)
   {
     String eventName = evt.getPropertyName();
-    // System.err.println(">>SeqCanvas propertyChange " + eventName);
+    // jalview.bin.Console.errPrintln(">>SeqCanvas propertyChange " + eventName);
     if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
     {
       fastPaint = true;
@@ -1675,7 +1689,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
     {
       fastPaint = false;
-      // System.err.println("!!!! fastPaint false from MOVE_VIEWPORT");
+      // jalview.bin.Console.errPrintln("!!!! fastPaint false from MOVE_VIEWPORT");
       repaint();
       return;
     }
diff --git a/src/jalview/gui/SeqCanvas.java.broken b/src/jalview/gui/SeqCanvas.java.broken
index c0a86df..3560efd 100755
--- a/src/jalview/gui/SeqCanvas.java.broken
+++ b/src/jalview/gui/SeqCanvas.java.broken
@@ -377,7 +377,7 @@ public class SeqCanvas extends JComponent
       } catch (OutOfMemoryError er)
       {
         System.gc();
-        System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
+        jalview.bin.Console.errPrintln("SeqCanvas OutOfMemory Redraw Error.\n" + er);
         new OOMWarning("Creating alignment image for display", er);
 
         return;
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 55f06fc..ce60be6 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -137,7 +137,7 @@ public class SeqPanel extends JPanel
       MousePos o = (MousePos) obj;
       boolean b = (column == o.column && seqIndex == o.seqIndex
               && annotationIndex == o.annotationIndex);
-      // System.out.println(obj + (b ? "= " : "!= ") + this);
+      // jalview.bin.Console.outPrintln(obj + (b ? "= " : "!= ") + this);
       return b;
     }
 
@@ -881,7 +881,7 @@ public class SeqPanel extends JPanel
 
     if (lastMessage == null || !lastMessage.equals(tmp))
     {
-      // System.err.println("mouseOver Sequence: "+tmp);
+      // jalview.bin.Console.errPrintln("mouseOver Sequence: "+tmp);
       ssm.mouseOverSequence(sequence, index, pos, av);
     }
     lastMessage = tmp;
@@ -1006,7 +1006,7 @@ public class SeqPanel extends JPanel
   @Override
   public void updateColours(SequenceI seq, int index)
   {
-    System.out.println("update the seqPanel colours");
+    jalview.bin.Console.outPrintln("update the seqPanel colours");
     // repaint();
   }
 
@@ -2861,7 +2861,7 @@ public class SeqPanel extends JPanel
     if (copycolsel && av.hasHiddenColumns()
             && (av.getAlignment().getHiddenColumns() == null))
     {
-      System.err.println("Bad things");
+      jalview.bin.Console.errPrintln("Bad things");
     }
     if (repaint) // always true!
     {
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 6b4c74a..137655f 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -599,7 +599,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                 + ((StringPair) database.getSelectedItem()).getDisplay());
         // error
         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
-        System.err.println("Retrieval failed for source ='"
+        jalview.bin.Console.errPrintln("Retrieval failed for source ='"
                 + ((StringPair) database.getSelectedItem()).getDisplay()
                 + "' and query\n'" + textArea.getText() + "'\n");
         e.printStackTrace();
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 0b7af0d..ff409e0 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -172,7 +172,7 @@ public class SplashScreen extends JPanel
           }
           if (mt.isErrorAny())
           {
-            System.err.println("Error when loading images!");
+            jalview.bin.Console.errPrintln("Error when loading images!");
           }
         } while (!mt.checkAll());
         Desktop.instance.setIconImages(ChannelProperties.getIconList());
@@ -228,7 +228,7 @@ public class SplashScreen extends JPanel
   protected boolean refreshText()
   {
     String newtext = Desktop.instance.getAboutMessage();
-    // System.err.println("Text found: \n"+newtext+"\nEnd of newtext.");
+    // jalview.bin.Console.errPrintln("Text found: \n"+newtext+"\nEnd of newtext.");
     if (oldTextLength != newtext.length())
     {
       iframe.setVisible(false);
diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index 08d6e03..73744b3 100644
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -900,6 +900,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
       });
       featureSettingsUI = new JInternalFrame(MessageManager.getString(
               "label.sequence_feature_settings_for_CDS_and_Protein"));
+      featureSettingsUI.setFrameIcon(null);
       featureSettingsPanels.setOpaque(true);
 
       JPanel dialog = new JPanel();
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 6fce984..d00b1c2 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -71,7 +71,6 @@ import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
 import jalview.gui.structurechooser.StructureChooserQuerySource;
 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
 import jalview.io.DataSourceType;
-import jalview.io.FileFormatException;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.FilterOption;
@@ -85,7 +84,6 @@ import jalview.util.StringUtils;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
-import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.sifts.SiftsSettings;
 
@@ -1525,7 +1523,7 @@ public class StructureChooser extends GStructureChooser
             // for moment, it will work fine as is because it is self-contained
             String searchTerm = text.toLowerCase(Locale.ROOT);
             searchTerm = searchTerm.split(":")[0];
-            // System.out.println(">>>>> search term : " + searchTerm);
+            // jalview.bin.Console.outPrintln(">>>>> search term : " + searchTerm);
             List wantedFields = new ArrayList<>();
             FTSRestRequest pdbRequest = new FTSRestRequest();
             pdbRequest.setAllowEmptySeq(false);
@@ -1801,7 +1799,9 @@ public class StructureChooser extends GStructureChooser
     sc.mainFrame.dispose();
 
     if (showRefAnnotations)
+    {
       showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+    }
 
     return sv;
   }
diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 6cef665..ad3fc6a 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -21,9 +21,11 @@
 package jalview.gui;
 
 import java.util.ArrayList;
+import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 
@@ -66,7 +68,27 @@ public class StructureViewer
 
   public enum ViewerType
   {
-    JMOL, CHIMERA, CHIMERAX, PYMOL
+    JMOL, CHIMERA, CHIMERAX, PYMOL;
+
+    public static ViewerType getFromString(String viewerString)
+    {
+      ViewerType viewerType = null;
+      if (!"none".equals(viewerString))
+      {
+        for (ViewerType v : EnumSet.allOf(ViewerType.class))
+        {
+          String name = v.name().toLowerCase(Locale.ROOT).replaceAll(" ",
+                  "");
+          if (viewerString.equals(name))
+          {
+            viewerType = v;
+            break;
+          }
+        }
+      }
+      return viewerType;
+    }
+
   };
 
   /**
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 01a3c2d..b8d2cce 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -1197,7 +1197,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       }
     } catch (Exception e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error retrieving PDB id " + pdbid + ": " + e.getMessage());
     } finally
     {
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 2eff542..0a0c1b8 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -261,7 +261,7 @@ public class TreePanel extends GTreePanel
         {
           if (tree == null)
           {
-            System.out.println("tree is null");
+            jalview.bin.Console.outPrintln("tree is null");
             // TODO: deal with case when a change event is received whilst a
             // tree is still being calculated - should save reference for
             // processing message later.
@@ -269,7 +269,7 @@ public class TreePanel extends GTreePanel
           }
           if (evt.getNewValue() == null)
           {
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "new alignment sequences vector value is null");
           }
 
@@ -896,7 +896,7 @@ public class TreePanel extends GTreePanel
       pg.close();
     } catch (Exception ex)
     {
-      System.err.println("Error writing tree as EPS");
+      jalview.bin.Console.errPrintln("Error writing tree as EPS");
       ex.printStackTrace();
     }
   }
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 8a8ba8d..28f6c59 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -614,7 +614,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       cdoc = null;
     } catch (Exception ee)
     {
-      System.err.println("Exception whilst updating :");
+      jalview.bin.Console.errPrintln("Exception whilst updating :");
       ee.printStackTrace(System.err);
       // recover object map backup, since its probably corrupted with references
       // to Vobjects that don't exist anymore.
@@ -803,7 +803,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               // we only care about AlignmentSequence selections
               SelectionMessage sm = (SelectionMessage) message;
               sm.validate();
-              System.err.println("Received\n" + sm.getRawMessage());
+              jalview.bin.Console.errPrintln("Received\n" + sm.getRawMessage());
               Object[] jvobjs = sm.getVorbaIDs() == null ? null
                       : new Object[sm.getVorbaIDs().length];
               if (jvobjs == null)
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 7eeee9a..961caa7 100644
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -359,7 +359,7 @@ public class WebserviceInfo extends GWebserviceInfo
       @Override
       public void internalFrameClosed(InternalFrameEvent evt)
       {
-        // System.out.println("Shutting down webservice client");
+        // jalview.bin.Console.outPrintln("Shutting down webservice client");
         WSClientI service = thisinfo.getthisService();
         if (service != null && service.isCancellable())
         {
diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index e1613da..196eb32 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -493,7 +493,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     else
     {
       // TODO: show warning
-      System.err.println("Invalid name. Not saved.");
+      jalview.bin.Console.errPrintln("Invalid name. Not saved.");
     }
   }
 
@@ -642,7 +642,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
           }
           else
           {
-            System.err.println("Ignoring unknown service argument type "
+            jalview.bin.Console.errPrintln("Ignoring unknown service argument type "
                     + myarg.getClass().getName());
           }
         }
@@ -685,7 +685,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         {
           if (arg instanceof OptionI)
           {
-            // System.out.println("Setting option "
+            // jalview.bin.Console.outPrintln("Setting option "
             // + System.identityHashCode(arg) + ":" + arg.getName()
             // + " with " + arg.getDefaultValue());
             opanp.selectOption((OptionI) arg, arg.getValue());
@@ -874,7 +874,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
         if (cw + 120 > panewidth)
         {
           jobOptions.add(pbox, "wrap");
-          // System.out.println("Wrap on "+pbox.option.getName());
+          // jalview.bin.Console.outPrintln("Wrap on "+pbox.option.getName());
           cw = hgap + pbox.getSize().width;
           fh = true;
         }
@@ -946,7 +946,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
     // TODO: waste some time trying to eliminate any unnecessary .validate calls
     // here
-    // System.out.println("Size will be : "+w+","+os);
+    // jalview.bin.Console.outPrintln("Size will be : "+w+","+os);
     // optsAndparams.setPreferredSize(null);
     // paramPane.getViewport().setView(optsAndparams);
     paramPane.getViewport().setAutoscrolls(true);
@@ -976,7 +976,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
       disc.run();
     } catch (Exception e)
     {
-      System.err.println("Aborting. Problem discovering services.");
+      jalview.bin.Console.errPrintln("Aborting. Problem discovering services.");
       e.printStackTrace();
       return;
     }
@@ -1023,7 +1023,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
               pr = en.next();
             }
             {
-              System.out.println("Testing opts dupes for "
+              jalview.bin.Console.outPrintln("Testing opts dupes for "
                       + lastserv.getUri() + " : " + lastserv.getActionText()
                       + ":" + pr.getName());
               List