Can run headless=true

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index e2477d9..d8a6d3d 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -105,8 +105,14 @@ public class Cache
           jnlpVersion = "Test";\r
         }\r
 \r
+\r
+        System.out.println("Version: "+codeVersion);\r
+\r
         // jnlpVersion will be null if we're using InstallAnywhere\r
-        if(jnlpVersion==null)\r
+        // Dont do this check if running in headless mode\r
+        if(jnlpVersion==null && (\r
+                System.getProperty("java.awt.headless")==null\r
+             || System.getProperty("java.awt.headless").equals("false")))\r
         {\r
           try{\r
             java.net.URL url = new java.net.URL("http://www.jalview.org/webstart/jalview.jnlp");\r
@@ -124,10 +130,9 @@ public class Cache
             }\r
           }catch(Exception ex)\r
           {  jnlpVersion =  codeVersion; }\r
-        }\r
 \r
-        System.out.println("Version: "+codeVersion);\r
-        System.out.println("Latest : "+jnlpVersion);\r
+          System.out.println("Latest : "+jnlpVersion);\r
+        }\r
 \r
         setProperty("LATEST_VERSION", jnlpVersion);\r
         setProperty("VERSION", codeVersion);\r

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 395875c..3ab3bf4 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -25,6 +25,9 @@ import org.apache.log4j.*;
 import javax.swing.*;\r
 \r
 import java.util.Vector;\r
+import jalview.datamodel.Alignment;\r
+import jalview.io.FormatAdapter;\r
+import jalview.datamodel.SequenceI;\r
 \r
 \r
 /**\r
@@ -73,17 +76,42 @@ public class Jalview
     public static void main(String[] args)\r
     {\r
       ArgsParser aparser = new ArgsParser(args);\r
+      boolean headless = false;\r
+\r
+      if( aparser.contains("help") || aparser.contains("h") )\r
+      {\r
+        System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"\r
+                           +"-nodisplay\tRun Jalview without User Interface.\n"\r
+                           +"-props FILE\tUse the given Jalview properties file instead of users default.\n"\r
+                           +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"\r
+                           +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\n"\r
+                           +"SequenceID is used in preference to SequenceIndex if both are provided.\n"\r
+                           +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"\r
+                           +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"\r
+                           +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"\r
+                           +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"\r
+                           +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"\r
+                           +"-msf FILE\tCreate alignment file FILE in MSF format.\n"\r
+                           +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"\r
+                           +"-pir FILE\tCreate alignment file FILE in PIR format.\n"\r
+                           +"-blc FILE\tCreate alignment file FILE in BLC format.\n"\r
+                           +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"\r
+                           +"-png FILE\tCreate PNG image FILE from alignment.\n"\r
+                           +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"\r
+                           +"-eps FILE\tCreate EPS file FILE from alignment.");\r
+        System.exit(0);\r
+          }\r
+\r
+\r
+     if (aparser.contains("nodisplay"))\r
+      System.setProperty("java.awt.headless", "true");\r
+\r
+    if(   System.getProperty("java.awt.headless") != null\r
+          && System.getProperty("java.awt.headless").equals("true"))\r
+      {\r
+        headless = true;\r
+      }\r
 \r
-      try\r
-        {\r
-            UIManager.setLookAndFeel(\r
-            //  "javax.swing.plaf.metal.MetalLookAndFeel"\r
-            //  "javax.swing.plaf.multi.MultiLookAndFeel"\r
-            UIManager.getSystemLookAndFeelClassName());\r
-        }\r
-        catch (Exception ex)\r
-        {\r
-        }\r
 \r
         Cache.loadProperties(aparser.getValue("props"));\r
         jalview.gui.Preferences.initPreferences();\r
@@ -97,125 +125,117 @@ public class Jalview
         }\r
 \r
 \r
-        String file = null, protocol = null, format = null, groups=null;\r
-        Desktop desktop = new Desktop();\r
-\r
-\r
-        if(args==null || args.length==0)\r
+        Desktop desktop = null;\r
+        if( !headless )\r
         {\r
+          try\r
+          {\r
+            UIManager.setLookAndFeel(\r
+                //  "javax.swing.plaf.metal.MetalLookAndFeel"\r
+                //  "javax.swing.plaf.multi.MultiLookAndFeel"\r
+                UIManager.getSystemLookAndFeelClassName());\r
+          }\r
+          catch (Exception ex)\r
+          {\r
+          }\r
+\r
+          desktop = new Desktop();\r
           desktop.setVisible(true);\r
         }\r
-        else\r
-        {\r
-          if( aparser.contains("help") || aparser.contains("h") )\r
-          {\r
-            System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"\r
-                               +"-nodisplay\tRun Jalview without User Interface.\n"\r
-                               +"-props FILE\tUse the given Jalview properties file instead of users default.\n"\r
-                               +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"\r
-                               +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\n"\r
-                               +"SequenceID is used in preference to SequenceIndex if both are provided.\n"\r
-                               +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"\r
-                               +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"\r
-                               +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"\r
-                               +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"\r
-                               +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"\r
-                               +"-msf FILE\tCreate alignment file FILE in MSF format.\n"\r
-                               +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"\r
-                               +"-pir FILE\tCreate alignment file FILE in PIR format.\n"\r
-                               +"-blc FILE\tCreate alignment file FILE in BLC format.\n"\r
-                               +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"\r
-                               +"-png FILE\tCreate PNG image FILE from alignment.\n"\r
-                               +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"\r
-                               +"-eps FILE\tCreate EPS file FILE from alignment.");\r
-            System.exit(0);\r
 \r
-          }\r
 \r
-          if (!aparser.contains("nodisplay"))\r
-            desktop.setVisible(true);\r
+         String file = null, protocol = null, format = null, groups=null;\r
+         jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();\r
 \r
           file = aparser.getValue("open");\r
 \r
-          if (file == null && !desktop.isVisible())\r
+          if (file == null && desktop==null)\r
           {\r
             System.out.println("No files to open!");\r
             System.exit(1);\r
           }\r
-          else if(!file.startsWith("http://"))\r
+\r
+          if(file!=null)\r
           {\r
-            if (!(new java.io.File(file)).exists())\r
+\r
+            if (!file.startsWith("http://"))\r
             {\r
-              System.out.println("Can't find " + file);\r
-              System.exit(1);\r
+              if (! (new java.io.File(file)).exists())\r
+              {\r
+                System.out.println("Can't find " + file);\r
+                System.exit(1);\r
+              }\r
             }\r
-          }\r
-\r
-          protocol = "File";\r
 \r
-          if (file.indexOf("http:") > -1)\r
-          {\r
-            protocol = "URL";\r
-          }\r
+            protocol = "File";\r
 \r
-          if(file.endsWith(".jar"))\r
-            format = "Jalview";\r
-          else\r
-            format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+            if (file.indexOf("http:") > -1)\r
+            {\r
+              protocol = "URL";\r
+            }\r
 \r
-          System.out.println("Opening: " + format + " file " + file);\r
+            if (file.endsWith(".jar"))\r
+              format = "Jalview";\r
+            else\r
+              format = jalview.io.IdentifyFile.Identify(file, protocol);\r
 \r
-          AlignFrame af = desktop.LoadFileWaitTillLoaded(file, protocol, format);\r
+            System.out.println("Opening: " + format + " file " + file);\r
 \r
-          groups = aparser.getValue("groups");\r
-          if(groups!=null)\r
-          {\r
-            af.parseGroupsFile(groups);\r
-          }\r
+            AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);\r
 \r
-          String imageName = "unnamed.png";\r
-          while (aparser.getSize() > 1)\r
-          {\r
-            format = aparser.nextValue();\r
-            file = aparser.nextValue();\r
-\r
-            if (format.equalsIgnoreCase("png"))\r
+            groups = aparser.getValue("groups");\r
+            if (groups != null)\r
             {\r
-              af.createPNG(new java.io.File(file));\r
-              imageName = (new java.io.File(file)).getName();\r
-              System.out.println("Creating PNG image: " + file);\r
-              continue;\r
+              af.parseGroupsFile(groups);\r
             }\r
-            else if (format.equalsIgnoreCase("imgMap"))\r
+\r
+            String imageName = "unnamed.png";\r
+            while (aparser.getSize() > 1)\r
             {\r
-              af.createImageMap(new java.io.File(file), imageName);\r
-              System.out.println("Creating image map: " + file);\r
-              continue;\r
+              format = aparser.nextValue();\r
+              file = aparser.nextValue();\r
+\r
+              if (format.equalsIgnoreCase("png"))\r
+              {\r
+                af.createPNG(new java.io.File(file));\r
+                imageName = (new java.io.File(file)).getName();\r
+                System.out.println("Creating PNG image: " + file);\r
+                continue;\r
+              }\r
+              else if (format.equalsIgnoreCase("imgMap"))\r
+              {\r
+                af.createImageMap(new java.io.File(file), imageName);\r
+                System.out.println("Creating image map: " + file);\r
+                continue;\r
+              }\r
+              else if (format.equalsIgnoreCase("eps"))\r
+              {\r
+                System.out.println("Creating EPS file: " + file);\r
+                af.createEPS(new java.io.File(file));\r
+                continue;\r
+              }\r
+\r
+              if (af.saveAlignment(file, format))\r
+                System.out.println("Written alignment in " + format +\r
+                                   " format to " + file);\r
+              else\r
+                System.out.println("Error writing file " + file + " in " + format +\r
+                                   " format!!");\r
+\r
             }\r
-            else if (format.equalsIgnoreCase("eps"))\r
+\r
+            while (aparser.getSize() > 0)\r
             {\r
-              System.out.println("Creating EPS file: " + file);\r
-              af.createEPS(new java.io.File(file));\r
-              continue;\r
+              System.out.println("Unknown arg: " + aparser.nextValue());\r
             }\r
-\r
-            if (af.saveAlignment(file, format))\r
-              System.out.println("Written alignment in " + format +\r
-                                 " format to " + file);\r
-            else\r
-              System.out.println("Error writing file " + file + " in " + format +\r
-                                 " format!!");\r
-\r
-          }\r
-\r
-          while (aparser.getSize() > 0)\r
-          {\r
-            System.out.println("Unknown arg: " + aparser.nextValue());\r
           }\r
-        }\r
 \r
-          if (jalview.gui.Preferences.showStartupFile &&\r
-              (jalview.gui.Preferences.startupFile != null))\r
+        // We'll only open the default file if the desktop is visible.\r
+        //////////////////////\r
+          if (\r
+              !headless &&\r
+              jalview.gui.Preferences.showStartupFile &&\r
+              jalview.gui.Preferences.startupFile != null)\r
           {\r
 \r
             file = jalview.gui.Preferences.startupFile;\r
@@ -237,7 +257,8 @@ public class Jalview
             }\r
           }\r
 \r
-          if (!desktop.isVisible())\r
+\r
+          if (desktop==null)\r
             System.exit(0);\r
     }\r
 }\r

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6c235a4..e4842ee 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -226,7 +226,6 @@ public class GAlignFrame
     }\r
     catch (Exception e)\r
     {\r
-      e.printStackTrace();\r
     }\r
 \r
   }\r