X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=bdfe3aedfcb50e37ed89433144d1690fa1ee1153;hb=47aec94b56baa5b666c3189280f4d1d5c7567a95;hp=910c94720665a082c0180d8244e051112e57bbc6;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 910c947..bdfe3ae 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -57,11 +57,8 @@ public class Jalview
         System.out.println("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"
-                           +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"
-                           +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\n"
-                           +"SequenceID is used in preference to SequenceIndex if both are provided.\n"
-                           +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"
-                           +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"
+                           +"-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+                           +"-features FILE\tUse the given file to mark features on the alignment.\n"
                            +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
                            +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
                            +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
@@ -72,14 +69,17 @@ public class Jalview
                            +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                            +"-png FILE\tCreate PNG image FILE from alignment.\n"
                            +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
-                           +"-eps FILE\tCreate EPS file FILE from alignment.");
+                           +"-eps FILE\tCreate EPS file FILE from alignment."
+            +"\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
         System.exit(0);
           }
 
+          Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!
 
           if (aparser.contains("nodisplay"))
+          {
             System.setProperty("java.awt.headless", "true");
-
+          }
           if (System.getProperty("java.awt.headless") != null
               && System.getProperty("java.awt.headless").equals("true"))
           {
@@ -99,8 +99,6 @@ public class Jalview
             System.exit(0);
           }
 
-        Cache.loadProperties(aparser.getValue("props"));
-
         Desktop desktop = null;
         if( !headless )
         {
@@ -126,7 +124,7 @@ public class Jalview
         }
 
 
-         String file = null, protocol = null, format = null, groups=null;
+         String file = null, protocol = null, format = null, data=null;
          jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
 
           file = aparser.getValue("open");
@@ -145,7 +143,8 @@ public class Jalview
               if (! (new java.io.File(file)).exists())
               {
                 System.out.println("Can't find " + file);
-                System.exit(1);
+                if(headless)
+                  System.exit(1);
               }
             }
 
@@ -159,18 +158,34 @@ public class Jalview
             if (file.endsWith(".jar"))
               format = "Jalview";
             else
-              format = jalview.io.IdentifyFile.Identify(file, protocol);
+              format = new jalview.io.IdentifyFile().Identify(file, protocol);
 
             System.out.println("Opening: " + format + " file " + file);
 
             AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
 
-            groups = aparser.getValue("groups");
-            if (groups != null)
+            // Must maintain ability to use the groups flag
+            data = aparser.getValue("groups");
+            if (data != null)
+            {
+              af.parseGroupsFile(data);
+              System.out.println("Added "+data);
+            }
+            data = aparser.getValue("features");
+            if (data != null)
+            {
+              af.parseGroupsFile(data);
+              System.out.println("Added "+data);
+            }
+
+            data = aparser.getValue("annotations");
+            if (data != null)
             {
-              af.parseGroupsFile(groups);
+              af.loadJalviewDataFile(data);
+              System.out.println("Added "+data);
             }
 
+
             String imageName = "unnamed.png";
             while (aparser.getSize() > 1)
             {
@@ -215,12 +230,14 @@ public class Jalview
         // We'll only open the default file if the desktop is visible.
         //////////////////////
           if (
-              !headless &&
-              jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+              !headless
+          && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
+                    )
           {
 
             file = jalview.bin.Cache.getDefault("STARTUP_FILE",
                                                 "http://www.jalview.org/examples/exampleFile.jar");
+
             protocol = "File";
 
             if (file.indexOf("http:") > -1)
@@ -230,18 +247,14 @@ public class Jalview
 
             if (file.endsWith(".jar"))
             {
-              Jalview2XML.LoadJalviewAlign(file);
+              new Jalview2XML().LoadJalviewAlign(file);
             }
             else
             {
-              format = jalview.io.IdentifyFile.Identify(file, protocol);
-              desktop.LoadFile(file, protocol, format);
+              format = new jalview.io.IdentifyFile().Identify(file, protocol);
+              new jalview.io.FileLoader().LoadFile(file, protocol, format);
             }
           }
-
-
-          if (desktop==null)
-            System.exit(0);
     }
 }