X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e5ad207ecd5b77f53c32f2e368c344d59c4ab5d0;hb=ec187a3251292293356cc9ee42f90d5c7d5a3a78;hp=1a67c05f9e52e917ad2541025b06286d0fbf8f7d;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 1a67c05..e5ad207 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -57,14 +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."
-                           +"\nThe first lines of the groups file lists the GroupName and GroupColours"
-                           +" to be used in the alignment. Use the GROUPNAME label for each of your sequences. "
-                           +"\nGROUPNAME<tab>GROUPCOLOUR\n"
-                           +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>GROUPNAME\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"
@@ -75,10 +69,12 @@ 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"))
           {
@@ -103,16 +99,14 @@ public class Jalview
             System.exit(0);
           }
 
-        Cache.loadProperties(aparser.getValue("props"));
-
         Desktop desktop = null;
         if( !headless )
         {
           try
           {
             UIManager.setLookAndFeel(
-                   UIManager.getSystemLookAndFeelClassName()
-            //        UIManager.getCrossPlatformLookAndFeelClassName()
+                UIManager.getSystemLookAndFeelClassName()
+                //        UIManager.getCrossPlatformLookAndFeelClassName()
 //"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
 //"javax.swing.plaf.metal.MetalLookAndFeel"
 //"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
@@ -130,7 +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");
@@ -164,18 +158,56 @@ 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)
+            data = aparser.getValue("colour");
+            if(data!=null)
             {
-              af.parseGroupsFile(groups);
+              data.replaceAll("%20", " ");
+
+              jalview.schemes.ColourSchemeI cs =
+                  jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().
+                  getAlignment(), data);
+
+              if(cs == null)
+              {
+                jalview.schemes.UserColourScheme ucs
+                    = new jalview.schemes.UserColourScheme("white");
+                ucs.parseAppletParameter(data);
+                cs = ucs;
+              }
+
+              System.out.println("colour is " + data);
+              af.changeColour( cs );
             }
 
+
+            // Must maintain ability to use the groups flag
+            data = aparser.getValue("groups");
+            if (data != null)
+            {
+              af.parseFeaturesFile(data, protocol);
+              System.out.println("Added "+data);
+            }
+            data = aparser.getValue("features");
+            if (data != null)
+            {
+              af.parseFeaturesFile(data, protocol);
+              System.out.println("Added "+data);
+            }
+
+            data = aparser.getValue("annotations");
+            if (data != null)
+            {
+              af.loadJalviewDataFile(data);
+              System.out.println("Added "+data);
+            }
+
+
             String imageName = "unnamed.png";
             while (aparser.getSize() > 1)
             {
@@ -218,14 +250,18 @@ public class Jalview
           }
 
         // We'll only open the default file if the desktop is visible.
+        // And the user
         //////////////////////
           if (
-              !headless &&
-              jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+              !headless
+          && file==null
+          && 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)
@@ -235,12 +271,12 @@ 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);
             }
           }
     }