X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1116fe404ec5733ba508dbdae70a5513b3b29d4f;hb=c766c1829042b039ea2ff56fc05f4a0100c2a73d;hp=a73405424d5743516bd7ae0325cadfdb209a439e;hpb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index a734054..1116fe4 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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"
@@ -75,7 +69,8 @@ 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);
           }
 
@@ -110,8 +105,8 @@ public class Jalview
           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"
@@ -129,7 +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");
@@ -142,6 +137,7 @@ public class Jalview
 
           if(file!=null)
           {
+            System.out.println("Opening file: " + file);
 
             if (!file.startsWith("http://"))
             {
@@ -155,26 +151,72 @@ public class Jalview
 
             protocol = "File";
 
-            if (file.indexOf("http:") > -1)
+            if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1)
             {
               protocol = "URL";
             }
 
+
+
             if (file.endsWith(".jar"))
               format = "Jalview";
             else
               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)
+            if(af==null)
+            {
+              System.out.println("error");
+              return;
+            }
+
+            data = aparser.getValue("colour");
+            if(data!=null)
+            {
+              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.parseGroupsFile(groups);
+              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)
             {
@@ -217,14 +259,18 @@ 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)
@@ -234,13 +280,15 @@ public class Jalview
 
             if (file.endsWith(".jar"))
             {
-              Jalview2XML.LoadJalviewAlign(file);
+              format = "Jalview";
             }
             else
             {
               format = new jalview.io.IdentifyFile().Identify(file, protocol);
-              desktop.LoadFile(file, protocol, format);
             }
+
+            fileLoader.LoadFile(file, protocol, format);
+
           }
     }
 }