X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3e8018bfc44d155f5a50bb1d0d791d8c6904b898;hb=aca26588a9857a2b71d7ca2450676521ca874eae;hp=e244d6742876dc33b7410e3a1d449010477e83fa;hpb=c09d2d06c71e7865bf36df59c9363a8fa698d7cd;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e244d67..3e8018b 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"
@@ -75,7 +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);
           }
 
@@ -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");
@@ -169,11 +164,27 @@ public class Jalview
 
             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(groups);
+              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.loadJalviewDataFile(data);
+              System.out.println("Added "+data);
+            }
+
 
             String imageName = "unnamed.png";
             while (aparser.getSize() > 1)