Add annoations from the command line

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e244d67..3e8018b 100755 (executable)
--- 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"\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."\r
-                           +"\nThe first lines of the groups file lists the GroupName and GroupColours"\r
-                           +" to be used in the alignment. Use the GROUPNAME label for each of your sequences. "\r
-                           +"\nGROUPNAME<tab>GROUPCOLOUR\n"\r
-                           +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>GROUPNAME\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
+                           +"-annotations FILE\tAdd precalculated annotations to the alignment.\n"\r
+                           +"-features FILE\tUse the given file to mark features on the alignment.\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
@@ -75,7 +69,8 @@ public class Jalview
                            +"-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
+                           +"-eps FILE\tCreate EPS file FILE from alignment."\r
+            +"\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");\r
         System.exit(0);\r
           }\r
 \r
@@ -129,7 +124,7 @@ public class Jalview
         }\r
 \r
 \r
-         String file = null, protocol = null, format = null, groups=null;\r
+         String file = null, protocol = null, format = null, data=null;\r
          jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();\r
 \r
           file = aparser.getValue("open");\r
@@ -169,11 +164,27 @@ public class Jalview
 \r
             AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);\r
 \r
-            groups = aparser.getValue("groups");\r
-            if (groups != null)\r
+            // Must maintain ability to use the groups flag\r
+            data = aparser.getValue("groups");\r
+            if (data != null)\r
             {\r
-              af.parseGroupsFile(groups);\r
+              af.parseGroupsFile(data);\r
+              System.out.println("Added "+data);\r
             }\r
+            data = aparser.getValue("features");\r
+            if (data != null)\r
+            {\r
+              af.parseGroupsFile(data);\r
+              System.out.println("Added "+data);\r
+            }\r
+\r
+            data = aparser.getValue("annotations");\r
+            if (data != null)\r
+            {\r
+              af.loadJalviewDataFile(data);\r
+              System.out.println("Added "+data);\r
+            }\r
+\r
 \r
             String imageName = "unnamed.png";\r
             while (aparser.getSize() > 1)\r