From: amwaterhouse Date: Tue, 4 Apr 2006 12:53:14 +0000 (+0000) Subject: Add annoations from the command line X-Git-Tag: Release_2_08~70 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aca26588a9857a2b71d7ca2450676521ca874eae;p=jalview.git Add annoations from the command line --- 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. " - +"\nGROUPNAMEGROUPCOLOUR\n" - +"TEXTSEQUENCE_IDSEQUENCE_INDEXSTART_RESIDUEEND_RESIDUEGROUPNAME\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)