- else\r
- {\r
- if( aparser.contains("help") || aparser.contains("h") )\r
- {\r
- 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. \nGroups file is in the following tab delimited format\n"\r
- +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\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
- +"-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
- +"-msf FILE\tCreate alignment file FILE in MSF format.\n"\r
- +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"\r
- +"-pir FILE\tCreate alignment file FILE in PIR format.\n"\r
- +"-blc FILE\tCreate alignment file FILE in BLC format.\n"\r
- +"-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
- System.exit(0);\r