/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\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."\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
+"-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
}\r
\r
Desktop desktop = null;\r
- if( !headless )\r
+\r
+\r
+ try\r
{\r
- try\r
- {\r
- UIManager.setLookAndFeel(\r
- UIManager.getSystemLookAndFeelClassName()\r
- // UIManager.getCrossPlatformLookAndFeelClassName()\r
-//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
-//"javax.swing.plaf.metal.MetalLookAndFeel"\r
-//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
-//"com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
-\r
- );\r
- }\r
- catch (Exception ex)\r
+ UIManager.setLookAndFeel(\r
+ UIManager.getSystemLookAndFeelClassName()\r
+ // UIManager.getCrossPlatformLookAndFeelClassName()\r
+ //"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
+ //"javax.swing.plaf.metal.MetalLookAndFeel"\r
+ //"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
+ //"com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
+\r
+ );\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+\r
+ if (!headless)\r
{\r
+ desktop = new Desktop();\r
+ desktop.setVisible(true);\r
+ desktop.discoverer.start();\r
}\r
\r
- desktop = new Desktop();\r
- desktop.setVisible(true);\r
- desktop.discoverer.start();\r
- }\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
\r
if(file!=null)\r
{\r
+ System.out.println("Opening file: " + file);\r
\r
if (!file.startsWith("http://"))\r
{\r
\r
protocol = "File";\r
\r
- if (file.indexOf("http:") > -1)\r
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1)\r
{\r
protocol = "URL";\r
}\r
\r
+\r
+\r
if (file.endsWith(".jar"))\r
format = "Jalview";\r
else\r
format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
\r
- System.out.println("Opening: " + format + " file " + file);\r
+\r
\r
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);\r
\r
- groups = aparser.getValue("groups");\r
- if (groups != null)\r
+ if(af==null)\r
+ {\r
+ System.out.println("error");\r
+ return;\r
+ }\r
+\r
+ data = aparser.getValue("colour");\r
+ if(data!=null)\r
+ {\r
+ data.replaceAll("%20", " ");\r
+\r
+ jalview.schemes.ColourSchemeI cs =\r
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().\r
+ getAlignment(), data);\r
+\r
+ if(cs == null)\r
+ {\r
+ jalview.schemes.UserColourScheme ucs\r
+ = new jalview.schemes.UserColourScheme("white");\r
+ ucs.parseAppletParameter(data);\r
+ cs = ucs;\r
+ }\r
+\r
+ System.out.println("colour is " + data);\r
+ af.changeColour( cs );\r
+ }\r
+\r
+\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.parseFeaturesFile(data, protocol);\r
+ System.out.println("Added "+data);\r
+ }\r
+ data = aparser.getValue("features");\r
+ if (data != null)\r
+ {\r
+ af.parseFeaturesFile(data, protocol);\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
{\r
}\r
\r
// We'll only open the default file if the desktop is visible.\r
+ // And the user\r
//////////////////////\r
if (\r
!headless\r
+ && file==null\r
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)\r
)\r
{\r
\r
if (file.endsWith(".jar"))\r
{\r
- new Jalview2XML().LoadJalviewAlign(file);\r
+ format = "Jalview";\r
}\r
else\r
{\r
format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
- desktop.LoadFile(file, protocol, format);\r
}\r
+\r
+ fileLoader.LoadFile(file, protocol, format);\r
+\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff