X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=272250e40f57232076afa737a076899bd7ce361a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=b599f0f663d4d98fb494bb790752cb9408d7b42f;hpb=dfd8d228991732db0871b4b2a9ea19838d9b45b9;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index b599f0f..272250e 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -24,6 +24,8 @@ import java.io.IOException; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.lang.reflect.Constructor; +import java.net.MalformedURLException; +import java.net.URI; import java.net.URL; import java.net.URLDecoder; import java.security.AllPermission; @@ -81,8 +83,9 @@ public class Jalview + System.getProperty("os.version")); if (new Platform().isAMac()) { - System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview"); - System.setProperty("apple.laf.useScreenMenuBar", "true"); + System.setProperty("com.apple.mrj.application.apple.menu.about.name", + "Jalview"); + System.setProperty("apple.laf.useScreenMenuBar", "true"); } ArgsParser aparser = new ArgsParser(args); @@ -247,7 +250,7 @@ public class Jalview { try { - String viprotocol = Jalview.checkProtocol(vamsasImport); + String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport); if (viprotocol == jalview.io.FormatAdapter.FILE) { inSession = desktop.vamsasImport(new File(vamsasImport)); @@ -315,9 +318,14 @@ public class Jalview } } } + long progress=-1; // Finally, deal with the remaining input data. if (file != null) { + if (!headless) + { + desktop.setProgressBar("Processing commandline arguments...", progress=System.currentTimeMillis()); + } System.out.println("Opening file: " + file); if (!file.startsWith("http://")) @@ -332,7 +340,7 @@ public class Jalview } } - protocol = checkProtocol(file); + protocol = jalview.io.AppletFormatAdapter.checkProtocol(file); format = new jalview.io.IdentifyFile().Identify(file, protocol); @@ -368,20 +376,20 @@ public class Jalview data = aparser.getValue("groups", true); if (data != null) { - af.parseFeaturesFile(data, checkProtocol(data)); + af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); System.out.println("Added " + data); } data = aparser.getValue("features", true); if (data != null) { - af.parseFeaturesFile(data, checkProtocol(data)); + af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); System.out.println("Added " + data); } data = aparser.getValue("annotations", true); if (data != null) { - af.loadJalviewDataFile(data); + af.loadJalviewDataFile(data, null, null, null); System.out.println("Added " + data); } // set or clear the sortbytree flag. @@ -399,7 +407,7 @@ public class Jalview jalview.io.NewickFile fin = null; try { - fin = new jalview.io.NewickFile(data, checkProtocol(data)); + fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); if (fin != null) { af.getViewport().setCurrentTree( @@ -412,7 +420,7 @@ public class Jalview ex.printStackTrace(System.err); } } - // todo - load PDB structure to alignment + // TODO - load PDB structure(s) to alignment JAL-629 // (associate with identical sequence in alignment, or a specified // sequence) @@ -441,7 +449,7 @@ public class Jalview if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, desktop); + executeGroovyScript(groovyscript, new Object[] {desktop,af}); } else { @@ -503,8 +511,15 @@ public class Jalview && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { file = jalview.bin.Cache.getDefault("STARTUP_FILE", - "http://www.jalview.org/examples/exampleFile_2_3.jar"); - + jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_7.jar"); + if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")) + { + // hardwire upgrade of the startup file + file.replace("_2_3.jar","_2_7.jar"); + // and remove the stale setting + jalview.bin.Cache.removeProperty("STARTUP_FILE"); + } + protocol = "File"; if (file.indexOf("http:") > -1) @@ -543,7 +558,7 @@ public class Jalview if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, desktop); + executeGroovyScript(groovyscript, new Object[] { desktop, startUpAlframe}); } else { @@ -553,8 +568,11 @@ public class Jalview } } // and finally, turn off batch mode indicator - if the desktop still exists - if (desktop!=null) + if (desktop != null) { + if (progress!=-1) { + desktop.setProgressBar(null, progress); + } desktop.setInBatchMode(false); } } @@ -600,22 +618,29 @@ public class Jalview * 'Jalview' object. */ private static void executeGroovyScript(String groovyscript, - Object jalviewContext) + Object[] jalviewContext) { if (jalviewContext == null) { System.err .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled."); } - File sfile = null; + /** + * for scripts contained in files + */ + File tfile = null; + /** + * script's URI + */ + URL sfile = null; if (groovyscript.trim().equals("STDIN")) { // read from stdin into a tempfile and execute it try { - sfile = File.createTempFile("jalview", "groovy"); + tfile = File.createTempFile("jalview", "groovy"); PrintWriter outfile = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(sfile))); + new FileOutputStream(tfile))); BufferedReader br = new BufferedReader( new java.io.InputStreamReader(System.in)); String line = null; @@ -630,30 +655,51 @@ public class Jalview } catch (Exception ex) { System.err.println("Failed to read from STDIN into tempfile " - + ((sfile == null) ? "(tempfile wasn't created)" : sfile + + ((tfile == null) ? "(tempfile wasn't created)" : tfile .toString())); ex.printStackTrace(); return; } + try { + sfile = tfile.toURI().toURL(); + } catch (Exception x) + { + System.err.println("Unexpected Malformed URL Exception for temporary file created from STDIN: "+tfile.toURI()); + x.printStackTrace(); + return; + } } else { - sfile = new File(groovyscript); - } - if (!sfile.exists()) - { - System.err.println("File '" + groovyscript + "' does not exist."); - return; - } - if (!sfile.canRead()) - { - System.err.println("File '" + groovyscript + "' cannot be read."); - return; - } - if (sfile.length() < 1) - { - System.err.println("File '" + groovyscript + "' is empty."); - return; + try + { + sfile = new URI(groovyscript).toURL(); + } catch (Exception x) + { + tfile = new File(groovyscript); + if (!tfile.exists()) + { + System.err.println("File '" + groovyscript + "' does not exist."); + return; + } + if (!tfile.canRead()) + { + System.err.println("File '" + groovyscript + "' cannot be read."); + return; + } + if (tfile.length() < 1) + { + System.err.println("File '" + groovyscript + "' is empty."); + return; + } + try { + sfile = tfile.getAbsoluteFile().toURI().toURL(); + } catch (Exception ex) + { + System.err.println("Failed to create a file URL for "+tfile.getAbsoluteFile()); + return; + } + } } boolean success = false; try @@ -669,25 +715,61 @@ public class Jalview * = new Binding(); binding.setVariable("input", "world"); * gse.run("hello.groovy", binding); */ - ClassLoader cl = jalviewContext.getClass().getClassLoader(); + Class[] bspec; + Object[] binding; + int blen = ((jalviewContext[0] == null) ? 0 : 1) + + ((jalviewContext[1] == null) ? 0 : 1); + String cnames[] = new String[] + { "Jalview", "currentAlFrame" }; + bspec = new Class[blen * 2]; + binding = new Object[blen * 2]; + blen = 0; + ClassLoader cl = null; + Map vbinding = new Hashtable(); + for (int jc = 0; jc < jalviewContext.length; jc++) + { + if (jalviewContext[jc] != null) + { + if (cl == null) + { + cl = jalviewContext[jc].getClass().getClassLoader(); + } + bspec[blen * 2] = String.class; + bspec[blen * 2 + 1] = Object.class; + binding[blen * 2] = cnames[jc]; + binding[blen * 2 + 1] = jalviewContext[jc]; + vbinding.put(cnames[jc], jalviewContext[jc]); + blen++; + } + } Class gbindingc = cl.loadClass("groovy.lang.Binding"); - Constructor gbcons = gbindingc.getConstructor(null); - Object gbinding = gbcons.newInstance(null); - java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", - new Class[] - { String.class, Object.class }); - setvar.invoke(gbinding, new Object[] - { "Jalview", jalviewContext }); + Constructor gbcons; + Object gbinding; + try + { + gbcons = gbindingc.getConstructor(Map.class); + gbinding = gbcons.newInstance(vbinding); + } catch (NoSuchMethodException x) + { + // old style binding config - using series of string/object values to + // setVariable. + gbcons = gbindingc.getConstructor(null); + gbinding = gbcons.newInstance(null); + java.lang.reflect.Method setvar = gbindingc.getMethod( + "setVariable", bspec); + setvar.invoke(gbinding, binding); + } + ; Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class }); // String[].class }); Object gse = gseccons.newInstance(new Object[] { new URL[] - { sfile.toURL() } }); // .toString() } }); + { sfile } }); // .toString() } }); java.lang.reflect.Method run = gsec.getMethod("run", new Class[] { String.class, gbindingc }); run.invoke(gse, new Object[] - { sfile.getName(), gbinding }); + { sfile.toString(), gbinding }); success = true; } catch (Exception e) { @@ -700,7 +782,7 @@ public class Jalview { // delete temp file that we made - but only if it was successfully // executed - sfile.delete(); + tfile.delete(); } } @@ -790,17 +872,6 @@ public class Jalview } return ff; } - - private static String checkProtocol(String file) - { - String protocol = jalview.io.FormatAdapter.FILE; - - if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1) - { - protocol = jalview.io.FormatAdapter.URL; - } - return protocol; - } } /**