X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=bfa7b1128bb5e1bb6ed9df75fc9f0fe543e14ab0;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=93836569cfcdd80047ea5b6869258d7f4f53e5d8;hpb=8ee6aadb9d5ce7a1922a5b1e8a086d9031ad6a32;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 9383656..bfa7b11 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 2.6) - * 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; @@ -214,6 +216,7 @@ public class Jalview } } } + desktop.checkForNews(); } String file = null, protocol = null, format = null, data = null; @@ -248,7 +251,8 @@ public class Jalview { try { - String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport); + String viprotocol = jalview.io.AppletFormatAdapter + .checkProtocol(vamsasImport); if (viprotocol == jalview.io.FormatAdapter.FILE) { inSession = desktop.vamsasImport(new File(vamsasImport)); @@ -316,9 +320,15 @@ 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://")) @@ -342,158 +352,164 @@ public class Jalview if (af == null) { System.out.println("error"); - return; } - - data = aparser.getValue("colour", true); - if (data != null) + else { - data.replaceAll("%20", " "); - - jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty - .getColour(af.getViewport().getAlignment(), data); - if (cs == null) + data = aparser.getValue("colour", true); + if (data != null) { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - "white"); - ucs.parseAppletParameter(data); - cs = ucs; - } + data.replaceAll("%20", " "); - System.out.println("colour is " + data); - af.changeColour(cs); - } + jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty + .getColour(af.getViewport().getAlignment(), data); - // Must maintain ability to use the groups flag - data = aparser.getValue("groups", true); - if (data != null) - { - af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); - } - data = aparser.getValue("features", true); - if (data != null) - { - af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); - } - - data = aparser.getValue("annotations", true); - if (data != null) - { - af.loadJalviewDataFile(data, null, null, null); - System.out.println("Added " + data); - } - // set or clear the sortbytree flag. - if (aparser.contains("sortbytree")) - { - af.getViewport().setSortByTree(true); - } - if (aparser.contains("nosortbytree")) - { - af.getViewport().setSortByTree(false); - } - data = aparser.getValue("tree", true); - if (data != null) - { - jalview.io.NewickFile fin = null; - try - { - fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - if (fin != null) + if (cs == null) { - af.getViewport().setCurrentTree( - af.ShowNewickTree(fin, data).getTree()); - System.out.println("Added tree " + data); + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( + "white"); + ucs.parseAppletParameter(data); + cs = ucs; } - } catch (IOException ex) - { - System.err.println("Couldn't add tree " + data); - ex.printStackTrace(System.err); - } - } - // TODO - load PDB structure(s) to alignment JAL-629 - // (associate with identical sequence in alignment, or a specified - // sequence) - getFeatures = checkDasArguments(aparser); - if (af != null && getFeatures != null) - { - FeatureFetcher ff = startFeatureFetching(getFeatures); - if (ff != null) - while (!ff.allFinished() || af.operationInProgress()) - { - // wait around until fetching is finished. - try - { - Thread.sleep(100); - } catch (Exception e) - { + System.out.println("colour is " + data); + af.changeColour(cs); + } - } - } - getFeatures = null; // have retrieved features - forget them now. - } - if (groovyscript != null) - { - // Execute the groovy script after we've done all the rendering stuff - // and before any images or figures are generated. - if (jalview.bin.Cache.groovyJarsPresent()) + // Must maintain ability to use the groups flag + data = aparser.getValue("groups", true); + if (data != null) { - System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] {desktop,af}); + af.parseFeaturesFile(data, + jalview.io.AppletFormatAdapter.checkProtocol(data)); + System.out.println("Added " + data); } - else + data = aparser.getValue("features", true); + if (data != null) { - System.err - .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " - + groovyscript); + af.parseFeaturesFile(data, + jalview.io.AppletFormatAdapter.checkProtocol(data)); + System.out.println("Added " + data); } - groovyscript = null; - } - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) - { - format = aparser.nextValue(); - file = aparser.nextValue(); - if (format.equalsIgnoreCase("png")) + data = aparser.getValue("annotations", true); + if (data != null) { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; + af.loadJalviewDataFile(data, null, null, null); + System.out.println("Added " + data); } - else if (format.equalsIgnoreCase("imgMap")) + // set or clear the sortbytree flag. + if (aparser.contains("sortbytree")) { - af.createImageMap(new java.io.File(file), imageName); - System.out.println("Creating image map: " + file); - continue; + af.getViewport().setSortByTree(true); } - else if (format.equalsIgnoreCase("eps")) + if (aparser.contains("nosortbytree")) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); - continue; + af.getViewport().setSortByTree(false); + } + data = aparser.getValue("tree", true); + if (data != null) + { + jalview.io.NewickFile fin = null; + try + { + fin = new jalview.io.NewickFile(data, + jalview.io.AppletFormatAdapter.checkProtocol(data)); + if (fin != null) + { + af.getViewport().setCurrentTree( + af.ShowNewickTree(fin, data).getTree()); + System.out.println("Added tree " + data); + } + } catch (IOException ex) + { + System.err.println("Couldn't add tree " + data); + ex.printStackTrace(System.err); + } } + // TODO - load PDB structure(s) to alignment JAL-629 + // (associate with identical sequence in alignment, or a specified + // sequence) - if (af.saveAlignment(file, format)) + getFeatures = checkDasArguments(aparser); + if (af != null && getFeatures != null) { - System.out.println("Written alignment in " + format - + " format to " + file); + FeatureFetcher ff = startFeatureFetching(getFeatures); + if (ff != null) + while (!ff.allFinished() || af.operationInProgress()) + { + // wait around until fetching is finished. + try + { + Thread.sleep(100); + } catch (Exception e) + { + + } + } + getFeatures = null; // have retrieved features - forget them now. } - else + if (groovyscript != null) { - System.out.println("Error writing file " + file + " in " + format - + " format!!"); + // Execute the groovy script after we've done all the rendering stuff + // and before any images or figures are generated. + if (jalview.bin.Cache.groovyJarsPresent()) + { + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, new Object[] + { desktop, af }); + } + else + { + System.err + .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + + groovyscript); + } + groovyscript = null; } + String imageName = "unnamed.png"; + while (aparser.getSize() > 1) + { + format = aparser.nextValue(); + file = aparser.nextValue(); - } + if (format.equalsIgnoreCase("png")) + { + af.createPNG(new java.io.File(file)); + imageName = (new java.io.File(file)).getName(); + System.out.println("Creating PNG image: " + file); + continue; + } + else if (format.equalsIgnoreCase("imgMap")) + { + af.createImageMap(new java.io.File(file), imageName); + System.out.println("Creating image map: " + file); + continue; + } + else if (format.equalsIgnoreCase("eps")) + { + System.out.println("Creating EPS file: " + file); + af.createEPS(new java.io.File(file)); + continue; + } - while (aparser.getSize() > 0) - { - System.out.println("Unknown arg: " + aparser.nextValue()); + if (af.saveAlignment(file, format)) + { + System.out.println("Written alignment in " + format + + " format to " + file); + } + else + { + System.out.println("Error writing file " + file + " in " + + format + " format!!"); + } + + } + + while (aparser.getSize() > 0) + { + System.out.println("Unknown arg: " + aparser.nextValue()); + } } } AlignFrame startUpAlframe = null; @@ -503,8 +519,18 @@ public class Jalview if (!headless && file == null && vamsasImport == null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { - file = jalview.bin.Cache.getDefault("STARTUP_FILE", - "http://www.jalview.org/examples/exampleFile_2_3.jar"); + file = jalview.bin.Cache.getDefault( + "STARTUP_FILE", + 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"; @@ -544,7 +570,8 @@ public class Jalview if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] { desktop, startUpAlframe}); + executeGroovyScript(groovyscript, new Object[] + { desktop, startUpAlframe }); } else { @@ -556,6 +583,10 @@ public class Jalview // and finally, turn off batch mode indicator - if the desktop still exists if (desktop != null) { + if (progress != -1) + { + desktop.setProgressBar(null, progress); + } desktop.setInBatchMode(false); } } @@ -588,7 +619,7 @@ public class Jalview Cache.log.info("Not enabling Google Tracking."); } }, null, true); - SwingUtilities.invokeLater(prompter); + desktop.addDialogThread(prompter); } /** @@ -608,15 +639,22 @@ public class Jalview 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; @@ -631,30 +669,56 @@ 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 @@ -672,44 +736,59 @@ public class Jalview */ 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; - for (int jc=0;jc