X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=ff5df66a1f09772281c00f65d56607f07d33660f;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=772f99eb090858939b318d32cd0474311844a91b;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 772f99e..ff5df66 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,24 +1,31 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; -import java.awt.FlowLayout; -import java.awt.Frame; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; + import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.BufferedReader; @@ -37,12 +44,11 @@ import java.security.CodeSource; import java.security.PermissionCollection; import java.security.Permissions; import java.security.Policy; -import java.util.*; - -import javax.swing.*; +import java.util.Hashtable; +import java.util.Map; +import java.util.Vector; -import jalview.gui.*; -import jalview.util.Platform; +import javax.swing.UIManager; /** * Main class for Jalview Application
@@ -71,7 +77,6 @@ public class Jalview } }); } - protected static boolean proteine; /** * main class for Jalview application @@ -98,44 +103,31 @@ public class Jalview if (aparser.contains("help") || aparser.contains("h")) { - 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" - + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" - + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" - + "-tree FILE\tLoad the given newick format tree file onto 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" - + "-msf FILE\tCreate alignment file FILE in MSF format.\n" - + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" - + "-pir FILE\tCreate alignment file FILE in PIR format.\n" - + "-blc FILE\tCreate alignment file FILE in BLC format.\n" - + "-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.\n" - + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n" - + "-noquestionnaire\tTurn off questionnaire check.\n" - + "-nousagestats\tTurn off google analytics tracking for this session.\n" - + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n" - // + - // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)" - + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" - + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" - + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" - + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" - // + - // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n" - // + "-vses vamsas-session\tJoin session with given URN\n" - + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n" - + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); + showUsage(); System.exit(0); } + if (aparser.contains("nodisplay") || aparser.contains("nogui") + || aparser.contains("headless")) + { + System.setProperty("java.awt.headless", "true"); + headless = true; + } Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! + + final String jabawsUrl = aparser.getValue("jabaws"); + if (jabawsUrl != null) + { + try + { + Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + } catch (MalformedURLException e) + { + System.err.println("Invalid jabaws parameter: " + jabawsUrl + + " ignored"); + } + } + String defs = aparser.getValue("setprop"); while (defs != null) { @@ -153,16 +145,13 @@ public class Jalview } defs = aparser.getValue("setprop"); } - if (aparser.contains("nodisplay")) - { - System.setProperty("java.awt.headless", "true"); - } if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) { headless = true; } - + System.setProperty("http.agent", + "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); try { Cache.initLogger(); @@ -221,6 +210,7 @@ public class Jalview } } } + desktop.checkForNews(); } String file = null, protocol = null, format = null, data = null; @@ -255,7 +245,8 @@ 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)); @@ -323,13 +314,14 @@ public class Jalview } } } - long progress=-1; + long progress = -1; // Finally, deal with the remaining input data. if (file != null) { if (!headless) { - desktop.setProgressBar("Processing commandline arguments...", progress=System.currentTimeMillis()); + desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"), + progress = System.currentTimeMillis()); } System.out.println("Opening file: " + file); @@ -354,197 +346,197 @@ 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); - } - - // 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); - } + jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty + .getColour(af.getViewport().getAlignment(), 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.loadJalviewDataFile(data, null, null, null); + System.out.println("Added " + data); + } + // set or clear the sortbytree flag. + if (aparser.contains("sortbytree")) { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; + af.getViewport().setSortByTree(true); } - else if (format.equalsIgnoreCase("imgMap")) + if (aparser.contains("nosortbytree")) { - af.createImageMap(new java.io.File(file), imageName); - System.out.println("Creating image map: " + file); - continue; + af.getViewport().setSortByTree(false); } - else if (format.equalsIgnoreCase("eps")) + data = aparser.getValue("tree", true); + if (data != null) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); - continue; + 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("svg")) + { + File imageFile = new java.io.File(file); + imageName = imageFile.getName(); + af.createSVG(imageFile); + System.out.println("Creating SVG 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; // We'll only open the default file if the desktop is visible. // And the user // //////////////////// - - JFrame Typechooser =new JFrame("choose molecule type"); - FlowLayout fl = new FlowLayout(); - Typechooser.setLayout(fl); - Typechooser.setSize(400,400); - Typechooser.setDefaultCloseOperation(Typechooser.DISPOSE_ON_CLOSE); - JLabel label = new JLabel("What would you open ? "); - JButton rnabutton = new JButton("RNA molecule"); - JButton pbutton = new JButton("Proteine molecule"); - - pbutton.addActionListener(new pbuttonlistener()); - rnabutton.addActionListener(new rnabuttonlistener()); - Typechooser.getContentPane().add(label); - Typechooser.getContentPane().add(rnabutton); - Typechooser.getContentPane().add(pbutton); - Typechooser.setVisible(true); - - - - + if (!headless && file == null && vamsasImport == null - && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && proteine == true) + && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { - file = jalview.bin.Cache.getDefault("STARTUP_FILE", - jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_7.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 + 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) @@ -583,7 +575,8 @@ 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 { @@ -595,14 +588,53 @@ public class Jalview // and finally, turn off batch mode indicator - if the desktop still exists if (desktop != null) { - if (progress!=-1) { + if (progress != -1) + { desktop.setProgressBar(null, progress); } desktop.setInBatchMode(false); } } - - + + private static void showUsage() + { + 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" + + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" + + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" + + "-tree FILE\tLoad the given newick format tree file onto 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" + + "-msf FILE\tCreate alignment file FILE in MSF format.\n" + + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" + + "-pir FILE\tCreate alignment file FILE in PIR format.\n" + + "-blc FILE\tCreate alignment file FILE in BLC format.\n" + + "-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.\n" + + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n" + + "-noquestionnaire\tTurn off questionnaire check.\n" + + "-nousagestats\tTurn off google analytics tracking for this session.\n" + + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n" + // + + // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)" + + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n" + + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" + + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" + + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" + + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" + // + + // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n" + // + "-vses vamsas-session\tJoin session with given URN\n" + + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n" + + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); + } + private static void startUsageStats(final Desktop desktop) { /** @@ -620,7 +652,7 @@ public class Jalview public void run() { Cache.log - .info("Initialising googletracker for usage stats."); + .debug("Initialising googletracker for usage stats."); Cache.initGoogleTracker(); Cache.log.debug("Tracking enabled."); } @@ -628,10 +660,10 @@ public class Jalview { public void run() { - Cache.log.info("Not enabling Google Tracking."); + Cache.log.debug("Not enabling Google Tracking."); } }, null, true); - SwingUtilities.invokeLater(prompter); + desktop.addDialogThread(prompter); } /** @@ -686,11 +718,14 @@ public class Jalview ex.printStackTrace(); return; } - try { + try + { sfile = tfile.toURI().toURL(); } catch (Exception x) { - System.err.println("Unexpected Malformed URL Exception for temporary file created from STDIN: "+tfile.toURI()); + System.err + .println("Unexpected Malformed URL Exception for temporary file created from STDIN: " + + tfile.toURI()); x.printStackTrace(); return; } @@ -718,11 +753,13 @@ public class Jalview System.err.println("File '" + groovyscript + "' is empty."); return; } - try { - sfile = tfile.getAbsoluteFile().toURI().toURL(); + try + { + sfile = tfile.getAbsoluteFile().toURI().toURL(); } catch (Exception ex) { - System.err.println("Failed to create a file URL for "+tfile.getAbsoluteFile()); + System.err.println("Failed to create a file URL for " + + tfile.getAbsoluteFile()); return; } } @@ -910,18 +947,21 @@ public class Jalview * */ -class rnabuttonlistener implements ActionListener{ - public void actionPerformed(ActionEvent arg0) { - System.out.println("Good idea ! "); +class rnabuttonlistener implements ActionListener +{ + public void actionPerformed(ActionEvent arg0) + { + System.out.println("Good idea ! "); - } + } } -class pbuttonlistener implements ActionListener{ - public void actionPerformed(ActionEvent arg0) { - - - } +class pbuttonlistener implements ActionListener +{ + public void actionPerformed(ActionEvent arg0) + { + + } } class ArgsParser @@ -1046,7 +1086,7 @@ class FeatureFetcher running++; } - af.setProgressBar("DAS features being retrieved...", id); + af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id); af.featureSettings_actionPerformed(null); af.featureSettings.fetchDasFeatures(dasSources, true); af.setProgressBar(null, id); @@ -1062,7 +1102,5 @@ class FeatureFetcher { return queued == 0 && running == 0; } - - - + };