X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=ed51cee49e9be2ccdb3e13ce8c36bb142c0dee84;hb=29ea678048298c63f589674ff35f6c026497550c;hp=faf98db719b17726410ba474a9d55f24b0190d47;hpb=2a6fdd3e8c315282db909efb520312505a0ceba1;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index faf98db..ed51cee 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,17 +1,17 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * * This program 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 2 * of the License, or (at your option) any later version. - * + * * This program 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 this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA @@ -25,6 +25,7 @@ import java.io.IOException; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.lang.reflect.Constructor; +import java.net.URL; import java.util.*; import javax.swing.*; @@ -79,19 +80,38 @@ public class Jalview + "-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." - + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires." - + "-noquestionnaire\tTurn off questionnaire check." - + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments." - + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them." - + "-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"); + + "-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"); System.exit(0); } - Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! - + String defs = aparser.getValue("setprop"); + while (defs!=null) + { + int p = defs.indexOf('='); + if ( p==-1 ) + { + System.err.println("Ignoring invalid setprop argument : "+defs); + } else { + System.out.println("Executing setprop argument: "+defs); + // DISABLED FOR SECURITY REASONS + // Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + } + defs = aparser.getValue("setprop"); + } if (aparser.contains("nodisplay")) { System.setProperty("java.awt.headless", "true"); @@ -125,6 +145,7 @@ public class Jalview // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel" // "com.sun.java.swing.plaf.motif.MotifLookAndFeel" + ); } catch (Exception ex) { @@ -134,6 +155,13 @@ public class Jalview desktop = new Desktop(); desktop.setVisible(true); desktop.discoverer.start(); + if (!aparser.contains("nousagestats") && Cache.getDefault("USAGESTATS", true)) { + Cache.log.info("Initialising googletracker for usage stats."); + Cache.initGoogleTracker(); + Cache.log.debug("Tracking enabled."); + } else { + Cache.log.info("Not enabling Google Tracking."); + } if (!aparser.contains("noquestionnaire")) { String url = aparser.getValue("questionnaire"); @@ -165,9 +193,11 @@ public class Jalview String file = null, protocol = null, format = null, data = null; jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); - Vector getFeatures = null; // vector of das source nicknames to fetch features from + Vector getFeatures = null; // vector of das source nicknames to fetch + // features from // loading is done. - String groovyscript = null; // script to execute after all loading is completed one way or another + String groovyscript = null; // script to execute after all loading is + // completed one way or another // extract groovy argument and execute if necessary groovyscript = aparser.getValue("groovy"); file = aparser.getValue("open"); @@ -177,7 +207,62 @@ public class Jalview System.out.println("No files to open!"); System.exit(1); } - + String vamsasImport=aparser.getValue("vdoc"),vamsasSession=aparser.getValue("vsess"); + if (vamsasImport!=null || vamsasSession!=null) + { + if (desktop==null || headless) + { + System.out.println("Headless vamsas sessions not yet supported. Sorry."); + System.exit(1); + } + // if we have a file, start a new session and import it. + boolean inSession = false; + if (vamsasImport!=null) + { + try { + String viprotocol = Jalview.checkProtocol(vamsasImport); + if (viprotocol == jalview.io.FormatAdapter.FILE) { + inSession = desktop.vamsasImport(new File(vamsasImport)); + } else if (viprotocol == jalview.io.FormatAdapter.URL) { + inSession = desktop.vamsasImport(new URL(vamsasImport)); + } + + } catch (Exception e) + { + System.err.println("Exeption when importing "+vamsasImport+" as a vamsas document."); + e.printStackTrace(); + } + if (!inSession) { + System.err.println("Failed to import "+vamsasImport+" as a vamsas document."); + } else { + System.out.println("Imported Successfully into new session "+desktop.getVamsasApplication().getCurrentSession()); + } + } + if (vamsasSession!=null) { + if (vamsasImport!=null) { + // close the newly imported session and import the Jalview specific remnants into the new session later on. + desktop.vamsasStop_actionPerformed(null); + } + // now join the new session + try { + if (desktop.joinVamsasSession(vamsasSession)) { + System.out.println("Successfully joined vamsas session "+vamsasSession); + } else { + System.err.println("WARNING: Failed to join vamsas session "+vamsasSession); + } + } catch (Exception e) + { + System.err.println("ERROR: Failed to join vamsas session "+vamsasSession); + e.printStackTrace(); + } + if (vamsasImport!=null) { + // the Jalview specific remnants can now be imported into the new session at the user's leisure. + Cache.log.info("Skipping Push for import of data into existing vamsas session."); // TODO: enable this when debugged + // desktop.getVamsasApplication().push_update(); + } + } + } + // Finally, deal with the remaining input data. if (file != null) { System.out.println("Opening file: " + file); @@ -247,6 +332,15 @@ public class Jalview af.loadJalviewDataFile(data); 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"); if (data != null) { @@ -267,31 +361,36 @@ public class Jalview } } getFeatures = checkDasArguments(aparser); - if (af != null && getFeatures!=null) + if (af != null && getFeatures != null) { - startFeatureFetching(getFeatures); + startFeatureFetching(getFeatures); // need to block until fetching is complete. while (af.operationInProgress()) { // wait around until fetching is finished. - try { + try + { Thread.sleep(10); } catch (Exception e) { - + } } } - if (groovyscript!=null) + if (groovyscript != null) { - // Execute the groovy script after we've done all the rendering stuff + // 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); + System.out.println("Executing script " + groovyscript); executeGroovyScript(groovyscript, desktop); - } else { - System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript); + } + else + { + System.err + .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + + groovyscript); } groovyscript = null; } @@ -343,7 +442,7 @@ public class Jalview // We'll only open the default file if the desktop is visible. // And the user // //////////////////// - if (!headless && file == null + if (!headless && file == null && vamsasImport==null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { file = jalview.bin.Cache.getDefault("STARTUP_FILE", @@ -371,169 +470,202 @@ public class Jalview // extract groovy arguments before anything else. } // Once all loading is done. Retrieve features. - if (getFeatures!=null) + if (getFeatures != null) { - if (startUpAlframe!=null) + if (startUpAlframe != null) { startFeatureFetching(getFeatures); } } - if (groovyscript!=null) + if (groovyscript != null) { if (jalview.bin.Cache.groovyJarsPresent()) { - System.out.println("Executing script "+groovyscript); + System.out.println("Executing script " + groovyscript); executeGroovyScript(groovyscript, desktop); - } else { - System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript); + } + else + { + System.err + .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + + groovyscript); } } // Once all other stuff is done, execute any groovy scripts (in order) } + /** * Locate the given string as a file and pass it to the groovy interpreter. - * @param groovyscript the script to execute - * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object. + * + * @param groovyscript + * the script to execute + * @param jalviewContext + * the Jalview Desktop object passed in to the groovy binding + * as the 'Jalview' object. */ - private static void executeGroovyScript(String groovyscript, Object jalviewContext) + private static void executeGroovyScript(String groovyscript, + Object jalviewContext) { - if (jalviewContext==null) + if (jalviewContext == null) { - System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled."); + System.err + .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled."); } File sfile = null; if (groovyscript.trim().equals("STDIN")) { // read from stdin into a tempfile and execute it - try { + try + { sfile = File.createTempFile("jalview", "groovy"); - PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(sfile))); - BufferedReader br = new BufferedReader(new java.io.InputStreamReader(System.in)); - String line=null; - while ((line=br.readLine())!=null) + PrintWriter outfile = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(sfile))); + BufferedReader br = new BufferedReader( + new java.io.InputStreamReader(System.in)); + String line = null; + while ((line = br.readLine()) != null) { - outfile.write(line+"\n"); + outfile.write(line + "\n"); } br.close(); outfile.flush(); outfile.close(); - + } catch (Exception ex) { - System.err.println("Failed to read from STDIN into tempfile "+((sfile==null) ? "(tempfile wasn't created)" : sfile.toString())); + System.err.println("Failed to read from STDIN into tempfile " + + ((sfile == null) ? "(tempfile wasn't created)" : sfile + .toString())); ex.printStackTrace(); return; } - } else { + } + else + { sfile = new File(groovyscript); } if (!sfile.exists()) { - System.err.println("File '"+groovyscript+"' does not exist."); + System.err.println("File '" + groovyscript + "' does not exist."); return; } if (!sfile.canRead()) { - System.err.println("File '"+groovyscript+"' cannot be read."); + System.err.println("File '" + groovyscript + "' cannot be read."); return; } - if (sfile.length()<1) + if (sfile.length() < 1) { - System.err.println("File '"+groovyscript+"' is empty."); + System.err.println("File '" + groovyscript + "' is empty."); return; } boolean success = false; - try { - /* The following code performs the GroovyScriptEngine invocation using reflection, - * and is equivalent to this fragment from the embedding groovy documentation on - * the groovy site: - * - import groovy.lang.Binding; - import groovy.util.GroovyScriptEngine; - - String[] roots = new String[] { "/my/groovy/script/path" }; - GroovyScriptEngine gse = new GroovyScriptEngine(roots); - Binding binding = new Binding(); - binding.setVariable("input", "world"); - gse.run("hello.groovy", binding); - * - */ - ClassLoader cl = jalviewContext.getClass().getClassLoader(); - 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}); - Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); - Constructor gseccons = gsec.getConstructor(new Class[] { String[].class }); - Object gse = gseccons.newInstance(new Object[] { new String[] { sfile.toURL().toString() } }); - java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc }); - run.invoke(gse, new Object[] { sfile.toURL().toString(), gbinding }); - success = true; + try + { + /* + * The following code performs the GroovyScriptEngine invocation using + * reflection, and is equivalent to this fragment from the embedding + * groovy documentation on the groovy site: import + * groovy.lang.Binding; import groovy.util.GroovyScriptEngine; + * + * String[] roots = new String[] { "/my/groovy/script/path" }; + * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding = + * new Binding(); binding.setVariable("input", "world"); + * gse.run("hello.groovy", binding); + */ + ClassLoader cl = jalviewContext.getClass().getClassLoader(); + 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 }); + 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() } }); + java.lang.reflect.Method run = gsec.getMethod("run", new Class[] + { String.class, gbindingc }); + run.invoke(gse, new Object[] + { sfile.getName(), gbinding }); + success = true; } catch (Exception e) { - System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script."); + System.err.println("Exception Whilst trying to execute file " + sfile + + " as a groovy script."); e.printStackTrace(System.err); - + } if (success && groovyscript.equals("STDIN")) { - // delete temp file that we made - but only if it was successfully executed + // delete temp file that we made - but only if it was successfully + // executed sfile.delete(); } } + /** * Check commandline for any das server definitions or any fetchfrom switches + * * @return vector of DAS source nicknames to retrieve from */ private static Vector checkDasArguments(ArgsParser aparser) { - Vector source=null; + Vector source = null; String data; String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE); - while ((data = aparser.getValue("dasserver"))!=null) + while ((data = aparser.getValue("dasserver")) != null) { String nickname = null; String url = null; + boolean seq=false,feat=true; int pos = data.indexOf('='); + // determine capabilities if (pos > 0) { nickname = data.substring(0, pos); } url = data.substring(pos + 1); - if (url != null && url.startsWith("http:")) + if (url != null && (url.startsWith("http:") || url.startsWith("sequence:http:"))) { if (nickname == null) { nickname = url; } - if (locsources==null) + if (locsources == null) { - locsources=""; - } else { - locsources+="\t"; + locsources = ""; } - locsources=locsources+nickname+"|"+url; + else + { + locsources += "\t"; + } + locsources = locsources + nickname + "|" + url; System.err .println("NOTE! dasserver parameter not yet really supported (got args of " + nickname + "|" + url); - if (source==null) + if (source == null) { source = new Vector(); } source.addElement(nickname); } } // loop until no more server entries are found. - if (locsources!=null && locsources.indexOf('|')>-1) + if (locsources != null && locsources.indexOf('|') > -1) { - Cache.log.debug("Setting local source list in properties file to:\n"+locsources); + Cache.log.debug("Setting local source list in properties file to:\n" + + locsources); Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources); } - while ((data = aparser.getValue("fetchfrom"))!=null) + while ((data = aparser.getValue("fetchfrom")) != null) { - System.out.println("adding source '"+data+"'"); - if (source==null) + System.out.println("adding source '" + data + "'"); + if (source == null) { source = new Vector(); } @@ -541,24 +673,27 @@ public class Jalview } return source; } + /** * start a feature fetcher for every alignment frame + * * @param dasSources */ private static void startFeatureFetching(final Vector dasSources) { AlignFrame afs[] = Desktop.getAlignframes(); - if (afs==null || afs.length==0) + if (afs == null || afs.length == 0) { return; } - for (int i = 0; i