X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=ff1b18099190bfec774bd1928ba20fc8a9325edd;hb=cf82c19425ee457a01c3f1a04aabfb0d9817af6f;hp=b6d6d3f090de5810e2fb587f54a689b7fd5db6ba;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index b6d6d3f..ff1b180 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,8 +20,12 @@ */ 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; @@ -31,6 +35,7 @@ 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; @@ -39,12 +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
@@ -75,11 +79,6 @@ public class Jalview } /** - * Put protein=true for get a protein example - */ - private static boolean protein = false; - - /** * main class for Jalview application * * @param args @@ -104,40 +103,7 @@ 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") @@ -148,6 +114,20 @@ public class Jalview } 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) { @@ -340,7 +320,7 @@ public class Jalview { if (!headless) { - desktop.setProgressBar("Processing commandline arguments...", + desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"), progress = System.currentTimeMillis()); } System.out.println("Opening file: " + file); @@ -450,6 +430,7 @@ public class Jalview { FeatureFetcher ff = startFeatureFetching(getFeatures); if (ff != null) + { while (!ff.allFinished() || af.operationInProgress()) { // wait around until fetching is finished. @@ -461,6 +442,7 @@ public class Jalview } } + } getFeatures = null; // have retrieved features - forget them now. } if (groovyscript != null) @@ -494,6 +476,14 @@ public class Jalview 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); @@ -532,8 +522,7 @@ public class Jalview // //////////////////// if (!headless && file == null && vamsasImport == null - && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) - && protein == true) + && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { file = jalview.bin.Cache.getDefault( "STARTUP_FILE", @@ -607,6 +596,45 @@ public class Jalview } } + 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) { /** @@ -624,7 +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."); } @@ -632,7 +660,7 @@ public class Jalview { public void run() { - Cache.log.info("Not enabling Google Tracking."); + Cache.log.debug("Not enabling Google Tracking."); } }, null, true); desktop.addDialogThread(prompter); @@ -1058,7 +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);