+
+ private static boolean setCrossPlatformLookAndFeel()
+ {
+ boolean set = false;
+ try
+ {
+ UIManager.setLookAndFeel(
+ UIManager.getCrossPlatformLookAndFeelClassName());
+ set = true;
+ } catch (Exception ex)
+ {
+ System.err.println("Unexpected Look and Feel Exception");
+ ex.printStackTrace();
+ }
+ return set;
+ }
+
+ private static boolean setSystemLookAndFeel()
+ {
+ boolean set = false;
+ try
+ {
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ set = true;
+ } catch (Exception ex)
+ {
+ System.err.println("Unexpected Look and Feel Exception");
+ ex.printStackTrace();
+ }
+ return set;
+ }
+
+ private static boolean setGtkLookAndFeel()
+ {
+ boolean set = false;
+ String laf = "com.sun.java.swing.plaf.gtk.GTKLookAndFeel";
+ try
+ {
+ for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {
+ if (info.getName() != null && info.getName().startsWith("Gtk")) {
+ laf = info.getClassName();
+ break;
+ }
+ }
+ UIManager.setLookAndFeel(laf);
+ set = true;
+ } catch (Exception ex)
+ {
+ System.err.println("Unexpected Look and Feel Exception");
+ ex.printStackTrace();
+ }
+ return set;
+ }
+
+ private static boolean setMetalLookAndFeel()
+ {
+ boolean set = false;
+ String laf = "javax.swing.plaf.metal.MetalLookAndFeel";
+ try
+ {
+ for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {
+ if (info.getName() != null && info.getName().equals("Metal")) {
+ laf = info.getClassName();
+ break;
+ }
+ }
+ UIManager.setLookAndFeel(laf);
+ set = true;
+ } catch (Exception ex)
+ {
+ System.err.println("Unexpected Look and Feel Exception");
+ ex.printStackTrace();
+ }
+ return set;
+ }
+
+ private static boolean setNimbusLookAndFeel()
+ {
+ boolean set = false;
+ String laf = "javax.swing.plaf.nimbus.NimbusLookAndFeel";
+ try
+ {
+ for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {
+ if (info.getName() != null && info.getName().equals("Nimbus")) {
+ laf = info.getClassName();
+ break;
+ }
+ }
+ UIManager.setLookAndFeel(laf);
+ set = true;
+ } catch (Exception ex)
+ {
+ System.err.println("Unexpected Look and Feel Exception");
+ ex.printStackTrace();
+ }
+ return set;
+ }
+
+ private static boolean setMacLookAndFeel()
+ {
+ boolean set = false;
+ LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
+ .getLookAndFeel();
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ if (lookAndFeel != null)
+ {
+ try
+ {
+ UIManager.setLookAndFeel(lookAndFeel);
+ set = true;
+ } catch (Throwable e)
+ {
+ System.err.println(
+ "Failed to set QuaQua look and feel: " + e.toString());
+ }
+ }
+ if (lookAndFeel == null
+ || !(lookAndFeel.getClass().isAssignableFrom(
+ UIManager.getLookAndFeel().getClass()))
+ || !UIManager.getLookAndFeel().getClass().toString()
+ .toLowerCase().contains("quaqua"))
+ {
+ try
+ {
+ System.err.println(
+ "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
+ UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+ set = true;
+ } catch (Throwable e)
+ {
+ System.err
+ .println("Failed to reset look and feel: " + e.toString());
+ }
+ }
+ return set;
+ }
+
+ 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"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ + "-png FILE\tCreate PNG image FILE from alignment.\n"
+ + "-svg FILE\tCreate SVG image FILE from alignment.\n"
+ + "-html FILE\tCreate HTML file from alignment.\n"
+ + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML 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"
+ + "-nonews\tTurn off check for Jalview news.\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"
+ + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\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");
+ }
+