X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=d0b3232b47d6658d3841be320b89b40e16b86086;hb=dafd78a3307dd856d328139887036c156b44a203;hp=8ad4cbd0e0568353cd79e4fa85dcaeff3d01d7ec;hpb=e9c752522f4b0b9ef072e7c1f198f9ec59de957d;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 8ad4cbd..d0b3232 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -51,7 +51,6 @@ import java.util.Map; import java.util.Vector; import javax.swing.UIManager; -import javax.swing.UnsupportedLookAndFeelException; /** * Main class for Jalview Application
@@ -68,6 +67,7 @@ public class Jalview // grab all the rights we can the JVM Policy.setPolicy(new Policy() { + @Override public PermissionCollection getPermissions(CodeSource codesource) { Permissions perms = new Permissions(); @@ -75,6 +75,7 @@ public class Jalview return (perms); } + @Override public void refresh() { } @@ -89,6 +90,7 @@ public class Jalview */ public static void main(String[] args) { + System.setSecurityManager(null); System.out.println("Java version: " + System.getProperty("java.version")); System.out.println(System.getProperty("os.arch") + " " @@ -178,7 +180,7 @@ public class Jalview } catch (Exception ex) { } - if (new Platform().isAMac()) + if (Platform.isAMac()) { System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview"); @@ -187,10 +189,10 @@ public class Jalview { UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager .getLookAndFeel()); - } catch (UnsupportedLookAndFeelException e) + } catch (Throwable e) { - // TODO Auto-generated catch block - e.printStackTrace(); + System.err.println("Failed to set QuaQua look and feel: " + + e.toString()); } } @@ -240,8 +242,7 @@ public class Jalview } else { - System.err -.println("CMD [-noquestionnaire] executed successfully!"); + System.err.println("CMD [-noquestionnaire] executed successfully!"); } desktop.checkForNews(); } @@ -358,7 +359,8 @@ public class Jalview { if (!headless) { - desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"), + desktop.setProgressBar(MessageManager + .getString("status.processing_commandline_args"), progress = System.currentTimeMillis()); } System.out.println("CMD [-open " + file + "] executed successfully!"); @@ -377,7 +379,7 @@ public class Jalview protocol = jalview.io.AppletFormatAdapter.checkProtocol(file); - format = new jalview.io.IdentifyFile().Identify(file, protocol); + format = new jalview.io.IdentifyFile().identify(file, protocol); AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); @@ -387,7 +389,7 @@ public class Jalview } else { - + Desktop.setCurrentAlignFrame(af); data = aparser.getValue("colour", true); if (data != null) { @@ -445,8 +447,7 @@ public class Jalview af.getViewport().setSortByTree(true); if (af.getViewport().getSortByTree()) { - System.out -.println("CMD [-sortbytree] executed successfully!"); + System.out.println("CMD [-sortbytree] executed successfully!"); } } if (aparser.contains("no-annotation")) @@ -454,8 +455,7 @@ public class Jalview af.getViewport().setShowAnnotation(false); if (!af.getViewport().isShowAnnotation()) { - System.out -.println("CMD no-annotation executed successfully!"); + System.out.println("CMD no-annotation executed successfully!"); } } if (aparser.contains("nosortbytree")) @@ -516,21 +516,10 @@ public class Jalview { // 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 }); - - System.out.println("CMD groovy[" + groovyscript - + "] executed successfully!"); - } - else - { - System.err - .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " - + groovyscript); - } + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, new Object[] { desktop, af }); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); groovyscript = null; } String imageName = "unnamed.png"; @@ -630,7 +619,7 @@ public class Jalview } else { - format = new jalview.io.IdentifyFile().Identify(file, protocol); + format = new jalview.io.IdentifyFile().identify(file, protocol); } startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, @@ -655,8 +644,8 @@ 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 { @@ -693,6 +682,7 @@ public class Jalview + "-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" @@ -731,6 +721,7 @@ public class Jalview + "\n\n(you can enable or disable usage tracking in the preferences)", new Runnable() { + @Override public void run() { Cache.log @@ -740,6 +731,7 @@ public class Jalview } }, new Runnable() { + @Override public void run() { Cache.log.debug("Not enabling Google Tracking."); @@ -864,8 +856,7 @@ public class Jalview Object[] binding; int blen = ((jalviewContext[0] == null) ? 0 : 1) + ((jalviewContext[1] == null) ? 0 : 1); - String cnames[] = new String[] - { "Jalview", "currentAlFrame" }; + String cnames[] = new String[] { "Jalview", "currentAlFrame" }; bspec = new Class[blen * 2]; binding = new Object[blen * 2]; blen = 0; @@ -906,15 +897,15 @@ public class Jalview } 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 } }); // .toString() } }); - java.lang.reflect.Method run = gsec.getMethod("run", new Class[] - { String.class, gbindingc }); - run.invoke(gse, new Object[] - { sfile.toString(), gbinding }); + Constructor gseccons = gsec + .getConstructor(new Class[] { URL[].class }); // String[].class + // }); + Object gse = gseccons + .newInstance(new Object[] { new URL[] { sfile } }); // .toString() + // } }); + java.lang.reflect.Method run = gsec.getMethod("run", new Class[] { + String.class, gbindingc }); + run.invoke(gse, new Object[] { sfile.toString(), gbinding }); success = true; } catch (Exception e) { @@ -1043,6 +1034,7 @@ public class Jalview class rnabuttonlistener implements ActionListener { + @Override public void actionPerformed(ActionEvent arg0) { System.out.println("Good idea ! "); @@ -1052,6 +1044,7 @@ class rnabuttonlistener implements ActionListener class pbuttonlistener implements ActionListener { + @Override public void actionPerformed(ActionEvent arg0) { @@ -1172,6 +1165,7 @@ class FeatureFetcher new Thread(new Runnable() { + @Override public void run() { synchronized (us) @@ -1180,7 +1174,8 @@ class FeatureFetcher running++; } - af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id); + af.setProgressBar(MessageManager + .getString("status.das_features_being_retrived"), id); af.featureSettings_actionPerformed(null); af.featureSettings.fetchDasFeatures(dasSources, true); af.setProgressBar(null, id);