X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;fp=src%2Fjalview%2Fbin%2FJalview.java;h=462f5a70511c834a7e49d3fd7deccfab641ce4ab;hb=9623cea766a766683243235557ad48e6f7659e6a;hp=00a042d6b1f6b11d39decfaf70a831f3009ae4d8;hpb=6066400ed6b0fe288ebbea82389f59838a534706;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 00a042d..462f5a7 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -109,7 +109,14 @@ public class Jalview System.setProperty("java.awt.headless", "true"); headless = true; } - Cache.loadProperties(aparser.getValue("props")); // must do this before + String usrPropsFile = aparser.getValue("props"); + Cache.loadProperties(usrPropsFile); // must do this before + if (usrPropsFile != null) + { + System.out.println("CMD [-props " + usrPropsFile + + "] executed successfully!"); + } + // anything else! final String jabawsUrl = aparser.getValue("jabaws"); @@ -118,6 +125,8 @@ public class Jalview try { Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + System.out.println("CMD [-jabaws " + jabawsUrl + + "] executed successfully!"); } catch (MalformedURLException e) { System.err.println("Invalid jabaws parameter: " + jabawsUrl @@ -195,6 +204,11 @@ public class Jalview { startUsageStats(desktop); } + else + { + System.err.println("CMD [-nousagestats] executed successfully!"); + } + if (!aparser.contains("noquestionnaire")) { String url = aparser.getValue("questionnaire"); @@ -204,6 +218,8 @@ public class Jalview // questionnaire Cache.log.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); + System.out.println("CMD questionnaire[-" + url + + "] executed successfully!"); } else { @@ -222,13 +238,20 @@ public class Jalview } } } + else + { + System.err.println("CMD [-noquestionnaire] executed successfully!"); + } desktop.checkForNews(); } - BioJsHTMLOutput.updateBioJS(); + if (!isHeadlessMode()) + { + BioJsHTMLOutput.updateBioJS(); + } String file = null, protocol = null, format = null, data = null; - jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); + jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless); Vector getFeatures = null; // vector of das source nicknames to fetch // features from // loading is done. @@ -334,10 +357,11 @@ 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("Opening file: " + file); + System.out.println("CMD [-open " + file + "] executed successfully!"); if (!file.startsWith("http://")) { @@ -363,7 +387,7 @@ public class Jalview } else { - + Desktop.setCurrentAlignFrame(af); data = aparser.getValue("colour", true); if (data != null) { @@ -379,8 +403,11 @@ public class Jalview ucs.parseAppletParameter(data); cs = ucs; } - - System.out.println("colour is " + data); + else + { + System.out.println("CMD [-color " + data + + "] executed successfully!"); + } af.changeColour(cs); } @@ -390,34 +417,53 @@ public class Jalview { af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); + // System.out.println("Added " + data); + System.out.println("CMD groups[-" + data + + "] executed successfully!"); } data = aparser.getValue("features", true); if (data != null) { af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); + // System.out.println("Added " + data); + System.out.println("CMD [-features " + data + + "] executed successfully!"); } data = aparser.getValue("annotations", true); if (data != null) { af.loadJalviewDataFile(data, null, null, null); - System.out.println("Added " + data); + // System.out.println("Added " + data); + System.out.println("CMD [-annotations " + data + + "] executed successfully!"); } // set or clear the sortbytree flag. if (aparser.contains("sortbytree")) { af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) + { + System.out.println("CMD [-sortbytree] executed successfully!"); + } } if (aparser.contains("no-annotation")) { af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + System.out.println("CMD no-annotation executed successfully!"); + } } if (aparser.contains("nosortbytree")) { af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) + { + System.out + .println("CMD [-nosortbytree] executed successfully!"); + } } data = aparser.getValue("tree", true); if (data != null) @@ -425,13 +471,14 @@ public class Jalview jalview.io.NewickFile fin = null; try { + System.out.println("CMD [-tree " + data + + "] executed successfully!"); 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) { @@ -470,8 +517,10 @@ public class Jalview if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] - { desktop, af }); + executeGroovyScript(groovyscript, new Object[] { desktop, af }); + + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); } else { @@ -518,8 +567,10 @@ public class Jalview } else if (format.equalsIgnoreCase("eps")) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); + File outputFile = new java.io.File(file); + System.out.println("Creating EPS file: " + + outputFile.getAbsolutePath()); + af.createEPS(outputFile); continue; } @@ -601,8 +652,8 @@ 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 { @@ -639,6 +690,7 @@ 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" @@ -810,8 +862,7 @@ 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; @@ -852,15 +903,15 @@ 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) { @@ -925,6 +976,8 @@ public class Jalview } source.addElement(nickname); } + System.out.println("CMD [-dasserver " + data + + "] executed successfully!"); } // loop until no more server entries are found. if (locsources != null && locsources.indexOf('|') > -1) { @@ -963,6 +1016,16 @@ public class Jalview } return ff; } + + public static boolean isHeadlessMode() + { + String isheadless = System.getProperty("java.awt.headless"); + if (isheadless != null && isheadless.equalsIgnoreCase("true")) + { + return true; + } + return false; + } } /** @@ -1114,7 +1177,8 @@ 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); @@ -1131,4 +1195,4 @@ class FeatureFetcher return queued == 0 && running == 0; } -}; +}