X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=362b15eb1fb880171a91d11df281be28c544bd5f;hb=c9f21b2f940ed83ee018f7651302e7d3cea489c5;hp=999e6ade6bdfe05f6677e6aed1794fa34a3e0c90;hpb=e66322bfd895b80f19ae39ec0367a6c1cd4a93a3;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 999e6ad..362b15e 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -250,7 +250,8 @@ public class Jalview { try { - String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport); + String viprotocol = jalview.io.AppletFormatAdapter + .checkProtocol(vamsasImport); if (viprotocol == jalview.io.FormatAdapter.FILE) { inSession = desktop.vamsasImport(new File(vamsasImport)); @@ -318,13 +319,14 @@ public class Jalview } } } - long progress=-1; + long progress = -1; // Finally, deal with the remaining input data. if (file != null) { if (!headless) { - desktop.setProgressBar("Processing commandline arguments...", progress=System.currentTimeMillis()); + desktop.setProgressBar("Processing commandline arguments...", + progress = System.currentTimeMillis()); } System.out.println("Opening file: " + file); @@ -349,158 +351,164 @@ public class Jalview if (af == null) { System.out.println("error"); - return; } - - data = aparser.getValue("colour", true); - if (data != null) + else { - data.replaceAll("%20", " "); - jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty - .getColour(af.getViewport().getAlignment(), data); - - if (cs == null) + data = aparser.getValue("colour", true); + if (data != null) { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - "white"); - ucs.parseAppletParameter(data); - cs = ucs; - } + data.replaceAll("%20", " "); - System.out.println("colour is " + data); - af.changeColour(cs); - } - - // Must maintain ability to use the groups flag - data = aparser.getValue("groups", true); - if (data != null) - { - af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); - } - data = aparser.getValue("features", true); - if (data != null) - { - af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); - } + jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty + .getColour(af.getViewport().getAlignment(), data); - data = aparser.getValue("annotations", true); - if (data != null) - { - af.loadJalviewDataFile(data, null, null, null); - 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", true); - if (data != null) - { - jalview.io.NewickFile fin = null; - try - { - fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - if (fin != null) + if (cs == null) { - af.getViewport().setCurrentTree( - af.ShowNewickTree(fin, data).getTree()); - System.out.println("Added tree " + data); + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( + "white"); + ucs.parseAppletParameter(data); + cs = ucs; } - } catch (IOException ex) - { - System.err.println("Couldn't add tree " + data); - ex.printStackTrace(System.err); - } - } - // TODO - load PDB structure(s) to alignment JAL-629 - // (associate with identical sequence in alignment, or a specified - // sequence) - getFeatures = checkDasArguments(aparser); - if (af != null && getFeatures != null) - { - FeatureFetcher ff = startFeatureFetching(getFeatures); - if (ff != null) - while (!ff.allFinished() || af.operationInProgress()) - { - // wait around until fetching is finished. - try - { - Thread.sleep(100); - } catch (Exception e) - { + System.out.println("colour is " + data); + af.changeColour(cs); + } - } - } - getFeatures = null; // have retrieved features - forget them now. - } - if (groovyscript != null) - { - // 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()) + // Must maintain ability to use the groups flag + data = aparser.getValue("groups", true); + if (data != null) { - System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] {desktop,af}); + af.parseFeaturesFile(data, + jalview.io.AppletFormatAdapter.checkProtocol(data)); + System.out.println("Added " + data); } - else + data = aparser.getValue("features", true); + if (data != null) { - System.err - .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " - + groovyscript); + af.parseFeaturesFile(data, + jalview.io.AppletFormatAdapter.checkProtocol(data)); + System.out.println("Added " + data); } - groovyscript = null; - } - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) - { - format = aparser.nextValue(); - file = aparser.nextValue(); - if (format.equalsIgnoreCase("png")) + data = aparser.getValue("annotations", true); + if (data != null) { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; + af.loadJalviewDataFile(data, null, null, null); + System.out.println("Added " + data); } - else if (format.equalsIgnoreCase("imgMap")) + // set or clear the sortbytree flag. + if (aparser.contains("sortbytree")) { - af.createImageMap(new java.io.File(file), imageName); - System.out.println("Creating image map: " + file); - continue; + af.getViewport().setSortByTree(true); } - else if (format.equalsIgnoreCase("eps")) + if (aparser.contains("nosortbytree")) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); - continue; + af.getViewport().setSortByTree(false); } + data = aparser.getValue("tree", true); + if (data != null) + { + jalview.io.NewickFile fin = null; + try + { + 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) + { + System.err.println("Couldn't add tree " + data); + ex.printStackTrace(System.err); + } + } + // TODO - load PDB structure(s) to alignment JAL-629 + // (associate with identical sequence in alignment, or a specified + // sequence) - if (af.saveAlignment(file, format)) + getFeatures = checkDasArguments(aparser); + if (af != null && getFeatures != null) { - System.out.println("Written alignment in " + format - + " format to " + file); + FeatureFetcher ff = startFeatureFetching(getFeatures); + if (ff != null) + while (!ff.allFinished() || af.operationInProgress()) + { + // wait around until fetching is finished. + try + { + Thread.sleep(100); + } catch (Exception e) + { + + } + } + getFeatures = null; // have retrieved features - forget them now. } - else + if (groovyscript != null) { - System.out.println("Error writing file " + file + " in " + format - + " format!!"); + // 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 }); + } + else + { + System.err + .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + + groovyscript); + } + groovyscript = null; } + String imageName = "unnamed.png"; + while (aparser.getSize() > 1) + { + format = aparser.nextValue(); + file = aparser.nextValue(); - } + if (format.equalsIgnoreCase("png")) + { + af.createPNG(new java.io.File(file)); + imageName = (new java.io.File(file)).getName(); + System.out.println("Creating PNG image: " + file); + continue; + } + else if (format.equalsIgnoreCase("imgMap")) + { + af.createImageMap(new java.io.File(file), imageName); + System.out.println("Creating image map: " + file); + continue; + } + else if (format.equalsIgnoreCase("eps")) + { + System.out.println("Creating EPS file: " + file); + af.createEPS(new java.io.File(file)); + continue; + } - while (aparser.getSize() > 0) - { - System.out.println("Unknown arg: " + aparser.nextValue()); + if (af.saveAlignment(file, format)) + { + System.out.println("Written alignment in " + format + + " format to " + file); + } + else + { + System.out.println("Error writing file " + file + " in " + + format + " format!!"); + } + + } + + while (aparser.getSize() > 0) + { + System.out.println("Unknown arg: " + aparser.nextValue()); + } } } AlignFrame startUpAlframe = null; @@ -510,16 +518,19 @@ public class Jalview if (!headless && file == null && vamsasImport == null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { - file = jalview.bin.Cache.getDefault("STARTUP_FILE", - jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_7.jar"); + file = jalview.bin.Cache.getDefault( + "STARTUP_FILE", + jalview.bin.Cache.getDefault("www.jalview.org", + "http://www.jalview.org") + + "/examples/exampleFile_2_7.jar"); if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")) { // hardwire upgrade of the startup file - file.replace("_2_3.jar","_2_7.jar"); - // and remove the stale setting + file.replace("_2_3.jar", "_2_7.jar"); + // and remove the stale setting jalview.bin.Cache.removeProperty("STARTUP_FILE"); } - + protocol = "File"; if (file.indexOf("http:") > -1) @@ -558,7 +569,8 @@ 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 { @@ -570,7 +582,8 @@ public class Jalview // and finally, turn off batch mode indicator - if the desktop still exists if (desktop != null) { - if (progress!=-1) { + if (progress != -1) + { desktop.setProgressBar(null, progress); } desktop.setInBatchMode(false); @@ -605,7 +618,7 @@ public class Jalview Cache.log.info("Not enabling Google Tracking."); } }, null, true); - SwingUtilities.invokeLater(prompter); + desktop.addDialogThread(prompter); } /** @@ -660,11 +673,14 @@ public class Jalview ex.printStackTrace(); return; } - try { + try + { sfile = tfile.toURI().toURL(); } catch (Exception x) { - System.err.println("Unexpected Malformed URL Exception for temporary file created from STDIN: "+tfile.toURI()); + System.err + .println("Unexpected Malformed URL Exception for temporary file created from STDIN: " + + tfile.toURI()); x.printStackTrace(); return; } @@ -692,11 +708,13 @@ public class Jalview System.err.println("File '" + groovyscript + "' is empty."); return; } - try { - sfile = tfile.getAbsoluteFile().toURI().toURL(); + try + { + sfile = tfile.getAbsoluteFile().toURI().toURL(); } catch (Exception ex) { - System.err.println("Failed to create a file URL for "+tfile.getAbsoluteFile()); + System.err.println("Failed to create a file URL for " + + tfile.getAbsoluteFile()); return; } }