From f77ee8eeaa83f2fc257e23f277b526b94a0e94ef Mon Sep 17 00:00:00 2001 From: hansonr Date: Thu, 16 May 2019 10:59:35 -0500 Subject: [PATCH] Jalview-JS/JAL-3253 applet param PDBFILE --- src/jalview/bin/Jalview.java | 449 ++++++++++++++++++--------------- src/jalview/bin/JalviewAppLoader.java | 21 +- src/jalview/bin/JalviewLite.java | 4 +- 3 files changed, 259 insertions(+), 215 deletions(-) diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 7bf0c72..808acc4 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -30,12 +30,14 @@ import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.Preferences; import jalview.gui.PromptUserConfig; +import jalview.gui.StructureViewer; import jalview.io.AppletFormatAdapter; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; @@ -279,7 +281,8 @@ public class Jalview implements ApplicationSingletonI void doMain(String[] args) { - if (!Platform.isJS()) + boolean isJS = Platform.isJS(); + if (!isJS) { System.setSecurityManager(null); } @@ -294,7 +297,7 @@ public class Jalview implements ApplicationSingletonI String usrPropsFile = aparser.getValue(ArgsParser.PROPS); Cache.loadProperties(usrPropsFile); - if (Platform.isJS()) + if (isJS) { isJavaAppletTag = aparser.isApplet(); if (isJavaAppletTag) @@ -363,7 +366,7 @@ public class Jalview implements ApplicationSingletonI else { System.out.println("Executing setprop argument: " + defs); - if (Platform.isJS()) + if (isJS) { Cache.setProperty(defs.substring(0, p), defs.substring(p + 1)); } @@ -446,7 +449,7 @@ public class Jalview implements ApplicationSingletonI desktop.setInBatchMode(true); // indicate we are starting up desktop.setVisible(true); - if (!Platform.isJS()) + if (!isJS) /** * Java only * @@ -507,108 +510,30 @@ public class Jalview implements ApplicationSingletonI } String data = null; - FileFormatI format = null; - DataSourceType protocol = null; FileLoader fileLoader = new FileLoader(!headless); // script to execute after all loading is // completed one way or another // extract groovy argument and execute if necessary - String groovyscript = aparser.getValue(ArgsParser.GROOVY, true); + String groovyscript = (isJS ? null + : aparser.getValue(ArgsParser.GROOVY, true)); String file = aparser.getValue(ArgsParser.OPEN, true); + String file2 = (isJavaAppletTag ? aparser.getAppletValue("file2", null) + : null); + String fileFormat = (isJavaAppletTag + ? aparser.getAppletValue("format", null) + : null); + FileFormatI format = null; + DataSourceType protocol = null; if (file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } - String vamsasImport = aparser.getValue(ArgsParser.VDOC); - String vamsasSession = aparser.getValue(ArgsParser.VSESS); - if (vamsasImport != null || vamsasSession != null) - { - if (desktop == null || headless) - { - System.out.println( - "Headless vamsas sessions not yet supported. Sorry."); - System.exit(1); - } - // if we have a file, start a new session and import it. - boolean inSession = false; - if (vamsasImport != null) - { - try - { - DataSourceType viprotocol = AppletFormatAdapter - .checkProtocol(vamsasImport); - if (viprotocol == DataSourceType.FILE) - { - inSession = desktop.vamsasImport(new File(vamsasImport)); - } - else if (viprotocol == DataSourceType.URL) - { - inSession = desktop.vamsasImport(new URL(vamsasImport)); - } - - } catch (Exception e) - { - System.err.println("Exeption when importing " + vamsasImport - + " as a vamsas document."); - e.printStackTrace(); - } - if (!inSession) - { - System.err.println("Failed to import " + vamsasImport - + " as a vamsas document."); - } - else - { - System.out.println("Imported Successfully into new session " - + desktop.getVamsasApplication().getCurrentSession()); - } - } - if (vamsasSession != null) - { - if (vamsasImport != null) - { - // close the newly imported session and import the Jalview specific - // remnants into the new session later on. - desktop.vamsasStop_actionPerformed(null); - } - // now join the new session - try - { - if (desktop.joinVamsasSession(vamsasSession)) - { - System.out.println( - "Successfully joined vamsas session " + vamsasSession); - } - else - { - System.err.println("WARNING: Failed to join vamsas session " - + vamsasSession); - } - } catch (Exception e) - { - System.err.println( - "ERROR: Failed to join vamsas session " + vamsasSession); - e.printStackTrace(); - } - if (vamsasImport != null) - { - // the Jalview specific remnants can now be imported into the new - // session at the user's leisure. - Cache.log.info( - "Skipping Push for import of data into existing vamsas session."); // TODO: - // enable - // this - // when - // debugged - // desktop.getVamsasApplication().push_update(); - } - } - } - long progress = -1; + boolean haveImport = checkStartVamas(aparser); // Finally, deal with the remaining input data. + long progress = -1; if (file != null) { if (!headless) @@ -620,7 +545,7 @@ public class Jalview implements ApplicationSingletonI } System.out.println("CMD [-open " + file + "] executed successfully!"); - if (!Platform.isJS()) + if (!isJS) /** * ignore in JavaScript -- can't just check file existence - could load * it? @@ -646,7 +571,13 @@ public class Jalview implements ApplicationSingletonI try { - format = new IdentifyFile().identify(file, protocol); + format = (isJavaAppletTag && fileFormat != null + ? FileFormats.getInstance().forName(fileFormat) + : null); + if (format == null) + { + format = new IdentifyFile().identify(file, protocol); + } } catch (FileFormatException e1) { // TODO ? @@ -661,6 +592,9 @@ public class Jalview implements ApplicationSingletonI else { setCurrentAlignFrame(af); + + // TODO: file2 How to implement file2 for the applet spit screen? + data = aparser.getValue(ArgsParser.COLOUR, true); if (data != null) { @@ -752,109 +686,28 @@ public class Jalview implements ApplicationSingletonI // TODO - load PDB structure(s) to alignment JAL-629 // (associate with identical sequence in alignment, or a specified // sequence) - if (groovyscript != null) - { - // Execute the groovy script after we've done all the rendering stuff - // and before any images or figures are generated. - System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, af); - System.out.println("CMD groovy[" + groovyscript - + "] executed successfully!"); - groovyscript = null; - } - if (isJavaAppletTag) { loadAppletParams(aparser, af); } - else + else if (!isJS) + /** + * Java only + * + * @j2sIgnore + */ { - - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) + if (groovyscript != null) { - // PNG filename - // SVG filename - // HTML filename - // biojsmsa filename - String outputFormat = aparser.nextValue(); - file = aparser.nextValue(); - - if (outputFormat.equalsIgnoreCase("png")) - { - af.createPNG(new File(file)); - imageName = (new File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("svg")) - { - File imageFile = new File(file); - imageName = imageFile.getName(); - af.createSVG(imageFile); - System.out.println("Creating SVG image: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("html")) - { - File imageFile = new File(file); - imageName = imageFile.getName(); - HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); - htmlSVG.exportHTML(file); - - System.out.println("Creating HTML image: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("biojsmsa")) - { - if (file == null) - { - System.err.println("The output html file must not be null"); - return; - } - try - { - BioJsHTMLOutput.refreshVersionInfo( - BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); - } catch (URISyntaxException e) - { - e.printStackTrace(); - } - BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); - bjs.exportHTML(file); - System.out.println( - "Creating BioJS MSA Viwer HTML file: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("imgMap")) - { - af.createImageMap(new File(file), imageName); - System.out.println("Creating image map: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("eps")) - { - File outputFile = new File(file); - System.out.println( - "Creating EPS file: " + outputFile.getAbsolutePath()); - af.createEPS(outputFile); - continue; - } - - af.saveAlignment(file, format); - if (af.isSaveAlignmentSuccessful()) - { - System.out.println("Written alignment in " + format - + " format to " + file); - } - else - { - 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. + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); + groovyscript = null; } - + checkOutputFile(aparser, af, format); while (aparser.getSize() > 0) { System.out.println("Unknown arg: " + aparser.nextValue()); @@ -867,8 +720,7 @@ public class Jalview implements ApplicationSingletonI // And the user // //////////////////// - if (!Platform.isJS() && !headless && file == null - && vamsasImport == null + if (!isJS && !headless && file == null && !haveImport && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) /** * Java only @@ -942,6 +794,185 @@ public class Jalview implements ApplicationSingletonI } } + private boolean checkStartVamas(ArgsParser aparser) + { + String vamsasImport = aparser.getValue(ArgsParser.VDOC); + String vamsasSession = aparser.getValue(ArgsParser.VSESS); + if (vamsasImport == null && vamsasSession == null) + { + return false; + } + if (desktop == null || headless) + { + System.out.println( + "Headless vamsas sessions not yet supported. Sorry."); + System.exit(1); + } + boolean haveImport = (vamsasImport != null); + if (haveImport) + { + // if we have a file, start a new session and import it. + boolean inSession = false; + try + { + DataSourceType viprotocol = AppletFormatAdapter + .checkProtocol(vamsasImport); + if (viprotocol == DataSourceType.FILE) + { + inSession = desktop.vamsasImport(new File(vamsasImport)); + } + else if (viprotocol == DataSourceType.URL) + { + inSession = desktop.vamsasImport(new URL(vamsasImport)); + } + + } catch (Exception e) + { + System.err.println("Exeption when importing " + vamsasImport + + " as a vamsas document."); + e.printStackTrace(); + } + if (!inSession) + { + System.err.println("Failed to import " + vamsasImport + + " as a vamsas document."); + } + else + { + System.out.println("Imported Successfully into new session " + + desktop.getVamsasApplication().getCurrentSession()); + } + } + if (vamsasSession != null) + { + if (vamsasImport != null) + { + // close the newly imported session and import the Jalview specific + // remnants into the new session later on. + desktop.vamsasStop_actionPerformed(null); + } + // now join the new session + try + { + if (desktop.joinVamsasSession(vamsasSession)) + { + System.out.println( + "Successfully joined vamsas session " + vamsasSession); + } + else + { + System.err.println("WARNING: Failed to join vamsas session " + + vamsasSession); + } + } catch (Exception e) + { + System.err.println( + "ERROR: Failed to join vamsas session " + vamsasSession); + e.printStackTrace(); + } + if (vamsasImport != null) + { + // the Jalview specific remnants can now be imported into the new + // session at the user's leisure. + Cache.log.info( + "Skipping Push for import of data into existing vamsas session."); // TODO: + // enable + // this + // when + // debugged + // desktop.getVamsasApplication().push_update(); + } + } + return haveImport; + } + + private void checkOutputFile(ArgsParser aparser, AlignFrame af, + FileFormatI format) + { + String imageName = "unnamed.png"; + while (aparser.getSize() > 1) + { + // PNG filename + // SVG filename + // HTML filename + // biojsmsa filename + String outputFormat = aparser.nextValue(); + String file = aparser.nextValue(); + if (outputFormat.equalsIgnoreCase("png")) + { + af.createPNG(new File(file)); + imageName = (new File(file)).getName(); + System.out.println("Creating PNG image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("svg")) + { + File imageFile = new File(file); + imageName = imageFile.getName(); + af.createSVG(imageFile); + System.out.println("Creating SVG image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("html")) + { + File imageFile = new File(file); + imageName = imageFile.getName(); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); + htmlSVG.exportHTML(file); + + System.out.println("Creating HTML image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("biojsmsa")) + { + if (file == null) + { + System.err.println("The output html file must not be null"); + return; + } + try + { + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(file); + System.out.println("Creating BioJS MSA Viwer HTML file: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("imgMap")) + { + af.createImageMap(new File(file), imageName); + System.out.println("Creating image map: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("eps")) + { + File outputFile = new File(file); + System.out.println( + "Creating EPS file: " + outputFile.getAbsolutePath()); + af.createEPS(outputFile); + continue; + } + + af.saveAlignment(file, format); + if (af.isSaveAlignmentSuccessful()) + { + System.out.println( + "Written alignment in " + format + " format to " + file); + } + else + { + System.out.println("Error writing file " + file + " in " + format + + " format!!"); + } + + } + } + private static void showUsage() { System.out.println( @@ -1185,10 +1216,11 @@ public class Jalview implements ApplicationSingletonI */ private void loadAppletParams(ArgsParser aparser, AlignFrame af) { - Jalview me = this; JalviewApp app = new JalviewApp() { + private boolean alignPDBStructures; // From JalviewLite; not implemented + @Override public String getParameter(String name) { @@ -1224,7 +1256,7 @@ public class Jalview implements ApplicationSingletonI @Override public AlignViewportI getViewport() { - return Jalview.getCurrentAlignFrame().getViewport(); + return af.getViewport(); } /** @@ -1245,7 +1277,7 @@ public class Jalview implements ApplicationSingletonI @Override public boolean loadScoreFile(String sScoreFile) throws IOException { - Jalview.getCurrentAlignFrame().loadJalviewDataFile(sScoreFile, null, + af.loadJalviewDataFile(sScoreFile, null, null, null); return true; } @@ -1257,7 +1289,7 @@ public class Jalview implements ApplicationSingletonI @Override public void updateForAnnotations() { - Jalview.getCurrentAlignFrame().updateForAnnotations(); + af.updateForAnnotations(); } @Override @@ -1270,38 +1302,35 @@ public class Jalview implements ApplicationSingletonI @Override public void setAlignPdbStructures(boolean defaultParameter) { - // TODO Auto-generated method stub - + alignPDBStructures = true; } @Override public void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol) { - // TODO Auto-generated method stub - + StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs); } @Override - public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs, - String[][] chains, String[] protocols) + public void setFeatureGroupState(String[] groups, boolean state) { - // TODO Auto-generated method stub - + af.setFeatureGroupState(groups, state); } @Override - public void setFeatureGroupState(String[] groups, boolean state) + public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs, + String[][] chains, String[] protocols) { - // TODO Auto-generated method stub - + System.err.println( + "Jalview applet interface alignedStructureView not implemented"); } @Override public void newFeatureSettings() { - // TODO Auto-generated method stub - + System.err.println( + "Jalview applet interface newFeatureSettings not implemented"); } }; diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java index 4ac4ffd..0bf922c 100644 --- a/src/jalview/bin/JalviewAppLoader.java +++ b/src/jalview/bin/JalviewAppLoader.java @@ -65,6 +65,7 @@ public class JalviewAppLoader loadAnnotations(); loadJnetFile(); loadPdbFiles(); + callInitCallback(); } /** @@ -93,7 +94,6 @@ public class JalviewAppLoader * */ - int pdbFileCount = 0; // Accumulate pdbs here if they are heading for the same view (if // alignPdbStructures is true) Vector pdbs = new Vector<>(); @@ -105,6 +105,7 @@ public class JalviewAppLoader .getSequencesArray()) : null; + int pdbFileCount = 0; String param; do { @@ -167,9 +168,9 @@ public class JalviewAppLoader chains = tmp2.toArray(new String[tmp2.size()]); } } + pdb.setId(param); ret[0] = param; - DataSourceType protocol = resolveFileProtocol(app, - ret); + DataSourceType protocol = resolveFileProtocol(app, ret); // TODO check JAL-357 for files in a jar (CLASSLOADER) pdb.setFile(ret[0]); @@ -650,4 +651,18 @@ public class JalviewAppLoader } } + public void callInitCallback() + { + String initjscallback = app.getParameter("oninit"); + if (initjscallback == null) + { + return; + } + initjscallback = initjscallback.trim(); + if (initjscallback.length() > 0) + { + // TODO + } + } + } diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 8c251cc..ba4f460 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1603,7 +1603,7 @@ public class JalviewLite extends Applet } } - private void callInitCallback() + void callInitCallback() { String initjscallback = getParameter("oninit"); if (initjscallback == null) @@ -1915,8 +1915,8 @@ public class JalviewLite extends Applet fileFound = false; applet.remove(launcher); applet.repaint(); + callInitCallback(); } - callInitCallback(); } /** -- 1.7.10.2