X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=e177a59b7c31806772c5f2feb4aa944d463f56e1;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=9aa573551fdb71a60b930eb5164f4fd5b74503ef;hpb=b3d648f529f35f8b7d67292b8be709bce9c8439d;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 9aa5735..e177a59 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -45,8 +45,10 @@ import jalview.io.NewickFile; import jalview.javascript.JSFunctionExec; import jalview.javascript.JalviewLiteJsApi; import jalview.javascript.JsCallBack; +import jalview.javascript.MouseOverStructureListener; import jalview.structure.SelectionListener; import jalview.structure.StructureSelectionManager; +import jalview.util.HttpUtils; import jalview.util.MessageManager; import java.applet.Applet; @@ -61,10 +63,9 @@ import java.awt.event.ActionEvent; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStream; import java.io.InputStreamReader; import java.net.URL; +import java.util.ArrayList; import java.util.Hashtable; import java.util.List; import java.util.StringTokenizer; @@ -92,7 +93,7 @@ public class JalviewLite extends Applet implements } // ///////////////////////////////////////// - // The following public methods maybe called + // The following public methods may be called // externally, eg via javascript in HTML page /* * (non-Javadoc) @@ -956,11 +957,16 @@ public class JalviewLite extends Applet implements } } - /* - * (non-Javadoc) - * + /** + * Callable from javascript to register a javascript function to pass events + * to a structure viewer. + * + * @param listener + * the name of a javascript function + * @param modelSet + * a token separated list of PDB file names listened for * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, - * java.lang.String) + * java.lang.String) */ public void setStructureListener(String listener, String modelSet) { @@ -974,8 +980,8 @@ public class JalviewLite extends Applet implements return; } } - jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener( - this, listener, separatorListToArray(modelSet)); + MouseOverStructureListener mol = new MouseOverStructureListener(this, + listener, separatorListToArray(modelSet)); javascriptListeners.addElement(mol); StructureSelectionManager.getStructureSelectionManager(this) .addStructureViewerListener(mol); @@ -1289,7 +1295,7 @@ public class JalviewLite extends Applet implements { builddate = "unknown"; version = "test"; - installation = "Webstart"; + installation = "applet"; java.net.URL url = JalviewLite.class .getResource("/.build_properties"); if (url != null) @@ -1345,9 +1351,10 @@ public class JalviewLite extends Applet implements /** * init method for Jalview Applet */ + @Override public void init() { - // remove any handlers that might be hanging around from an earlier instance + debug = TRUE.equalsIgnoreCase(getParameter("debug")); try { if (debug) @@ -1370,23 +1377,17 @@ public class JalviewLite extends Applet implements ex.printStackTrace(); } } - /** - * turn on extra applet debugging - */ - debug = TRUE.equalsIgnoreCase(getParameter("debug")); + if (debug) { - System.err.println("JalviewLite Version " + getVersion()); System.err.println("Build Date : " + getBuildDate()); System.err.println("Installation : " + getInstallation()); - } String externalsviewer = getParameter("externalstructureviewer"); if (externalsviewer != null) { - useXtrnalSviewer = externalsviewer.trim().toLowerCase() - .equals(TRUE); + useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE); } /** * if true disable the check for jmol @@ -1412,7 +1413,9 @@ public class JalviewLite extends Applet implements } else { - throw new Error(MessageManager.getString("error.invalid_separator_parameter")); + throw new Error( + MessageManager + .getString("error.invalid_separator_parameter")); } } int r = 255; @@ -1459,7 +1462,7 @@ public class JalviewLite extends Applet implements file = data.toString(); } } - if (TRUE.equalsIgnoreCase(getParameter("enableSplitFrame"))) + if (getDefaultParameter("enableSplitFrame", true)) { file2 = getParameter("file2"); } @@ -1788,27 +1791,72 @@ public class JalviewLite extends Applet implements * update the protocol state variable for accessing the datasource located * by file. * - * @param file + * @param path * @return possibly updated datasource string */ - public String setProtocolState(String file) + public String resolveFileProtocol(String path) { - if (file.startsWith("PASTE")) + /* + * is it paste data? + */ + if (path.startsWith("PASTE")) { - file = file.substring(5); protocol = AppletFormatAdapter.PASTE; + return path.substring(5); } - else if (inArchive(file)) + + /* + * is it a URL? + */ + if (path.indexOf("://") != -1) { - protocol = AppletFormatAdapter.CLASSLOADER; + protocol = AppletFormatAdapter.URL; + return path; } - else + + /* + * try relative to document root + */ + URL documentBase = getDocumentBase(); + String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase); + if (HttpUtils.isValidUrl(withDocBase)) + { + if (debug) + { + System.err.println("Prepended document base '" + documentBase + + "' to make: '" + withDocBase + "'"); + } + protocol = AppletFormatAdapter.URL; + return withDocBase; + } + + /* + * try relative to codebase (if different to document base) + */ + URL codeBase = getCodeBase(); + String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path, + codeBase); + if (!withCodeBase.equals(withDocBase) + && HttpUtils.isValidUrl(withCodeBase)) { - file = addProtocol(file); protocol = AppletFormatAdapter.URL; + if (debug) + { + System.err.println("Prepended codebase '" + codeBase + + "' to make: '" + withCodeBase + "'"); + } + return withCodeBase; + } + + /* + * try locating by classloader; try this last so files in the directory + * are resolved using document base + */ + if (inArchive(path)) + { + protocol = AppletFormatAdapter.CLASSLOADER; } - dbgMsg("Protocol identified as '" + protocol + "'"); - return file; + return path; } public LoadingThread(String file, String file2, JalviewLite _applet) @@ -1884,8 +1932,11 @@ public class JalviewLite extends Applet implements { AlignmentI al1 = af.viewport.getAlignment(); AlignmentI al2 = af2.viewport.getAlignment(); - if (AlignmentUtils.isMappable(al1, al2)) + AlignmentI cdna = al1.isNucleotide() ? al1 : al2; + AlignmentI prot = al1.isNucleotide() ? al2 : al1; + if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna)) { + al2.alignAs(al1); SplitFrame sf = new SplitFrame(af, af2); sf.addToDisplay(embedded, JalviewLite.this); return; @@ -1915,13 +1966,14 @@ public class JalviewLite extends Applet implements { return null; } - String resolvedFile = setProtocolState(fileParam); + String resolvedFile = resolveFileProtocol(fileParam); String format = new IdentifyFile().Identify(resolvedFile, protocol); dbgMsg("File identified as '" + format + "'"); AlignmentI al = null; try { - al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format); + al = new AppletFormatAdapter().readFile(resolvedFile, protocol, + format); if ((al != null) && (al.getHeight() > 0)) { dbgMsg("Successfully loaded file."); @@ -1939,13 +1991,13 @@ public class JalviewLite extends Applet implements if (protocol == AppletFormatAdapter.PASTE) { newAlignFrame.setTitle(MessageManager.formatMessage( - "label.sequences_from", new Object[] - { applet.getDocumentBase().toString() })); + "label.sequences_from", new Object[] { applet + .getDocumentBase().toString() })); } newAlignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new Object[] - { resolvedFile })); + "label.successfully_loaded_file", + new Object[] { resolvedFile })); return newAlignFrame; } @@ -2040,18 +2092,17 @@ public class JalviewLite extends Applet implements String sequence = applet.getParameter("PDBSEQ"); if (sequence != null) { - seqs = new SequenceI[] - { matcher == null ? (Sequence) alignFrame.getAlignViewport() - .getAlignment().findName(sequence) : matcher - .findIdMatch(sequence) }; + seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame + .getAlignViewport().getAlignment().findName(sequence) + : matcher.findIdMatch(sequence) }; } } else { param = st.nextToken(); - Vector tmp = new Vector(); - Vector tmp2 = new Vector(); + List tmp = new ArrayList(); + List tmp2 = new ArrayList(); while (st.hasMoreTokens()) { @@ -2060,39 +2111,22 @@ public class JalviewLite extends Applet implements if (st2.countTokens() > 1) { // This is the chain - tmp2.addElement(st2.nextToken()); + tmp2.add(st2.nextToken()); seqstring = st2.nextToken(); } - tmp.addElement(matcher == null ? (Sequence) alignFrame + tmp.add(matcher == null ? (Sequence) alignFrame .getAlignViewport().getAlignment() .findName(seqstring) : matcher.findIdMatch(seqstring)); } - seqs = new SequenceI[tmp.size()]; - tmp.copyInto(seqs); + seqs = tmp.toArray(new SequenceI[tmp.size()]); if (tmp2.size() == tmp.size()) { - chains = new String[tmp2.size()]; - tmp2.copyInto(chains); + chains = tmp2.toArray(new String[tmp2.size()]); } } - param = setProtocolState(param); - - if (// !jmolAvailable - // && - protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer) - { - // Re: JAL-357 : the bug isn't a problem if we are using an - // external viewer! - // TODO: verify this Re: - // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 - // This exception preserves the current behaviour where, even if - // the local pdb file was identified in the class loader - protocol = AppletFormatAdapter.URL; // this is probably NOT - // CORRECT! - param = addProtocol(param); // - } - + param = resolveFileProtocol(param); + // TODO check JAL-357 for files in a jar (CLASSLOADER) pdb.setFile(param); if (seqs != null) @@ -2125,8 +2159,8 @@ public class JalviewLite extends Applet implements } else { - pdbs.addElement(new Object[] - { pdb, seqs, chains, new String(protocol) }); + pdbs.addElement(new Object[] { pdb, seqs, chains, + new String(protocol) }); } } } @@ -2169,7 +2203,7 @@ public class JalviewLite extends Applet implements { try { - param = setProtocolState(param); + param = resolveFileProtocol(param); JPredFile predictions = new JPredFile(param, protocol); JnetAnnotationMaker.add_annotation(predictions, alignFrame.viewport.getAlignment(), 0, false); @@ -2204,7 +2238,7 @@ public class JalviewLite extends Applet implements String param = applet.getParameter("annotations"); if (param != null) { - param = setProtocolState(param); + param = resolveFileProtocol(param); if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, param, protocol)) @@ -2257,7 +2291,7 @@ public class JalviewLite extends Applet implements param = applet.getParameter("features"); if (param != null) { - param = setProtocolState(param); + param = resolveFileProtocol(param); result = alignFrame.parseFeaturesFile(param, protocol); } @@ -2326,7 +2360,7 @@ public class JalviewLite extends Applet implements { try { - treeFile = setProtocolState(treeFile); + treeFile = resolveFileProtocol(treeFile); NewickFile fin = new NewickFile(treeFile, protocol); fin.parse(); @@ -2351,113 +2385,29 @@ public class JalviewLite extends Applet implements /** * Discovers whether the given file is in the Applet Archive * - * @param file + * @param f * String * @return boolean */ - boolean inArchive(String file) + boolean inArchive(String f) { // This might throw a security exception in certain browsers // Netscape Communicator for instance. try { - boolean rtn = (getClass().getResourceAsStream("/" + file) != null); + boolean rtn = (getClass().getResourceAsStream("/" + f) != null); if (debug) { - System.err.println("Resource '" + file + "' was " - + (rtn ? "" : "not") + " located by classloader."); + System.err.println("Resource '" + f + "' was " + + (rtn ? "" : "not ") + "located by classloader."); } return rtn; } catch (Exception ex) { - System.out.println("Exception checking resources: " + file + " " - + ex); + System.out.println("Exception checking resources: " + f + " " + ex); return false; } } - - /** - * If the file is not already in URL format, tries to locate it by resolving - * as a URL. - * - * @param file - * @return - */ - String addProtocol(final String file) - { - if (file.indexOf("://") == -1) - { - /* - * Try relative to document base - */ - String url = applet.resolveUrlForLocalOrAbsolute(file, - getDocumentBase()); - if (urlExists(url)) - { - if (debug) - { - System.err.println("Prepended document base for resource: '" - + file + "'"); - } - return url; - } - - /* - * Try relative to codebase - */ - url = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase()); - if (urlExists(url)) - { - if (debug) - { - System.err.println("Prepended codebase for resource: '" + file - + "'"); - } - return url; - } - } - - /* - * Not resolved, leave unchanged - */ - return file; - } - - /** - * Returns true if an input stream can be opened on the specified URL, else - * false. - * - * @param url - * @return - */ - private boolean urlExists(String url) - { - InputStream is = null; - try - { - is = new URL(url).openStream(); - if (is != null) - { - return true; - } - } catch (Exception x) - { - // ignore - } finally - { - if (is != null) - { - try - { - is.close(); - } catch (IOException e) - { - // ignore - } - } - } - return false; - } } /** @@ -2510,9 +2460,9 @@ public class JalviewLite extends Applet implements * @param separator * @return elements separated by separator */ - public String[] separatorListToArray(String list, String separator) + public static String[] separatorListToArray(String list, String separator) { - // note separator local variable intentionally masks object field + // TODO use StringUtils version (slightly different...) int seplen = separator.length(); if (list == null || list.equals("") || list.equals(separator)) { @@ -2578,8 +2528,9 @@ public class JalviewLite extends Applet implements * @param separator * @return concatenated string */ - public String arrayToSeparatorList(String[] list, String separator) + public static String arrayToSeparatorList(String[] list, String separator) { + // TODO use StringUtils version StringBuffer v = new StringBuffer(); if (list != null && list.length > 0) { @@ -2736,7 +2687,7 @@ public class JalviewLite extends Applet implements { return def; } - if (stn.toLowerCase().equals(TRUE)) + if (TRUE.equalsIgnoreCase(stn)) { return true; } @@ -2897,27 +2848,61 @@ public class JalviewLite extends Applet implements * form a complete URL given a path to a resource and a reference location on * the same server * - * @param url + * @param targetPath * - an absolute path on the same server as localref or a document * located relative to localref * @param localref * - a URL on the same server as url * @return a complete URL for the resource located by url */ - private String resolveUrlForLocalOrAbsolute(String url, URL localref) + private String resolveUrlForLocalOrAbsolute(String targetPath, + URL localref) { - String codebase = localref.toString(); - if (url.indexOf("/") == 0) + String resolvedPath = ""; + if (targetPath.startsWith("/")) { - url = codebase.substring(0, codebase.length() - - localref.getFile().length()) - + url; + String codebase = localref.toString(); + String localfile = localref.getFile(); + resolvedPath = codebase.substring(0, + codebase.length() - localfile.length()) + + targetPath; + return resolvedPath; + } + + /* + * get URL path and strip off any trailing file e.g. + * www.jalview.org/examples/index.html#applets?a=b is trimmed to + * www.jalview.org/examples/ + */ + String urlPath = localref.toString(); + String directoryPath = urlPath; + int lastSeparator = directoryPath.lastIndexOf("/"); + if (lastSeparator > 0) + { + directoryPath = directoryPath.substring(0, lastSeparator + 1); + } + + if (targetPath.startsWith("/")) + { + /* + * construct absolute URL to a file on the server - this is not allowed? + */ + // String localfile = localref.getFile(); + // resolvedPath = urlPath.substring(0, + // urlPath.length() - localfile.length()) + // + targetPath; + resolvedPath = directoryPath + targetPath.substring(1); } else { - url = localref + url; + resolvedPath = directoryPath + targetPath; + } + if (debug) + { + System.err.println("resolveUrlForLocalOrAbsolute returning " + + resolvedPath); } - return url; + return resolvedPath; } /** @@ -2939,8 +2924,8 @@ public class JalviewLite extends Applet implements URL prepend; url = resolveUrlForLocalOrAbsolute( url, - prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase() - : getCodeBase()); + prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase() + : getDocumentBase()); if (debug) { System.err