X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=0ebebc2670bf021eba053ba01b4dcedcc978806c;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=a026c57005d64302e4093078ca1981d29e47c75b;hpb=4660fcf0745dbc1f6f6e7241b398301f93edb548;p=jalview.git diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java index a026c57..0ebebc2 100644 --- a/src/jalview/io/BioJsHTMLOutput.java +++ b/src/jalview/io/BioJsHTMLOutput.java @@ -1,11 +1,34 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.io; +import jalview.api.AlignExportSettingI; +import jalview.api.AlignmentViewPanel; +import jalview.datamodel.AlignmentExportData; import jalview.exceptions.NoFileSelectedException; -import jalview.gui.AlignViewport; -import jalview.gui.AlignmentPanel; -import jalview.gui.FeatureRenderer; -import jalview.json.binding.v1.BioJSReleasePojo; -import jalview.json.binding.v1.BioJSRepositoryPojo; +import jalview.gui.AlignFrame; +import jalview.gui.IProgressIndicator; +import jalview.gui.OOMWarning; +import jalview.json.binding.biojs.BioJSReleasePojo; +import jalview.json.binding.biojs.BioJSRepositoryPojo; import jalview.util.MessageManager; import java.io.BufferedInputStream; @@ -20,10 +43,15 @@ import java.net.URL; import java.util.Objects; import java.util.TreeMap; - public class BioJsHTMLOutput { - private AlignViewport av; + private AlignmentViewPanel ap; + + private long pSessionId; + + private IProgressIndicator pIndicator; + + private boolean headless; private static File currentBJSTemplateFile; @@ -38,28 +66,78 @@ public class BioJsHTMLOutput public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache .getDefault( "biojs_template_git_repo", - "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json"); + "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json"); - public BioJsHTMLOutput(AlignmentPanel ap, FeatureRenderer fr1) + public BioJsHTMLOutput(AlignmentViewPanel ap, + IProgressIndicator pIndicator) { if (ap != null) { - this.av = ap.av; - av.setFeatureRenderer(new FeatureRenderer(ap)); + this.ap = ap; + this.pSessionId = System.currentTimeMillis(); + this.pIndicator = pIndicator; + this.headless = (System.getProperty("java.awt.headless") != null && System + .getProperty("java.awt.headless").equals("true")); } } public void exportJalviewAlignmentAsBioJsHtmlFile() { + String outputFile = null; try { - String outputFile = getOutputFile(); - String jalviewAlignmentJson = JSONFile.getJSONData(av); + outputFile = getOutputFile(); + AlignExportSettingI exportSettings = new AlignExportSettingI() + { + @Override + public boolean isExportHiddenSequences() + { + return true; + } + + @Override + public boolean isExportHiddenColumns() + { + return true; + } + + @Override + public boolean isExportAnnotations() + { + return true; + } + + @Override + public boolean isExportFeatures() + { + return true; + } + + @Override + public boolean isExportGroups() + { + return true; + } + + @Override + public boolean isCancelled() + { + return false; + } + + }; + AlignmentExportData exportData = AlignFrame + .getAlignmentForExport(FileFormat.Json, + ap.getAlignViewport(), exportSettings); + String bioJSON = new FormatAdapter(ap, exportData.getSettings()) + .formatSequences(FileFormat.Json, exportData + .getAlignment(), exportData.getOmitHidden(), + exportData.getStartEndPostions(), ap + .getAlignViewport().getColumnSelection()); + String bioJSTemplateString = getBioJsTemplateAsString(); String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString - .replaceAll( -"#sequenceData#", jalviewAlignmentJson) - .toString(); + .replaceAll("#sequenceData#", bioJSON).toString(); PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter( outputFile)); @@ -67,11 +145,23 @@ public class BioJsHTMLOutput out.flush(); out.close(); jalview.util.BrowserLauncher.openURL("file:///" + outputFile); + if (pIndicator != null && !headless) + { + pIndicator.setProgressBar(MessageManager.formatMessage( + "status.export_complete", "BioJS"), pSessionId); + } } catch (NoFileSelectedException ex) { // do noting if no file was selected + } catch (OutOfMemoryError err) + { + System.out.println("########################\n" + "OUT OF MEMORY " + + outputFile + "\n" + "########################"); + new OOMWarning("Creating Image for " + outputFile, err); } catch (Exception e) { + pIndicator.setProgressBar(MessageManager.formatMessage( + "info.error_creating_file", "HTML"), pSessionId); e.printStackTrace(); } } @@ -79,16 +169,21 @@ public class BioJsHTMLOutput public String getOutputFile() throws NoFileSelectedException { String selectedFile = null; + if (pIndicator != null && !headless) + { + pIndicator.setProgressBar(MessageManager.formatMessage( + "status.waiting_for_user_to_select_output_file", "HTML"), + pSessionId); + } + JalviewFileChooser jvFileChooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "html" }, new String[] - { "HTML files" }, "HTML files"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "html" }, new String[] { "HTML files" }, + "HTML files"); jvFileChooser.setFileView(new JalviewFileView()); - // TODO uncomment when supported by MassageManager jvFileChooser.setDialogTitle(MessageManager .getString("label.save_as_biojs_html")); - jvFileChooser.setDialogTitle("save as BioJs HTML"); jvFileChooser.setToolTipText(MessageManager.getString("action.save")); int fileChooserOpt = jvFileChooser.showSaveDialog(null); @@ -100,14 +195,15 @@ public class BioJsHTMLOutput } else { + pIndicator.setProgressBar(MessageManager.formatMessage( + "status.cancelled_image_export_operation", "BioJS"), + pSessionId); throw new NoFileSelectedException("No file was selected."); } return selectedFile; } - - public static String getBioJsTemplateAsString() - throws IOException + public static String getBioJsTemplateAsString() throws IOException { InputStreamReader isReader = null; BufferedReader buffReader = null; @@ -185,15 +281,19 @@ public class BioJsHTMLOutput { Thread updateThread = new Thread() { + @Override public void run() { try { String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO); - BioJSRepositoryPojo release = new BioJSRepositoryPojo( - gitRepoPkgJson); - syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release); - refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY); + if (gitRepoPkgJson != null) + { + BioJSRepositoryPojo release = new BioJSRepositoryPojo( + gitRepoPkgJson); + syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release); + refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY); + } } catch (URISyntaxException e) { e.printStackTrace(); @@ -204,7 +304,6 @@ public class BioJsHTMLOutput } - public static void syncUpdates(String localDir, BioJSRepositoryPojo repo) { for (BioJSReleasePojo bjsRelease : repo.getReleases())