X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=54e7e4b6c3012d5fbe286554b5a8048bad468b95;hb=08c7bee16c16563cc7cec7ea4d336b3e0c4c937a;hp=81cdd3c78fcdfe65c72bd83f66e84a24ea776276;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java old mode 100755 new mode 100644 index 81cdd3c..54e7e4b --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@ -1,8 +1,29 @@ +/* + * 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.AlignExportSettingsI; +import jalview.bin.Cache; +import jalview.datamodel.AlignExportSettingsAdapter; import jalview.datamodel.AlignmentExportData; -import jalview.exceptions.NoFileSelectedException; import jalview.gui.AlignmentPanel; import jalview.gui.IProgressIndicator; import jalview.util.MessageManager; @@ -18,82 +39,61 @@ public abstract class HTMLOutput implements Runnable { protected AlignmentPanel ap; + /* + * key for progress or status messages + */ protected long pSessionId; + /* + * (optional) place to write progress messages to + */ protected IProgressIndicator pIndicator; protected File generatedFile; - public HTMLOutput(AlignmentPanel ap) - { - if (ap != null) - { - this.ap = ap; - this.pIndicator = ap.alignFrame; - } - } + String _bioJson = null; - public String getBioJSONData() + private String description; + + /** + * Constructor given an alignment panel (which should not be null) + * + * @param ap + * @param desc + */ + public HTMLOutput(AlignmentPanel ap, String desc) { - return getBioJSONData(null); + this.ap = ap; + this.pIndicator = ap.alignFrame; + this.description = desc; + this.pSessionId = System.currentTimeMillis(); } - public String getBioJSONData(AlignExportSettingI exportSettings) + /** + * Gets the BioJSON data as a string, with lazy evaluation (first time called + * only). If the output format is configured not to embed BioJSON, returns + * null. + * + * @return + */ + public String getBioJSONData() { if (!isEmbedData()) { return null; } - if (exportSettings == null) + if (_bioJson == null) { - 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; - } - }; + AlignExportSettingsI options = new AlignExportSettingsAdapter(true); + AlignmentExportData exportData = ap.getAlignViewport() + .getAlignExportData(options); + _bioJson = new FormatAdapter(ap, options).formatSequences( + FileFormat.Json, exportData.getAlignment(), + exportData.getOmitHidden(), exportData.getStartEndPostions(), + ap.getAlignViewport().getAlignment().getHiddenColumns()); } - AlignmentExportData exportData = jalview.gui.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() - .getAlignment().getHiddenColumns()); - return bioJSON; + + return _bioJson; } /** @@ -198,16 +198,18 @@ public abstract class HTMLOutput implements Runnable } - public String getOutputFile() throws NoFileSelectedException + /** + * Prompts the user to choose an output file and returns the file path, or + * null on Cancel + * + * @return + */ + public String getOutputFile() { String selectedFile = null; - if (pIndicator != null && !isHeadless()) - { - pIndicator.setProgressBar(MessageManager.formatMessage( - "status.waiting_for_user_to_select_output_file", "HTML"), - pSessionId); - } + // TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or + // Jalview HTML rendering system- probably not required for Jalview-JS) JalviewFileChooser jvFileChooser = new JalviewFileChooser("html", "HTML files"); jvFileChooser.setFileView(new JalviewFileView()); @@ -219,14 +221,11 @@ public abstract class HTMLOutput implements Runnable int fileChooserOpt = jvFileChooser.showSaveDialog(null); if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION) { - jalview.bin.Cache.setProperty("LAST_DIRECTORY", + Cache.setProperty("LAST_DIRECTORY", jvFileChooser.getSelectedFile().getParent()); selectedFile = jvFileChooser.getSelectedFile().getPath(); } - else - { - throw new NoFileSelectedException("No file was selected."); - } + return selectedFile; } @@ -255,16 +254,6 @@ public abstract class HTMLOutput implements Runnable /** * This method provides implementation of consistent behaviour which should - * occur before a HTML file export. It MUST be called at the start of the - * exportHTML() method implementation. - */ - protected void exportStarted() - { - pSessionId = System.currentTimeMillis(); - } - - /** - * This method provides implementation of consistent behaviour which should * occur after a HTML file export. It MUST be called at the end of the * exportHTML() method implementation. */ @@ -304,13 +293,51 @@ public abstract class HTMLOutput implements Runnable * * @return */ - public abstract File getExportedFile(); + public File getExportedFile() + { + return generatedFile; + } + + public void exportHTML(String outputFile) + { + setProgressMessage(MessageManager.formatMessage( + "status.exporting_alignment_as_x_file", getDescription())); + try + { + if (outputFile == null) + { + /* + * prompt for output file + */ + outputFile = getOutputFile(); + if (outputFile == null) + { + setProgressMessage(MessageManager.formatMessage( + "status.cancelled_image_export_operation", + getDescription())); + return; + } + } + generatedFile = new File(outputFile); + } catch (Exception e) + { + setProgressMessage(MessageManager + .formatMessage("info.error_creating_file", getDescription())); + e.printStackTrace(); + return; + } + new Thread(this).start(); + + } /** - * This is the main method to handle the HTML generation. + * Answers a short description of the image format suitable for display in + * messages * - * @param outputFile - * the file path of the generated HTML + * @return */ - public abstract void exportHTML(String outputFile); + protected final String getDescription() + { + return description; + } } \ No newline at end of file