X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=eb44180a9095157205893ec98f1c05f6de52b2f3;hb=f4b18ae31d37e694b59875f26e0863179de248f1;hp=fd51823c9277734de36dd88550ef599f111df726;hpb=505e70d1af8a25642843387160b1ef199c5cbb04;p=jalview.git diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java old mode 100755 new mode 100644 index fd51823..eb44180 --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@ -1,237 +1,346 @@ -package jalview.io; - -import jalview.gui.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import java.awt.*; -import javax.swing.*; -import java.io.*; -import java.util.*; - - -public class HTMLOutput -{ - AlignViewport av; - SequenceRenderer sr; - Color color; - - public HTMLOutput(AlignViewport av) - { - this.av = av; - sr = new SequenceRenderer(av); - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY") - , new String[]{"html"}, "HTML files"); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save as HTML"); - chooser.setToolTipText("Save"); - int value = chooser.showSaveDialog(null); - if(value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - try{ - PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice)); - out.println(""); - out.println(""); - out.println(""); - - - if(av.getWrapAlignment()) - drawWrappedAlignment(out); - else - drawUnwrappedAlignment(out); - - out.println("\n\n"); - out.close(); - jalview.util.BrowserLauncher.openURL( "file:///"+choice ); - } - catch(Exception ex){ex.printStackTrace();} - } - } - - void drawUnwrappedAlignment(PrintWriter out) - { - - out.println("
\n"); - out.println("\n"); - - - ////////////// - SequenceGroup [] groups; - SequenceI seq; - ColourSchemeI cs = null; - AlignmentI alignment = av.getAlignment(); - String r,g,b; - - // draws the top row, the measure rule - out.println(""); - int i=0; - for(i=10; i"+i+"
|"); - - out.println(""); - out.println(""); - - for (i = 0; i < alignment.getHeight(); i++) - { - seq = alignment.getSequenceAt(i); - groups = alignment.findAllGroups( seq ); - if(av.getShowFullId()) - out.println(""); - else - out.println(""); - - - - for (int res = 0; res < seq.getLength(); res++) - { - cs = av.getGlobalColourScheme(); - - if(groups!=null) - { - for (int k = 0; k < groups.length; k++) - if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res) - { - cs = groups[k].cs; - break; - } - } - - - color = sr.getResidueBoxColour(cs, seq, res); - - if(color.getRGB()<-1) - { - r = Integer.toHexString(color.getRed()); - if(r.length()<2) - r = "0"+r; - g = Integer.toHexString(color.getGreen()); - if(g.length()<2) - g = "0"+g; - b = Integer.toHexString(color.getBlue()); - if(b.length()<2) - b = "0"+b; - out.println(""); - } - else - out.println(""); - - } - - out.println(""); - } - ////////////// - out.println("
"+i+"
|
"+seq.getDisplayId()+"  
"+seq.getName()+"  "+seq.getCharAt(res)+""+seq.getCharAt(res)+"
"); - out.println("
"); - - } - - void drawWrappedAlignment(PrintWriter out) - { - //////////////////////////////////// - /// How many sequences and residues can we fit on a printable page? - AlignmentI al = av.getAlignment(); - SequenceGroup [] groups; - SequenceI seq; - ColourSchemeI cs = null; - String r,g,b; - - out.println("
\n"); - out.println("\n"); - - for(int startRes=0; startResal.getWidth()) - endRes = al.getWidth(); - - out.println(""); - out.println(""); - for (int i = startRes+10; i < endRes; i += 10) - out.println(""); - - // out.println(""); - out.println(""); - - - - for (int s = 0; s < al.getHeight(); s++) - { - out.println(""); - seq = al.getSequenceAt(s); - groups = al.findAllGroups( seq ); - if(av.getShowFullId()) - out.println(""); - else - out.println(""); - - for (int res = startRes; res < endRes; res++) - { - cs = av.getGlobalColourScheme(); - if(groups!=null) - { - for (int k = 0; k < groups.length; k++) - if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res) - { - cs = groups[k].cs; - break; - } - } - - color = sr.getResidueBoxColour(cs, seq, res); - - if(color.getRGB()<-1) - { - r = Integer.toHexString(color.getRed()); - if(r.length()<2) - r = "0"+r; - g = Integer.toHexString(color.getGreen()); - if(g.length()<2) - g = "0"+g; - b = Integer.toHexString(color.getBlue()); - if(b.length()<2) - b = "0"+b; - out.println(""); - } - else - out.println(""); - - } - - out.println(""); - - } - if(endRes"); - - - - } - - out.println("
 " + i + "
|		" + i + - // "
|
"+seq.getDisplayId()+"  "+seq.getName()+"  "+seq.getCharAt(res)+""+seq.getCharAt(res)+"
"); - out.println("
"); - - - - } - - -} +/* + * 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 java.io.BufferedReader; +import java.io.File; +import java.io.IOException; +import java.io.InputStreamReader; +import java.net.URL; +import java.util.Objects; + +import jalview.api.AlignExportSettingsI; +import jalview.bin.Cache; +import jalview.datamodel.AlignExportSettingsAdapter; +import jalview.datamodel.AlignmentExportData; +import jalview.gui.AlignmentPanel; +import jalview.gui.IProgressIndicator; +import jalview.util.MessageManager; + +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; + + String _bioJson = null; + + private String description; + + /** + * Constructor given an alignment panel (which should not be null) + * + * @param ap + * @param desc + */ + public HTMLOutput(AlignmentPanel ap, String desc) + { + this.ap = ap; + this.pIndicator = ap.alignFrame; + this.description = desc; + this.pSessionId = System.currentTimeMillis(); + } + + /** + * 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 (_bioJson == null) + { + 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()); + } + + return _bioJson; + } + + /** + * Read a template file content as string + * + * @param file + * - the file to be read + * @return File content as String + * @throws IOException + */ + public static String readFileAsString(File file) throws IOException + { + InputStreamReader isReader = null; + BufferedReader buffReader = null; + StringBuilder sb = new StringBuilder(); + Objects.requireNonNull(file, "File must not be null!"); + @SuppressWarnings("deprecation") + URL url = file.toURL(); + if (url != null) + { + try + { + isReader = new InputStreamReader(url.openStream()); + buffReader = new BufferedReader(isReader); + String line; + String lineSeparator = System.getProperty("line.separator"); + while ((line = buffReader.readLine()) != null) + { + sb.append(line).append(lineSeparator); + } + + } catch (Exception ex) + { + ex.printStackTrace(); + } finally + { + if (isReader != null) + { + isReader.close(); + } + + if (buffReader != null) + { + buffReader.close(); + } + } + } + return sb.toString(); + } + + public static String getImageMapHTML() + { + return new String("\n" + "\n" + + "\n" + "\n" + "\n" + + "
\n" + + "\n"); + + } + + /** + * Prompts the user to choose an output file and returns the file path, or + * null on Cancel + * + * @return + */ + public String getOutputFile() + { + String selectedFile = null; + + // 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()); + + jvFileChooser + .setDialogTitle(MessageManager.getString("label.save_as_html")); + jvFileChooser.setToolTipText(MessageManager.getString("action.save")); + + int fileChooserOpt = jvFileChooser.showSaveDialog(null); + if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION) + { + Cache.setProperty("LAST_DIRECTORY", + jvFileChooser.getSelectedFile().getParent()); + selectedFile = jvFileChooser.getSelectedFile().getPath(); + } + + return selectedFile; + } + + protected void setProgressMessage(String message) + { + if (pIndicator != null && !isHeadless()) + { + pIndicator.setProgressBar(message, pSessionId); + } + else + { + System.out.println(message); + } + } + + /** + * Answers true if HTML export is invoke in headless mode or false otherwise + * + * @return + */ + protected boolean isHeadless() + { + return System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true"); + } + + /** + * 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. + */ + protected void exportCompleted() + { + if (isLaunchInBrowserAfterExport() && !isHeadless()) + { + /* + try + { + */ + jalview.util.BrowserLauncher.openURL("file:///" + getExportedFile()); + /* + } catch (IOException e) + { + e.printStackTrace(); + } + */ + } + } + + /** + * if this answers true then BioJSON data will be embedded to the exported + * HTML file otherwise it won't be embedded. + * + * @return + */ + public abstract boolean isEmbedData(); + + /** + * if this answers true then the generated HTML file is opened for viewing in + * a browser after its generation otherwise it won't be opened in a browser + * + * @return + */ + public abstract boolean isLaunchInBrowserAfterExport(); + + /** + * handle to the generated HTML file + * + * @return + */ + 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(); + + } + + /** + * Answers a short description of the image format suitable for display in + * messages + * + * @return + */ + protected final String getDescription() + { + return description; + } +} \ No newline at end of file