X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;h=a943a813e80cc726385960f68c73a77bd110ab39;hb=f9f0b83445a2da848d21614d94a909888484e25e;hp=b79d35d1917c22f5e3d19445d83fb8f0dce2309d;hpb=e18a55983523b534b2317b64104d32948275b1cd;p=jalview.git diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index b79d35d..a943a81 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -1,271 +1,358 @@ +/* + * 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.datamodel.SequenceI; -import jalview.gui.AlignViewport; +import jalview.bin.Cache; import jalview.gui.AlignmentPanel; -import jalview.gui.AnnotationPanel; -import jalview.gui.FeatureRenderer; -import jalview.gui.HTMLOptions; +import jalview.gui.LineartOptions; +import jalview.gui.OOMWarning; import jalview.math.AlignmentDimension; import jalview.util.MessageManager; +import jalview.util.dialogrunner.RunResponse; -import java.awt.Color; -import java.awt.FontMetrics; import java.awt.Graphics; -import java.awt.print.Printable; import java.awt.print.PrinterException; import java.io.File; import java.io.FileOutputStream; +import java.io.IOException; +import java.util.concurrent.atomic.AtomicBoolean; + +import javax.swing.JOptionPane; import org.jfree.graphics2d.svg.SVGGraphics2D; import org.jfree.graphics2d.svg.SVGHints; -public class HtmlSvgOutput +public class HtmlSvgOutput extends HTMLOutput { - AlignViewport av; - - FeatureRenderer fr; - AlignmentPanel ap; - - AnnotationPanel annotationPanel; - - public HtmlSvgOutput(File file, AlignmentPanel ap) + public HtmlSvgOutput(AlignmentPanel ap) { - - this.av = ap.av; - this.ap = ap; - this.annotationPanel = ap.getAnnotationPanel(); - generateHtmlSvgOutput(file); + super(ap); } - public void generateHtmlSvgOutput(File file) + @Override + public void exportHTML(String outputFile) { + exportStarted(); try { - if (file == null /* - * && !(System.getProperty("java.awt.headless") != null - * && System - * .getProperty("java.awt.headless").equals("true")) - */) - { - - JalviewFileChooser chooser = getHTMLChooser(); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(ap.alignFrame.getTitle()); - chooser.setToolTipText(MessageManager.getString("action.save")); - int value = chooser.showSaveDialog(ap.alignFrame); - - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + if (outputFile == null) { - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); - file = chooser.getSelectedFile(); - } - } - - AlignmentDimension aDimension = ap.getAlignmentDimension(); - SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(), - aDimension.getHeight()); - SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(), - aDimension.getHeight()); - - String renderStyle = jalview.bin.Cache.getDefault("HTML_RENDERING", - "Prompt each time"); - - // If we need to prompt, and if the GUI is visible then - // Prompt for rendering style - if (renderStyle.equalsIgnoreCase("Prompt each time") - && !(System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true"))) - { - HTMLOptions svgOption = new HTMLOptions(); - renderStyle = svgOption.getValue(); - - if (renderStyle == null || svgOption.cancelled) + outputFile = getOutputFile(); + if (outputFile == null) { + setProgressMessage(MessageManager.formatMessage( + "status.cancelled_image_export_operation", "HTML")); return; } } - - if (renderStyle.equalsIgnoreCase("lineart")) - { - g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE, - SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR); - g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE, - SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR); - } - printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1, - g2); - FileOutputStream out = new FileOutputStream(file); - - String titleSvgData = g1.getSVGDocument(); - String alignSvgData = g2.getSVGDocument(); - String htmlData = getHtml(titleSvgData, alignSvgData); - - out.write(htmlData.getBytes()); - out.flush(); - out.close(); - - jalview.util.BrowserLauncher.openURL("file:///" + file); + generatedFile = new File(outputFile); } catch (Exception e) { + setProgressMessage(MessageManager + .formatMessage("info.error_creating_file", "HTML")); e.printStackTrace(); + return; } + new Thread(this).start(); } - - static JalviewFileChooser getHTMLChooser() + + public int printUnwrapped(int pwidth, int pheight, int pi, + Graphics idGraphics, Graphics alignmentGraphics) + throws PrinterException { - return new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "html" }, new String[] - { "Hypertext Markup Language" }, "Hypertext Markup Language"); + return ap.printUnwrapped(pwidth, pheight, pi, idGraphics, + alignmentGraphics); } - public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg) + public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg) throws PrinterException { - int idWidth = ap.getVisibleIdWidth(false); - FontMetrics fm = ap.getFontMetrics(av.getFont()); - int scaleHeight = av.getCharHeight() + fm.getDescent(); - - pg[0].setColor(Color.white); - pg[0].fillRect(0, 0, pwidth, pheight); - pg[0].setFont(av.getFont()); - - // ////////////////////////////////// - // / How many sequences and residues can we fit on a printable page? - int totalRes = (pwidth - idWidth) / av.getCharWidth(); - int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1; - int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; - - // /////////////////////////// - // / Only print these sequences and residues on this page - int startRes; - - // /////////////////////////// - // / Only print these sequences and residues on this page - int endRes; - - // /////////////////////////// - // / Only print these sequences and residues on this page - int startSeq; - - // /////////////////////////// - // / Only print these sequences and residues on this page - int endSeq; - startRes = (pi % pagesWide) * totalRes; - endRes = (startRes + totalRes) - 1; + return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]); + } - if (endRes > (av.getAlignment().getWidth() - 1)) + String getHtml(String titleSvg, String alignmentSvg, + String jsonData, boolean wrapped) + { + StringBuilder htmlSvg = new StringBuilder(); + htmlSvg.append("\n"); + if (jsonData != null) { - endRes = av.getAlignment().getWidth() - 1; + htmlSvg.append( + "  "); + htmlSvg.append( + ""); + htmlSvg.append( + "
" + + jsonData + "
"); + htmlSvg.append("
 "); } - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; - if (endSeq > av.getAlignment().getHeight()) + htmlSvg.append("\n"); + if (!wrapped) { - pagesHigh += ap.getAnnotationPanel().adjustPanelHeight() + 3; + htmlSvg.append("
"); + htmlSvg.append("
\n"); + htmlSvg.append("
\n"); + htmlSvg.append(titleSvg); + htmlSvg.append("
"); + htmlSvg.append( + "
\n\n\n\n"); + htmlSvg.append("
"); + htmlSvg.append( + "
") + .append(alignmentSvg).append("
").append("
"); + htmlSvg.append("
"); + + htmlSvg.append( + "\n" + + "\n" + + "\n"); } - pagesHigh /= pheight; - if (pi >= (pagesWide * pagesHigh)) + else { - return Printable.NO_SUCH_PAGE; + htmlSvg.append("
\n").append(alignmentSvg).append("
"); + htmlSvg.append( + "\n" + + "\n"); } - // draw Scale - pg[1].translate(0, 0); - ap.getScalePanel().drawScale(pg[1], startRes, endRes, pwidth - idWidth, - scaleHeight); - pg[1].translate(-idWidth, scaleHeight); - - // ////////////// - // Draw the ids - Color currentColor = null; - Color currentTextColor = null; - pg[0].translate(0, scaleHeight); - pg[0].setFont(ap.getIdPanel().getIdCanvas().getIdfont()); - SequenceI seq; - for (int i = startSeq; i < endSeq; i++) + // javascript for launching file in Jalview + htmlSvg.append("\n"); + htmlSvg.append(""); + return htmlSvg.toString(); + } + + @Override + public boolean isEmbedData() + { + return Boolean.valueOf( + jalview.bin.Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true")); + } + + @Override + public boolean isLaunchInBrowserAfterExport() + { + return true; + } + + @Override + public void run() + { + try + { + setProgressMessage(null); + setProgressMessage(MessageManager.formatMessage( + "status.exporting_alignment_as_x_file", getDescription())); + + String renderStyle = Cache.getDefault("HTML_RENDERING", + "Prompt each time"); + AtomicBoolean textOption = new AtomicBoolean( + !"Lineart".equals(renderStyle)); + + /* + * configure the action to run on OK in the dialog + */ + RunResponse okAction = new RunResponse(JOptionPane.OK_OPTION) + { + @Override + public void run() + { + doOutput(textOption.get()); + } + }; + + /* + * Prompt for character rendering style if preference is not set + */ + if (renderStyle.equalsIgnoreCase("Prompt each time") && !isHeadless()) { - currentColor = av.getSequenceColour(seq); - currentTextColor = Color.black; + LineartOptions svgOption = new LineartOptions("HTML", textOption); + svgOption.setResponseAction(new RunResponse(JOptionPane.NO_OPTION) + { + @Override + public void run() + { + setProgressMessage(MessageManager.formatMessage( + "status.cancelled_image_export_operation", + getDescription())); + } + }); + svgOption.setResponseAction(okAction); + svgOption.showDialog(); + /* no code here - JalviewJS cannot execute it */ } - pg[0].setColor(currentColor); - pg[0].fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, - av.getCharHeight()); - pg[0].setColor(currentTextColor); - int xPos = 0; - if (av.isRightAlignIds()) + else { - fm = pg[0].getFontMetrics(); - xPos = idWidth - - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) - - 4; + /* + * else (if preference set) just do the export action + */ + doOutput(textOption.get()); } - pg[0].drawString( - seq.getDisplayId(av.getShowJVSuffix()), - xPos, - (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - - (av.getCharHeight() / 5)); + } catch (OutOfMemoryError err) + { + System.out.println("########################\n" + "OUT OF MEMORY " + + generatedFile + "\n" + "########################"); + new OOMWarning("Creating Image for " + generatedFile, err); + } catch (Exception e) + { + e.printStackTrace(); + setProgressMessage(MessageManager + .formatMessage("info.error_creating_file", getDescription())); } - pg[0].setFont(av.getFont()); - pg[0].translate(idWidth, 0); + } - // draw main sequence panel - pg[1].translate(idWidth, 0); - ap.getSeqPanel().seqCanvas.drawPanel(pg[1], startRes, endRes, startSeq, - endSeq, 0); - if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) + /** + * Builds and writes the image to the file specified by field + * generatedFile + * + * @param textCharacters + * true for Text character rendering, false for Lineart + */ + protected void doOutput(boolean textCharacters) + { + try { - // draw annotation label - need to offset for current scroll position - int offset = -ap.getAlabels().getScrollOffset(); - pg[0].translate(0, offset); - pg[0].translate(-idWidth - 3, - (endSeq - startSeq) * av.getCharHeight() + 3); - ap.getAlabels().drawComponent(pg[0], idWidth); - pg[0].translate(idWidth + 3, 0); - pg[0].translate(0, -offset); + AlignmentDimension aDimension = ap.getAlignmentDimension(); + SVGGraphics2D idPanelGraphics = new SVGGraphics2D( + aDimension.getWidth(), aDimension.getHeight()); + SVGGraphics2D alignPanelGraphics = new SVGGraphics2D( + aDimension.getWidth(), aDimension.getHeight()); + if (!textCharacters) // Lineart selected + { + idPanelGraphics.setRenderingHint( + SVGHints.KEY_DRAW_STRING_TYPE, + SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR); + alignPanelGraphics.setRenderingHint( + SVGHints.KEY_DRAW_STRING_TYPE, + SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR); + } + if (ap.av.getWrapAlignment()) + { + printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0, + alignPanelGraphics); + } + else + { + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), + 0, idPanelGraphics, alignPanelGraphics); + } - // draw annotation - need to offset for current scroll position - pg[1].translate(0, offset); - pg[1].translate(-idWidth - 3, - (endSeq - startSeq) * av.getCharHeight() + 3); - pg[1].translate(idWidth + 3, 0); - ap.getAnnotationPanel().renderer.drawComponent( - ap.getAnnotationPanel(), av, pg[1], -1, startRes, endRes + 1); - pg[1].translate(0, -offset); + String idPanelSvgData = idPanelGraphics.getSVGDocument(); + String alignPanelSvgData = alignPanelGraphics.getSVGDocument(); + String jsonData = getBioJSONData(); + String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, + jsonData, ap.av.getWrapAlignment()); + FileOutputStream out = new FileOutputStream(generatedFile); + out.write(htmlData.getBytes()); + out.flush(); + out.close(); + setProgressMessage(MessageManager + .formatMessage("status.export_complete", getDescription())); + exportCompleted(); + } catch (Exception e) + { + e.printStackTrace(); + setProgressMessage(MessageManager + .formatMessage("info.error_creating_file", getDescription())); } - - return Printable.PAGE_EXISTS; } - - private String getHtml(String titleSvg, String alignmentSvg) + + @Override + protected String getDescription() { - StringBuilder htmlSvg = new StringBuilder(); - htmlSvg.append("" - + "
" - + "
"); - htmlSvg.append(titleSvg); - htmlSvg.append("
").append(alignmentSvg); - htmlSvg.append("
"); - return htmlSvg.toString(); + return "HTML"; } }