X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;h=a943a813e80cc726385960f68c73a77bd110ab39;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=00af2425a4ebedbe0d761bb66c7e31729a353c10;hpb=ee409dd34f8aff73c4b2b7d425e1154add8e2142;p=jalview.git diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index 00af242..a943a81 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -20,355 +20,88 @@ */ package jalview.io; -import jalview.api.AlignExportSettingI; -import jalview.api.FeatureRenderer; -import jalview.datamodel.AlignmentExportData; -import jalview.datamodel.SequenceI; -import jalview.gui.AlignViewport; +import jalview.bin.Cache; import jalview.gui.AlignmentPanel; -import jalview.gui.HTMLOptions; -import jalview.gui.IProgressIndicator; +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; - - public HtmlSvgOutput(File file, AlignmentPanel ap) + public HtmlSvgOutput(AlignmentPanel ap) { - this.av = ap.av; - this.ap = ap; - fr = ap.cloneFeatureRenderer(); - generateHtmlSvgOutput(file); + super(ap); } - public void generateHtmlSvgOutput(File file) + @Override + public void exportHTML(String outputFile) { - IProgressIndicator pIndicator = ap.alignFrame; - long pSessionId = System.currentTimeMillis(); + exportStarted(); try { - boolean headless = (System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true")); - if (file == null) + if (outputFile == null) { - if (pIndicator != null && !headless) - { - pIndicator.setProgressBar(MessageManager.formatMessage( - "status.waiting_for_user_to_select_output_file", "HTML"), - pSessionId); - } - 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) - { - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); - file = chooser.getSelectedFile(); - } - else - { - - if (pIndicator != null && !headless) - { - pIndicator.setProgressBar(MessageManager.formatMessage( - "status.cancelled_image_export_operation", "HTML"), - pSessionId); - } - return; - } - } - - 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); - - String titleSvgData = g1.getSVGDocument(); - String alignSvgData = g2.getSVGDocument(); - String jsonData = null; - boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache - .getDefault("EXPORT_EMBBED_BIOJSON", "true")); - if (isEmbbedBioJSON) - { - 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 = jalview.gui.AlignFrame - .getAlignmentForExport(JSONFile.FILE_DESC, av, - exportSettings); - jsonData = new FormatAdapter(ap, exportData.getSettings()) - .formatSequences(JSONFile.FILE_DESC, - exportData.getAlignment(), - exportData.getOmitHidden(), - exportData.getStartEndPostions(), - av.getColumnSelection()); - } - String htmlData = getHtml(titleSvgData, alignSvgData, jsonData); - FileOutputStream out = new FileOutputStream(file); - out.write(htmlData.getBytes()); - out.flush(); - out.close(); - if (!(System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true"))) - { - jalview.util.BrowserLauncher.openURL("file:///" + file); - } - if (pIndicator != null && !headless) - { - pIndicator.setProgressBar(MessageManager.formatMessage( - "status.export_complete", "HTML"), pSessionId); - } - } catch (OutOfMemoryError err) - { - System.out.println("########################\n" + "OUT OF MEMORY " - + file + "\n" + "########################"); - new OOMWarning("Creating Image for " + file, err); + generatedFile = new File(outputFile); } catch (Exception e) { + setProgressMessage(MessageManager + .formatMessage("info.error_creating_file", "HTML")); e.printStackTrace(); - pIndicator.setProgressBar(MessageManager.formatMessage( - "info.error_creating_file", "HTML"), pSessionId); + 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; - - if (endRes > (av.getAlignment().getWidth() - 1)) - { - endRes = av.getAlignment().getWidth() - 1; - } - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; - if (endSeq > av.getAlignment().getHeight()) - { - endSeq = av.getAlignment().getHeight(); - } - int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) - * pheight; - if (av.isShowAnnotation()) - { - pagesHigh += ap.getAnnotationPanel().adjustPanelHeight() + 3; - } - pagesHigh /= pheight; - if (pi >= (pagesWide * pagesHigh)) - { - return Printable.NO_SUCH_PAGE; - } - - // 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++) - { - seq = av.getAlignment().getSequenceAt(i); - if ((av.getSelectionGroup() != null) - && av.getSelectionGroup().getSequences(null).contains(seq)) - { - currentColor = Color.gray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getSequenceColour(seq); - currentTextColor = Color.black; - } - 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()) - { - fm = pg[0].getFontMetrics(); - xPos = idWidth - - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) - - 4; - } - pg[0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, - (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - - (av.getCharHeight() / 5)); - } - 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())) - { - // 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); - - // 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); - } - - return Printable.PAGE_EXISTS; + return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]); } - private String getHtml(String titleSvg, String alignmentSvg, - String jsonData) + String getHtml(String titleSvg, String alignmentSvg, + String jsonData, boolean wrapped) { StringBuilder htmlSvg = new StringBuilder(); htmlSvg.append("\n"); if (jsonData != null) { - htmlSvg.append(" "); - htmlSvg.append(""); - htmlSvg.append("
generatedFile
+ *
+ * @param textCharacters
+ * true for Text character rendering, false for Lineart
+ */
+ protected void doOutput(boolean textCharacters)
+ {
+ try
+ {
+ 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);
+ }
+ 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()));
}
+ }
- htmlSvg.append("\n");
- htmlSvg.append("