*/
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.LineartOptions;
+import jalview.gui.OOMWarning;
import jalview.math.AlignmentDimension;
import jalview.util.MessageManager;
-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 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, "HTML");
}
- public void generateHtmlSvgOutput(File file)
- {
- try
- {
- if (file == null)
- {
-
- 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();
- }
- }
-
- 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)
- {
- 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);
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- }
-
- 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("<html>\n");
if (jsonData != null)
{
- htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> ");
- htmlSvg.append("<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
- htmlSvg.append("<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
- + jsonData + "</div>");
+ htmlSvg.append(
+ "<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> ");
+ htmlSvg.append(
+ "<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
+ htmlSvg.append(
+ "<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
+ + jsonData + "</div>");
htmlSvg.append("<br/> ");
}
htmlSvg.append("\n<style type=\"text/css\"> "
if (jsonData != null)
{
// facebox style sheet for displaying raw BioJSON data
- htmlSvg.append("#facebox { position: absolute; top: 0; left: 0; z-index: 100; text-align: left; }\n"
- + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
- + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
- + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
- + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
- + " border-radius:4px; }\n"
- + "#facebox .content > p:first-child{ margin-top:0; }\n"
- + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
- + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
- + "#facebox .close img{ opacity:0.3; }\n"
- + "#facebox .close:hover img{ opacity:1.0; }\n"
- + "#facebox .loading { text-align: center; }\n"
- + "#facebox .image { text-align: center;}\n"
- + "#facebox img { border: 0; margin: 0; }\n"
- + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
- + ".facebox_hide { z-index:-100; }\n"
- + ".facebox_overlayBG { background-color: #000; z-index: 99; }");
+ htmlSvg.append(
+ "#facebox { position: absolute; top: 0; left: 0; z-index: 100; text-align: left; }\n"
+ + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
+ + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
+ + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
+ + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
+ + " border-radius:4px; }\n"
+ + "#facebox .content > p:first-child{ margin-top:0; }\n"
+ + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
+ + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
+ + "#facebox .close img{ opacity:0.3; }\n"
+ + "#facebox .close:hover img{ opacity:1.0; }\n"
+ + "#facebox .loading { text-align: center; }\n"
+ + "#facebox .image { text-align: center;}\n"
+ + "#facebox img { border: 0; margin: 0; }\n"
+ + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
+ + ".facebox_hide { z-index:-100; }\n"
+ + ".facebox_overlayBG { background-color: #000; z-index: 99; }");
}
-
htmlSvg.append("</style>");
- htmlSvg.append("<div class=\"main-container\" \n>");
- htmlSvg.append("<div class=\"titlex\">\n");
- htmlSvg.append("<div class=\"sub-category-container\"> \n");
- htmlSvg.append(titleSvg);
- htmlSvg.append("</div>");
- htmlSvg.append("</div>\n\n<!-- ========================================================================================== -->\n\n");
- htmlSvg.append("<div class=\"align\" >");
- htmlSvg.append(
- "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
- .append(alignmentSvg).append("</div></div>").append("</div>");
- htmlSvg.append("</div>");
-
- htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
- + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
- + "<script>\n"
- + "var subCatContainer = $(\".sub-category-container\");\n"
- + "subCatContainer.scroll(\nfunction() {\n"
- + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
-
- htmlSvg.append("</script>\n");
+ if (!wrapped)
+ {
+ htmlSvg.append("<div class=\"main-container\" \n>");
+ htmlSvg.append("<div class=\"titlex\">\n");
+ htmlSvg.append("<div class=\"sub-category-container\"> \n");
+ htmlSvg.append(titleSvg);
+ htmlSvg.append("</div>");
+ htmlSvg.append(
+ "</div>\n\n<!-- ========================================================================================== -->\n\n");
+ htmlSvg.append("<div class=\"align\" >");
+ htmlSvg.append(
+ "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
+ .append(alignmentSvg).append("</div></div>").append("</div>");
+ htmlSvg.append("</div>");
+
+ htmlSvg.append(
+ "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+ + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
+ + "<script>\n"
+ + "var subCatContainer = $(\".sub-category-container\");\n"
+ + "subCatContainer.scroll(\nfunction() {\n"
+ + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
+
+ htmlSvg.append("</script>\n");
+ }
+ else
+ {
+ htmlSvg.append("<div>\n").append(alignmentSvg).append("</div>");
+ htmlSvg.append(
+ "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+ + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
+ }
// javascript for launching file in Jalview
-
htmlSvg.append("<script language=\"JavaScript\">\n");
htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
- htmlSvg.append(" var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
- htmlSvg.append(" var jalviewVersion = json['appSettings'].version;\n");
+ htmlSvg.append(
+ " var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
+ htmlSvg.append(
+ " var jalviewVersion = json['appSettings'].version;\n");
htmlSvg.append(" var url = json['appSettings'].webStartUrl;\n");
- htmlSvg.append(" var myForm = document.createElement(\"form\");\n\n");
+ htmlSvg.append(
+ " var myForm = document.createElement(\"form\");\n\n");
htmlSvg.append(" var heap = document.createElement(\"input\");\n");
htmlSvg.append(" heap.setAttribute(\"name\", \"jvm-max-heap\") ;\n");
htmlSvg.append(" heap.setAttribute(\"value\", \"2G\");\n\n");
htmlSvg.append(" var target = document.createElement(\"input\");\n");
htmlSvg.append(" target.setAttribute(\"name\", \"open\");\n");
htmlSvg.append(" target.setAttribute(\"value\", document.URL);\n\n");
- htmlSvg.append(" var jvVersion = document.createElement(\"input\");\n");
+ htmlSvg.append(
+ " var jvVersion = document.createElement(\"input\");\n");
htmlSvg.append(" jvVersion.setAttribute(\"name\", \"version\") ;\n");
- htmlSvg.append(" jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
+ htmlSvg.append(
+ " jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
htmlSvg.append(" myForm.action = url;\n");
htmlSvg.append(" myForm.appendChild(heap);\n");
htmlSvg.append(" myForm.appendChild(target);\n");
htmlSvg.append(" document.body.removeChild(myForm);\n");
htmlSvg.append("}\n");
- // jquery facebox for displaying raw BioJSON data");
if (jsonData != null)
{
- htmlSvg.append("/* Facebox (for jQuery)\n");
- htmlSvg.append("* version: 1.3\n");
- htmlSvg.append(" * @requires jQuery v1.2 or later\n");
- htmlSvg.append(" * @homepage https://github.com/defunkt/facebox\n");
- htmlSvg.append(" * Licensed under the MIT:\n");
- htmlSvg.append(" * http://www.opensource.org/licenses/mit-license.php\n");
- htmlSvg.append(" * Copyright Forever Chris Wanstrath, Kyle Neath\n");
- htmlSvg.append(" * Usage:\n");
- htmlSvg.append(" * jQuery(document).ready(function() {\n");
- htmlSvg.append(" * jQuery('a[rel*=facebox]').facebox()\n");
- htmlSvg.append(" * })\n");
- htmlSvg.append(" * <a href=\"#terms\" rel=\"facebox\">Terms</a>\n");
- htmlSvg.append(" * Loads the #terms div in the box\n");
- htmlSvg.append(" * <a href=\"terms.html\" rel=\"facebox\">Terms</a>\n");
- htmlSvg.append(" * Loads the terms.html page in the box\n");
- htmlSvg.append(" * <a href=\"terms.png\" rel=\"facebox\">Terms</a>\n");
- htmlSvg.append(" * Loads the terms.png image in the box\n");
- htmlSvg.append(" * You can also use it programmatically:\n");
- htmlSvg.append(" * jQuery.facebox('some html')\n");
- htmlSvg.append(" * jQuery.facebox('some html', 'my-groovy-style')\n");
- htmlSvg.append(" * The above will open a facebox with \"some html\" as the content.\n");
- htmlSvg.append(" * jQuery.facebox(function($) {\n");
- htmlSvg.append(" * $.get('blah.html', function(data) { $.facebox(data) })\n");
- htmlSvg.append(" * })\n");
- htmlSvg.append(" * The above will show a loading screen before the passed function is called,\n");
- htmlSvg.append(" * allowing for a better ajaxy experience.\n");
- htmlSvg.append(" * The facebox function can also display an ajax page, an image, or the contents of a div:\n");
- htmlSvg.append(" * jQuery.facebox({ ajax: 'remote.html' })\n");
- htmlSvg.append(" * jQuery.facebox({ ajax: 'remote.html' }, 'my-groovy-style')\n");
- htmlSvg.append(" * jQuery.facebox({ image: 'stairs.jpg' })\n");
- htmlSvg.append(" * jQuery.facebox({ image: 'stairs.jpg' }, 'my-groovy-style')\n");
- htmlSvg.append(" * jQuery.facebox({ div: '#box' })\n");
- htmlSvg.append(" * jQuery.facebox({ div: '#box' }, 'my-groovy-style')\n");
- htmlSvg.append(" * Want to close the facebox? Trigger the 'close.facebox' document event:\n");
- htmlSvg.append(" * jQuery(document).trigger('close.facebox')\n");
- htmlSvg.append(" * Facebox also has a bunch of other hooks:\n");
- htmlSvg.append(" * loading.facebox\n");
- htmlSvg.append(" * beforeReveal.facebox\n");
- htmlSvg.append(" * reveal.facebox (aliased as 'afterReveal.facebox')\n");
- htmlSvg.append(" * init.facebox\n");
- htmlSvg.append(" * afterClose.facebox\n");
- htmlSvg.append(" * Simply bind a function to any of these hooks:\n");
- htmlSvg.append(" * $(document).bind('reveal.facebox', function() { ...stuff to do after the facebox and contents are revealed... })\n");
- htmlSvg.append(" *\n");
- htmlSvg.append(" */\n");
- htmlSvg.append("(function($) {\n");
- htmlSvg.append(" $.facebox = function(data, klass) {\n");
- htmlSvg.append(" $.facebox.loading()\n");
- htmlSvg.append(" if (data.ajax) fillFaceboxFromAjax(data.ajax, klass)\n");
- htmlSvg.append(" else if (data.image) fillFaceboxFromImage(data.image, klass)\n");
- htmlSvg.append(" else if (data.div) fillFaceboxFromHref(data.div, klass)\n");
- htmlSvg.append(" else if ($.isFunction(data)) data.call($)\n");
- htmlSvg.append(" else $.facebox.reveal(data, klass)\n");
- htmlSvg.append(" }\n");
-
- htmlSvg.append(" $.extend($.facebox, {\n");
- htmlSvg.append(" settings: {\n");
- htmlSvg.append(" opacity : 0.2,\n");
- htmlSvg.append(" overlay : true,\n");
- htmlSvg.append(" loadingImage : 'https://raw.githubusercontent.com/jalview/biojson/gh-pages/images/loading.gif',\n");
- htmlSvg.append(" closeImage : 'https://raw.githubusercontent.com/jalview/biojson/gh-pages/images/cancel.png',\n");
- htmlSvg.append(" imageTypes : [ 'png', 'jpg', 'jpeg', 'gif' ],\n");
- htmlSvg.append(" faceboxHtml : '<div id=\"facebox\" style=\"display:none; width: 95%; height: 85%; overflow: auto;\"> ");
- htmlSvg.append(" <div class=\"popup\"> ");
- htmlSvg.append(" <div class=\"content\"> ");
- htmlSvg.append(" </div> ");
- htmlSvg.append(" <a href=\"#\" class=\"close\"></a> ");
- htmlSvg.append(" </div> ");
- htmlSvg.append(" </div>'\n");
- htmlSvg.append(" }, \n");
- htmlSvg.append(" loading: function() {\n");
- htmlSvg.append(" init()\n");
- htmlSvg.append(" if ($('#facebox .loading').length == 1) return true\n");
- htmlSvg.append(" showOverlay() \n");
- htmlSvg.append(" $('#facebox .content').empty().\n");
- htmlSvg.append(" append('<div class=\"loading\"><img src=\"'+$.facebox.settings.loadingImage+'\"/></div>')\n");
- htmlSvg.append(" $('#facebox').show().css({\n");
- htmlSvg.append(" top: getPageScroll()[1] + (getPageHeight() / 10),\n");
- htmlSvg.append(" left: $(window).width() / 2 - ($('#facebox .popup').outerWidth() / 2)\n");
- htmlSvg.append(" }) \n");
- htmlSvg.append(" $(document).bind('keydown.facebox', function(e) {\n");
- htmlSvg.append(" if (e.keyCode == 27) $.facebox.close()\n");
- htmlSvg.append(" return true\n");
- htmlSvg.append(" })\n");
- htmlSvg.append(" $(document).trigger('loading.facebox')\n");
- htmlSvg.append(" },\n");
- htmlSvg.append(" reveal: function(data, klass) {\n");
- htmlSvg.append(" $(document).trigger('beforeReveal.facebox')\n");
- htmlSvg.append(" if (klass) $('#facebox .content').addClass(klass)\n");
- htmlSvg.append(" $('#facebox .content').empty().append('<pre><code>'+JSON.stringify(JSON.parse(data),null,4)+'</pre></code>')\n");
- htmlSvg.append(" $('#facebox .popup').children().fadeIn('normal')\n");
- htmlSvg.append(" $('#facebox').css('left', $(window).width() / 2 - ($('#facebox .popup').outerWidth() / 2))\n");
- htmlSvg.append(" $(document).trigger('reveal.facebox').trigger('afterReveal.facebox')\n");
- htmlSvg.append(" }, \n");
- htmlSvg.append(" close: function() {\n");
- htmlSvg.append(" $(document).trigger('close.facebox')\n");
- htmlSvg.append(" return false\n");
- htmlSvg.append(" }\n");
- htmlSvg.append(" })\n");
- htmlSvg.append(" $.fn.facebox = function(settings) {\n");
- htmlSvg.append(" if ($(this).length == 0) return \n");
- htmlSvg.append(" init(settings) \n");
- htmlSvg.append(" function clickHandler() {\n");
- htmlSvg.append(" $.facebox.loading(true) \n");
- htmlSvg.append(" // support for rel=\"facebox.inline_popup\" syntax, to add a class\n");
- htmlSvg.append(" // also supports deprecated \"facebox[.inline_popup]\" syntax\n");
- htmlSvg.append(" var klass = this.rel.match(/facebox\\[?\\.(\\w+)\\]?/)\n");
- htmlSvg.append(" if (klass) klass = klass[1]\n");
- htmlSvg.append(" fillFaceboxFromHref(this.href, klass)\n");
- htmlSvg.append(" return false\n");
- htmlSvg.append(" } \n");
- htmlSvg.append(" return this.bind('click.facebox', clickHandler)\n");
- htmlSvg.append(" }\n");
- htmlSvg.append(" // called one time to setup facebox on this page\n");
- htmlSvg.append(" function init(settings) {\n");
- htmlSvg.append(" if ($.facebox.settings.inited) return true\n");
- htmlSvg.append(" else $.facebox.settings.inited = true\n");
- htmlSvg.append(" $(document).trigger('init.facebox')\n");
- htmlSvg.append(" makeCompatible()\n");
- htmlSvg.append(" var imageTypes = $.facebox.settings.imageTypes.join('|')\n");
- htmlSvg.append(" $.facebox.settings.imageTypesRegexp = new RegExp('\\\\.(' + imageTypes + ')(\\\\?.*)?$', 'i')\n");
-
- htmlSvg.append(" if (settings) $.extend($.facebox.settings, settings)\n");
- htmlSvg.append(" $('body').append($.facebox.settings.faceboxHtml)\n");
-
- htmlSvg.append(" var preload = [ new Image(), new Image() ]\n");
- htmlSvg.append(" preload[0].src = $.facebox.settings.closeImage\n");
- htmlSvg.append(" preload[1].src = $.facebox.settings.loadingImage\n");
-
- htmlSvg.append(" $('#facebox').find('.b:first, .bl').each(function() {\n");
- htmlSvg.append(" preload.push(new Image())\n");
- htmlSvg.append(" preload.slice(-1).src = $(this).css('background-image').replace(/url\\((.+)\\)/, '$1')\n");
- htmlSvg.append(" })\n");
-
- htmlSvg.append(" $('#facebox .close')\n");
- htmlSvg.append(" .click($.facebox.close)\n");
- htmlSvg.append(" .append('<img src=\"'\n");
- htmlSvg.append(" + $.facebox.settings.closeImage\n");
- htmlSvg.append(" + '\" class=\"close_image\" title=\"close\">')\n");
- htmlSvg.append(" }\n");
-
- htmlSvg.append(" // getPageScroll() by quirksmode.com\n");
- htmlSvg.append(" function getPageScroll() {\n");
- htmlSvg.append(" var xScroll, yScroll;\n");
- htmlSvg.append(" if (self.pageYOffset) {\n");
- htmlSvg.append(" yScroll = self.pageYOffset;\n");
- htmlSvg.append(" xScroll = self.pageXOffset;\n");
- htmlSvg.append(" } else if (document.documentElement && document.documentElement.scrollTop) { // Explorer 6 Strict\n");
- htmlSvg.append(" yScroll = document.documentElement.scrollTop;\n");
- htmlSvg.append(" xScroll = document.documentElement.scrollLeft;\n");
- htmlSvg.append(" } else if (document.body) {// all other Explorers\n");
- htmlSvg.append(" yScroll = document.body.scrollTop;\n");
- htmlSvg.append(" xScroll = document.body.scrollLeft;\n");
- htmlSvg.append(" }\n");
- htmlSvg.append(" return new Array(xScroll,yScroll)\n");
- htmlSvg.append(" }\n");
-
- // Adapted from getPageSize() by quirksmode.com");
- htmlSvg.append(" function getPageHeight() {\n");
- htmlSvg.append(" var windowHeight\n");
- htmlSvg.append(" if (self.innerHeight) { // all except Explorer\n");
- htmlSvg.append(" windowHeight = self.innerHeight;\n");
- htmlSvg.append(" } else if (document.documentElement && document.documentElement.clientHeight) { // Explorer 6 Strict Mode\n");
- htmlSvg.append(" windowHeight = document.documentElement.clientHeight;\n");
- htmlSvg.append(" } else if (document.body) { // other Explorers\n");
- htmlSvg.append(" windowHeight = document.body.clientHeight;\n");
- htmlSvg.append(" }\n");
- htmlSvg.append(" return windowHeight\n");
- htmlSvg.append(" }\n");
-
- htmlSvg.append(" // Backwards compatibility\n");
- htmlSvg.append(" function makeCompatible() {\n");
- htmlSvg.append(" var $s = $.facebox.settings \n");
- htmlSvg.append(" $s.loadingImage = $s.loading_image || $s.loadingImage\n");
- htmlSvg.append(" $s.closeImage = $s.close_image || $s.closeImage\n");
- htmlSvg.append(" $s.imageTypes = $s.image_types || $s.imageTypes\n");
- htmlSvg.append(" $s.faceboxHtml = $s.facebox_html || $s.faceboxHtml\n");
- htmlSvg.append(" }\n");
-
- htmlSvg.append(" // Figures out what you want to display and displays it\n");
- htmlSvg.append(" // formats are:\n");
- htmlSvg.append(" // div: #id\n");
- htmlSvg.append(" // image: blah.extension\n");
- htmlSvg.append(" // ajax: anything else\n");
- htmlSvg.append(" function fillFaceboxFromHref(href, klass) {\n");
- htmlSvg.append(" // div\n");
- htmlSvg.append(" if (href.match(/#/)) {\n");
- htmlSvg.append(" var url = window.location.href.split('#')[0]\n");
- htmlSvg.append(" var target = href.replace(url,'')\n");
- htmlSvg.append(" if (target == '#') return\n");
- htmlSvg.append(" $.facebox.reveal($(target).html(), klass)\n");
-
- htmlSvg.append(" // image\n");
- htmlSvg.append(" } else if (href.match($.facebox.settings.imageTypesRegexp)) {\n");
- htmlSvg.append(" fillFaceboxFromImage(href, klass)\n");
- htmlSvg.append(" // ajax\n");
- htmlSvg.append(" } else {\n");
- htmlSvg.append(" fillFaceboxFromAjax(href, klass)\n");
- htmlSvg.append(" }\n");
- htmlSvg.append(" }\n");
-
- htmlSvg.append(" function fillFaceboxFromImage(href, klass) {\n");
- htmlSvg.append(" var image = new Image()\n");
- htmlSvg.append(" image.onload = function() {\n");
- htmlSvg.append(" $.facebox.reveal('<div class=\"image\"><img src=\"' + image.src + '\" /></div>', klass)\n");
- htmlSvg.append(" }\n");
- htmlSvg.append(" image.src = href\n");
- htmlSvg.append(" }\n");
-
- htmlSvg.append(" function fillFaceboxFromAjax(href, klass) {\n");
- htmlSvg.append(" $.facebox.jqxhr = $.get(href, function(data) { $.facebox.reveal(data, klass) })\n");
- htmlSvg.append(" }\n");
+ // JQuery FaceBox for displaying raw BioJSON data");
+ File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
+ try
+ {
+ htmlSvg.append(HTMLOutput.readFileAsString(faceBoxJsFile));
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
- htmlSvg.append(" function skipOverlay() {\n");
- htmlSvg.append(" return $.facebox.settings.overlay == false || $.facebox.settings.opacity === null\n");
- htmlSvg.append(" }\n");
+ htmlSvg.append("</script>\n");
+ htmlSvg.append("</html>");
+ return htmlSvg.toString();
+ }
- htmlSvg.append(" function showOverlay() {\n");
- htmlSvg.append(" if (skipOverlay()) return\n");
+ @Override
+ public boolean isEmbedData()
+ {
+ return Boolean.valueOf(
+ Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ }
- htmlSvg.append(" if ($('#facebox_overlay').length == 0)\n");
- htmlSvg.append(" $(\"body\").append('<div id=\"facebox_overlay\" class=\"facebox_hide\"></div>')\n");
+ @Override
+ public boolean isLaunchInBrowserAfterExport()
+ {
+ return true;
+ }
- htmlSvg.append(" $('#facebox_overlay').hide().addClass(\"facebox_overlayBG\")\n");
- htmlSvg.append(" .css('opacity', $.facebox.settings.opacity)\n");
- htmlSvg.append(" .click(function() { $(document).trigger('close.facebox') })\n");
- htmlSvg.append(" .fadeIn(200)\n");
- htmlSvg.append(" return false\n");
- htmlSvg.append(" }\n");
+ @Override
+ public void run()
+ {
+ try
+ {
+ String renderStyle = Cache.getDefault("HTML_RENDERING",
+ "Prompt each time");
+ AtomicBoolean textOption = new AtomicBoolean(
+ !"Lineart".equals(renderStyle));
- htmlSvg.append(" function hideOverlay() {\n");
- htmlSvg.append(" if (skipOverlay()) return \n");
- htmlSvg.append(" $('#facebox_overlay').fadeOut(200, function(){\n");
- htmlSvg.append(" $(\"#facebox_overlay\").removeClass(\"facebox_overlayBG\")\n");
- htmlSvg.append(" $(\"#facebox_overlay\").addClass(\"facebox_hide\")\n");
- htmlSvg.append(" $(\"#facebox_overlay\").remove()\n");
- htmlSvg.append(" }) \n");
- htmlSvg.append(" return false\n");
- htmlSvg.append(" }\n");
+ /*
+ * configure the action to run on OK in the dialog
+ */
+ Runnable okAction = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ doOutput(textOption.get());
+ }
+ };
- htmlSvg.append(" $(document).bind('close.facebox', function() {\n");
- htmlSvg.append(" if ($.facebox.jqxhr) {\n");
- htmlSvg.append(" $.facebox.jqxhr.abort()\n");
- htmlSvg.append(" $.facebox.jqxhr = null\n");
- htmlSvg.append(" }\n");
- htmlSvg.append(" $(document).unbind('keydown.facebox')\n");
- htmlSvg.append(" $('#facebox').fadeOut(function() {\n");
- htmlSvg.append(" $('#facebox .content').removeClass().addClass('content')\n");
- htmlSvg.append(" $('#facebox .loading').remove()\n");
- htmlSvg.append(" $(document).trigger('afterClose.facebox')\n");
- htmlSvg.append(" })\n");
- htmlSvg.append(" hideOverlay()\n");
- htmlSvg.append(" })\n");
+ /*
+ * Prompt for character rendering style if preference is not set
+ */
+ if (renderStyle.equalsIgnoreCase("Prompt each time") && !isHeadless())
+ {
+ LineartOptions svgOption = new LineartOptions("HTML", textOption);
+ svgOption.setResponseAction(1, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation",
+ getDescription()));
+ }
+ });
+ svgOption.setResponseAction(0, okAction);
+ svgOption.showDialog();
+ /* no code here - JalviewJS cannot execute it */
+ }
+ else
+ {
+ /*
+ * else (if preference set) just do the export action
+ */
+ doOutput(textOption.get());
+ }
+ } 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()));
+ }
+ }
- htmlSvg.append("})(jQuery);\n");
+ /**
+ * Builds and writes the image to the file specified by field
+ * <code>generatedFile</code>
+ *
+ * @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("</script>\n");
- htmlSvg.append("</html>");
- return htmlSvg.toString();
}
}
git://source.jalview.org / jalview.git / blobdiff