package jalview.io;
+import jalview.api.FeatureRenderer;
+import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
-import jalview.gui.AnnotationPanel;
-import jalview.gui.FeatureRenderer;
import jalview.gui.HTMLOptions;
import jalview.math.AlignmentDimension;
import jalview.util.MessageManager;
FeatureRenderer fr;
AlignmentPanel ap;
- AnnotationPanel annotationPanel;
- public HtmlSvgOutput(AlignmentPanel ap)
+ public HtmlSvgOutput(File file, AlignmentPanel ap)
{
-
- this.av = ap.av;
- this.ap = ap;
- this.annotationPanel = ap.getAnnotationPanel();
- generateHtmlSvgOutput();
+ this.av = ap.av;
+ this.ap = ap;
+ fr = ap.cloneFeatureRenderer();
+ generateHtmlSvgOutput(file);
}
- public void generateHtmlSvgOutput()
+ public void generateHtmlSvgOutput(File file)
{
- File file = null;
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());
.getSelectedFile().getParent());
file = chooser.getSelectedFile();
}
+ }
AlignmentDimension aDimension = ap.getAlignmentDimension();
SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
}
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);
-
+ String jsonData = null;
+ boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
+ .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ if (isEmbbedBioJSON)
+ {
+ AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport(
+ JSONFile.FILE_DESC, av);
+ if (exportData.getSettings().isCancelled())
+ {
+ return;
+ }
+ jsonData = new FormatAdapter(ap, exportData.getSettings())
+ .formatSequences(JSONFile.FILE_DESC, exportData
+ .getAlignment(), exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap
+ .getAlignViewport().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();
return Printable.PAGE_EXISTS;
}
- private String getHtml(String titleSvg, String alignmentSvg)
+ private String getHtml(String titleSvg, String alignmentSvg,
+ String jsonData)
{
StringBuilder htmlSvg = new StringBuilder();
- htmlSvg.append("<html><style type=\"text/css\">" + "div.title {"
- + "height: 100%;" + "width: 9%;" + "float: left;" + "}"
- + "div.align {" + "height: 100%;" + "width: 91%;"
- + "overflow: scroll;" + "float: right;" + "}" + "</style>"
- + "<div style=\"width:100%; height:100%; overflow: hidden\">"
- + "<div class=\"title\">");
- htmlSvg.append(titleSvg);
- htmlSvg.append("</div><div class=\"align\">").append(alignmentSvg);
+ htmlSvg.append("<html>\n");
+ if (jsonData != null)
+ {
+ htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button>");
+ htmlSvg.append("<input type=\"hidden\" name=\"seqData\" id=\"seqData\" value='"
+ + jsonData + "'>");
+ }
+ htmlSvg.append("\n<style type=\"text/css\"> "
+ + "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
+ + "div.titlex{ width:11%; float: left; }\n"
+ + "div.align{ width:89%; float: right; }\n"
+ + ".sub-category-container {overflow-y: scroll; overflow-x: hidden; width: 100%; height: 100%;}\n"
+ + "object {pointer-events: none;}"
+ + "</style>");
+ htmlSvg.append("<div>");
+ htmlSvg.append(
+"<div class=\"titlex\">");
+ htmlSvg.append(
+"<div class=\"sub-category-container\"> ")
+ .append(titleSvg)
+ .append("</div>")
+ .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=\"//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");
+
+ // 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\").value);\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 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(" jvVersion.setAttribute(\"name\", \"version\") ;\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(" myForm.appendChild(jvVersion);\n");
+ htmlSvg.append(" document.body.appendChild(myForm);\n");
+ htmlSvg.append(" myForm.submit() ;\n");
+ htmlSvg.append(" document.body.removeChild(myForm);\n");
+ htmlSvg.append("}\n");
+ htmlSvg.append("</script>\n");
+ htmlSvg.append("</hmtl>");
return htmlSvg.toString();
}
}
git://source.jalview.org / jalview.git / blobdiff