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.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(File file, AlignmentPanel ap)
{
-
- this.av = ap.av;
- this.ap = ap;
- this.annotationPanel = ap.getAnnotationPanel();
+ this.av = ap.av;
+ this.ap = ap;
+ fr = ap.cloneFeatureRenderer();
generateHtmlSvgOutput(file);
}
{
try
{
- if (file == null /*
- * && !(System.getProperty("java.awt.headless") != null
- * && System
- * .getProperty("java.awt.headless").equals("true"))
- */)
+ if (file == null)
{
JalviewFileChooser chooser = getHTMLChooser();
}
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)
+ {
+ 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();
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\"> "
+ 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"
+ "subCatContainer.scroll(\nfunction() {\n"
+ "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
- htmlSvg.append("</script></hmtl>");
-
+ 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();
}
}