X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;fp=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;h=6612db3d99ec77389534cec1df24355471531f56;hb=f06554784411ddbf871d642e66c8dcb7f147d4a8;hp=781eace903475dc0479ed19daad9b060d10492d3;hpb=cf06ee5d732af6cc874115aece1138adafca8ad7;p=jalview.git
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 781eace..6612db3 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -40,11 +40,7 @@ public class HtmlSvgOutput
{
try
{
- if (file == null /*
- * && !(System.getProperty("java.awt.headless") != null
- * && System
- * .getProperty("java.awt.headless").equals("true"))
- */)
+ if (file == null)
{
JalviewFileChooser chooser = getHTMLChooser();
@@ -97,22 +93,25 @@ public class HtmlSvgOutput
String titleSvgData = g1.getSVGDocument();
String alignSvgData = g2.getSVGDocument();
-
- AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport(
+ String jsonData = null;
+ boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
+ .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ if (isEmbbedBioJSON)
+ {
+ AlignmentExportData exportData = jalview.gui.AlignFrame
+ .getAlignmentForExport(
JSONFile.FILE_DESC, av);
if (exportData.getSettings().isCancelled())
{
return;
}
- String jsonData = new FormatAdapter(ap, exportData.getSettings())
+ jsonData = new FormatAdapter(ap, exportData.getSettings())
.formatSequences(JSONFile.FILE_DESC, exportData
.getAlignment(), exportData.getOmitHidden(),
- exportData.getStartEndPostions(), ap
- .getAlignViewport().getColumnSelection());
-
- // String jsonData = JSONFile.getJSONData(ap);
+ exportData.getStartEndPostions(),
+ av.getColumnSelection());
+ }
String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
-
FileOutputStream out = new FileOutputStream(file);
out.write(htmlData.getBytes());
out.flush();
@@ -276,6 +275,7 @@ public class HtmlSvgOutput
htmlSvg.append("\n");
if (jsonData != null)
{
+ htmlSvg.append("");
htmlSvg.append("");
}
@@ -310,8 +310,35 @@ public class HtmlSvgOutput
+ "subCatContainer.scroll(\nfunction() {\n"
+ "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
- htmlSvg.append("");
-
+ htmlSvg.append("\n");
+
+ // javascript for launching file in Jalview
+
+ htmlSvg.append("\n");
+ htmlSvg.append("");
return htmlSvg.toString();
}
}