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JAL-2322 Refactored unified architecture for data + html exporting for SVG & BioJS...
[jalview.git]
/
src
/
jalview
/
bin
/
Jalview.java
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
d0cabb2
..
bcb4e7b
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-51,6
+51,7
@@
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.net.MalformedURLException;
import java.net.URI;
import java.io.PrintWriter;
import java.net.MalformedURLException;
import java.net.URI;
+import java.net.URISyntaxException;
import java.net.URL;
import java.security.AllPermission;
import java.security.CodeSource;
import java.net.URL;
import java.security.AllPermission;
import java.security.CodeSource;
@@
-651,23
+652,28
@@
public class Jalview
File imageFile = new File(file);
imageName = imageFile.getName();
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
File imageFile = new File(file);
imageName = imageFile.getName();
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.generateHtmlSvgOutput(new File(file));
+ htmlSVG.exportHTML(file);
System.out.println("Creating HTML image: " + file);
continue;
}
else if (format.equalsIgnoreCase("biojsmsa"))
{
System.out.println("Creating HTML image: " + file);
continue;
}
else if (format.equalsIgnoreCase("biojsmsa"))
{
- BioJsHTMLOutput.updateBioJS();
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
try
{
try
{
- Thread.sleep(1500);
- } catch (InterruptedException e)
+ BioJsHTMLOutput
+ .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
{
e.printStackTrace();
}
{
e.printStackTrace();
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
- bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
System.out.println("Creating BioJS MSA Viwer HTML file: "
+ file);
continue;
System.out.println("Creating BioJS MSA Viwer HTML file: "
+ file);
continue;