import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
- FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
fileFormat, viewport.getAlignment(),
viewport.getShowJVSuffix()));
url.append(appendProtocol(viewport.applet.getParameter("annotations")));
}
- if (viewport.applet.getParameter("jnetfile") != null)
+ if (viewport.applet.getParameter("jnetfile") != null
+ || viewport.applet.getParameter("jpredfile") != null)
{
url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
+ .getParameter("jnetfile") : viewport.applet
+ .getParameter("jpredfile")));
}
if (viewport.applet.getParameter("defaultColour") != null)
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
MenuItem item = new MenuItem(ff);