import jalview.datamodel.AlignmentI;
import jalview.gui.AlignFrame;
import jalview.gui.SplitFrame;
-import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
// TODO or format as file=/examples/uniref50.fa (etc)?
public class JalviewJS
{
+
+ static
+ {
+ /**
+ * @j2sNative
+ *
+ * thisApplet.__Info.args =
+ * ["file","examples/uniref50.fa","features",
+ * "examples/exampleFeatures.txt",
+ * "props","/Users/gmcarstairs/.jalview_properties"];
+ */
+
+ }
+
private static final String PARAM_FILE = "file";
private static final String PARAM_FILE2 = "file2";
private List<String> pdbFileParams;
- public static void main(String[] args)
+ public static void main(String[] args) throws Exception
{
- try
- {
- new JalviewJS().doMain(args);
- } catch (Throwable e)
- {
- e.printStackTrace();
- }
+ new JalviewJS().doMain(args);
}
/**
// todo extract helper for protocol resolution from JalviewLite
DataSourceType sourceType = featureFile.startsWith("http")
? DataSourceType.URL
- : DataSourceType.FILE;
+ : DataSourceType.RELATIVE_URL;
alignFrame.parseFeaturesFile(featureFile, sourceType);
}
}
String file = getParameter(fileParam);
if (file != null)
{
- DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+ DataSourceType protocol = file.startsWith("http") ? DataSourceType.URL
+ : DataSourceType.RELATIVE_URL;
+ // DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
FileFormatI format = new IdentifyFile().identify(file, protocol);
FileLoader fileLoader = new FileLoader(false);
af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);