*/
package jalview.bin;
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
System.err.println("CMD [-noquestionnaire] executed successfully!");
}
- if (!aparser.contains("nonews"))
+ if (!aparser.contains("nonews")
+ || Cache.getProperty("NONEWS") == null)
{
desktop.checkForNews();
}
}
System.out.println("CMD [-open " + file + "] executed successfully!");
-
-
protocol = AppletFormatAdapter.checkProtocol(file);
-
+
if (protocol == DataSourceType.FILE)
{
if (!(new File(file)).exists())
af.createEPS(outputFile);
continue;
}
- FileFormatI outFormat=null;
- try {
+ FileFormatI outFormat = null;
+ try
+ {
outFormat = FileFormats.getInstance().forName(outputFormat);
- } catch (Exception formatP) {
- System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
+ } catch (Exception formatP)
+ {
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
}
if (outFormat != null)
{
jalview.bin.Cache.getDefault("www.jalview.org",
"https://www.jalview.org")
+ "/examples/exampleFile_2_7.jvp");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+ || file.equals(
"http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
file.replace("http:", "https:");
jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
- protocol = DataSourceType.FILE;
-
- if (file.indexOf("http:") > -1)
- {
- protocol = DataSourceType.URL;
- }
+ protocol = AppletFormatAdapter.checkProtocol(file);
if (file.endsWith(".jar"))
{