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.ChannelProperties;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
- if (aparser.contains("help") || aparser.contains("h"))
- {
- showUsage();
- System.exit(0);
- }
- if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
- {
- System.setProperty("java.awt.headless", "true");
- headless = true;
- }
String usrPropsFile = aparser.getValue("props");
Cache.loadProperties(usrPropsFile); // must do this before
if (usrPropsFile != null)
if (!headless)
{
+ Desktop.nosplash = aparser.contains("nosplash");
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
// t.printStackTrace();
}
+ // set Proxy settings before all the internet calls
+ Cache.setProxyPropertiesFromPreferences();
+
desktop.setVisible(true);
if (!Platform.isJS())
* @j2sIgnore
*/
{
- desktop.startServiceDiscovery();
+ if (!aparser.contains("nowebservicediscovery"))
+ {
+ desktop.startServiceDiscovery();
+ }
if (!aparser.contains("nousagestats"))
{
startUsageStats(desktop);
af.createEPS(outputFile);
continue;
}
-
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
+ FileFormatI outFormat = null;
+ try
{
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
+ {
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
}
- else
+ if (outFormat != null)
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ if (!outFormat.isWritable())
+ {
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
+ }
+ else
+ {
+ af.saveAlignment(file, outFormat);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in "
+ + outFormat.getName() + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + outFormat.getName() + " format!!");
+ }
+ }
}
}
Cache.removeProperty("STARTUP_FILE");
}
- protocol = DataSourceType.FILE;
-
- if (file.indexOf("http:") > -1)
- {
- protocol = DataSourceType.URL;
- }
+ protocol = AppletFormatAdapter.checkProtocol(file);
if (file.endsWith(".jar"))
{
private static void setLookAndFeel()
{
- // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
- // "mac"
+ // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
+ // "mac" or "flat"
// If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
// try Quaqua/Vaqua.
String lafProp = System.getProperty("laf");
Cache.log.error("Could not set requested laf=" + laf);
}
break;
+ case "flat":
+ lafSet = setFlatLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
case "quaqua":
lafSet = setQuaquaLookAndFeel();
if (!lafSet)
if (info.getName() != null && nameStartsWith
? info.getName().toLowerCase()
.startsWith(name.toLowerCase())
- : info.getName().toLowerCase().equals(name.toLowerCase()))
+ : info.getName().equalsIgnoreCase(name.toLowerCase()))
{
className = info.getClassName();
break;
"javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
}
+ private static boolean setFlatLookAndFeel()
+ {
+ return setSpecificLookAndFeel("flatlaf light",
+ "com.formdev.flatlaf.FlatLightLaf", false);
+ }
+
private static boolean setQuaquaLookAndFeel()
{
return setSpecificLookAndFeel("quaqua",
{
boolean set = false;
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
+ ChannelProperties.getProperty("app_name"));
System.setProperty("apple.laf.useScreenMenuBar", "true");
set = setQuaquaLookAndFeel();
if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
+ "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
}
git://source.jalview.org / jalview.git / blobdiff