import jalview.structure.StructureImportSettings;
import jalview.urls.IdOrgSettings;
import jalview.util.ColorUtils;
- import jalview.ws.dbsources.das.api.DasSourceRegistryI;
- import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import jalview.ws.sifts.SiftsSettings;
import java.awt.Color;
/** Default file is ~/.jalview_properties */
static String propertiesFile;
- private static boolean propsAreReadOnly = false;
+ private static boolean propsAreReadOnly = /** @j2sNative true || */
+ false;
public static void initLogger()
{
// LOAD THE AUTHORS FROM THE authors.props file
try
{
- String authorDetails = "jar:"
+ String authorDetails = /** @j2sNative "xxx" || */
+ "jar:"
.concat(Cache.class.getProtectionDomain().getCodeSource()
.getLocation().toString().concat("!/authors.props"));
// VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
try
{
- String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+ String buildDetails = /** @j2sNative "xxx" || */
+ "jar:".concat(Cache.class.getProtectionDomain()
.getCodeSource().getLocation().toString()
.concat("!/.build_properties"));
return null;
}
- private static DasSourceRegistryI sourceRegistry = null;
-
- /**
- * initialise and ..
- *
- * @return instance of the das source registry
- */
- public static DasSourceRegistryI getDasSourceRegistry()
- {
- if (sourceRegistry == null)
- {
- sourceRegistry = new DasSourceRegistry();
- }
- return sourceRegistry;
- }
-
/**
* Set the specified value, or remove it if null or empty. Does not save the
* properties file.
*/
public class Jalview
{
+
+ // BH 6/19/2018 starting to work on JS version - just discovering issues
+
/*
* singleton instance of this class
*/
public static AlignFrame currentAlignFrame;
+ public static boolean isJS = /** @j2sNative true || */ // BH 2018
+ false;
+
static
{
+
+ if (!isJS)
+ { // BH 2018
// grab all the rights we can the JVM
Policy.setPolicy(new Policy()
{
{
}
});
+
+ }
}
/**
af.setProgressBar(MessageManager
.getString("status.das_features_being_retrived"), id);
af.featureSettings_actionPerformed(null);
- af.featureSettings.fetchDasFeatures(dasSources, true);
af.setProgressBar(null, id);
synchronized (us)
{
*/
void doMain(String[] args)
{
- System.setSecurityManager(null);
+
+ if (!isJS)
+ {
+ System.setSecurityManager(null);
+ }
+
System.out
.println("Java version: " + System.getProperty("java.version"));
System.out.println(System.getProperty("os.arch") + " "
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)
"CMD [-props " + usrPropsFile + "] executed successfully!");
}
- // anything else!
-
- final String jabawsUrl = aparser.getValue("jabaws");
- if (jabawsUrl != null)
+ /**
+ * BH 2018 ignoring this section for JS
+ *
+ * @j2sNative
+ */
{
- try
+ if (aparser.contains("help") || aparser.contains("h"))
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- System.out.println(
- "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
- } catch (MalformedURLException e)
+ showUsage();
+ System.exit(0);
+ }
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
- System.err.println(
- "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ System.setProperty("java.awt.headless", "true");
+ headless = true;
+ }
+ // anything else!
+
+ final String jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println(
+ "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+ } catch (MalformedURLException e)
+ {
+ System.err.println(
+ "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ }
}
- }
+ }
String defs = aparser.getValue("setprop");
while (defs != null)
{
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
- desktop.startServiceDiscovery();
- if (!aparser.contains("nousagestats"))
- {
- startUsageStats(desktop);
- }
- else
- {
- System.err.println("CMD [-nousagestats] executed successfully!");
- }
- if (!aparser.contains("noquestionnaire"))
+ /**
+ * BH 2018 JS bypass this section
+ *
+ * @j2sNative
+ *
+ */
{
- String url = aparser.getValue("questionnaire");
- if (url != null)
+ desktop.startServiceDiscovery();
+ if (!aparser.contains("nousagestats"))
{
- // Start the desktop questionnaire prompter with the specified
- // questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
- desktop.checkForQuestionnaire(url);
- System.out.println(
- "CMD questionnaire[-" + url + "] executed successfully!");
+ startUsageStats(desktop);
}
else
{
- if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
+ if (!aparser.contains("noquestionnaire"))
+ {
+ String url = aparser.getValue("questionnaire");
+ if (url != null)
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
- // String defurl =
- // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
- // //
- String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug(
- "Starting questionnaire with default url: " + defurl);
- desktop.checkForQuestionnaire(defurl);
+ Cache.log.debug("Starting questionnaire url at " + url);
+ desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
+ }
+ else
+ {
+ if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ {
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ // String defurl =
+ // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+ // //
+ String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+ Cache.log.debug(
+ "Starting questionnaire with default url: " + defurl);
+ desktop.checkForQuestionnaire(defurl);
+ }
}
}
- }
- else
- {
- System.err.println("CMD [-noquestionnaire] executed successfully!");
- }
+ else
+ {
+ System.err
+ .println("CMD [-noquestionnaire] executed successfully!");
+ }
- if (!aparser.contains("nonews"))
- {
- desktop.checkForNews();
- }
+ if (!aparser.contains("nonews"))
+ {
+ desktop.checkForNews();
+ }
- BioJsHTMLOutput.updateBioJS();
+ BioJsHTMLOutput.updateBioJS();
+ }
}
String file = null, data = null;
}
System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!file.startsWith("http://"))
+ if (!isJS && !file.startsWith("http://"))
{
if (!(new File(file)).exists())
{
}
}
- protocol = AppletFormatAdapter.checkProtocol(file);
+ protocol = AppletFormatAdapter.checkProtocol(file);
try
{
// And the user
// ////////////////////
- if (!headless && file == null && vamsasImport == null
+ if (/** @j2sNative false && */ // BH 2018
+ !headless && file == null && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
file = jalview.bin.Cache.getDefault("STARTUP_FILE",
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.fts.core.GFTSPanel;
import jalview.fts.service.pdb.PDBFTSPanel;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
- import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
private static jalview.ws.SequenceFetcher sfetch = null;
- private static long lastDasSourceRegistry = -3;
-
- private static DasSourceRegistryI dasRegistry = null;
-
private static boolean _initingFetcher = false;
private static Thread initingThread = null;
Thread.currentThread().hashCode());
}
}
- if (sfetch == null || dasRegistry != Cache.getDasSourceRegistry()
- || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
- .getDasRegistryURL()
- + Cache.getDasSourceRegistry().getLocalSourceString())
- .hashCode())
+ if (sfetch == null)
{
_initingFetcher = true;
initingThread = Thread.currentThread();
"status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
- dasRegistry = Cache.getDasSourceRegistry();
- dasRegistry.refreshSources();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
if (guiWindow != null)
{
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
}
- lastDasSourceRegistry = (dasRegistry.getDasRegistryURL()
- + dasRegistry.getLocalSourceString()).hashCode();
sfetch = sf;
_initingFetcher = false;
initingThread = null;
dbeg.setText(MessageManager.formatMessage("label.example_query_param",
new String[]
{ eq }));
+ // TODO this should be a property of the SequenceFetcher whether commas are and
+ // colons are allowed in the IDs...
+
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
- for (DbSourceProxy dbs : database.getSelectedSources())
- {
- if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
- {
- enablePunct = false;
- break;
- }
- }
replacePunctuation.setEnabled(enablePunct);
} catch (Exception ex)
// Alignments?
}
- SequenceFeature[] sfs = null;
- List<SequenceI> alsqs;
- synchronized (alsqs = al.getSequences())
+ List<SequenceI> alsqs = al.getSequences();
+ synchronized (alsqs)
{
for (SequenceI sq : alsqs)
{
git://source.jalview.org / jalview.git / commitdiff