import jalview.structure.StructureImportSettings;
import jalview.urls.IdOrgSettings;
import jalview.util.ColorUtils;
+import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
import java.awt.Color;
* service</li>
* <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
* <li>SHOW_OVERVIEW boolean for overview window display</li>
* <li>ANTI_ALIAS boolean for smooth fonts</li>
* <li>RIGHT_ALIGN_IDS boolean</li>
* sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info</li>
- * <li>DAS_REGISTRY_URL the registry to query</li>
* <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
* <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)</li>
* <li>VERSION_CHECK (true) check for the latest release version from
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
- public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
- public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
-
/**
* Sifts settings
*/
/** Default file is ~/.jalview_properties */
static String propertiesFile;
- private static boolean propsAreReadOnly = /** @j2sNative true || */
- false;
+ private static boolean propsAreReadOnly = Platform.isJS();/// ** @j2sNative
+ /// true || */false;
public static void initLogger()
{
}
// LOAD THE AUTHORS FROM THE authors.props file
- try
+ boolean ignore = Platform.isJS();
+ if (!ignore)
+ /**
+ * @j2sNative
+ */
{
- String authorDetails = /** @j2sNative "xxx" || */
- "jar:"
- .concat(Cache.class.getProtectionDomain().getCodeSource()
- .getLocation().toString().concat("!/authors.props"));
+ try
+ {
+ String authorDetails = "jar:"
+ .concat(Cache.class.getProtectionDomain().getCodeSource()
+ .getLocation().toString().concat("!/authors.props"));
- java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+ java.net.URL localJarFileURL = new java.net.URL(authorDetails);
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading author details: " + ex);
- applicationProperties.remove("AUTHORS");
- applicationProperties.remove("AUTHORFNAMES");
- applicationProperties.remove("YEAR");
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading author details: " + ex);
+ ignore = true;
+ }
}
+ if (ignore) {
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
+ }
+
// FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
// MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
// VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
- try
+ // BH 2019.01.25 switching to Platform.isJS()
+ ignore = Platform.isJS();
+ if (!ignore)
+ /**
+ * @j2sNative
+ */
{
- String buildDetails = /** @j2sNative "xxx" || */
- "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties"));
+ try
+ {
+ String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/.build_properties"));
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+ java.net.URL localJarFileURL = new java.net.URL(buildDetails);
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading build details: " + ex);
- applicationProperties.remove("VERSION");
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ ignore = true;
+ }
+ }
+
+ if (ignore) {
+ applicationProperties.remove("VERSION");
}
String jnlpVersion = System.getProperty("jalview.version");
return def;
}
+ public static int getDefault(String property, int def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ try
+ {
+ def = Integer.parseInt(string);
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing int property '" + property
+ + "' with value '" + string + "'");
+ }
+ }
+
+ return def;
+ }
+
/**
* Answers the value of the given property, or the supplied default value if
* the property is not set
}
}
}
+
+ /**
+ * Add a known domain that implements access-control-allow-origin:* bh 2018
+ *
+ * @param defaultUniprotDomain
+ */
+ public static void addJ2SDirectDatabaseCall(String domain)
+ {
+
+ /**
+ * @j2sNative
+ *
+ * J2S.addDirectDatabaseCall(domain);
+ */
+ }
}