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.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();
+
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
public static void initLogger()
{
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
- if (propsFile == null)
+ if (propsFile == null && !propsAreReadOnly)
{
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ ".jalview_properties";
propsAreReadOnly = true;
}
- try
+ if (propertiesFile == null)
+ { // BH 2019
+ Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+ applicationProperties);
+ }
+ else
{
- InputStream fis;
try
{
- fis = new java.net.URL(propertiesFile).openStream();
- System.out.println(
- "Loading jalview properties from : " + propertiesFile);
- System.out.println(
- "Disabling Jalview writing to user's local properties file.");
- propsAreReadOnly = true;
+ InputStream fis;
+ try
+ {
+ fis = new java.net.URL(propertiesFile).openStream();
+ System.out.println(
+ "Loading jalview properties from : " + propertiesFile);
+ System.out.println(
+ "Disabling Jalview writing to user's local properties file.");
+ propsAreReadOnly = true;
+
+ } catch (Exception ex)
+ {
+ fis = null;
+ }
+ if (fis == null)
+ {
+ fis = new FileInputStream(propertiesFile);
+ }
+ applicationProperties.clear();
+ applicationProperties.load(fis);
+ // remove any old build properties
+
+ deleteBuildProperties();
+ fis.close();
} catch (Exception ex)
{
- fis = null;
- }
- if (fis == null)
- {
- fis = new FileInputStream(propertiesFile);
+ System.out.println("Error reading properties file: " + ex);
}
- applicationProperties.clear();
- applicationProperties.load(fis);
-
- // remove any old build properties
-
- deleteBuildProperties();
- fis.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading properties file: " + ex);
}
-
if (getDefault("USE_PROXY", false))
{
String proxyServer = getDefault("PROXY_SERVER", ""),
}
// LOAD THE AUTHORS FROM THE authors.props file
+ String authorDetails = (Platform.isJS() ? null
+ : "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/authors.props")));
+
try
{
- String authorDetails = /** @j2sNative "xxx" || */
- "jar:"
- .concat(Cache.class.getProtectionDomain().getCodeSource()
- .getLocation().toString().concat("!/authors.props"));
-
- java.net.URL localJarFileURL = new java.net.URL(authorDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
+ if (authorDetails != null)
+ {
+ 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");
+ authorDetails = null;
+ }
+ if (authorDetails == null)
+ {
+ 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
+ String buildDetails = (Platform.isJS() ? null
+ : "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/.build_properties")));
+ if (buildDetails != null)
{
- String buildDetails = /** @j2sNative "xxx" || */
- "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties"));
-
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
+ try
+ {
+ 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);
+ buildDetails = null;
+ }
+ }
+ if (buildDetails == null)
{
- System.out.println("Error reading build details: " + ex);
- applicationProperties.remove("VERSION");
+ applicationProperties.remove("VERSION");
}
-
String jnlpVersion = System.getProperty("jalview.version");
String codeVersion = getProperty("VERSION");
String codeInstallation = getProperty("INSTALLATION");
false);
}
+
private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
*/
public static String getProperty(String key)
{
- return applicationProperties.getProperty(key);
+ String prop = applicationProperties.getProperty(key);
+ if (prop == null && Platform.isJS())
+ {
+ prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ + "_" + JS_PROPERTY_PREFIX + key);
+ }
+ return prop;
}
/**
return def;
}
- /**
- * These methods are used when checking if the saved preference is different
- * to the default setting
- */
- public static String getDefault(String property, String def)
+ public static int getDefault(String property, int def)
{
String string = getProperty(property);
if (string != null)
{
- return string;
+ 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
+ */
+ public static String getDefault(String property, String def)
+ {
+ String value = getProperty(property);
+ return value == null ? def : value;
+ }
+
+ /**
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
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.
}
}
}
+
+ /**
+ * Add a known domain that implements access-control-allow-origin:* bh 2018
+ *
+ * @param defaultUniprotDomain
+ */
+ public static void addJ2SDirectDatabaseCall(String domain)
+ {
+
+ /**
+ * @j2sNative
+ *
+ * J2S.addDirectDatabaseCall(domain);
+ */
+ }
}
git://source.jalview.org / jalview.git / blobdiff