*/
package jalview.bin;
-import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.UserColourScheme;
-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;
import java.io.BufferedReader;
-import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ColorUtils;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
+
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* list entries are separated by '|' symbols unless otherwise stated (|) clauses
* @author $author$
* @version $Revision$
*/
-public class Cache
+public class Cache implements ApplicationSingletonI
{
+
+ private Cache()
+ {
+ // private singleton
+ }
+
+ /**
+ * In Java, this will be a static field instance, which will be
+ * application-specific; in JavaScript it will be an applet-specific instance
+ * tied to the applet's ThreadGroup.
+ *
+ * @return
+ */
+ public static Cache getInstance()
+ {
+ return (Cache) ApplicationSingletonProvider.getInstance(Cache.class);
+ }
+
/**
* property giving log4j level for CASTOR loggers
*/
/**
* Sifts settings
*/
- public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
- .getProperty("user.home") + File.separatorChar
- + ".sifts_downloads" + File.separatorChar;
-
+ public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = Platform.getUserPath(".sifts_downloads/");
+
private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
/**
* Identifiers.org download settings
*/
- private static final String ID_ORG_FILE = System.getProperty("user.home")
- + File.separatorChar + ".identifiers.org.ids.json";
+ private static final String ID_ORG_FILE = Platform.getUserPath(".identifiers.org.ids.json");
/**
* Allowed values are PDB or mmCIF
public static Logger log;
/** Jalview Properties */
- public static Properties applicationProperties = new Properties()
+ private Properties applicationProperties = new Properties()
{
// override results in properties output in alphabetical order
@Override
*/
public static void loadProperties(String propsFile)
{
+
+ getInstance().loadPropertiesImpl(propsFile);
+
+ }
+
+ private void loadPropertiesImpl(String propsFile)
+ {
+
propertiesFile = propsFile;
if (propsFile == null && !propsAreReadOnly)
{
- propertiesFile = System.getProperty("user.home") + File.separatorChar
- + ".jalview_properties";
+ propertiesFile = Platform.getUserPath(".jalview_properties");
}
else
{
}
if (authorDetails == null)
{
- applicationProperties.remove("AUTHORS");
- applicationProperties.remove("AUTHORFNAMES");
- applicationProperties.remove("YEAR");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
}
loadBuildProperties(false);
String jnlpVersion = System.getProperty("jalview.version");
- // jnlpVersion will be null if a latest version check for the channel needs to
+ // jnlpVersion will be null if a latest version check for the channel needs
+ // to
// be done
// Dont do this check if running in headless mode
url = Cache.class.getResource(resourcePath).toString();
} catch (Exception ex)
{
- System.err.println("Failed to resolve resource " + resourcePath + ": "
- + ex.getMessage());
+ System.err.println("Failed to resolve resource " + resourcePath
+ + ": " + ex.getMessage());
}
}
else
return url;
}
- public static void loadBuildProperties(boolean reportVersion)
+ public void loadBuildProperties(boolean reportVersion)
{
String codeInstallation = getProperty("INSTALLATION");
boolean printVersion = codeInstallation == null;
new BuildDetails(codeVersion, null, codeInstallation);
if (printVersion && reportVersion)
{
- System.out
- .println("Jalview Version: " + codeVersion + codeInstallation);
+ System.out.println(
+ "Jalview Version: " + codeVersion + codeInstallation);
}
}
- private static void deleteBuildProperties()
+ private void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
applicationProperties.remove("VERSION");
*/
public static String getProperty(String key)
{
- String prop = applicationProperties.getProperty(key);
- if (prop == null && Platform.isJS())
- {
- prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
- + "_" + JS_PROPERTY_PREFIX + key);
- }
+ String prop = getInstance().applicationProperties.getProperty(key);
+ // if (prop == null && Platform.isJS())
+ // {
+ // prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ // + "_" + JS_PROPERTY_PREFIX + key);
+ // }
return prop;
}
*/
public static Object setProperty(String key, String obj)
{
- Object oldValue = null;
- try
- {
- oldValue = applicationProperties.setProperty(key, obj);
- if (propertiesFile != null && !propsAreReadOnly)
- {
- FileOutputStream out = new FileOutputStream(propertiesFile);
- applicationProperties.store(out, "---JalviewX Properties File---");
- out.close();
- }
- } catch (Exception ex)
- {
- System.out.println(
- "Error setting property: " + key + " " + obj + "\n" + ex);
- }
- return oldValue;
+ return getInstance().setPropertyImpl(key, obj, true);
}
/**
- * remove the specified property from the jalview properties file
+ * Removes the specified property from the jalview properties file
*
- * @param string
+ * @param key
*/
- public static void removeProperty(String string)
+ public static void removeProperty(String key)
{
- applicationProperties.remove(string);
- saveProperties();
+ getInstance().removePropertyImpl(key, true);
+ }
+
+ /**
+ * Removes the named property for the running application, without saving the
+ * properties file
+ *
+ * BH noting that ColourMenuHelper calls this. If the intent is to save, then
+ * simply chanet that call to removeProperty(key).
+ *
+ * @param key
+ */
+ public static void removePropertyNoSave(String key)
+ {
+
+ getInstance().
+
+ removePropertyImpl(key, false);
+ }
+
+ /**
+ * Removes the named property, and optionally saves the current properties to
+ * file
+ *
+ * @param key
+ * @param andSave
+ */
+ private void removePropertyImpl(String key, boolean andSave)
+ {
+ applicationProperties.remove(key);
+ if (andSave)
+ saveProperties();
}
/**
*/
public static void saveProperties()
{
+ getInstance().savePropertiesImpl();
+ }
+
+ /**
+ * save the properties to the jalview properties path
+ */
+ private void savePropertiesImpl()
+
+ {
if (!propsAreReadOnly)
{
try
* @param property
* @param colour
*/
- public static void setColourProperty(String property, Color colour)
+ public static void setColourPropertyNoSave(String property, Color colour)
{
- setProperty(property, jalview.util.Format.getHexString(colour));
+ setPropertyNoSave(property, jalview.util.Format.getHexString(colour));
}
/**
public static Date getDateProperty(String propertyName)
{
String val = getProperty(propertyName);
+
if (val != null)
{
try
{
- return date_format.parse(val);
+ if ((val = val.trim()).indexOf(",") < 0 && val.indexOf("-") >= 0 && val.indexOf(" ") == val.lastIndexOf(" ")) {
+ val = val.replace(" ",", ").replace('-',' ');
+ }
+ Date date = date_format.parse(val);
+ return date;
} catch (Exception ex)
{
System.err.println("Invalid or corrupt date in property '"
}
if (value == null || value.trim().length() < 1)
{
- Cache.applicationProperties.remove(propName);
+ getInstance().applicationProperties.remove(propName);
}
else
{
- Cache.applicationProperties.setProperty(propName, value);
+ getInstance().applicationProperties.setProperty(propName, value);
}
}
}
else
{
- applicationProperties
+ getInstance().applicationProperties
.remove(UserDefinedColours.USER_DEFINED_COLOURS);
}
}
}
/**
+ * Initial logging information helper for various versions output
+ *
+ * @param prefix
+ * @param value
+ * @param defaultValue
+ */
+ private static void appendIfNotNull(StringBuilder sb, String prefix,
+ String value, String suffix, String defaultValue)
+ {
+ if (value == null && defaultValue == null)
+ {
+ return;
+ }
+ String line = prefix + (value != null ? value : defaultValue) + suffix;
+ sb.append(line);
+ }
+
+ /**
*
* @return Jalview version, build details and JVM platform version for console
*/
public static String getVersionDetailsForConsole()
{
- return "Jalview Version: "
- + jalview.bin.Cache.getDefault("VERSION", "TEST")
- + "\n" + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION",
- "unknown")
- + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "\n" + "Java version: "
- + System.getProperty("java.version") + "\n"
- + System.getProperty("os.arch") + " "
+ StringBuilder sb = new StringBuilder();
+ sb.append("Jalview Version: "
+ + jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append("\n");
+ sb.append("Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("\n");
+ sb.append("Build Date: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("\n");
+ sb.append("Java version: " + System.getProperty("java.version"));
+ sb.append("\n");
+ sb.append(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
- + System.getProperty("os.version")
- + (jalview.bin.Cache.getDefault("VERSION", "TEST")
- .equals("DEVELOPMENT")
- ? "\nGetdown appdir: " + System.getProperty("getdownappdir") + "\nJava path: "
- + System.getProperty(
- "java.home")
- + File.separator + "bin"
- + File.separator + "java"
- : "");
+ + System.getProperty("os.version"));
+ sb.append("\n");
+ appendIfNotNull(sb, "Install4j version: ",
+ System.getProperty("sys.install4jVersion"), "\n", null);
+ appendIfNotNull(sb, "Install4j template version: ",
+ System.getProperty("installer_template_version"), "\n", null);
+ appendIfNotNull(sb, "Launcher version: ",
+ System.getProperty("launcher_version"), "\n", null);
+ if (jalview.bin.Cache.getDefault("VERSION", "TEST")
+ .equals("DEVELOPMENT"))
+ {
+ appendIfNotNull(sb, "Getdown appdir: ",
+ System.getProperty("getdownappdir"), "\n", null);
+ appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+ "\n", "unknown");
+ }
+ return sb.toString();
}
/**
// eg 'built from Source' or update channel
return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
}
+
+ /**
+ *
+ * For AppletParams and Preferences ok_actionPerformed and
+ * startupFileTextfield_mouseClicked
+ *
+ * Sets a property value for the running application, without saving it to the
+ * properties file
+ *
+ * @param key
+ * @param obj
+ */
+ public static void setPropertyNoSave(String key, String obj)
+ {
+ getInstance().setPropertyImpl(key, obj, false);
+ }
+
+ /**
+ * Sets a property value, and optionally also saves the current properties to
+ * file
+ *
+ * @param key
+ * @param obj
+ * @param andSave
+ * @return
+ */
+ private Object setPropertyImpl(
+ String key, String obj, boolean andSave)
+ {
+ Object oldValue = null;
+ try
+ {
+ oldValue = applicationProperties.setProperty(key, obj);
+ if (andSave && !propsAreReadOnly && propertiesFile != null)
+ {
+ FileOutputStream out = new FileOutputStream(propertiesFile);
+ applicationProperties.store(out, "---JalviewX Properties File---");
+ out.close();
+ }
+ } catch (Exception ex)
+ {
+ System.out.println(
+ "Error setting property: " + key + " " + obj + "\n" + ex);
+ }
+ return oldValue;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff