import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
+ import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+ import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
+ import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.Enumeration;
+ import java.util.HashMap;
import java.util.List;
import java.util.Locale;
+ import java.util.Map;
import java.util.Properties;
import java.util.StringTokenizer;
import java.util.TreeSet;
import javax.swing.UIManager;
import jalview.analytics.Plausible;
+ import jalview.bin.argparser.Arg;
+ import jalview.bin.argparser.ArgParser;
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
* <li>WRAP_ALIGNMENT</li>
* <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
* style check</li>
+ * <li>BITMAP_SCALE - scale factor for PNG export - default 0.0 - native
+ * resolution</li>
+ * <li>BITMAP_HEIGHT - height bound for PNG export or 0 for unbound</li>
+ * <li>BITMAP_WIDTH - width bound for PNG export or 0 for unbound</li>
* <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
* <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$</li>
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+ // for tests
+ public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
+
/**
* Sifts settings
*/
// in-memory only storage of proxy password, safer to use char array
public static char[] proxyAuthPassword = null;
+ /**
+ * Session properties, set by command line, try not to affect stored
+ * properties!
+ */
+ private static Map<String, String> sessionProperties = new HashMap<>();
+
+ private static boolean bypassSessionProperties = false;
+
+ public static void enableSessionProperties()
+ {
+ bypassSessionProperties = false;
+ }
+
+ public static void disableSessionProperties()
+ {
+ bypassSessionProperties = true;
+ }
+
/** Jalview Properties */
public static Properties applicationProperties = new Properties()
{
/** Default file is ~/.jalview_properties */
static String propertiesFile;
+ private static final String fallbackPropertiesFile = ".jalview_properties";
+
private static boolean propsAreReadOnly = Platform.isJS();
+ public static boolean isPropsAreReadOnly()
+ {
+ return propsAreReadOnly;
+ }
+
+ public static void setPropsAreReadOnly(boolean propsAreReadOnly)
+ {
+ Cache.propsAreReadOnly = propsAreReadOnly;
+ }
+
private final static String JS_PROPERTY_PREFIX = "jalview_";
/**
{
String channelPrefsFilename = ChannelProperties
.getProperty("preferences.filename");
- String releasePrefsFilename = ".jalview_properties";
+ String releasePrefsFilename = fallbackPropertiesFile;
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ channelPrefsFilename;
releasePropertiesFile = System.getProperty("user.home")
{
// props file provided as URL
fis = new URL(propertiesFile).openStream();
- System.out.println(
- "Loading jalview properties from : " + propertiesFile);
- System.out.println(
- "Disabling Jalview writing to user's local properties file.");
+ if (!Jalview.quiet())
+ {
+ jalview.bin.Console.outPrintln(
+ "Loading jalview properties from : " + propertiesFile);
+ jalview.bin.Console.outPrintln(
+ "Disabling Jalview writing to user's local properties file.");
+ }
propsAreReadOnly = true;
} catch (Exception ex)
{
fis.close();
} catch (Exception ex)
{
- System.out.println("Error reading properties file: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error reading properties file: " + ex);
}
}
}
} catch (Exception ex)
{
- System.out.println("Error reading author details: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error reading author details: " + ex);
authorDetails = null;
}
if (authorDetails == null)
if (orgtimeout == null)
{
orgtimeout = "30";
- System.out.println("# INFO: Setting default net timeout to "
- + orgtimeout + " seconds.");
+ Console.debug("Setting default net timeout to " + orgtimeout
+ + " seconds.");
}
String remoteVersion = null;
if (remoteBuildPropertiesUrl.startsWith("http"))
remoteVersion = remoteBuildProperties.getProperty("VERSION");
} catch (Exception ex)
{
- System.out.println(
- "Non-fatal exception when checking version at "
- + remoteBuildPropertiesUrl + ":");
- System.out.println(ex);
+ if (!Jalview.quiet())
+ {
+ jalview.bin.Console.errPrintln(
+ "Non-fatal exception when checking version at "
+ + remoteBuildPropertiesUrl + ":");
+ jalview.bin.Console.printStackTrace(ex);
+ }
remoteVersion = getProperty("VERSION");
}
}
url = Cache.class.getResource(resourcePath).toString();
} catch (Exception ex)
{
- System.err.println("Failed to resolve resource " + resourcePath
- + ": " + ex.getMessage());
+ jalview.bin.Console.errPrintln("Failed to resolve resource "
+ + resourcePath + ": " + ex.getMessage());
}
}
else
}
} catch (Exception ex)
{
- System.out.println("Error reading build details: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error reading build details: " + ex);
applicationProperties.remove("VERSION");
}
String codeVersion = getProperty("VERSION");
new BuildDetails(codeVersion, null, codeInstallation);
if (printVersion && reportVersion)
{
- System.out.println(ChannelProperties.getProperty("app_name")
- + " Version: " + codeVersion + codeInstallation);
+ jalview.bin.Console
+ .outPrintln(ChannelProperties.getProperty("app_name")
+ + " version: " + codeVersion + codeInstallation);
}
}
*/
public static String getProperty(String key)
{
- String prop = applicationProperties.getProperty(key);
+ return getProperty(key, false);
+ }
+
+ public static String getProperty(String key,
+ boolean skipSessionProperties)
+ {
+ String prop = null;
+ if (!(skipSessionProperties || bypassSessionProperties))
+ {
+ prop = getSessionProperty(key);
+ }
+ if (prop == null)
+ {
+ prop = applicationProperties.getProperty(key);
+ }
if (prop == null && Platform.isJS())
{
prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
def = Integer.parseInt(string);
} catch (NumberFormatException e)
{
- System.out.println("Error parsing int property '" + property
- + "' with value '" + string + "'");
+ if (!Jalview.quiet())
+ jalview.bin.Console.errPrintln("Error parsing int property '"
+ + property + "' with value '" + string + "'");
+ }
+ }
+
+ return def;
+ }
+
+ public static float getDefault(String property, float def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ try
+ {
+ def = Float.parseFloat(string);
+ } catch (NumberFormatException e)
+ {
+ if (!Jalview.quiet())
+ jalview.bin.Console.errPrintln("Error parsing float property '"
+ + property + "' with value '" + string + "'");
}
}
try
{
oldValue = applicationProperties.setProperty(key, obj);
- if (propertiesFile != null && !propsAreReadOnly)
+ if (propertiesFile != null && !propsAreReadOnly
+ // don't rewrite if new value is same as old value
+ && !((obj == null && oldValue == null)
+ || (obj != null && obj.equals(oldValue))))
{
+ // reset the session property too
+ if (sessionProperties.containsKey(key))
+ {
+ sessionProperties.remove(key);
+ }
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);
+ if (!Jalview.quiet())
+ jalview.bin.Console.errPrintln(
+ "Error setting property: " + key + " " + obj + "\n" + ex);
}
return oldValue;
}
out.close();
} catch (Exception ex)
{
- System.out.println("Error saving properties: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console.errPrintln("Error saving properties: " + ex);
}
}
}
return date_format.parse(val);
} catch (Exception ex)
{
- System.err.println("Invalid or corrupt date in property '"
- + propertyName + "' : value was '" + val + "'");
+ jalview.bin.Console
+ .errPrintln("Invalid or corrupt date in property '"
+ + propertyName + "' : value was '" + val + "'");
}
}
return null;
return Integer.valueOf(val);
} catch (NumberFormatException x)
{
- System.err.println("Invalid integer in property '" + property
- + "' (value was '" + val + "')");
+ jalview.bin.Console.errPrintln("Invalid integer in property '"
+ + property + "' (value was '" + val + "')");
}
}
return null;
}
} catch (Exception ex)
{
- System.out.println("Error loading User ColourFile\n" + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error loading User ColourFile\n" + ex);
}
}
if (!files.equals(coloursFound.toString()))
sb.append("Java version: ");
sb.append(System.getProperty("java.version"));
sb.append("\n");
+ sb.append("Java platform: ");
sb.append(System.getProperty("os.arch"));
sb.append(" ");
sb.append(System.getProperty("os.name"));
sb.append(" (");
sb.append(lafClass);
sb.append(")\n");
+ appendIfNotNull(sb, "Channel: ",
+ ChannelProperties.getProperty("channel"), "\n", null);
if (Console.isDebugEnabled()
|| !"release".equals(ChannelProperties.getProperty("channel")))
{
- appendIfNotNull(sb, "Channel: ",
- ChannelProperties.getProperty("channel"), "\n", null);
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdowninstanceappdir"), "\n", null);
appendIfNotNull(sb, "Getdown appbase: ",
System.getProperty("getdowninstanceappbase"), "\n", null);
appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
"\n", "unknown");
+ appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n",
+ "unknown");
}
return sb.toString();
}
if (customProxySet &&
// we have a username but no password for the scheme being
// requested
- (protocol.equalsIgnoreCase("http")
- && (httpUser != null && httpUser.length() > 0
- && (httpPassword == null
- || httpPassword.length == 0)))
+ (protocol.equalsIgnoreCase("http")
+ && (httpUser != null
+ && httpUser.length() > 0
+ && (httpPassword == null
+ || httpPassword.length == 0)))
|| (protocol.equalsIgnoreCase("https")
&& (httpsUser != null
&& httpsUser.length() > 0
String appbase = getGetdownAppbase();
return appbase + "/" + getdownDistDir + "/build_properties";
}
+
+ private static final Collection<String> bootstrapProperties = new ArrayList<>(
+ Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
+
+ public static Properties bootstrapProperties(String filename)
+ {
+ Properties bootstrapProps = new Properties();
+ File file = null;
+ if (filename != null)
+ {
+ file = new File(filename);
+ }
+ if (file == null || !file.exists())
+ {
+ if (file != null)
+ {
+ jalview.bin.Console
+ .errPrintln("Could not load bootstrap preferences file '"
+ + file.getPath() + "'");
+ }
+ String channelPrefsFilename = ChannelProperties
+ .getProperty("preferences.filename");
+ String propertiesFilename = System.getProperty("user.home")
+ + File.separatorChar + channelPrefsFilename;
+ jalview.bin.Console.errPrintln(
+ "Using default properties file '" + propertiesFilename + "'");
+ file = new File(propertiesFilename);
+ }
+ if (file == null || !file.exists())
+
+ {
+ String releasePrefsFilename = fallbackPropertiesFile;
+ String releasePropertiesFilename = System.getProperty("user.home")
+ + File.separatorChar + releasePrefsFilename;
+ jalview.bin.Console.errPrintln("Falling back to properties file '"
+ + releasePropertiesFilename + "'");
+ file = new File(releasePropertiesFilename);
+ }
+
+ if (!file.exists())
+ {
+ jalview.bin.Console
+ .errPrintln("Could not load bootstrap preferences file '"
+ + file.getPath() + "'");
+ return null;
+ }
+
+ try
+ {
+ FileInputStream in = new FileInputStream(file.getAbsoluteFile());
+ Properties props = new Properties();
+ props.load(in);
+ for (String prop : bootstrapProperties)
+ {
+ if (props.containsKey(prop))
+ bootstrapProps.put(prop, props.getProperty(prop));
+ }
+ } catch (FileNotFoundException e)
+ {
+ jalview.bin.Console
+ .errPrintln("Could not find bootstrap preferences file '"
+ + file.getAbsolutePath() + "'");
+ } catch (IOException e)
+ {
+ jalview.bin.Console.errPrintln(
+ "IOException when loading bootstrap preferences file '"
+ + file.getAbsolutePath() + "'");
+ }
+ return bootstrapProps;
+ }
+
+ public static void setSessionProperty(String key, String val)
+ {
+ if (key != null)
+ {
+ sessionProperties.put(key, val);
+ }
+ }
+
+ public static String getSessionProperty(String key)
+ {
+ return key == null ? null : sessionProperties.get(key);
+ }
+
+ public static boolean getArgCacheDefault(Arg a, String pref, boolean def)
+ {
+ ArgParser ap = Jalview.getInstance().getArgParser();
+ return ap.isSet(a) ? ap.getBoolean(a) : getDefault(pref, def);
+ }
}
git://source.jalview.org / jalview.git / commitdiff