*/
package jalview.bin;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+
import java.awt.Color;
import java.io.*;
import java.text.DateFormat;
import java.util.*;
import org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* histogram.</li>
* <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
* logo.</li>
+ * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.</li>
* <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
* </li>
* <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation when shading by annotation</li>
* <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP requests to be redirected to a mirror of http://www.jalview.org</li>
*
+ * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported alignment figure to accommodate even the longest sequence ID or annotation label.</li>
+ * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true will override this).</li>
* <li></li>
*
* </ul>
if (getDefault("USE_PROXY", false))
{
+ String proxyServer=getDefault("PROXY_SERVER", ""), proxyPort=getDefault("PROXY_PORT", "8080");
+
System.out.println("Using proxyServer: "
- + getDefault("PROXY_SERVER", null) + " proxyPort: "
- + getDefault("PROXY_PORT", null));
- System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
- System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
+ + proxyServer + " proxyPort: "
+ + proxyPort );
+
+ System.setProperty("http.proxyHost", proxyServer);
+ System.setProperty("http.proxyPort", proxyPort);
}
// LOAD THE AUTHORS FROM THE authors.props file
}
/**
- * generate Das1Sources from the local das source list
- *
- * @return Vector of Das1Sources
- */
- public static Vector getLocalDasSources()
- {
- Vector localSources = new Vector();
- String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
- if (local != null)
- {
- StringTokenizer st = new StringTokenizer(local, "\t");
- while (st.hasMoreTokens())
- {
- String token = st.nextToken();
- int bar = token.indexOf("|");
- Das1Source source = new Das1Source();
- source.setUrl(token.substring(bar + 1));
- if (source.getUrl().startsWith("sequence:"))
- {
- source.setUrl(source.getUrl().substring(9));
- // this source also serves sequences as well as features
- source.setCapabilities(new String[]
- { "sequence", "features" });
- }
- else
- {
- // default is that all user added sources serve features
- source.setCapabilities(new String[]
- { "features" });
- }
-
- source.setNickname(token.substring(0, bar));
-
- localSources.addElement(source);
- }
- }
- return localSources;
- }
-
- /**
* GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
* enabled.
*/
}
return null;
}
+
+ /**
+ * get and parse a property as an integer. send any parsing problems to System.err
+ * @param property
+ * @return null or Integer
+ */
+ public static Integer getIntegerProperty(String property)
+ {
+ String val=getProperty(property);
+ if (val!=null && (val=val.trim()).length()>0)
+ {
+ try {
+ return Integer.valueOf(val);
+ } catch (NumberFormatException x)
+ {
+ System.err.println("Invalid integer in property '"+property+"' (value was '"+val+"')");
+ }
+ }
+ 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;
+ }
}