import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import java.awt.Color;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.io.InputStreamReader;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
-import java.util.*;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.Properties;
+import java.util.TreeSet;
-import org.apache.log4j.*;
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* <li>SHOW_QUALITY show alignment quality annotation</li>
* <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
* <li>SHOW_CONSERVATION show alignment conservation annotation</li>
+ * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
+ * LABEL_AND_SEQUENCE</li>
+ * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
+ * sequence annotations</li>
* <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
* annotation row</li>
* <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
* 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>
+ * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
+ * record</li>
+ * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
+ * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
+ * display</li>
+ * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
+ * display</li>
+ * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
+ * display</li>
*
* </ul>
* Deprecated settings:
public static Logger log;
/** Jalview Properties */
- public static Properties applicationProperties = new Properties();
+ public static Properties applicationProperties = new Properties() {
+ // override results in properties output in alphabetical order
+ @Override
+ public synchronized Enumeration<Object> keys() {
+ return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ }
+ };
/** Default file is ~/.jalview_properties */
static String propertiesFile;
if (log != null)
{
if (re != null)
+ {
log.debug("Caught runtime exception in googletracker init:", re);
+ }
if (ex != null)
+ {
log.warn(
"Failed to initialise GoogleTracker for Jalview Desktop with version "
+ vrs, ex);
+ }
if (err != null)
+ {
log.error(
"Whilst initing GoogleTracker for Jalview Desktop version "
+ vrs, err);
+ }
}
else
{