SHOW_CONSERVATION show alignment conservation annotation
+ *
SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
+ * LABEL_AND_SEQUENCE
+ *
SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
+ * sequence annotations
*
CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
* annotation row
*
DEFAULT_COLOUR default colour scheme to apply for a new alignment
@@ -142,14 +158,21 @@ import org.apache.log4j.*;
* when shading by annotation
*
www.jalview.org (http://www.jalview.org) a property enabling all HTTP
* requests to be redirected to a mirror of http://www.jalview.org
- *
*
FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.
*
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).
- *
+ *
STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
+ * record
+ *
USE_RNAVIEW (false) use RNAViewer to derive secondary structure
ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
+ * display
+ *
STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
+ * display
*
*
* Deprecated settings:
@@ -197,7 +220,13 @@ public class Cache
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