FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
*
+ *
JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services
*
SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* warning dialog box is displayed.
*
ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
@@ -158,14 +163,22 @@ import org.apache.log4j.SimpleLayout;
* 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
+ *
CHIMERA_PATH specify full path to Chimera program (if non-standard)
*
*
* Deprecated settings:
@@ -207,12 +220,32 @@ public class Cache
public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
- /*
- * Property key/value constants
+ public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
+ .getProperty("user.home")
+ + File.separatorChar
+ + ".sifts_downloads" + File.separatorChar;
+
+ private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
+
+ private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
+
+ /**
+ * Allowed values are PDB or mmCIF
*/
- public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+ private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+ .toString();
- public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+ private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString();
+
+ /*
+ * a date formatter using a fixed (rather than the user's) locale;
+ * this ensures that date properties can be written and re-read successfully
+ * even if the user changes their locale setting
+ */
+ private static final DateFormat date_format = SimpleDateFormat
+ .getDateTimeInstance(SimpleDateFormat.LONG,
+ SimpleDateFormat.LONG, Locale.UK);
/**
* Initialises the Jalview Application Log
@@ -220,11 +253,13 @@ 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