X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=641815d1fad408c3f1782800efa103ef921c7242;hb=7fef0501bb64f11080bdb93ee0824416d84784cc;hp=2a9f53d212f0fe193fc1e560324cd2cb72f31e58;hpb=eaf9092bfa74b5162589c8775f68a19dd79dbb1d;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 2a9f53d..641815d 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
@@ -32,8 +32,11 @@ import java.io.InputStream;
import java.io.InputStreamReader;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
+import java.util.Collections;
import java.util.Date;
+import java.util.Enumeration;
import java.util.Properties;
+import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
@@ -147,6 +150,7 @@ import org.apache.log4j.SimpleLayout;
*
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
@@ -155,14 +159,22 @@ 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:
@@ -210,7 +222,13 @@ 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