X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=7911cd5bab0728fb6976ab5b4d2a60c25c04a801;hb=2f5b2fa149a0bdedff23293ce7c0522b3a3c77ec;hp=d5c54b284b07e79ffc41e79e5d24ee64004ea688;hpb=be5a6a44e9eb355110f3b414d6b0fd5419f5936c;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index d5c54b2..7911cd5 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,28 +1,50 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
-import java.io.*;
-import java.util.*;
-
-import org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
+import jalview.datamodel.DBRefSource;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.ws.sifts.SiftsSettings;
+
+import java.awt.Color;
+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.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;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
@@ -40,9 +62,6 @@ import org.biojava.dasobert.dasregistry.Das1Source;
*
*
SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$
- *
GROUP_LINKS list of name|URL[|<separator>] tuples - see jalview.utils.GroupURLLink for more info
- *
+ *
GROUP_LINKS list of name|URL[|<separator>] tuples - see
+ * jalview.utils.GroupURLLink for more info
*
DAS_REGISTRY_URL the registry to query
*
DEFAULT_BROWSER for unix
*
DAS_ACTIVE_SOURCE list of active sources
*
SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)
- *
VERSION_CHECK (true) check for the latest release version from www.jalview.org
+ *
VERSION_CHECK (true) check for the latest release version from
+ * www.jalview.org (or the alias given by the www.jalview.org property)
*
SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
* ID tooltip
*
SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
@@ -114,17 +138,60 @@ import org.biojava.dasobert.dasregistry.Das1Source;
* displayed as '.'
*
SORT_BY_TREE (false) sort the current alignment view according to the
* order of a newly displayed tree
- *
DBFETCH_USEPICR (false) use PICR to recover valid DB references from sequence ID strings before attempting retrieval from any datasource
- *
SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the alignment.
- *
SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups in the alignment.
- *
SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's histogram.
- *
SHOW_CONSENSUS_PROFILE (false) Show consensus annotation row's sequence logo.
- *
- *
- *
- *
+ *
DBFETCH_USEPICR (false) use PICR to recover valid DB references from
+ * sequence ID strings before attempting retrieval from any datasource
+ *
SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
+ * alignment.
+ *
SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
+ * in the alignment.
+ *
SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
+ * histogram.
+ *
SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo.
+ *
NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.
+ *
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
+ * when shading by annotation
+ *
ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
+ * 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