X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=00c8b86fbd116038da11e4b864a77ec6e55c08df;hb=3ea56b3730e5115138af264f5b5408104ebd9c20;hp=d2f400d3f94ed49f3dba42e133ac6fc130611b84;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index d2f400d..00c8b86 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,30 +1,51 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
- *
+ * 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
+import jalview.datamodel.PDBEntry;
+import jalview.structure.StructureImportSettings;
+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.*;
+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 org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.Locale;
+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
@@ -58,6 +79,10 @@ import org.biojava.dasobert.dasregistry.Das1Source;
*
SHOW_QUALITY show alignment quality annotation
*
SHOW_ANNOTATIONS show alignment annotation rows
*
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
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
- *
- *
+ *
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
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:
*
- * *
DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * *
+ *
DISCOVERY_START - Boolean - controls if discovery services are queried on
* startup (JWS1 services only)
- *
DISCOVERY_URLS - comma separated list of Discovery Service endpoints. (JWS1 services only)
- *
SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2 services in the desktop GUI
+ *
DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
+ * (JWS1 services only)
+ *
SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
+ * services in the desktop GUI
+ *
ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
+ * panel in web service preferences
*
+ *
* @author $author$
* @version $Revision$
*/
@@ -169,18 +220,53 @@ public class Cache
public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+ 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
+ */
+ private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
+ .toString();
+
+ 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.MEDIUM,
+ SimpleDateFormat.MEDIUM, Locale.UK);
+
/**
* Initialises the Jalview Application Log
*/
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