X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=9e51d67b32e11de34d9dde2b3d2259e009008c4d;hb=76cfeb5e50dd69a3ba963096556f9677c9eea55a;hp=5d26b850de6d3dfbacc14c301031d670909d33ae;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 5d26b85..9e51d67 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,32 +1,62 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
-
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.io.PrintWriter;
+import java.io.StringWriter;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
-import java.util.*;
-
-import org.apache.log4j.*;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.Locale;
+import java.util.Properties;
+import java.util.StringTokenizer;
+import java.util.TreeSet;
+import java.util.regex.Pattern;
+
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+
+import jalview.datamodel.PDBEntry;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ColorUtils;
+import jalview.ws.sifts.SiftsSettings;
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
@@ -51,7 +81,8 @@ import org.apache.log4j.*;
*
SHOW_FULLSCREEN boolean
*
FONT_NAME java font name for alignment text display
*
FONT_SIZE size of displayed alignment text
- *
FONT_STYLE style of font displayed (sequence labels are always italic)
+ *
FONT_STYLE style of font displayed (sequence labels are always
+ * italic)
*
GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
*
LAST_DIRECTORY last directory for browsing alignment
*
USER_DEFINED_COLOURS list of user defined colour scheme files
@@ -60,6 +91,10 @@ import org.apache.log4j.*;
*
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
@@ -85,7 +120,6 @@ import org.apache.log4j.*;
* service
*
USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics
- *
DAS_LOCAL_SOURCE list of local das sources
*
SHOW_OVERVIEW boolean for overview window display
*
ANTI_ALIAS boolean for smooth fonts
*
RIGHT_ALIGN_IDS boolean
@@ -99,11 +133,13 @@ import org.apache.log4j.*;
*
SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
*
SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$
+ *
STORED_LINKS list of name|url pairs which user has entered but are not
+ * currently used
+ *
DEFAULT_LINK name of single url to be used when user double clicks a
+ * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
*
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
@@ -131,23 +167,40 @@ import org.apache.log4j.*;
*
FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
*
+ *
SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services
+ *
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
- *
+ *
www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://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)
+ *
ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
+ *
*
+ *
NONEWS - when set disables Jalview News from automatically appearing
+ *
NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically
*
* Deprecated settings:
*
@@ -182,11 +235,40 @@ public class Cache
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
- public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
+ /**
+ * Sifts settings
+ */
+ 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";
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
+ private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
- public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+ /**
+ * Identifiers.org download settings
+ */
+ private static final String ID_ORG_FILE = System.getProperty("user.home")
+ + File.separatorChar + ".identifiers.org.ids.json";
+
+ /**
+ * 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
@@ -194,7 +276,15 @@ 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