X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FCache.java;h=da3cb92bc07a4c333c8ec36e5a981dd9eff10a39;hb=864558097ceffef983b15f24598cfdaf20efd52d;hp=8e5e240ac112920acdfa2887180ac591054ba04a;hpb=62737d15c0edb48128eb9ac6fe7fa419ab984125;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 8e5e240..da3cb92 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,168 +1,1068 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
- */
-package jalview.bin;
-
-import java.io.*;
-
-import java.util.*;
-
-import java.net.*;
-
-
-/**
- * Stores and retrieves Jalview Application Properties
- *
Current properties include:
- * logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
- * logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
- * jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.
- * SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN
- * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
- * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
- * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE
-
- * @author $author$
- * @version $Revision$
- */
-public class Cache
-{
-
- /** Jalview Properties */
- public static Properties applicationProperties;
-
- /** Default file is ~/.jalview_properties */
- static String propertiesFile;
-
- /** Called when Jalview is started */
- public static void loadProperties(String propsFile)
- {
- applicationProperties = new Properties();
-
- propertiesFile = propsFile;
- if (propsFile == null)
- {
- propertiesFile = System.getProperty("user.home") + "/.jalview_properties";
- }
-
- try
- {
- FileInputStream fis = new FileInputStream(propertiesFile);
- applicationProperties.load(fis);
- fis.close();
- }
- catch (Exception ex)
- {
- System.out.println("Error reading properties file: "+ex);
- }
-
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
- // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
- // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
- try
- {
- String buildDetails = "jar:"
- .concat(
- Cache.class.getProtectionDomain().getCodeSource().getLocation().toString()
- .concat("!/.build_properties")
- );
-
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- }
- catch (Exception ex)
- {
- System.out.println("Error reading build details: "+ex);
- applicationProperties.remove("VERSION");
- }
-
- String jnlpVersion = System.getProperty("jalview.version");
- String codeVersion = getProperty("VERSION");
-
- if(codeVersion==null)
- {
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
- codeVersion = "Test";
- jnlpVersion = "Test";
- setProperty("jalview.version", jnlpVersion);
- setProperty("VERSION", codeVersion);
- }
-
-
- // jnlpVersion will be null if we're using InstallAnywhere
- if(jnlpVersion==null)
- {
- try{
- java.net.URL url = new java.net.URL("http://www.jalview.org/webstart/jalview.jnlp");
- BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
- String line = null;
- while( (line = in.readLine()) !=null)
- {
- if(line.indexOf("jalview.version")==-1)
- continue;
-
- line = line.substring(line.indexOf("value=")+7);
- line = line.substring(0, line.lastIndexOf("\""));
- setProperty("jalview.version", line);
- }
- }catch(Exception ex)
- { setProperty("jalview.version", codeVersion); }
- }
- }
-
- /**
- * Gets Jalview application property of given key. Returns null
- * if key not found
- *
- * @param key Name of property
- *
- * @return Property value
- */
- public static String getProperty(String key)
- {
- return applicationProperties.getProperty(key);
- }
-
- /**
- * Stores property in the file "HOME_DIR/.jalview_properties"
- *
- * @param key Name of object
- * @param obj String value of property
- *
- * @return String value of property
- */
- public static String setProperty(String key, String obj)
- {
- try
- {
- FileOutputStream out = new FileOutputStream(propertiesFile);
-
- applicationProperties.setProperty(key, obj);
-
- applicationProperties.store(out, "---JalviewX Properties File---");
- out.close();
- }
- catch (Exception ex)
- {
- }
-
- return obj;
- }
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.bin;
+
+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.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.Locale;
+import java.util.Properties;
+import java.util.StringTokenizer;
+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
+ * list entries are separated by '|' symbols unless otherwise stated (|) clauses
+ * are alternative values for a tag.
+ *
+ * Current properties include:
+ *
+ *
+ * logs.Axis.Level - one of the stringified Levels for log4j controlling the
+ * logging level for axis (used for web services)
+ *
+ *
logs.Castor.Level - one of the stringified Levels for log4j controlling
+ * the logging level for castor (used for serialization)
+ *
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)
+ *
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
+ *
SHOW_FULL_ID show id with '/start-end' numbers appended
+ *
SHOW_IDENTITY show percentage identity annotation
+ *
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
+ *
DEFAULT_FILE_FORMAT file format used to save
+ *
STARTUP_FILE file loaded on startup (may be a fully qualified url)
+ *
SHOW_STARTUP_FILE flag to control loading of startup file
+ *
VERSION the version of the jalview build
+ *
BUILD_DATE date of this build
+ *
LATEST_VERSION the latest jalview version advertised on the
+ * www.jalview.org
+ *
PIR_MODELLER boolean indicating if PIR files are written with MODELLER
+ * descriptions
+ *
(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
+ * suffix to file
+ *
RECENT_URL list of recently retrieved URLs
+ *
RECENT_FILE list of recently opened files
+ *
USE_PROXY flag for whether a http proxy is to be used
+ *
PROXY_SERVER the proxy
+ *
PROXY_PORT
+ *
NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
+ * service
+ *
QUESTIONNAIRE last questionnaire:responder id string from questionnaire
+ * 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
+ *
AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
+ *
PAD_GAPS boolean
+ *
ID_ITALICS boolean
+ *
SHOW_JV_SUFFIX
+ *
WRAP_ALIGNMENT
+ *
EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
+ * style check
+ *
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
+ * 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
+ * ID tooltip
+ *
SHOW_UNCONSERVED (false) only render unconserved residues - conserved
+ * 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_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