X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=dc5084347e9bc01cab00b33cf6a8a44479085053;hb=0b93ce8953aaec40a5e06f076cd0b7378f44291d;hp=60fae3739f8a24c94dcc019b6293134d44134e03;hpb=74666bccffce69d865cfc5479f81f394e2d14d5e;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 60fae37..dc50843 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,28 +1,58 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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 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 org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
+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
@@ -40,76 +70,143 @@ import org.biojava.dasobert.dasregistry.Das1Source;
*
*
DISCOVERY_START - Boolean - controls if discovery services are queried
- * on startup
- *
DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
- *
- *
SCREEN_WIDTH
- *
SCREEN_HEIGHT
- *
SCREEN_Y=285
- *
SCREEN_X=371
- *
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)
- *
- *
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
+ *
SCREEN_WIDTH
+ *
SCREEN_HEIGHT
+ *
SCREEN_Y=285
+ *
SCREEN_X=371
+ *
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)
+ *
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
+ * 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
+ * www.jalview.org
*
PIR_MODELLER boolean indicating if PIR files are written with MODELLER
- * descriptions
+ * 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
+ * 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
+ * service
*
QUESTIONNAIRE last questionnaire:responder id string from questionnaire
- * service
- *
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
+ * 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)
+ * style check
+ *
SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
*
SEQUENCE_LINKS list of name|URL pairs for opening a url with
- * $SEQUENCE_ID$
- *
DAS_REGISTRY_URL the registry to query
- *
DEFAULT_BROWSER for unix
- *
DAS_ACTIVE_SOURCE list of active sources
+ * $SEQUENCE_ID$
+ *
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)
- *
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 '.'
- *
+ * (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