X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=4be78302bbacc10b62ed83a86438be1a081c927d;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=ab0814070c48bb0c8fa52e0eff7bdddc9a25454c;hpb=06931e7445db77675739e0f206d7b5fafc3f9c05;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index ab08140..4be7830 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,28 +1,50 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 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 java.awt.Color;
-import java.io.*;
-import java.util.*;
+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 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.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
@@ -56,6 +78,10 @@ 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