X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=21a030b075468c8009ad3565e7cae53f57b88d92;hb=7c5e7c1c51a48eab1b217a221df82748c35b76b1;hp=2ba6e3a63469303eea0d8f3ec4f746b6c80bef59;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 2ba6e3a..21a030b 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.bin;
 
@@ -21,12 +24,24 @@ 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.text.DateFormat;
 import java.text.SimpleDateFormat;
-import java.util.*;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.Properties;
+import java.util.TreeSet;
 
-import org.apache.log4j.*;
+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
@@ -60,6 +75,10 @@ import org.apache.log4j.*;
  * <li>SHOW_QUALITY show alignment quality annotation</li>
  * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
  * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
+ * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
+ * LABEL_AND_SEQUENCE</li>
+ * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
+ * sequence annotations</li>
  * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
  * annotation row</li>
  * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
@@ -188,13 +207,26 @@ public class Cache
 
   public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
 
+  /*
+   * Property key/value constants
+   */
+  public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+  public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
   /**
    * 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<Object> keys() {
+        return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+    }
+  };
 
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
@@ -281,8 +313,10 @@ public class Cache
         fis = new FileInputStream(propertiesFile);
       }
       applicationProperties.load(fis);
-      applicationProperties.remove("LATEST_VERSION");
-      applicationProperties.remove("VERSION");
+      
+      // remove any old build properties
+      
+      deleteBuildProperties();
       fis.close();
     } catch (Exception ex)
     {
@@ -434,6 +468,15 @@ public class Cache
             false);
   }
 
+  private static void deleteBuildProperties()
+  {
+    applicationProperties.remove("LATEST_VERSION");
+    applicationProperties.remove("VERSION");
+    applicationProperties.remove("AUTHORS");
+    applicationProperties.remove("AUTHORFNAMES");
+    applicationProperties.remove("YEAR");
+  }
+
   /**
    * Gets Jalview application property of given key. Returns null if key not
    * found
@@ -695,15 +738,21 @@ public class Cache
         if (log != null)
         {
           if (re != null)
+          {
             log.debug("Caught runtime exception in googletracker init:", re);
+          }
           if (ex != null)
+          {
             log.warn(
                     "Failed to initialise GoogleTracker for Jalview Desktop with version "
                             + vrs, ex);
+          }
           if (err != null)
+          {
             log.error(
                     "Whilst initing GoogleTracker for Jalview Desktop version "
                             + vrs, err);
+          }
         }
         else
         {