X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=a3950937e94cc35d907da9f791c9658192eb1586;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=09ebadddced7b7ee2cac1139e9c1e3fceba0c865;hpb=6243301a956bb45508ba97bbb2ab6f627eb86de9;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 09ebadd..a395093 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,28 +1,33 @@
 /*
- * 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 2.8.1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * 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.text.DateFormat;
+import java.text.SimpleDateFormat;
 import java.util.*;
 
 import org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
 
 /**
  * Stores and retrieves Jalview Application Properties Lists and fields within
@@ -40,9 +45,6 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * </li>
  * <li>logs.Jalview.Level - Cache.log stringified level. <br>
  * </li>
- * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
- * startup</li>
- * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.</li>
  * <li>SCREEN_WIDTH</li>
  * <li>SCREEN_HEIGHT</li>
  * <li>SCREEN_Y=285</li>
@@ -106,7 +108,7 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
  * (false)</li>
  * <li>VERSION_CHECK (true) check for the latest release version from
- * www.jalview.org</li>
+ * www.jalview.org (or the alias given by the www.jalview.org property)</li>
  * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
  * ID tooltip</li>
  * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
@@ -125,19 +127,41 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * histogram.</li>
  * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
  * logo.</li>
+ * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.</li>
  * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
  * respond to selections made in other alignments containing the same sequences.
  * </li>
  * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
  * warning dialog box is displayed.</li>
- * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation when shading by annotation</li>
- * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation when shading by annotation</li>
- * 
- * <li></li>
+ * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
+ * when shading by annotation</li>
+ * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
+ * when shading by annotation</li>
+ * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of http://www.jalview.org</li>
  * 
+ * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
+ * alignment figure to accommodate even the longest sequence ID or annotation
+ * label.</li>
+ * <li>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).</li>
  * <li></li>
  * 
  * </ul>
+ * Deprecated settings:
+ * <ul>
+ * *
+ * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * startup (JWS1 services only)</li>
+ * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
+ * (JWS1 services only)</li>
+ * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
+ * services in the desktop GUI</li>
+ * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
+ * panel in web service preferences</li>
+ * </ul>
  * 
  * @author $author$
  * @version $Revision$
@@ -176,7 +200,7 @@ public class Cache
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
-  private static boolean propsAreReadOnly=false;
+  private static boolean propsAreReadOnly = false;
 
   public static void initLogger()
   {
@@ -230,7 +254,9 @@ public class Cache
     {
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
-    } else {
+    }
+    else
+    {
       // don't corrupt the file we've been given.
       propsAreReadOnly = true;
     }
@@ -266,11 +292,34 @@ public class Cache
 
     if (getDefault("USE_PROXY", false))
     {
-      System.out.println("Using proxyServer: "
-              + getDefault("PROXY_SERVER", null) + " proxyPort: "
-              + getDefault("PROXY_PORT", null));
-      System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
-      System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
+      String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
+              "PROXY_PORT", "8080");
+
+      System.out.println("Using proxyServer: " + proxyServer
+              + " proxyPort: " + proxyPort);
+
+      System.setProperty("http.proxyHost", proxyServer);
+      System.setProperty("http.proxyPort", proxyPort);
+    }
+
+    // LOAD THE AUTHORS FROM THE authors.props file
+    try
+    {
+      String authorDetails = "jar:".concat(Cache.class
+              .getProtectionDomain().getCodeSource().getLocation()
+              .toString().concat("!/authors.props"));
+
+      java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+
+      InputStream in = localJarFileURL.openStream();
+      applicationProperties.load(in);
+      in.close();
+    } catch (Exception ex)
+    {
+      System.out.println("Error reading author details: " + ex);
+      applicationProperties.remove("AUTHORS");
+      applicationProperties.remove("AUTHORFNAMES");
+      applicationProperties.remove("YEAR");
     }
 
     // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
@@ -330,8 +379,9 @@ public class Cache
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
-            java.net.URL url = new java.net.URL(
-                    "http://www.jalview.org/webstart/jalview.jnlp");
+            java.net.URL url = new java.net.URL(Cache.getDefault(
+                    "www.jalview.org", "http://www.jalview.org")
+                    + "/webstart/jalview.jnlp");
             BufferedReader in = new BufferedReader(new InputStreamReader(
                     url.openStream()));
             String line = null;
@@ -573,46 +623,6 @@ public class Cache
   }
 
   /**
-   * generate Das1Sources from the local das source list
-   * 
-   * @return Vector of Das1Sources
-   */
-  public static Vector getLocalDasSources()
-  {
-    Vector localSources = new Vector();
-    String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
-    if (local != null)
-    {
-      StringTokenizer st = new StringTokenizer(local, "\t");
-      while (st.hasMoreTokens())
-      {
-        String token = st.nextToken();
-        int bar = token.indexOf("|");
-        Das1Source source = new Das1Source();
-        source.setUrl(token.substring(bar + 1));
-        if (source.getUrl().startsWith("sequence:"))
-        {
-          source.setUrl(source.getUrl().substring(9));
-          // this source also serves sequences as well as features
-          source.setCapabilities(new String[]
-          { "sequence", "features" });
-        }
-        else
-        {
-          // default is that all user added sources serve features
-          source.setCapabilities(new String[]
-          { "features" });
-        }
-
-        source.setNickname(token.substring(0, bar));
-
-        localSources.addElement(source);
-      }
-    }
-    return localSources;
-  }
-
-  /**
    * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
    * enabled.
    */
@@ -731,6 +741,7 @@ public class Cache
 
   /**
    * get the user's default colour if available
+   * 
    * @param property
    * @param defcolour
    * @return
@@ -738,20 +749,113 @@ public class Cache
   public static Color getDefaultColour(String property, Color defcolour)
   {
     String colprop = getProperty(property);
-    if (colprop==null) {
+    if (colprop == null)
+    {
       return defcolour;
     }
-    Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop);
-    if (col==null)
+    Color col = jalview.schemes.ColourSchemeProperty
+            .getAWTColorFromName(colprop);
+    if (col == null)
     {
-      try {
+      try
+      {
         col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
       } catch (Exception ex)
       {
-        log.warn("Couldn't parse '"+colprop+"' as a colour for "+property);
-        col=null;
+        log.warn("Couldn't parse '" + colprop + "' as a colour for "
+                + property);
+        col = null;
+      }
+    }
+    return (col == null) ? defcolour : col;
+  }
+
+  /**
+   * store a colour as a Jalview user default property
+   * 
+   * @param property
+   * @param colour
+   */
+  public static void setColourProperty(String property, Color colour)
+  {
+    setProperty(property, jalview.util.Format.getHexString(colour));
+  }
+
+  public static final DateFormat date_format = SimpleDateFormat
+          .getDateTimeInstance();
+
+  /**
+   * store a date in a jalview property
+   * 
+   * @param string
+   * @param time
+   */
+  public static void setDateProperty(String property, Date time)
+  {
+    setProperty(property, date_format.format(time));
+  }
+
+  /**
+   * read a date stored in a jalview property
+   * 
+   * @param property
+   * @return valid date as stored by setDateProperty, or null
+   * 
+   */
+  public static Date getDateProperty(String property)
+  {
+    String val = getProperty(property);
+    if (val != null)
+    {
+      try
+      {
+        return date_format.parse(val);
+      } catch (Exception ex)
+      {
+        System.err.println("Invalid or corrupt date in property '"
+                + property + "' : value was '" + val + "'");
+      }
+    }
+    return null;
+  }
+
+  /**
+   * get and parse a property as an integer. send any parsing problems to
+   * System.err
+   * 
+   * @param property
+   * @return null or Integer
+   */
+  public static Integer getIntegerProperty(String property)
+  {
+    String val = getProperty(property);
+    if (val != null && (val = val.trim()).length() > 0)
+    {
+      try
+      {
+        return Integer.valueOf(val);
+      } catch (NumberFormatException x)
+      {
+        System.err.println("Invalid integer in property '" + property
+                + "' (value was '" + val + "')");
       }
     }
-    return (col==null) ? defcolour: col;
+    return null;
+  }
+
+  private static DasSourceRegistryI sourceRegistry = null;
+
+  /**
+   * initialise and ..
+   * 
+   * @return instance of the das source registry
+   */
+  public static DasSourceRegistryI getDasSourceRegistry()
+  {
+    if (sourceRegistry == null)
+    {
+      sourceRegistry = new DasSourceRegistry();
+    }
+    return sourceRegistry;
   }
 }