X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=b24304af8e1cebef630a7919ba7e2b03aca088b1;hb=a79f9e113c51c032070c670e45ce3eb464691166;hp=d666b0197c8ca691e73fe5d19349171665fda3ec;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index d666b01..b24304a 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,11 +17,16 @@
  */
 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
@@ -39,9 +44,6 @@ 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>
@@ -105,7 +107,7 @@ 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
@@ -124,16 +126,30 @@ 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>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></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 $Revision$
  */
@@ -171,6 +187,8 @@ public class Cache
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
+  private static boolean propsAreReadOnly=false;
+
   public static void initLogger()
   {
     if (log != null)
@@ -223,11 +241,31 @@ public class Cache
     {
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
+    } else {
+      // don't corrupt the file we've been given.
+      propsAreReadOnly = true;
     }
 
     try
     {
-      FileInputStream fis = new FileInputStream(propertiesFile);
+      InputStream fis;
+      try
+      {
+        fis = new java.net.URL(propertiesFile).openStream();
+        System.out.println("Loading jalview properties from : "
+                + propertiesFile);
+        System.out
+                .println("Disabling Jalview writing to user's local properties file.");
+        propsAreReadOnly = true;
+
+      } catch (Exception ex)
+      {
+        fis = null;
+      }
+      if (fis == null)
+      {
+        fis = new FileInputStream(propertiesFile);
+      }
       applicationProperties.load(fis);
       applicationProperties.remove("LATEST_VERSION");
       applicationProperties.remove("VERSION");
@@ -246,6 +284,26 @@ public class Cache
       System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
     }
 
+    // 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
     // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
     // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
@@ -304,7 +362,7 @@ 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");
+                    Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp");
             BufferedReader in = new BufferedReader(new InputStreamReader(
                     url.openStream()));
             String line = null;
@@ -415,12 +473,16 @@ public class Cache
    */
   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();
+      if (!propsAreReadOnly)
+      {
+        FileOutputStream out = new FileOutputStream(propertiesFile);
+        applicationProperties.store(out, "---JalviewX Properties File---");
+        out.close();
+      }
     } catch (Exception ex)
     {
       System.out.println("Error setting property: " + key + " " + obj
@@ -445,14 +507,17 @@ public class Cache
    */
   public static void saveProperties()
   {
-    try
-    {
-      FileOutputStream out = new FileOutputStream(propertiesFile);
-      applicationProperties.store(out, "---JalviewX Properties File---");
-      out.close();
-    } catch (Exception ex)
+    if (!propsAreReadOnly)
     {
-      System.out.println("Error saving properties: " + ex);
+      try
+      {
+        FileOutputStream out = new FileOutputStream(propertiesFile);
+        applicationProperties.store(out, "---JalviewX Properties File---");
+        out.close();
+      } catch (Exception ex)
+      {
+        System.out.println("Error saving properties: " + ex);
+      }
     }
   }
 
@@ -539,46 +604,6 @@ 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.
    */
@@ -695,4 +720,106 @@ public class Cache
     }
   }
 
+  /**
+   * get the user's default colour if available
+   * @param property
+   * @param defcolour
+   * @return
+   */
+  public static Color getDefaultColour(String property, Color defcolour)
+  {
+    String colprop = getProperty(property);
+    if (colprop==null) {
+      return defcolour;
+    }
+    Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop);
+    if (col==null)
+    {
+      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;
+      }
+    }
+    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 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;
+  }
 }