X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=dcd6546ad8bd27f2210c9261761a56f33cbb46f3;hb=4bb7ef2feb729af8a320e9c090e39aee12028375;hp=fc18f587b62697ada089897609858b90da80b487;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index fc18f58..dcd6546 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 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,7 +21,13 @@
 package jalview.bin;
 
 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;
@@ -40,6 +46,7 @@ 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;
@@ -70,7 +77,8 @@ import org.apache.log4j.SimpleLayout;
  * <li>SHOW_FULLSCREEN boolean</li>
  * <li>FONT_NAME java font name for alignment text display</li>
  * <li>FONT_SIZE size of displayed alignment text</li>
- * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always
+ * italic)</li>
  * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
  * <li>LAST_DIRECTORY last directory for browsing alignment</li>
  * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
@@ -122,6 +130,10 @@ import org.apache.log4j.SimpleLayout;
  * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
  * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
  * $SEQUENCE_ID$</li>
+ * <li>STORED_LINKS list of name|url pairs which user has entered but are not
+ * currently used
+ * <li>DEFAULT_LINK name of single url to be used when user double clicks a
+ * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
  * <li>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see
  * jalview.utils.GroupURLLink for more info</li>
  * <li>DAS_REGISTRY_URL the registry to query</li>
@@ -179,6 +191,8 @@ import org.apache.log4j.SimpleLayout;
  * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
  * display</li>
  * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
+ * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
+ * </li>
  * 
  * </ul>
  * Deprecated settings:
@@ -220,9 +234,11 @@ public class Cache
 
   public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
 
+  /**
+   * Sifts settings
+   */
   public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
-          .getProperty("user.home")
-          + File.separatorChar
+          .getProperty("user.home") + File.separatorChar
           + ".sifts_downloads" + File.separatorChar;
 
   private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
@@ -230,6 +246,12 @@ public class Cache
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
 
   /**
+   * Identifiers.org download settings
+   */
+  private static final String ID_ORG_FILE = System.getProperty("user.home")
+          + File.separatorChar + ".identifiers.org.ids.json";
+
+  /**
    * Allowed values are PDB or mmCIF
    */
   private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
@@ -259,7 +281,7 @@ public class Cache
     @Override
     public synchronized Enumeration<Object> keys()
     {
-      return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+      return Collections.enumeration(new TreeSet<>(super.keySet()));
     }
   };
 
@@ -288,8 +310,8 @@ public class Cache
       Logger lcastor = Logger.getLogger("org.exolab.castor");
       jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
 
-      laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
-              Level.INFO.toString())));
+      laxis.setLevel(Level.toLevel(
+              Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
       lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
               Level.INFO.toString())));
       lcastor = Logger.getLogger("org.exolab.castor.xml");
@@ -298,8 +320,8 @@ public class Cache
       // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
       // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
       // Level.INFO.toString())));
-      jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
-              "logs.Jalview.level", Level.INFO.toString())));
+      jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
+              .getDefault("logs.Jalview.level", Level.INFO.toString())));
       // laxis.addAppender(ap);
       // lcastor.addAppender(ap);
       // jalview.bin.Cache.log.addAppender(ap);
@@ -312,7 +334,10 @@ public class Cache
     }
   }
 
-  /** Called when Jalview is started */
+  /**
+   * Loads properties from the given properties file. Any existing properties
+   * are first cleared.
+   */
   public static void loadProperties(String propsFile)
   {
     propertiesFile = propsFile;
@@ -333,10 +358,10 @@ public class Cache
       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.");
+        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)
@@ -347,6 +372,7 @@ public class Cache
       {
         fis = new FileInputStream(propertiesFile);
       }
+      applicationProperties.clear();
       applicationProperties.load(fis);
 
       // remove any old build properties
@@ -360,8 +386,8 @@ public class Cache
 
     if (getDefault("USE_PROXY", false))
     {
-      String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
-              "PROXY_PORT", "8080");
+      String proxyServer = getDefault("PROXY_SERVER", ""),
+              proxyPort = getDefault("PROXY_PORT", "8080");
 
       System.out.println("Using proxyServer: " + proxyServer
               + " proxyPort: " + proxyPort);
@@ -373,9 +399,9 @@ public class Cache
     // LOAD THE AUTHORS FROM THE authors.props file
     try
     {
-      String authorDetails = "jar:".concat(Cache.class
-              .getProtectionDomain().getCodeSource().getLocation()
-              .toString().concat("!/authors.props"));
+      String authorDetails = "jar:"
+              .concat(Cache.class.getProtectionDomain().getCodeSource()
+                      .getLocation().toString().concat("!/authors.props"));
 
       java.net.URL localJarFileURL = new java.net.URL(authorDetails);
 
@@ -429,16 +455,20 @@ public class Cache
     SiftsSettings
             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 
-    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
-            "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+            .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
 
-    SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
-            "sifts_fail_safe_pid_threshold",
-            DEFAULT_FAIL_SAFE_PID_THRESHOLD));
+    SiftsSettings.setFailSafePIDThreshold(
+            jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+                    DEFAULT_FAIL_SAFE_PID_THRESHOLD));
 
-    SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
-            "sifts_cache_threshold_in_days",
-            DEFAULT_CACHE_THRESHOLD_IN_DAYS));
+    SiftsSettings.setCacheThresholdInDays(
+            jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+                    DEFAULT_CACHE_THRESHOLD_IN_DAYS));
+
+    IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+            "http://www.jalview.org/services/identifiers"));
+    IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
@@ -452,8 +482,7 @@ public class Cache
     // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
-    if (jnlpVersion == null
-            && getDefault("VERSION_CHECK", true)
+    if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
             && (System.getProperty("java.awt.headless") == null || System
                     .getProperty("java.awt.headless").equals("false")))
     {
@@ -476,11 +505,11 @@ public class Cache
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
-            java.net.URL url = new java.net.URL(Cache.getDefault(
-                    "www.jalview.org", "http://www.jalview.org")
+            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()));
+            BufferedReader in = new BufferedReader(
+                    new InputStreamReader(url.openStream()));
             String line = null;
             while ((line = in.readLine()) != null)
             {
@@ -496,8 +525,8 @@ public class Cache
             }
           } catch (Exception ex)
           {
-            System.out
-                    .println("Non-fatal exception when checking version at www.jalview.org :");
+            System.out.println(
+                    "Non-fatal exception when checking version at www.jalview.org :");
             System.out.println(ex);
             remoteVersion = getProperty("VERSION");
           }
@@ -526,7 +555,7 @@ public class Cache
     setProperty("VERSION", codeVersion);
 
     // LOAD USERDEFINED COLOURS
-    jalview.gui.UserDefinedColours
+    jalview.bin.Cache
             .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
     jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
             false);
@@ -596,14 +625,14 @@ public class Cache
    * @param obj
    *          String value of property
    * 
-   * @return String value of property
+   * @return previous value of property (or null)
    */
-  public static String setProperty(String key, String obj)
+  public static Object setProperty(String key, String obj)
   {
-
+    Object oldValue = null;
     try
     {
-      applicationProperties.setProperty(key, obj);
+      oldValue = applicationProperties.setProperty(key, obj);
       if (!propsAreReadOnly)
       {
         FileOutputStream out = new FileOutputStream(propertiesFile);
@@ -612,10 +641,10 @@ public class Cache
       }
     } catch (Exception ex)
     {
-      System.out.println("Error setting property: " + key + " " + obj
-              + "\n" + ex);
+      System.out.println(
+              "Error setting property: " + key + " " + obj + "\n" + ex);
     }
-    return obj;
+    return oldValue;
   }
 
   /**
@@ -664,15 +693,15 @@ public class Cache
     {
       try
       {
-        if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
-                "uk.ac.vamsas.client.VorbaId") != null)
+        if (jalview.jbgui.GDesktop.class.getClassLoader()
+                .loadClass("uk.ac.vamsas.client.VorbaId") != null)
         {
-          jalview.bin.Cache.log
-                  .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+          jalview.bin.Cache.log.debug(
+                  "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
           vamsasJarsArePresent = 1;
           Logger lvclient = Logger.getLogger("uk.ac.vamsas");
-          lvclient.setLevel(Level.toLevel(Cache.getDefault(
-                  "logs.Vamsas.Level", Level.INFO.toString())));
+          lvclient.setLevel(Level.toLevel(Cache
+                  .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
 
           lvclient.addAppender(log.getAppender("JalviewLogger"));
           // Tell the user that debug is enabled
@@ -703,15 +732,15 @@ public class Cache
     {
       try
       {
-        if (Cache.class.getClassLoader().loadClass(
-                "groovy.lang.GroovyObject") != null)
+        if (Cache.class.getClassLoader()
+                .loadClass("groovy.lang.GroovyObject") != null)
         {
-          jalview.bin.Cache.log
-                  .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
+          jalview.bin.Cache.log.debug(
+                  "Found Groovy (groovy.lang.GroovyObject can be loaded)");
           groovyJarsArePresent = 1;
           Logger lgclient = Logger.getLogger("groovy");
-          lgclient.setLevel(Level.toLevel(Cache.getDefault(
-                  "logs.Groovy.Level", Level.INFO.toString())));
+          lgclient.setLevel(Level.toLevel(Cache
+                  .getDefault("logs.Groovy.Level", Level.INFO.toString())));
 
           lgclient.addAppender(log.getAppender("JalviewLogger"));
           // Tell the user that debug is enabled
@@ -752,15 +781,14 @@ public class Cache
         // try to get the tracker class
         try
         {
-          jgoogleanalyticstracker = Cache.class
-                  .getClassLoader()
-                  .loadClass(
-                          "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
-          trackerfocus = Cache.class.getClassLoader().loadClass(
-                  "com.boxysystems.jgoogleanalytics.FocusPoint");
+          jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
+                  "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+          trackerfocus = Cache.class.getClassLoader()
+                  .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
         } catch (Exception e)
         {
-          log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+          log.debug(
+                  "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
           tracker = null;
           jgoogleanalyticstracker = null;
           trackerfocus = null;
@@ -774,22 +802,22 @@ public class Cache
       try
       {
         // Google analytics tracking code for Library Finder
-        tracker = jgoogleanalyticstracker.getConstructor(
-                new Class[] { String.class, String.class, String.class })
-                .newInstance(
-                        new Object[] {
-                            "Jalview Desktop",
-                            (vrs = jalview.bin.Cache.getProperty("VERSION")
-                                    + "_"
-                                    + jalview.bin.Cache.getDefault(
-                                            "BUILD_DATE", "unknown")),
-                            "UA-9060947-1" });
-        jgoogleanalyticstracker.getMethod("trackAsynchronously",
-                new Class[] { trackerfocus }).invoke(
-                tracker,
-                new Object[] { trackerfocus.getConstructor(
-                        new Class[] { String.class }).newInstance(
-                        new Object[] { "Application Started." }) });
+        tracker = jgoogleanalyticstracker
+                .getConstructor(new Class[]
+                { String.class, String.class, String.class })
+                .newInstance(new Object[]
+                { "Jalview Desktop",
+                    (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
+                            + jalview.bin.Cache.getDefault("BUILD_DATE",
+                                    "unknown")),
+                    "UA-9060947-1" });
+        jgoogleanalyticstracker
+                .getMethod("trackAsynchronously", new Class[]
+                { trackerfocus })
+                .invoke(tracker, new Object[]
+                { trackerfocus.getConstructor(new Class[] { String.class })
+                        .newInstance(new Object[]
+                        { "Application Started." }) });
       } catch (RuntimeException e)
       {
         re = e;
@@ -806,42 +834,45 @@ public class Cache
         {
           if (re != null)
           {
-            log.debug("Caught runtime exception in googletracker init:", re);
+            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);
+                            + vrs,
+                    ex);
           }
           if (err != null)
           {
             log.error(
                     "Whilst initing GoogleTracker for Jalview Desktop version "
-                            + vrs, err);
+                            + vrs,
+                    err);
           }
         }
         else
         {
           if (re != null)
           {
-            System.err
-                    .println("Debug: Caught runtime exception in googletracker init:"
+            System.err.println(
+                    "Debug: Caught runtime exception in googletracker init:"
                             + vrs);
             re.printStackTrace();
           }
           if (ex != null)
           {
-            System.err
-                    .println("Warning:  Failed to initialise GoogleTracker for Jalview Desktop with version "
+            System.err.println(
+                    "Warning:  Failed to initialise GoogleTracker for Jalview Desktop with version "
                             + vrs);
             ex.printStackTrace();
           }
 
           if (err != null)
           {
-            System.err
-                    .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+            System.err.println(
+                    "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
                             + vrs);
             err.printStackTrace();
           }
@@ -868,19 +899,11 @@ public class Cache
     {
       return defcolour;
     }
-    Color col = jalview.schemes.ColourSchemeProperty
-            .getAWTColorFromName(colprop);
+    Color col = ColorUtils.parseColourString(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;
-      }
+      log.warn("Couldn't parse '" + colprop + "' as a colour for "
+              + property);
     }
     return (col == null) ? defcolour : col;
   }
@@ -997,4 +1020,56 @@ public class Cache
       Cache.applicationProperties.setProperty(propName, value);
     }
   }
+
+  /**
+   * Loads in user colour schemes from files.
+   * 
+   * @param files
+   *          a '|'-delimited list of file paths
+   */
+  public static void initUserColourSchemes(String files)
+  {
+    if (files == null || files.length() == 0)
+    {
+      return;
+    }
+
+    // In case colours can't be loaded, we'll remove them
+    // from the default list here.
+    StringBuffer coloursFound = new StringBuffer();
+    StringTokenizer st = new StringTokenizer(files, "|");
+    while (st.hasMoreElements())
+    {
+      String file = st.nextToken();
+      try
+      {
+        UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
+        if (ucs != null)
+        {
+          if (coloursFound.length() > 0)
+          {
+            coloursFound.append("|");
+          }
+          coloursFound.append(file);
+          ColourSchemes.getInstance().registerColourScheme(ucs);
+        }
+      } catch (Exception ex)
+      {
+        System.out.println("Error loading User ColourFile\n" + ex);
+      }
+    }
+    if (!files.equals(coloursFound.toString()))
+    {
+      if (coloursFound.toString().length() > 1)
+      {
+        setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
+                coloursFound.toString());
+      }
+      else
+      {
+        applicationProperties
+                .remove(UserDefinedColours.USER_DEFINED_COLOURS);
+      }
+    }
+  }
 }