Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

[jalview.git] / src / jalview / bin / Cache.java

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 76fdb69..9363c23 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -21,7 +21,11 @@
 package jalview.bin;
 
 import jalview.datamodel.PDBEntry;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureImportSettings;
+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 +44,7 @@ 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;
@@ -228,11 +233,11 @@ public class Cache
   private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
 
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
-  
+
   /**
    * Allowed values are PDB or mmCIF
    */
-  private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+  private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
           .toString();
 
   private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
@@ -244,8 +249,8 @@ public class Cache
    * even if the user changes their locale setting
    */
   private static final DateFormat date_format = SimpleDateFormat
-          .getDateTimeInstance(SimpleDateFormat.LONG,
-                  SimpleDateFormat.LONG, Locale.UK);
+          .getDateTimeInstance(SimpleDateFormat.MEDIUM,
+                  SimpleDateFormat.MEDIUM, Locale.UK);
 
   /**
    * Initialises the Jalview Application Log
@@ -444,11 +449,12 @@ public class Cache
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
-            .getDefault(
-            "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
+            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
     StructureImportSettings
-            .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
-                    "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
+            .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+    // "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
@@ -525,7 +531,7 @@ 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);
@@ -867,19 +873,11 @@ 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;
   }
@@ -894,7 +892,7 @@ public class Cache
   {
     setProperty(property, jalview.util.Format.getHexString(colour));
   }
-  
+
   /**
    * Stores a formatted date in a jalview property, using a fixed locale.
    * 
@@ -996,4 +994,54 @@ 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 = ColourSchemes.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);
+      }
+    }
+  }
 }