X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=9dcc949ee84d8b111e81d0964b0496d31d9f4aca;hb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;hp=6764430447e8e51547331df5c08c645ad9626772;hpb=2d18ff6c5ccbd11297b80f70591dc0cb2f6aace6;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 6764430..9dcc949 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -21,10 +21,14 @@
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.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.util.ColorUtils;
+import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
import java.awt.Color;
@@ -41,6 +45,7 @@ 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;
@@ -71,7 +76,8 @@ import org.apache.log4j.SimpleLayout;
*
SHOW_FULLSCREEN boolean
* FONT_NAME java font name for alignment text display
* FONT_SIZE size of displayed alignment text
- * FONT_STYLE style of font displayed (sequence labels are always italic)
+ * FONT_STYLE style of font displayed (sequence labels are always
+ * italic)
* GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
* LAST_DIRECTORY last directory for browsing alignment
* USER_DEFINED_COLOURS list of user defined colour scheme files
@@ -109,7 +115,6 @@ import org.apache.log4j.SimpleLayout;
* service
* USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics
- * DAS_LOCAL_SOURCE list of local das sources
* SHOW_OVERVIEW boolean for overview window display
* ANTI_ALIAS boolean for smooth fonts
* RIGHT_ALIGN_IDS boolean
@@ -129,9 +134,7 @@ import org.apache.log4j.SimpleLayout;
* sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info
- * DAS_REGISTRY_URL the registry to query
* DEFAULT_BROWSER for unix
- * DAS_ACTIVE_SOURCE list of active sources
* SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)
* VERSION_CHECK (true) check for the latest release version from
@@ -184,6 +187,8 @@ import org.apache.log4j.SimpleLayout;
* STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
* display
* CHIMERA_PATH specify full path to Chimera program (if non-standard)
+ * ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
+ *
*
*
* Deprecated settings:
@@ -219,18 +224,11 @@ public class Cache
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
- public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
- 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";
@@ -241,9 +239,7 @@ public class Cache
* Identifiers.org download settings
*/
private static final String ID_ORG_FILE = System.getProperty("user.home")
- + File.separatorChar + ".jalview_identifiers";
-
- private static final String ID_ORG_URL = "http://identifiers.org/rest/collections/";
+ + File.separatorChar + ".identifiers.org.ids.json";
/**
* Allowed values are PDB or mmCIF
@@ -275,14 +271,16 @@ public class Cache
@Override
public synchronized Enumeration