X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=dcd6546ad8bd27f2210c9261761a56f33cbb46f3;hb=a60d992b2ca2df9bcd0934959c16d40112f3136b;hp=6764430447e8e51547331df5c08c645ad9626772;hpb=2d18ff6c5ccbd11297b80f70591dc0cb2f6aace6;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 6764430..dcd6546 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -21,8 +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;
@@ -41,6 +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;
@@ -71,7 +77,8 @@ 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
@@ -184,6 +191,8 @@ 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:
@@ -229,8 +238,7 @@ public class Cache
* 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 +249,7 @@ 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
@@ -275,7 +281,7 @@ public class Cache
@Override
public synchronized Enumeration