X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=f4b4aac17624c6aba3228ecb88e31308ad444ace;hb=88153d5bb04acd2b8e7fbc3e6789622b77b6cf58;hp=8412dabcc0bbd700627fdcb1189a00fa924fc774;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 8412dab..f4b4aac 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -21,9 +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.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ColorUtils;
import jalview.ws.sifts.SiftsSettings;
import java.awt.Color;
@@ -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;
@@ -70,7 +75,8 @@ 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
@@ -108,7 +114,6 @@ 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
@@ -122,11 +127,13 @@ import org.apache.log4j.SimpleLayout;
* SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
* SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$
+ * STORED_LINKS list of name|url pairs which user has entered but are not
+ * currently used
+ * DEFAULT_LINK name of single url to be used when user double clicks a
+ * 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
@@ -179,6 +186,8 @@ 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:
@@ -214,15 +223,11 @@ 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";
@@ -230,6 +235,12 @@ 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 +270,7 @@ public class Cache
@Override
public synchronized Enumeration