X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=da3cb92bc07a4c333c8ec36e5a981dd9eff10a39;hb=73f4373f0ad3d76ca36a32201d3ed53c255180c5;hp=9363c233c17ebe530e8ee62cf39f80a809a01a5b;hpb=dfb3daaf3d75deda32e7622713ffb759aaadd18c;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 9363c23..da3cb92 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,9 +22,11 @@ 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;
@@ -127,6 +129,10 @@ 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
@@ -184,6 +190,8 @@ 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:
@@ -225,6 +233,9 @@ 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
@@ -235,6 +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
@@ -445,6 +462,10 @@ public class Cache
"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);
@@ -1017,7 +1038,7 @@ public class Cache
String file = st.nextToken();
try
{
- UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+ UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
if (ucs != null)
{
if (coloursFound.length() > 0)