X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=da3cb92bc07a4c333c8ec36e5a981dd9eff10a39;hb=73f4373f0ad3d76ca36a32201d3ed53c255180c5;hp=6b1aef949e6dc1d90cc6b217fcd0487a9b9a3380;hpb=b0cee3aaf7d8873910939f97b6acb217d518968d;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 6b1aef9..da3cb92 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -21,7 +21,12 @@
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;
@@ -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;
@@ -123,6 +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
@@ -180,6 +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:
@@ -221,6 +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
@@ -231,6 +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
@@ -441,6 +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);
@@ -527,7 +552,7 @@ 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);
@@ -990,4 +1015,54 @@ 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 = ColourSchemeLoader.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);
+ }
+ }
+ }
}