git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'features/JAL-2446NCList' into features/JAL-2574findFeaturesByColumn
[jalview.git]
/
src
/
jalview
/
bin
/
Cache.java
diff --git
a/src/jalview/bin/Cache.java
b/src/jalview/bin/Cache.java
index
9363c23
..
da3cb92
100755
(executable)
--- 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.datamodel.PDBEntry;
import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.UserColourScheme;
import jalview.structure.StructureImportSettings;
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.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;
* <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
* <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$</li>
* <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
* <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$</li>
+ * <li>STORED_LINKS list of name|url pairs which user has entered but are not
+ * currently used
+ * <li>DEFAULT_LINK name of single url to be used when user double clicks a
+ * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info</li>
* <li>DAS_REGISTRY_URL the registry to query</li>
* <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info</li>
* <li>DAS_REGISTRY_URL the registry to query</li>
@@
-184,6
+190,8
@@
import org.apache.log4j.SimpleLayout;
* <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
* display</li>
* <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
* <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
* display</li>
* <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
+ * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
+ * </li>
*
* </ul>
* Deprecated settings:
*
* </ul>
* Deprecated settings:
@@
-225,6
+233,9
@@
public class Cache
public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
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
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";
/**
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
* 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));
"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);
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
@@
-1017,7
+1038,7
@@
public class Cache
String file = st.nextToken();
try
{
String file = st.nextToken();
try
{
- UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+ UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
if (ucs != null)
{
if (coloursFound.length() > 0)
if (ucs != null)
{
if (coloursFound.length() > 0)