X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=19aa800c54b96bd5c4ee8ee34268cf4f7ffc4e16;hb=d71391d37943d1f6a5bf0af74996229f4d290cb0;hp=c9b6d89587e7e067b2335553635298bbebedd604;hpb=4306800413a28da102c15fe7301bcac7816445fe;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index c9b6d89..19aa800 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -28,8 +28,6 @@ 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;
import java.awt.Color;
@@ -116,7 +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
@@ -136,9 +133,7 @@ import org.apache.log4j.SimpleLayout;
* 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
@@ -178,7 +173,7 @@ import org.apache.log4j.SimpleLayout;
* FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.
- * FIGURE_USERIDWIDTH Specifies the width to use for the left-hand column
+ * FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
* when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
* will override this).
* STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
@@ -228,12 +223,6 @@ 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
*/
@@ -260,8 +249,6 @@ public class Cache
private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
.toString();
- private static String HMMER_PATH;
-
/*
* a date formatter using a fixed (rather than the user's) locale;
* this ensures that date properties can be written and re-read successfully
@@ -604,6 +591,24 @@ public class Cache
return def;
}
+ public static int getDefault(String property, int def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ try
+ {
+ def = Integer.parseInt(string);
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing int property '" + property
+ + "' with value '" + string + "'");
+ }
+ }
+
+ return def;
+ }
+
/**
* These methods are used when checking if the saved preference is different
* to the default setting
@@ -984,22 +989,6 @@ public class Cache
return null;
}
- private static DasSourceRegistryI sourceRegistry = null;
-
- /**
- * initialise and ..
- *
- * @return instance of the das source registry
- */
- public static DasSourceRegistryI getDasSourceRegistry()
- {
- if (sourceRegistry == null)
- {
- sourceRegistry = new DasSourceRegistry();
- }
- return sourceRegistry;
- }
-
/**
* Set the specified value, or remove it if null or empty. Does not save the
* properties file.