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JAL-1191 configure full SO for desktop, SOLite for applet (without
[jalview.git]
/
src
/
jalview
/
bin
/
Jalview.java
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
3294c26
..
ce29f01
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-23,6
+23,7
@@
package jalview.bin;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
+import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.PromptUserConfig;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.PromptUserConfig;
@@
-33,6
+34,7
@@
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
@@
-288,6
+290,14
@@
public class Jalview
}
}
}
}
+ /*
+ * configure 'full' SO model unless preferences say not to
+ */
+ if (!Cache.getDefault("USE_SO_LITE", false))
+ {
+ SequenceOntologyFactory.setInstance(new SequenceOntology());
+ }
+
if (!headless)
{
desktop = new Desktop();
if (!headless)
{
desktop = new Desktop();