JWS-50 refactored the valid AACon method parameters as a series of options in the...

[jabaws.git] / conf / settings / AAConPresets.xml

diff --git a/conf/settings/AAConPresets.xml b/conf/settings/AAConPresets.xml
index cdf8d37..f2e3cde 100644 (file)
--- a/conf/settings/AAConPresets.xml
+++ b/conf/settings/AAConPresets.xml
@@ -1,30 +1,25 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <presets>\r
- <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
+<runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
        <preset>\r
                <name>Quick conservation</name>\r
                <description>Collection of fast conservation methods</description>\r
                <optlist>\r
-                       <option>-m=KABAT,JORES,SCHNEIDER,SHENKIN,GERSTEIN,TAYLOR_GAPS,TAYLOR_NO_GAPS,ZVELIBIL,ARMON,THOMPSON,NOT_LANCET,MIRNY,WILLIAMSON</option>\r
+                       <option>-m=KABAT</option><option>-m=JORES</option><option>-m=SCHNEIDER</option><option>-m=SHENKIN</option><option>-m=GERSTEIN</option><option>-m=TAYLOR_GAPS</option><option>-m=TAYLOR_NO_GAPS</option><option>-m=ZVELIBIL</option><option>-m=ARMON</option><option>-m=THOMPSON</option><option>-m=NOT_LANCET</option><option>-m=MIRNY</option><option>-m=WILLIAMSON</option>\r
                </optlist>\r
        </preset>\r
        <preset>\r
                <name>Slow conservation</name>\r
                <description>Collection of most expensive (slow) conservation methods</description>\r
                <optlist>\r
-                       <option>-m=LANDGRAF,KARLIN,SANDER,VALDAR,SMERFS</option>\r
+                       <option>-m=LANDGRAF</option><option>-m=KARLIN</option><option>-m=SANDER</option><option>-m=VALDAR</option><option>-m=SMERFS</option>\r
                </optlist>\r
        </preset>\r
        <preset>\r
                <name>Complete conservation</name>\r
                <description>Calculate conservation with all supported methods</description>\r
                <optlist>\r
-                       <option>-m=KABAT,JORES,SCHNEIDER,SHENKIN,GERSTEIN,TAYLOR_GAPS,TAYLOR_NO_GAPS,ZVELIBIL,ARMON,THOMPSON,NOT_LANCET,MIRNY,WILLIAMSON,LANDGRAF,KARLIN,SANDER,VALDAR,SMERFS</option>\r
+                       <option>-m=KABAT</option><option>-m=JORES</option><option>-m=SCHNEIDER</option><option>-m=SHENKIN</option><option>-m=GERSTEIN</option><option>-m=TAYLOR_GAPS</option><option>-m=TAYLOR_NO_GAPS</option><option>-m=ZVELIBIL</option><option>-m=ARMON</option><option>-m=THOMPSON</option><option>-m=NOT_LANCET</option><option>-m=MIRNY</option><option>-m=WILLIAMSON</option><option>-m=LANDGRAF</option><option>-m=KARLIN</option><option>-m=SANDER</option><option>-m=VALDAR</option><option>-m=SMERFS</option>\r
                </optlist>\r
        </preset>\r
 </presets>\r
-\r
-\r
-\r
- \r
-\r