New Jpred parameters and new set of Jpred presets

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

diff --git a/conf/settings/TcoffeeLimits.xml b/conf/settings/TcoffeeLimits.xml
index 660d27c..f45c633 100644 (file)
--- a/conf/settings/TcoffeeLimits.xml
+++ b/conf/settings/TcoffeeLimits.xml
@@ -1,22 +1,22 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <limits>\r
- <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
-       <limit isDefault="true">\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
-       </limit>\r
-       <limit isDefault="false">\r
-               <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>100000</seqNumber>\r
-               <seqLength>100000</seqLength>\r
-       </limit>\r
-       \r
-       <!-- Uncomment/edit these if you would like to have separate limits for presets -->\r
-       <!-- \r
-       <limit isDefault="false">\r
-               <preset>Quick align. Very fast approximate (Speed-oriented)</preset>\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>3000</seqLength>\r
-       </limit>\r
-        -->\r
+    <runnerClassName>compbio.runner.msa.Tcoffee</runnerClassName>\r
+\r
+    <limit isDefault="true">\r
+        <seqNumber>1000</seqNumber>\r
+        <seqLength>1000</seqLength>\r
+    </limit>\r
+    <limit isDefault="false">\r
+        <preset># LocalEngineExecutionLimit #</preset>\r
+        <seqNumber>15</seqNumber>\r
+        <seqLength>400</seqLength>\r
+    </limit>\r
+\r
+    <!-- Limits for presets    -->\r
+    <limit isDefault="false">\r
+        <preset>Quick align. Very fast approximate (Speed-oriented)</preset>\r
+        <seqNumber>1000</seqNumber>\r
+        <seqLength>3000</seqLength>\r
+    </limit>\r
+\r
 </limits>\r