Dundee specific settings from JWS2 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3384 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/dundee-conf/settings/ClustalLimits.xml b/dundee-conf/settings/ClustalLimits.xml
index ebbe206..28adf27 100644 (file)
--- a/dundee-conf/settings/ClustalLimits.xml
+++ b/dundee-conf/settings/ClustalLimits.xml
@@ -12,7 +12,7 @@
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>40</seqNumber>\r
+               <seqNumber>30</seqNumber>\r
                <seqLength>500</seqLength>\r
        </limit>\r
 </limits>\r

diff --git a/dundee-conf/settings/MafftLimits.xml b/dundee-conf/settings/MafftLimits.xml
index 7db541e..4cd787f 100644 (file)
--- a/dundee-conf/settings/MafftLimits.xml
+++ b/dundee-conf/settings/MafftLimits.xml
@@ -6,8 +6,38 @@
                <seqLength>1000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
+               <preset>L-INS-i (Accuracy-oriented)</preset>\r
+               <seqNumber>500</seqNumber>\r
+               <seqLength>1000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
+               <preset>G-INS-i (Accuracy-oriented)</preset>\r
+               <seqNumber>500</seqNumber>\r
+               <seqLength>1000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
+               <preset>E-INS-i (Accuracy-oriented)</preset>\r
+               <seqNumber>500</seqNumber>\r
+               <seqLength>1000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
+               <preset>FFT-NS-i (Speed oriented)</preset>\r
+               <seqNumber>2000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
+               <preset>FFT-NS-1 (Speed oriented)</preset>\r
+               <seqNumber>2000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
+               <preset>NW-NS-PartTree-1 (Speed oriented)</preset>\r
+               <seqNumber>2000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>40</seqNumber>\r
+               <seqNumber>20</seqNumber>\r
                <seqLength>500</seqLength>\r
        </limit>\r
 </limits>\r

diff --git a/dundee-conf/settings/MuscleLimits.xml b/dundee-conf/settings/MuscleLimits.xml
index 88cfc61..75d66d9 100644 (file)
--- a/dundee-conf/settings/MuscleLimits.xml
+++ b/dundee-conf/settings/MuscleLimits.xml
@@ -6,8 +6,23 @@
                <seqLength>1000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
+               <preset>Protein alignment(Fastest speed)</preset>\r
+               <seqNumber>2000</seqNumber>\r
+               <seqLength>1000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
+               <preset>Nucleotide alignment(Fastest speed)</preset>\r
+               <seqNumber>1000</seqNumber>\r
+               <seqLength>3000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
+               <preset>Huge alignments (speed-oriented)</preset>\r
+               <seqNumber>2000</seqNumber>\r
+               <seqLength>3000</seqLength>\r
+       </limit>\r
+       <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>40</seqNumber>\r
+               <seqNumber>20</seqNumber>\r
                <seqLength>500</seqLength>\r
        </limit>\r
 </limits>\r

diff --git a/dundee-conf/settings/ProbconsLimits.xml b/dundee-conf/settings/ProbconsLimits.xml
index 96c8b31..e530fb9 100644 (file)
--- a/dundee-conf/settings/ProbconsLimits.xml
+++ b/dundee-conf/settings/ProbconsLimits.xml
@@ -7,7 +7,7 @@
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>30</seqNumber>\r
+               <seqNumber>20</seqNumber>\r
                <seqLength>500</seqLength>\r
        </limit>\r
 </limits>\r

diff --git a/dundee-conf/settings/TcoffeeLimits.xml b/dundee-conf/settings/TcoffeeLimits.xml
index f21fb03..84b3f50 100644 (file)
--- a/dundee-conf/settings/TcoffeeLimits.xml
+++ b/dundee-conf/settings/TcoffeeLimits.xml
@@ -6,8 +6,14 @@
                <seqLength>1000</seqLength>\r
        </limit>\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
+       <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>40</seqNumber>\r
-               <seqLength>500</seqLength>\r
+               <seqNumber>15</seqNumber>\r
+               <seqLength>400</seqLength>\r
        </limit>\r
 </limits>\r
+\r