Add limits for presets from jws2 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3752 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/conf/settings/ClustalLimits.xml b/conf/settings/ClustalLimits.xml
index d490402..52b0ef3 100644 (file)
--- a/conf/settings/ClustalLimits.xml
+++ b/conf/settings/ClustalLimits.xml
@@ -1,18 +1,22 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <limits>\r
  <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
-       <limit isDefault="false">\r
-               <preset>Disable gap weighting (Speed-oriented)</preset>\r
-               <seqNumber>2000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
-       </limit>\r
        <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
+               <seqNumber>100000</seqNumber>\r
+               <seqLength>100000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>500</seqNumber>\r
-               <seqLength>1000</seqLength>\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>Disable gap weighting (Speed-oriented)</preset>\r
+               <seqNumber>1000</seqNumber>\r
+               <seqLength>3000</seqLength>\r
        </limit>\r
+        -->\r
 </limits>\r

diff --git a/conf/settings/MafftLimits.xml b/conf/settings/MafftLimits.xml
index 06a6324..7067ff5 100644 (file)
--- a/conf/settings/MafftLimits.xml
+++ b/conf/settings/MafftLimits.xml
@@ -2,12 +2,47 @@
 <limits>\r
  <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\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>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
+        -->\r
+       \r
 </limits>\r

diff --git a/conf/settings/MuscleLimits.xml b/conf/settings/MuscleLimits.xml
index feb6fc7..2aceb46 100644 (file)
--- a/conf/settings/MuscleLimits.xml
+++ b/conf/settings/MuscleLimits.xml
@@ -2,12 +2,32 @@
 <limits>\r
  <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
+               <seqNumber>100000</seqNumber>\r
+               <seqLength>100000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>500</seqNumber>\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>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
+        -->\r
+        \r
 </limits>\r

diff --git a/conf/settings/ProbconsLimits.xml b/conf/settings/ProbconsLimits.xml
index 179d0dc..1d871d7 100644 (file)
--- a/conf/settings/ProbconsLimits.xml
+++ b/conf/settings/ProbconsLimits.xml
@@ -2,12 +2,12 @@
 <limits>\r
  <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
+               <seqNumber>100000</seqNumber>\r
+               <seqLength>100000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>500</seqNumber>\r
-               <seqLength>1000</seqLength>\r
+               <seqNumber>100000</seqNumber>\r
+               <seqLength>100000</seqLength>\r
        </limit>\r
 </limits>\r

diff --git a/conf/settings/TcoffeeLimits.xml b/conf/settings/TcoffeeLimits.xml
index 3416ca3..660d27c 100644 (file)
--- a/conf/settings/TcoffeeLimits.xml
+++ b/conf/settings/TcoffeeLimits.xml
@@ -2,12 +2,21 @@
 <limits>\r
  <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
        <limit isDefault="true">\r
-               <seqNumber>1000</seqNumber>\r
-               <seqLength>1000</seqLength>\r
+               <seqNumber>100000</seqNumber>\r
+               <seqLength>100000</seqLength>\r
        </limit>\r
        <limit isDefault="false">\r
                <preset># LocalEngineExecutionLimit #</preset>\r
-               <seqNumber>500</seqNumber>\r
-               <seqLength>1000</seqLength>\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
 </limits>\r