X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2Fsettings%2FMuscleParameters.xml;h=08ff4524e51a9d3d20f0252715d9c95dfbfba1ef;hb=dc8f4078acc94bd711079355d3cdf60dde467dae;hp=89ad920afc4ce31d3df62cd2d5ba7103544d673c;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/conf/settings/MuscleParameters.xml b/conf/settings/MuscleParameters.xml
index 89ad920..08ff452 100644
--- a/conf/settings/MuscleParameters.xml
+++ b/conf/settings/MuscleParameters.xml
@@ -1,6 +1,8 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
 <runnerConfig>
  <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>
+    <!--
+    This is the only option possible so no point in having it  
     <options isRequired="false">
         <name>Group sequences</name>
         <description>Group sequences by similarity (this is the default) or preserve the input order</description>
@@ -8,6 +10,7 @@
         <furtherDetails>prog_docs/muscle.html</furtherDetails>
         <defaultValue>-group</defaultValue>
     </options>
+     -->
     <!-- optionNames>-stable</optionNames  this is commented out as it contain bug see muscle web site-->
     <options isRequired="false">
         <name>Anchor optimisation</name>
@@ -17,6 +20,15 @@
         <furtherDetails>prog_docs/muscle.html</furtherDetails>
         <defaultValue>-anchors</defaultValue>
     </options>
+    <!-- Programs failures often with this option 
+    <options isRequired="false">
+        <name>Window refine</name>
+        <description>Refine an alignment by dividing it into non-overlapping windows and re-aligning each window. Typically used for whole-genome nucleotide alignments</description>
+        <optionNames>-refinew</optionNames>
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>
+        <defaultValue>-refinew</defaultValue>
+    </options>
+     -->
     <options isRequired="false">
         <name>Root alignment computation method</name>
         <description>Use Steven Brenner's method for computing the root alignment.</description>
@@ -69,7 +81,8 @@
         <defaultValue>auto</defaultValue>
         <possibleValues>auto</possibleValues>
         <possibleValues>protein</possibleValues>
-        <possibleValues>nucleo</possibleValues>
+        <possibleValues>dna</possibleValues>
+        <possibleValues>rna</possibleValues>
     </parameters>
 	<parameters isRequired="false">
         <name>Maxiters</name>
@@ -83,6 +96,68 @@
             <max>100</max>
         </validValue>
     </parameters>
+    <!-- disable as refinew is disabled 
+    <parameters isRequired="false">
+        <name>Maxiters</name>
+        <description>Length of window for Window Refine (-refinew)</description>
+        <optionNames>-refinewindow</optionNames>
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>
+        <defaultValue>200</defaultValue>
+        <validValue>
+        	<type>Integer</type>
+            <min>1</min>
+            <max>1000</max>
+        </validValue>
+    </parameters>
+     -->
+    <parameters isRequired="false">
+        <name>Diagonal break</name>
+        <description>Maximum distance between two diagonals that allows them to merge into one diagonal</description>
+        <optionNames>-diagbreak</optionNames>
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>
+        <defaultValue>1</defaultValue>
+        <validValue>
+        	<type>Integer</type>
+            <min>1</min>
+            <max>100</max>
+        </validValue>
+    </parameters>
+    <parameters isRequired="false">
+        <name>Diagonal length</name>
+        <description>Minimum length of diagonal</description>
+        <optionNames>-diaglength</optionNames>
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>
+        <defaultValue>24</defaultValue>
+        <validValue>
+        	<type>Integer</type>
+            <min>2</min>
+            <max>100</max>
+        </validValue>
+    </parameters>
+    <parameters isRequired="false">
+        <name>Diagonal margin</name>
+        <description>Discard this many positions at ends of diagonal</description>
+        <optionNames>-diagmargin</optionNames>
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>
+        <defaultValue>5</defaultValue>
+        <validValue>
+        	<type>Integer</type>
+            <min>1</min>
+            <max>100</max>
+        </validValue>
+    </parameters>
+    <parameters isRequired="false">
+        <name>Anchor spacing</name>
+        <description>Minimum spacing between anchor columns</description>
+        <optionNames>-anchorspacing</optionNames>
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>
+        <defaultValue>32</defaultValue>
+        <validValue>
+        	<type>Integer</type>
+            <min>2</min>
+            <max>1000</max>
+        </validValue>
+    </parameters>
   	<parameters isRequired="false">
         <name>Matrix</name>
         <description>Substitution Matrix to use</description>
@@ -222,6 +297,30 @@
             <max>10</max>
         </validValue>
     </parameters>
+     <parameters>
+        <name>Minimum anchor score</name>
+        <description>Minimum score a column must have to be an anchor (default depends on the profile scoring function!)</description>
+        <optionNames>-minbestcolscore</optionNames>
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>
+        <defaultValue>1.2</defaultValue>
+        <validValue>
+        	<type>Float</type>
+            <min>0</min>
+            <max>10</max>
+        </validValue>
+    </parameters>
+    <parameters>
+        <name>Minimum smoothed anchor score</name>
+        <description>Minimum smoothed score a column must have to be an anchor (default depends on the profile scoring function!)</description>
+        <optionNames>-minsmoothscore</optionNames>
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>
+        <defaultValue>1.2</defaultValue>
+        <validValue>
+        	<type>Float</type>
+            <min>0</min>
+            <max>10</max>
+        </validValue>
+    </parameters>
   	<parameters isRequired="false">
         <name>cluster1</name>
         <description>Clustering method to use on the iteration 1</description>