Add testing dirs

[proteocache.git] / testsrc / testdata / MafftPresets.xml

diff --git a/testsrc/testdata/MafftPresets.xml b/testsrc/testdata/MafftPresets.xml
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+++ b/testsrc/testdata/MafftPresets.xml
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+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<presets>\r
+       <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>\r
+       <preset>\r
+               <name>L-INS-i (Accuracy-oriented)</name>\r
+               <description>L-INS-i (probably most accurate; recommended for &lt;200\r
+                       sequences; iterative refinement method incorporating local pairwise\r
+                       alignment information)</description>\r
+               <optlist>\r
+                       <option>--localpair</option>\r
+                       <option>--maxiterate 1000</option>\r
+               </optlist>\r
+       </preset>\r
+       <preset>\r
+               <name>G-INS-i (Accuracy-oriented)</name>\r
+               <description>G-INS-i (suitable for sequences of similar lengths;\r
+                       recommended for &lt;200 sequences; iterative refinement method\r
+                       incorporating global pairwise alignment information)</description>\r
+               <optlist>\r
+                       <option>--globalpair</option>\r
+                       <option>--maxiterate 1000</option>\r
+               </optlist>\r
+       </preset>\r
+       <preset>\r
+               <name>E-INS-i (Accuracy-oriented)</name>\r
+               <description>E-INS-i (suitable for sequences containing large\r
+                       unalignable regions; recommended for &lt;200 sequences)</description>\r
+               <optlist>\r
+                       <option>--ep 0</option>\r
+                       <option>--genafpair</option>\r
+                       <option>--maxiterate 1000</option>\r
+               </optlist>\r
+       </preset>\r
+       <preset>\r
+               <name>FFT-NS-i (Speed oriented)</name>\r
+               <description>FFT-NS-i (iterative refinement method; two cycles only)</description>\r
+               <optlist>\r
+                       <option>--retree 2</option>\r
+                       <option>--maxiterate 2</option>\r
+               </optlist>\r
+       </preset>\r
+       <preset>\r
+               <name>FFT-NS-1 (Speed oriented)</name>\r
+               <description>FFT-NS-1 (very fast; recommended for &gt;2000 sequences;\r
+                       progressive method with a rough guide tree)</description>\r
+               <optlist>\r
+                       <option>--retree 1</option>\r
+                       <option>--maxiterate 0</option>\r
+               </optlist>\r
+       </preset>\r
+       <preset>\r
+               <name>NW-NS-PartTree-1 (Speed oriented)</name>\r
+               <description>NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000\r
+                       sequences; progressive method with the PartTree algorithm)</description>\r
+               <optlist>\r
+                       <option>--retree 1</option>\r
+                       <option>--maxiterate 0</option>\r
+                       <option>--nofft</option>\r
+                       <option>--parttree</option>\r
+               </optlist>\r
+       </preset>\r
+</presets>\r