1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>
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5 <name>Normalize</name>
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6 <description>Normalize the results.
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7 Normalized results have values between 0 and 1. Please note however, that
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8 some results cannot be normalized. In such a case, the system returns not
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9 normalized value. The following formula is used for normalization
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10 n = (d - dmin)/(dmax - dmin)
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11 Negative results first converted to positive by adding a greatest absolute
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12 result value.</description>
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13 <optionNames>-n</optionNames>
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14 <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>
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16 <prmSeparator>=</prmSeparator>
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18 <name>Calculation method</name>
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19 <description>The method of the calculation to use</description>
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20 <optionNames>-m</optionNames>
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21 <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>
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22 <defaultValue>SHENKIN</defaultValue>
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23 <possibleValues>KABAT</possibleValues>
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24 <possibleValues>JORES</possibleValues>
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25 <possibleValues>SCHNEIDER</possibleValues>
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26 <possibleValues>SHENKIN</possibleValues>
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27 <possibleValues>GERSTEIN</possibleValues>
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28 <possibleValues>TAYLOR_GAPS</possibleValues>
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29 <possibleValues>TAYLOR_NO_GAPS</possibleValues>
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30 <possibleValues>ZVELIBIL</possibleValues>
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31 <possibleValues>KARLIN</possibleValues>
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32 <possibleValues>ARMON</possibleValues>
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33 <possibleValues>THOMPSON</possibleValues>
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34 <possibleValues>NOT_LANCET</possibleValues>
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35 <possibleValues>MIRNY</possibleValues>
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36 <possibleValues>WILLIAMSON</possibleValues>
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37 <possibleValues>LANDGRAF</possibleValues>
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38 <possibleValues>SANDER</possibleValues>
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39 <possibleValues>VALDAR</possibleValues>
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40 <possibleValues>SMERFS</possibleValues>
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43 <name>SMERFS Window Width</name>
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44 <description>The width of the window for SMERFS. Optional, defaults to 7</description>
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45 <optionNames>-smerfsWW</optionNames>
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46 <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>
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47 <defaultValue>7</defaultValue>
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49 <type>Integer</type>
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55 <name>SMERFS Column Scoring Method</name>
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56 <description>SMERFS Column Score algorithm defines the window scores to
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57 columns allocation, two methods are possible:
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58 MID_SCORE - gives the window score to the middle column
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59 MAX_SCORE - gives the column the highest score of all the windows it
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60 belongs to. Optional defaults to MID_SCORE. </description>
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61 <optionNames>-smerfsCS</optionNames>
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62 <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>
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63 <defaultValue>MID_SCORE</defaultValue>
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64 <possibleValues>MAX_SCORE</possibleValues>
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65 <possibleValues>MID_SCORE</possibleValues>
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68 <name>SMERFS Gap Threshhold</name>
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69 <description>a gap percentage cutoff - a float greater than 0 and smaller or equal 1. Optional defaults to 0.1</description>
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70 <optionNames>-smerfsGT</optionNames>
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71 <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>
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72 <defaultValue>0.1</defaultValue>
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