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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7 Normalize the results. Normalized results have values between 0 and 1. Please note however,
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8 that 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 n = (d - dmin)/(dmax - dmin)
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10 Negative results first converted to positive by adding a greatest absolute result value.
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12 <optionNames>-n</optionNames>
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13 <defaultValue>-n</defaultValue>
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14 <furtherDetails>prog_docs/aacon.txt</furtherDetails>
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16 <options><name>KABAT</name><description></description><optionNames>-m=KABAT</optionNames><furtherDetails>prog_docs/aacon.txt#KABAT</furtherDetails></options>
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17 <options><name>JORES</name><description></description><optionNames>-m=JORES</optionNames><furtherDetails>prog_docs/aacon.txt#JORES</furtherDetails></options>
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18 <options><name>SCHNEIDER</name><description></description><optionNames>-m=SCHNEIDER</optionNames><furtherDetails>prog_docs/aacon.txt#SCHNEIDER</furtherDetails></options>
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19 <options><name>SHENKIN</name><description></description><optionNames>-m=SHENKIN</optionNames><furtherDetails>prog_docs/aacon.txt#SHENKIN</furtherDetails><defaultValue>-m=SHENKIN</defaultValue></options>
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20 <options><name>GERSTEIN</name><description></description><optionNames>-m=GERSTEIN</optionNames><furtherDetails>prog_docs/aacon.txt#GERSTEIN</furtherDetails></options>
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21 <options><name>TAYLOR_GAPS</name><description></description><optionNames>-m=TAYLOR_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_GAPS</furtherDetails></options>
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22 <options><name>TAYLOR_NO_GAPS</name><description></description><optionNames>-m=TAYLOR_NO_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_NO_GAPS</furtherDetails></options>
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23 <options><name>ZVELIBIL</name><description></description><optionNames>-m=ZVELIBIL</optionNames><furtherDetails>prog_docs/aacon.txt#ZVELIBIL</furtherDetails></options>
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24 <options><name>KARLIN</name><description></description><optionNames>-m=KARLIN</optionNames><furtherDetails>prog_docs/aacon.txt#KARLIN</furtherDetails></options>
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25 <options><name>ARMON</name><description></description><optionNames>-m=ARMON</optionNames><furtherDetails>prog_docs/aacon.txt#ARMON</furtherDetails></options>
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26 <options><name>THOMPSON</name><description></description><optionNames>-m=THOMPSON</optionNames><furtherDetails>prog_docs/aacon.txt#THOMPSON</furtherDetails></options>
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27 <options><name>NOT_LANCET</name><description></description><optionNames>-m=NOT_LANCET</optionNames><furtherDetails>prog_docs/aacon.txt#NOT_LANCET</furtherDetails></options>
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28 <options><name>MIRNY</name><description></description><optionNames>-m=MIRNY</optionNames><furtherDetails>prog_docs/aacon.txt#MIRNY</furtherDetails></options>
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29 <options><name>WILLIAMSON</name><description></description><optionNames>-m=WILLIAMSON</optionNames><furtherDetails>prog_docs/aacon.txt#WILLIAMSON</furtherDetails></options>
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30 <options><name>LANDGRAF</name><description></description><optionNames>-m=LANDGRAF</optionNames><furtherDetails>prog_docs/aacon.txt#LANDGRAF</furtherDetails></options>
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31 <options><name>SANDER</name><description></description><optionNames>-m=SANDER</optionNames><furtherDetails>prog_docs/aacon.txt#SANDER</furtherDetails></options>
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32 <options><name>VALDAR</name><description></description><optionNames>-m=VALDAR</optionNames><furtherDetails>prog_docs/aacon.txt#VALDAR</furtherDetails></options>
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33 <options><name>SMERFS</name><description></description><optionNames>-m=SMERFS</optionNames><furtherDetails>prog_docs/aacon.txt#SMERFS</furtherDetails></options>
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35 <prmSeparator>=</prmSeparator>
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37 <name>SMERFS Window Width</name>
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38 <description>The width of the window for SMERFS. Optional, defaults to 7</description>
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39 <optionNames>-smerfsWW</optionNames>
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40 <furtherDetails>prog_docs/aacon.txt</furtherDetails>
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41 <defaultValue>7</defaultValue>
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43 <type>Integer</type>
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50 <name>SMERFS Column Scoring Method</name>
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51 <description>SMERFS Column Score algorithm defines the window scores to
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52 columns allocation, two methods are possible: MID_SCORE - gives the window score to the middle column
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53 MAX_SCORE - gives the column the highest score of all the windows it belongs to. Optional defaults to MID_SCORE. </description>
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54 <optionNames>-smerfsCS</optionNames>
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55 <furtherDetails>prog_docs/aacon.txt</furtherDetails>
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56 <defaultValue>MID_SCORE</defaultValue>
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57 <possibleValues>MAX_SCORE</possibleValues>
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58 <possibleValues>MID_SCORE</possibleValues>
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62 <name>SMERFS Gap Threshhold</name>
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63 <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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64 <optionNames>-smerfsGT</optionNames>
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65 <furtherDetails>prog_docs/aacon.txt</furtherDetails>
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66 <defaultValue>0.1</defaultValue>
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