Mercurial > repos > rnateam > sshmm

view test-data/test_shapes_final_model.xml @ 0:4b01f0d7b350 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
author rnateam
date Fri, 06 Jul 2018 09:01:40 -0400
parents
children
line wrap: on
line source

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE mixture PUBLIC "-//ghmm.org//DOCUMENT ghmm V1.0//EN" "http://ghmm.sourceforge.net/xml/1.0/ghmm.dtd">
<mixture version="1.0" noComponents="1">
 <HMM name="stateHMM" type="labeled discrete">
  <alphabet id="0">
   <symbol code="0">A</symbol>
   <symbol code="1">C</symbol>
   <symbol code="2">G</symbol>
   <symbol code="3">T</symbol>
   <symbol code="4">+</symbol>
   <symbol code="5">#</symbol>
  </alphabet>
  <classAlphabet>
   <symbol code="0">St</symbol>
   <symbol code="1">E1</symbol>
   <symbol code="2">I1</symbol>
   <symbol code="3">S1</symbol>
   <symbol code="4">H1</symbol>
   <symbol code="5">M1</symbol>
   <symbol code="6">E2</symbol>
   <symbol code="7">I2</symbol>
   <symbol code="8">S2</symbol>
   <symbol code="9">H2</symbol>
   <symbol code="10">M2</symbol>
   <symbol code="11">E3</symbol>
   <symbol code="12">I3</symbol>
   <symbol code="13">S3</symbol>
   <symbol code="14">H3</symbol>
   <symbol code="15">M3</symbol>
   <symbol code="16">E4</symbol>
   <symbol code="17">I4</symbol>
   <symbol code="18">S4</symbol>
   <symbol code="19">H4</symbol>
   <symbol code="20">M4</symbol>
   <symbol code="21">E5</symbol>
   <symbol code="22">I5</symbol>
   <symbol code="23">S5</symbol>
   <symbol code="24">H5</symbol>
   <symbol code="25">M5</symbol>
   <symbol code="26">E6</symbol>
   <symbol code="27">I6</symbol>
   <symbol code="28">S6</symbol>
   <symbol code="29">H6</symbol>
   <symbol code="30">M6</symbol>
   <symbol code="31">En</symbol>
  </classAlphabet>
  <state id="0" initial="1.00000000">
   <discrete id="0">0, 0, 0, 0, 1, 0</discrete>
   <class>0</class>
  </state>
  <state id="1" initial="0.00000000">
   <discrete id="0">0.33333333, 0.16666667, 0.33333333, 0.16666667, 0, 0</discrete>
   <class>1</class>
  </state>
  <state id="2" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>2</class>
  </state>
  <state id="3" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>3</class>
  </state>
  <state id="4" initial="0.00000000">
   <discrete id="0">0.5625, 0.1875, 0.1875, 0.0625, 0, 0</discrete>
   <class>4</class>
  </state>
  <state id="5" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>5</class>
  </state>
  <state id="6" initial="0.00000000">
   <discrete id="0">0.16666667, 0.33333333, 0.16666667, 0.33333333, 0, 0</discrete>
   <class>6</class>
  </state>
  <state id="7" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>7</class>
  </state>
  <state id="8" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>8</class>
  </state>
  <state id="9" initial="0.00000000">
   <discrete id="0">0.3125, 0.3125, 0.1875, 0.1875, 0, 0</discrete>
   <class>9</class>
  </state>
  <state id="10" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>10</class>
  </state>
  <state id="11" initial="0.00000000">
   <discrete id="0">0.33333333, 0.16666667, 0.16666667, 0.33333333, 0, 0</discrete>
   <class>11</class>
  </state>
  <state id="12" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>12</class>
  </state>
  <state id="13" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>13</class>
  </state>
  <state id="14" initial="0.00000000">
   <discrete id="0">0.1875, 0.1875, 0.1875, 0.4375, 0, 0</discrete>
   <class>14</class>
  </state>
  <state id="15" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>15</class>
  </state>
  <state id="16" initial="0.00000000">
   <discrete id="0">0.33333333, 0.16666667, 0.16666667, 0.33333333, 0, 0</discrete>
   <class>16</class>
  </state>
  <state id="17" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>17</class>
  </state>
  <state id="18" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>18</class>
  </state>
  <state id="19" initial="0.00000000">
   <discrete id="0">0.3125, 0.0625, 0.125, 0.5, 0, 0</discrete>
   <class>19</class>
  </state>
  <state id="20" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>20</class>
  </state>
  <state id="21" initial="0.00000000">
   <discrete id="0">0.16666667, 0.16666667, 0.33333333, 0.33333333, 0, 0</discrete>
   <class>21</class>
  </state>
  <state id="22" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>22</class>
  </state>
  <state id="23" initial="0.00000000">
   <discrete id="0">0.2, 0.1, 0.5, 0.2, 0, 0</discrete>
   <class>23</class>
  </state>
  <state id="24" initial="0.00000000">
   <discrete id="0">0.6, 0.2, 0.1, 0.1, 0, 0</discrete>
   <class>24</class>
  </state>
  <state id="25" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>25</class>
  </state>
  <state id="26" initial="0.00000000">
   <discrete id="0">0.16666667, 0.16666667, 0.16666667, 0.5, 0, 0</discrete>
   <class>26</class>
  </state>
  <state id="27" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>27</class>
  </state>
  <state id="28" initial="0.00000000">
   <discrete id="0">0.33333333, 0.16666667, 0.25, 0.25, 0, 0</discrete>
   <class>28</class>
  </state>
  <state id="29" initial="0.00000000">
   <discrete id="0">0.375, 0.375, 0.125, 0.125, 0, 0</discrete>
   <class>29</class>
  </state>
  <state id="30" initial="0.00000000">
   <discrete id="0">0.25, 0.25, 0.25, 0.25, 0, 0</discrete>
   <class>30</class>
  </state>
  <state id="31" initial="0.00000000">
   <discrete id="0">0, 0, 0, 0, 0, 1</discrete>
   <class>31</class>
  </state>
  <transition source="0" target="1">
   <probability>0.15789474</probability>
  </transition>
  <transition source="0" target="2">
   <probability>0.052631579</probability>
  </transition>
  <transition source="0" target="3">
   <probability>0.052631579</probability>
  </transition>
  <transition source="0" target="4">
   <probability>0.68421053</probability>
  </transition>
  <transition source="0" target="5">
   <probability>0.052631579</probability>
  </transition>
  <transition source="1" target="6">
   <probability>0.42857143</probability>
  </transition>
  <transition source="1" target="7">
   <probability>0.14285714</probability>
  </transition>
  <transition source="1" target="8">
   <probability>0.14285714</probability>
  </transition>
  <transition source="1" target="9">
   <probability>0.14285714</probability>
  </transition>
  <transition source="1" target="10">
   <probability>0.14285714</probability>
  </transition>
  <transition source="2" target="6">
   <probability>0.2</probability>
  </transition>
  <transition source="2" target="7">
   <probability>0.2</probability>
  </transition>
  <transition source="2" target="8">
   <probability>0.2</probability>
  </transition>
  <transition source="2" target="9">
   <probability>0.2</probability>
  </transition>
  <transition source="2" target="10">
   <probability>0.2</probability>
  </transition>
  <transition source="3" target="6">
   <probability>0.2</probability>
  </transition>
  <transition source="3" target="7">
   <probability>0.2</probability>
  </transition>
  <transition source="3" target="8">
   <probability>0.2</probability>
  </transition>
  <transition source="3" target="9">
   <probability>0.2</probability>
  </transition>
  <transition source="3" target="10">
   <probability>0.2</probability>
  </transition>
  <transition source="4" target="6">
   <probability>0.058823529</probability>
  </transition>
  <transition source="4" target="7">
   <probability>0.058823529</probability>
  </transition>
  <transition source="4" target="8">
   <probability>0.058823529</probability>
  </transition>
  <transition source="4" target="9">
   <probability>0.76470588</probability>
  </transition>
  <transition source="4" target="10">
   <probability>0.058823529</probability>
  </transition>
  <transition source="5" target="6">
   <probability>0.2</probability>
  </transition>
  <transition source="5" target="7">
   <probability>0.2</probability>
  </transition>
  <transition source="5" target="8">
   <probability>0.2</probability>
  </transition>
  <transition source="5" target="9">
   <probability>0.2</probability>
  </transition>
  <transition source="5" target="10">
   <probability>0.2</probability>
  </transition>
  <transition source="6" target="11">
   <probability>0.42857143</probability>
  </transition>
  <transition source="6" target="12">
   <probability>0.14285714</probability>
  </transition>
  <transition source="6" target="13">
   <probability>0.14285714</probability>
  </transition>
  <transition source="6" target="14">
   <probability>0.14285714</probability>
  </transition>
  <transition source="6" target="15">
   <probability>0.14285714</probability>
  </transition>
  <transition source="7" target="11">
   <probability>0.2</probability>
  </transition>
  <transition source="7" target="12">
   <probability>0.2</probability>
  </transition>
  <transition source="7" target="13">
   <probability>0.2</probability>
  </transition>
  <transition source="7" target="14">
   <probability>0.2</probability>
  </transition>
  <transition source="7" target="15">
   <probability>0.2</probability>
  </transition>
  <transition source="8" target="11">
   <probability>0.2</probability>
  </transition>
  <transition source="8" target="12">
   <probability>0.2</probability>
  </transition>
  <transition source="8" target="13">
   <probability>0.2</probability>
  </transition>
  <transition source="8" target="14">
   <probability>0.2</probability>
  </transition>
  <transition source="8" target="15">
   <probability>0.2</probability>
  </transition>
  <transition source="9" target="11">
   <probability>0.058823529</probability>
  </transition>
  <transition source="9" target="12">
   <probability>0.058823529</probability>
  </transition>
  <transition source="9" target="13">
   <probability>0.058823529</probability>
  </transition>
  <transition source="9" target="14">
   <probability>0.76470588</probability>
  </transition>
  <transition source="9" target="15">
   <probability>0.058823529</probability>
  </transition>
  <transition source="10" target="11">
   <probability>0.2</probability>
  </transition>
  <transition source="10" target="12">
   <probability>0.2</probability>
  </transition>
  <transition source="10" target="13">
   <probability>0.2</probability>
  </transition>
  <transition source="10" target="14">
   <probability>0.2</probability>
  </transition>
  <transition source="10" target="15">
   <probability>0.2</probability>
  </transition>
  <transition source="11" target="16">
   <probability>0.42857143</probability>
  </transition>
  <transition source="11" target="17">
   <probability>0.14285714</probability>
  </transition>
  <transition source="11" target="18">
   <probability>0.14285714</probability>
  </transition>
  <transition source="11" target="19">
   <probability>0.14285714</probability>
  </transition>
  <transition source="11" target="20">
   <probability>0.14285714</probability>
  </transition>
  <transition source="12" target="16">
   <probability>0.2</probability>
  </transition>
  <transition source="12" target="17">
   <probability>0.2</probability>
  </transition>
  <transition source="12" target="18">
   <probability>0.2</probability>
  </transition>
  <transition source="12" target="19">
   <probability>0.2</probability>
  </transition>
  <transition source="12" target="20">
   <probability>0.2</probability>
  </transition>
  <transition source="13" target="16">
   <probability>0.2</probability>
  </transition>
  <transition source="13" target="17">
   <probability>0.2</probability>
  </transition>
  <transition source="13" target="18">
   <probability>0.2</probability>
  </transition>
  <transition source="13" target="19">
   <probability>0.2</probability>
  </transition>
  <transition source="13" target="20">
   <probability>0.2</probability>
  </transition>
  <transition source="14" target="16">
   <probability>0.058823529</probability>
  </transition>
  <transition source="14" target="17">
   <probability>0.058823529</probability>
  </transition>
  <transition source="14" target="18">
   <probability>0.058823529</probability>
  </transition>
  <transition source="14" target="19">
   <probability>0.76470588</probability>
  </transition>
  <transition source="14" target="20">
   <probability>0.058823529</probability>
  </transition>
  <transition source="15" target="16">
   <probability>0.2</probability>
  </transition>
  <transition source="15" target="17">
   <probability>0.2</probability>
  </transition>
  <transition source="15" target="18">
   <probability>0.2</probability>
  </transition>
  <transition source="15" target="19">
   <probability>0.2</probability>
  </transition>
  <transition source="15" target="20">
   <probability>0.2</probability>
  </transition>
  <transition source="16" target="21">
   <probability>0.42857143</probability>
  </transition>
  <transition source="16" target="22">
   <probability>0.14285714</probability>
  </transition>
  <transition source="16" target="23">
   <probability>0.14285714</probability>
  </transition>
  <transition source="16" target="24">
   <probability>0.14285714</probability>
  </transition>
  <transition source="16" target="25">
   <probability>0.14285714</probability>
  </transition>
  <transition source="17" target="21">
   <probability>0.2</probability>
  </transition>
  <transition source="17" target="22">
   <probability>0.2</probability>
  </transition>
  <transition source="17" target="23">
   <probability>0.2</probability>
  </transition>
  <transition source="17" target="24">
   <probability>0.2</probability>
  </transition>
  <transition source="17" target="25">
   <probability>0.2</probability>
  </transition>
  <transition source="18" target="21">
   <probability>0.2</probability>
  </transition>
  <transition source="18" target="22">
   <probability>0.2</probability>
  </transition>
  <transition source="18" target="23">
   <probability>0.2</probability>
  </transition>
  <transition source="18" target="24">
   <probability>0.2</probability>
  </transition>
  <transition source="18" target="25">
   <probability>0.2</probability>
  </transition>
  <transition source="19" target="21">
   <probability>0.058823529</probability>
  </transition>
  <transition source="19" target="22">
   <probability>0.058823529</probability>
  </transition>
  <transition source="19" target="23">
   <probability>0.41176471</probability>
  </transition>
  <transition source="19" target="24">
   <probability>0.41176471</probability>
  </transition>
  <transition source="19" target="25">
   <probability>0.058823529</probability>
  </transition>
  <transition source="20" target="21">
   <probability>0.2</probability>
  </transition>
  <transition source="20" target="22">
   <probability>0.2</probability>
  </transition>
  <transition source="20" target="23">
   <probability>0.2</probability>
  </transition>
  <transition source="20" target="24">
   <probability>0.2</probability>
  </transition>
  <transition source="20" target="25">
   <probability>0.2</probability>
  </transition>
  <transition source="21" target="26">
   <probability>0.42857143</probability>
  </transition>
  <transition source="21" target="27">
   <probability>0.14285714</probability>
  </transition>
  <transition source="21" target="28">
   <probability>0.14285714</probability>
  </transition>
  <transition source="21" target="29">
   <probability>0.14285714</probability>
  </transition>
  <transition source="21" target="30">
   <probability>0.14285714</probability>
  </transition>
  <transition source="22" target="26">
   <probability>0.2</probability>
  </transition>
  <transition source="22" target="27">
   <probability>0.2</probability>
  </transition>
  <transition source="22" target="28">
   <probability>0.2</probability>
  </transition>
  <transition source="22" target="29">
   <probability>0.2</probability>
  </transition>
  <transition source="22" target="30">
   <probability>0.2</probability>
  </transition>
  <transition source="23" target="26">
   <probability>0.090909091</probability>
  </transition>
  <transition source="23" target="27">
   <probability>0.090909091</probability>
  </transition>
  <transition source="23" target="28">
   <probability>0.63636364</probability>
  </transition>
  <transition source="23" target="29">
   <probability>0.090909091</probability>
  </transition>
  <transition source="23" target="30">
   <probability>0.090909091</probability>
  </transition>
  <transition source="24" target="26">
   <probability>0.090909091</probability>
  </transition>
  <transition source="24" target="27">
   <probability>0.090909091</probability>
  </transition>
  <transition source="24" target="28">
   <probability>0.27272727</probability>
  </transition>
  <transition source="24" target="29">
   <probability>0.45454545</probability>
  </transition>
  <transition source="24" target="30">
   <probability>0.090909091</probability>
  </transition>
  <transition source="25" target="26">
   <probability>0.2</probability>
  </transition>
  <transition source="25" target="27">
   <probability>0.2</probability>
  </transition>
  <transition source="25" target="28">
   <probability>0.2</probability>
  </transition>
  <transition source="25" target="29">
   <probability>0.2</probability>
  </transition>
  <transition source="25" target="30">
   <probability>0.2</probability>
  </transition>
  <transition source="26" target="31">
   <probability>1</probability>
  </transition>
  <transition source="27" target="31">
   <probability>1</probability>
  </transition>
  <transition source="28" target="31">
   <probability>1</probability>
  </transition>
  <transition source="29" target="31">
   <probability>1</probability>
  </transition>
  <transition source="30" target="31">
   <probability>1</probability>
  </transition>
  <transition source="31" target="31">
   <probability>1</probability>
  </transition>
 </HMM>
</mixture>