Mercurial > repos > grau > dimont_motif_discovery

comparison test-data/predictor_test.xml @ 0:b7d6db3ba6bc draft

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author grau
date Wed, 13 Nov 2013 04:25:23 -0500
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1 <gendismix-classifier>
2 <alphabetcontainer><className>de.jstacs.data.alphabets.DNAAlphabetContainer</className></alphabetcontainer><length><className>java.lang.Integer</className>0</length><classWeights><className>[D</className><length>2</length><pos val="0">-2.034267647272289</pos><pos val="1">-0.2525781403291907</pos></classWeights><params><className>de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.GenDisMixClassifierParameterSet</className><sequenceScoringParameterSet>
3 <superParameters>
4 <instanceParameterSet>
5 <superParameterSet>
6 <parameterSet>
7 <set>
8 <numberOfParameters><className>java.lang.Integer</className>8</numberOfParameters><parameter><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
9 <name><className>java.lang.String</className>algorithm</name><comment><className>java.lang.String</className>the algorithm that should be used for numerical optimization</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>true</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
10 <set>
11 <numberOfParameters><className>java.lang.Integer</className>13</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
12 <name><className>java.lang.String</className>steepest descent</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>16</value></simpleParameter>
13 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
14 <name><className>java.lang.String</className>conjugate gradients (F., R.)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>17</value></simpleParameter>
15 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
16 <name><className>java.lang.String</className>conjugate gradients (P., R. positive)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>18</value></simpleParameter>
17 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
18 <name><className>java.lang.String</className>quasi newton (D., F., P.)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>19</value></simpleParameter>
19 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
20 <name><className>java.lang.String</className>quasi newton (B., F., G., S.)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>20</value></simpleParameter>
21 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
22 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=3)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>3</value></simpleParameter>
23 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
24 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=4)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>4</value></simpleParameter>
25 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
26 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=5)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>5</value></simpleParameter>
27 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
28 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=6)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>6</value></simpleParameter>
29 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
30 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=7)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>7</value></simpleParameter>
31 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
32 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=8)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>8</value></simpleParameter>
33 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
34 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=9)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>9</value></simpleParameter>
35 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
36 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=10)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>10</value></simpleParameter>
37 </parameter></set>
38 </parameterSet>
39 </collection><selected><className>java.lang.Integer</className>2</selected><defaultSelected><className>java.lang.Integer</className>4</defaultSelected></collectionParameter>
40 </parameter><parameter><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
41 <name><className>java.lang.String</className>termination condition</name><comment><className>java.lang.String</className>the terminantion condition for stopping the training algorithm</comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>true</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
42 <set>
43 <numberOfParameters><className>java.lang.Integer</className>8</numberOfParameters><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
44 <name><className>java.lang.String</className>AbsoluteValueConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.AbsoluteValueCondition$AbsoluteValueConditionParameterSet</name></parameterClass></parameterSetContainer>
45 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
46 <name><className>java.lang.String</className>CombinedConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.CombinedCondition$CombinedConditionParameterSet</name></parameterClass></parameterSetContainer>
47 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
48 <name><className>java.lang.String</className>IterationConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.IterationCondition$IterationConditionParameterSet</name></parameterClass></parameterSetContainer>
49 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
50 <name><className>java.lang.String</className>MultipleIterationsConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.MultipleIterationsCondition$MultipleIterationsConditionParameterSet</name></parameterClass></parameterSetContainer>
51 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
52 <name><className>java.lang.String</className>SmallDifferenceOfFunctionEvaluationsConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.algorithms.optimization.termination.SmallDifferenceOfFunctionEvaluationsCondition$SmallDifferenceOfFunctionEvaluationsConditionParameterSet</className><instanceParameterSet>
53 <superParameterSet>
54 <parameterSet>
55 <set>
56 <numberOfParameters><className>java.lang.Integer</className>1</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
57 <name><className>java.lang.String</className>epsilon</name><comment><className>java.lang.String</className>the epsilon for the difference of function evaluations used for deciding whether to stop the algorithm or not</comment><datatype><className>de.jstacs.DataType</className><name>DOUBLE</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
58 <className><className>java.lang.String</className>java.lang.Double</className><lowerBound><className>java.lang.String</className>0.0</lowerBound><upperBound><className>java.lang.String</className>1.7976931348623157E308</upperBound></NumberValidator>
59 </validator><defaultValue><className>java.lang.Double</className>1.0E-6</defaultValue><value><className>java.lang.Double</className>1.0E-4</value></simpleParameter>
60 </parameter></set>
61 </parameterSet>
62 </superParameterSet>
63 <instanceClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.SmallDifferenceOfFunctionEvaluationsCondition</name></instanceClass></instanceParameterSet>
64 </parameters></parameterSetContainer>
65 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
66 <name><className>java.lang.String</className>SmallGradientConditonParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.SmallGradientConditon$SmallGradientConditonParameterSet</name></parameterClass></parameterSetContainer>
67 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
68 <name><className>java.lang.String</className>SmallStepConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.SmallStepCondition$SmallStepConditionParameterSet</name></parameterClass></parameterSetContainer>
69 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
70 <name><className>java.lang.String</className>TimeConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.TimeCondition$TimeConditionParameterSet</name></parameterClass></parameterSetContainer>
71 </parameter></set>
72 </parameterSet>
73 </collection><selected><className>java.lang.Integer</className>4</selected><defaultSelected><className>java.lang.Integer</className>4</defaultSelected></collectionParameter>
74 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
75 <name><className>java.lang.String</className>line epsilon</name><comment><className>java.lang.String</className>the threshold for stopping the line search in the numerical training</comment><datatype><className>de.jstacs.DataType</className><name>DOUBLE</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
76 <className><className>java.lang.String</className>java.lang.Double</className><lowerBound><className>java.lang.String</className>0.0</lowerBound><upperBound><className>java.lang.String</className>1.7976931348623157E308</upperBound></NumberValidator>
77 </validator><defaultValue><className>java.lang.Double</className>1.0E-9</defaultValue><value><className>java.lang.Double</className>1.0E-5</value></simpleParameter>
78 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
79 <name><className>java.lang.String</className>start distance</name><comment><className>java.lang.String</className>the start distance for the line search in the numerical training</comment><datatype><className>de.jstacs.DataType</className><name>DOUBLE</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
80 <className><className>java.lang.String</className>java.lang.Double</className><lowerBound><className>java.lang.String</className>0.0</lowerBound><upperBound><className>java.lang.String</className>1.7976931348623157E308</upperBound></NumberValidator>
81 </validator><defaultValue><className>java.lang.Double</className>1.0</defaultValue><value><className>java.lang.Double</className>1.0</value></simpleParameter>
82 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
83 <name><className>java.lang.String</className>free parameters</name><comment><className>java.lang.String</className>Indicates whether only the free parameters or all parameters should be used.</comment><datatype><className>de.jstacs.DataType</className><name>BOOLEAN</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue><className>java.lang.Boolean</className>false</defaultValue><value><className>java.lang.Boolean</className>false</value></simpleParameter>
84 </parameter><parameter><className>de.jstacs.parameters.EnumParameter</className><collectionParameter>
85 <name><className>java.lang.String</className>KindOfParameter</name><comment><className>java.lang.String</className>Indicates whether special plugIn parameters or the zero vector should be used as start parameters. For non-concave problems it is highly recommended to use plugIn parameters.</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>true</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
86 <set>
87 <numberOfParameters><className>java.lang.Integer</className>3</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
88 <name><className>java.lang.String</className>ZEROS</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.String</className>ZEROS</value></simpleParameter>
89 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
90 <name><className>java.lang.String</className>LAST</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.String</className>LAST</value></simpleParameter>
91 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
92 <name><className>java.lang.String</className>PLUGIN</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.String</className>PLUGIN</value></simpleParameter>
93 </parameter></set>
94 </parameterSet>
95 </collection><selected><className>java.lang.Integer</className>2</selected><defaultSelected><className>java.lang.Integer</className>2</defaultSelected><selectedEnum><className>java.lang.String</className>PLUGIN</selectedEnum><defaultSelectedEnum><className>java.lang.String</className>PLUGIN</defaultSelectedEnum><enumName><className>java.lang.Class</className><name>de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction$KindOfParameter</name></enumName></collectionParameter>
96 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
97 <name><className>java.lang.String</className>Normalize</name><comment><className>java.lang.String</className>If true the conditional likelihood will be normalized to the number of data sets.</comment><datatype><className>de.jstacs.DataType</className><name>BOOLEAN</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue><className>java.lang.Boolean</className>true</defaultValue><value><className>java.lang.Boolean</className>true</value></simpleParameter>
98 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
99 <name><className>java.lang.String</className>Threads</name><comment><className>java.lang.String</className>The number of threads that is used during an optimization.</comment><datatype><className>de.jstacs.DataType</className><name>INT</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
100 <className><className>java.lang.String</className>java.lang.Integer</className><lowerBound><className>java.lang.String</className>1</lowerBound><upperBound><className>java.lang.String</className>128</upperBound></NumberValidator>
101 </validator><defaultValue><className>java.lang.Integer</className>1</defaultValue><value><className>java.lang.Integer</className>1</value></simpleParameter>
102 </parameter></set>
103 </parameterSet>
104 </superParameterSet>
105 <instanceClass><className>java.lang.Class</className><name>de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.GenDisMixClassifier</name></instanceClass></instanceParameterSet>
106 </superParameters>
107 <variableLength><className>java.lang.Boolean</className>true</variableLength><alphabet><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
108 <name><className>java.lang.String</className>Alphabet</name><comment><className>java.lang.String</className>The alphabet the model works on</comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>true</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
109 <set>
110 <numberOfParameters><className>java.lang.Integer</className>2</numberOfParameters><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
111 <name><className>java.lang.String</className>AlphabetContainerParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.AlphabetContainerParameterSet</className><alphabetContainerParameterSet>
112 <superParameters>
113 <instanceParameterSet>
114 <superParameterSet>
115 <parameterSet>
116 <set>
117 <numberOfParameters><className>java.lang.Integer</className>1</numberOfParameters><parameter><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
118 <name><className>java.lang.String</className>Alphabet</name><comment><className>java.lang.String</className>Select a discrete alphabet</comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>false</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
119 <set>
120 <numberOfParameters><className>java.lang.Integer</className>4</numberOfParameters><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
121 <name><className>java.lang.String</className>DNAAlphabetParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.DNAAlphabet$DNAAlphabetParameterSet</className></parameters></parameterSetContainer>
122 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
123 <name><className>java.lang.String</className>ProteinAlphabetParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.ProteinAlphabet$ProteinAlphabetParameterSet</className></parameters></parameterSetContainer>
124 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
125 <name><className>java.lang.String</className>GenericComplementableDiscreteAlphabetParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.GenericComplementableDiscreteAlphabet$GenericComplementableDiscreteAlphabetParameterSet</className><instanceParameterSet>
126 <superParameterSet>
127 <parameterSet>
128 <set>
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130 <name><className>java.lang.String</className>Values of the index for computings the reverse complement</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>false</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value>null</value></simpleParameter>
131 </parameter></set>
132 </parameterSet>
133 </superParameterSet>
134 <instanceClass><className>java.lang.Class</className><name>de.jstacs.data.alphabets.GenericComplementableDiscreteAlphabet</name></instanceClass></instanceParameterSet>
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136 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
137 <name><className>java.lang.String</className>DiscreteAlphabetParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.DiscreteAlphabet$DiscreteAlphabetParameterSet</className><instanceParameterSet>
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142 <name><className>java.lang.String</className>Values of the alphabet</name><comment><className>java.lang.String</className>The possible values of the discrete alphabet.If the alphabet consists of single characters, e.g. A, C, G, and T, the values may be set as a single string, e.g. &amp;quot;ACGT&amp;quot;.If the alphabet consists of multi-character symbols, e.g. Gly, Asp, Ser,the symbols must be separated by spaces.</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>false</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value>null</value></simpleParameter>
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151 </parameterSet>
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154 </parameterSet>
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158 </parameter></set>
159 </parameterSet>
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162 </parameterSet>
163 </superParameterSet>
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171 </parameterSet>
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174 <name><className>java.lang.String</className>Length</name><comment><className>java.lang.String</className>The length of sequences the model can work on</comment><datatype><className>de.jstacs.DataType</className><name>INT</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
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