1 package jalview.datamodel;
3 import java.util.ArrayList;
7 * stores data for each node in the hmm model
13 //contains the match emissions for each symbol
14 List<Double> matchEmissions = new ArrayList<>();
15 //contains the insert emissions for each symbol
16 List<Double> insertEmissions = new ArrayList<>();
17 //contains the state transitions for each possible transition. These are bm, bi, bd, im, ii, dm and dd in order (0th position in
18 // the array indicates the probability of a bm transition)
19 List<Double> stateTransitions = new ArrayList<>();
22 Integer alignmentColumn = null;
23 char consensusResidue;
24 char referenceAnnotation;
26 char consensusStructure;
32 public HMMNode(HMMNode node)
34 matchEmissions = new ArrayList<>(node.getMatchEmissions());
35 insertEmissions = new ArrayList<>(node.getInsertEmissions());
36 stateTransitions = new ArrayList<>(node.getStateTransitions());
37 alignmentColumn = new Integer(node.getAlignmentColumn());
38 consensusResidue = node.getConsensusResidue();
39 referenceAnnotation = node.getReferenceAnnotation();
40 maskValue = node.getMaskValue();
41 consensusStructure = node.getConsensusStructure();
44 public List<Double> getMatchEmissions()
46 return matchEmissions;
49 public void setMatchEmissions(List<Double> matchEmissionsL)
51 this.matchEmissions = matchEmissionsL;
53 public List<Double> getInsertEmissions()
55 return insertEmissions;
58 public void setInsertEmissions(List<Double> insertEmissionsL)
60 this.insertEmissions = insertEmissionsL;
63 public List<Double> getStateTransitions()
65 return stateTransitions;
68 public void setStateTransitions(List<Double> stateTransitionsM)
70 this.stateTransitions = stateTransitionsM;
73 public Integer getAlignmentColumn()
75 return alignmentColumn;
77 public void setAlignmentColumn(int alignmentColumn)
79 this.alignmentColumn = alignmentColumn;
81 public char getConsensusResidue()
83 return consensusResidue;
85 public void setConsensusResidue(char consensusResidue)
87 this.consensusResidue = consensusResidue;
89 public char getReferenceAnnotation()
91 return referenceAnnotation;
93 public void setReferenceAnnotation(char referenceAnnotation)
95 this.referenceAnnotation = referenceAnnotation;
97 public char getMaskValue()
101 public void setMaskValue(char maskValue)
103 this.maskValue = maskValue;
105 public char getConsensusStructure()
107 return consensusStructure;
109 public void setConsensusStructure(char consensusStructure)
111 this.consensusStructure = consensusStructure;