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;
27 public List<Double> getMatchEmissions()
29 return matchEmissions;
32 public void setMatchEmissions(List<Double> matchEmissionsL)
34 this.matchEmissions = matchEmissionsL;
36 public List<Double> getInsertEmissions()
38 return insertEmissions;
41 public void setInsertEmissions(List<Double> insertEmissionsL)
43 this.insertEmissions = insertEmissionsL;
45 public List<Double> getStateTransitions()
47 return stateTransitions;
50 public void setStateTransitions(List<Double> stateTransitionsL)
52 this.stateTransitions = stateTransitionsL;
55 public Integer getAlignmentColumn()
57 return alignmentColumn;
59 public void setAlignmentColumn(int alignmentColumn)
61 this.alignmentColumn = alignmentColumn;
63 public char getConsensusResidue()
65 return consensusResidue;
67 public void setConsensusResidue(char consensusResidue)
69 this.consensusResidue = consensusResidue;
71 public char getReferenceAnnotation()
73 return referenceAnnotation;
75 public void setReferenceAnnotation(char referenceAnnotation)
77 this.referenceAnnotation = referenceAnnotation;
79 public char getMaskValue()
83 public void setMaskValue(char maskValue)
85 this.maskValue = maskValue;
87 public char getConsensusStructure()
89 return consensusStructure;
91 public void setConsensusStructure(char consensusStructure)
93 this.consensusStructure = consensusStructure;