1 package jalview.datamodel;
4 * stores data for each node in the hmm model
10 //contains the match emissions for each symbol
11 double[] matchEmissions;
13 //contains the insert emissions for each symbol
14 double[] insertEmissions;
16 // contains the state transitions for each possible transition. These are mm,
17 // mi, md, im, ii, dm and dd in order
18 double[] stateTransitions;
21 Integer alignmentColumn = null;
22 char consensusResidue;
23 char referenceAnnotation;
25 char consensusStructure;
34 public double[] getMatchEmissions()
36 return matchEmissions;
39 public double getMatchEmission(int symbolIndex)
41 return matchEmissions[symbolIndex];
44 public void setMatchEmissions(double[] matches)
46 this.matchEmissions = matches;
49 public double[] getInsertEmissions()
51 return insertEmissions;
54 public double getInsertEmission(int symbolIndex)
56 return insertEmissions[symbolIndex];
59 public void setInsertEmissions(double[] insertEmissionsL)
61 this.insertEmissions = insertEmissionsL;
64 public double[] getStateTransitions()
66 return stateTransitions;
69 public double getStateTransition(int transition)
71 return stateTransitions[transition];
74 public void setStateTransitions(double[] stateTransitionsM)
76 this.stateTransitions = stateTransitionsM;
79 public Integer getAlignmentColumn()
81 return alignmentColumn;
83 public void setAlignmentColumn(int alignmentColumn)
85 this.alignmentColumn = alignmentColumn;
87 public char getConsensusResidue()
89 return consensusResidue;
91 public void setConsensusResidue(char consensusResidue)
93 this.consensusResidue = consensusResidue;
95 public char getReferenceAnnotation()
97 return referenceAnnotation;
99 public void setReferenceAnnotation(char referenceAnnotation)
101 this.referenceAnnotation = referenceAnnotation;
103 public char getMaskValue()
107 public void setMaskValue(char maskValue)
109 this.maskValue = maskValue;
111 public char getConsensusStructure()
113 return consensusStructure;
115 public void setConsensusStructure(char consensusStructure)
117 this.consensusStructure = consensusStructure;