restructure file exporter

[jalview.git] / src / jalview / datamodel / HMMNode.java

diff --git a/src/jalview/datamodel/HMMNode.java b/src/jalview/datamodel/HMMNode.java
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+++ b/src/jalview/datamodel/HMMNode.java
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+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * stores data for each node in the hmm model
+ * @author TZVanaalten
+ *
+ */
+public class HMMNode
+{
+  //contains the match emissions for each symbol 
+  List<Double> matchEmissions = new ArrayList<>();
+  //contains the insert emissions for each symbol 
+  List<Double> insertEmissions = new ArrayList<>();
+  //contains the state transitions for each possible transition. These are bm, bi, bd, im, ii, dm and dd in order (0th position in
+  // the array indicates the probability of a bm transition)
+  List<Double> stateTransitions = new ArrayList<>();
+  
+  //annotations
+  Integer alignmentColumn = null;
+  char consensusResidue;
+  char referenceAnnotation;
+  char maskValue;
+  char consensusStructure;
+  public List<Double> getMatchEmissions()
+  {
+    return matchEmissions;
+  }
+
+  public void setMatchEmissions(List<Double> matchEmissionsL)
+  {
+    this.matchEmissions = matchEmissionsL;
+  }
+  public List<Double> getInsertEmissions()
+  {
+    return insertEmissions;
+  }
+
+  public void setInsertEmissions(List<Double> insertEmissionsL)
+  {
+    this.insertEmissions = insertEmissionsL;
+  }
+  public List<Double> getStateTransitions()
+  {
+    return stateTransitions;
+  }
+
+  public void setStateTransitions(List<Double> stateTransitionsL)
+  {
+    this.stateTransitions = stateTransitionsL;
+  }
+
+  public Integer getAlignmentColumn()
+  {
+    return alignmentColumn;
+  }
+  public void setAlignmentColumn(int alignmentColumn)
+  {
+    this.alignmentColumn = alignmentColumn;
+  }
+  public char getConsensusResidue()
+  {
+    return consensusResidue;
+  }
+  public void setConsensusResidue(char consensusResidue)
+  {
+    this.consensusResidue = consensusResidue;
+  }
+  public char getReferenceAnnotation()
+  {
+    return referenceAnnotation;
+  }
+  public void setReferenceAnnotation(char referenceAnnotation)
+  {
+    this.referenceAnnotation = referenceAnnotation;
+  }
+  public char getMaskValue()
+  {
+    return maskValue;
+  }
+  public void setMaskValue(char maskValue)
+  {
+    this.maskValue = maskValue;
+  }
+  public char getConsensusStructure()
+  {
+    return consensusStructure;
+  }
+  public void setConsensusStructure(char consensusStructure)
+  {
+    this.consensusStructure = consensusStructure;
+  }
+}
+   
+