Package edu.duke.cs.osprey.markstar.visualizer

Class KStarTreeNode

java.lang.Object
edu.duke.cs.osprey.markstar.visualizer.KStarTreeNode
All Implemented Interfaces:
Comparable<KStarTreeNode>
public class KStarTreeNode extends Object implements Comparable<KStarTreeNode>

  • Field Details

    • p

      public static final Pattern p

  • Constructor Details

    • KStarTreeNode

      public KStarTreeNode(int level, String[] assignments, int[] confAssignments, BigDecimal lowerBound, BigDecimal upperBound, double confLowerBound, double confUpperBound, double epsilon)

  • Method Details

    • setColorStyle

      public void setColorStyle(KStarTreeNode.ColorStyle style)

    • parseTree

      public static KStarTreeNode parseTree(File file, boolean render, Map<Integer,BigDecimal> zCutoffsByLevel)

    • parseTree

      public static KStarTreeNode parseTree(String fileName)

    • getLowerBound

      public BigDecimal getLowerBound()

    • getUpperBound

      public BigDecimal getUpperBound()

    • assign

      public KStarTreeNode assign(int pos, int rc, String assignment, BigDecimal lowerBound, BigDecimal upperBound, double confLowerBound, double confUpperBound)

    • updateBoundsFromChildren

      public void updateBoundsFromChildren(MathContext mathContext)

    • numStatesAtLevel

      public int numStatesAtLevel(int level)

    • maxWeightedErrorBound

      public BigDecimal maxWeightedErrorBound()

    • maxConfErrorBound

      public double maxConfErrorBound()

    • computeEntropy

      public double computeEntropy(int maxLevel)

    • computeEntropy

      public double computeEntropy()

    • computeEnthalpyWithEnergiesFrom

      public double computeEnthalpyWithEnergiesFrom(Map<String,Double> energyMap, int maxLevel)

    • computeEnergyMap

      public Map<String,Double> computeEnergyMap(int maxLevel)

    • computeEnthalpy

      public double computeEnthalpy(int maxLevel)

    • computeEnthalpy

      public double computeEnthalpy()

    • initStatText

      public void initStatText()

    • setRender

      public void setRender(boolean render)

    • preprocess

      public void preprocess()

    • showRoot

      public void showRoot()

    • setGroup

      public void setGroup(javafx.scene.Group g)

    • computeLevelMaxOccupancies

      public void computeLevelMaxOccupancies()

    • numConfsWithin

      public int numConfsWithin(double diffFromGMEC)

    • computeEnergyErrorWithinEnergyRange

      public double[] computeEnergyErrorWithinEnergyRange(double diffFromGMEC)

    • recenter

      public void recenter(double x, double y)

    • autoExpand

      public void autoExpand(double v)

    • autoExpand

      public void autoExpand(double v, int maxLevel)

    • getTopSamples

      public Map<KStarTreeNode,List<KStarTreeNode>> getTopSamples(int numSamples, int levelThreshold)

    • getTopSamplesInSubtree

      public List<KStarTreeNode> getTopSamplesInSubtree(int numSubtreeSamples)

    • getTopSamples

      public void getTopSamples(int numSamples, int levelThreshold, Map<KStarTreeNode,List<KStarTreeNode>> lists)

    • getAssignments

      public String[] getAssignments()

    • getConfAssignments

      public int[] getConfAssignments()

    • getConfLowerBound

      public double getConfLowerBound()

    • getConfUpperBound

      public double getConfUpperBound()

    • getEnsemblePDBName

      public String getEnsemblePDBName()

    • pieChart

      public void pieChart(int... levels)

    • pieChart

      public void pieChart(int targetLevel)

    • setTextRoot

      public void setTextRoot(javafx.scene.Group textGroup)

    • toggleCenter

      public void toggleCenter()

    • getLevelNodes

      public Set<KStarTreeNode> getLevelNodes(int targetLevel)

    • isChildOf

      public boolean isChildOf(KStarTreeNode otherNode)

    • isParentOf

      public boolean isParentOf(KStarTreeNode otherNode)

    • addChild

      protected void addChild(KStarTreeNode newNode)

    • parent

      public KStarTreeNode parent()

    • removeFromParent

      public void removeFromParent()

    • getAssignmentIndex

      public Integer getAssignmentIndex()

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • toStringVisual

      public String toStringVisual()

    • render

      public void render()

    • compareTo

      public int compareTo(KStarTreeNode other)
      Specified by:
      compareTo in interface Comparable<KStarTreeNode>

    • render

      public void render(javafx.scene.Group g)

    • printTree

      public void printTree(String prefix, FileWriter writer)

    • printTree

      public void printTree()

    • printTreeLikeMARKStar

      public void printTreeLikeMARKStar(Writer out) throws IOException
      printTree uses a different format than MARK* apparently
      Throws:
      IOException

    • printTreeLikeMARKStar

      public void printTreeLikeMARKStar(Writer out, String prefix) throws IOException
      Throws:
      IOException