refactors biWeight to sqBiWeight and adds labels

CIRDLES · Mar 25, 2017 · d2878fc · d2878fc
1 parent bf672a3
commit d2878fc
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Showing 4 changed files with 48 additions and 20 deletions.
diff --git a/appfx/src/main/java/org/cirdles/calamari/FXMLDocumentController.java b/appfx/src/main/java/org/cirdles/calamari/FXMLDocumentController.java
@@ -36,6 +36,7 @@
 import org.cirdles.calamari.tasks.expressions.builtinExpressions.SquidExpressionMinus4;
 import org.cirdles.calamari.tasks.expressions.customExpressions.CustomExpression_LnPbR_U;
 import org.cirdles.calamari.tasks.expressions.customExpressions.CustomExpression_LnUO_U;
+import org.cirdles.calamari.tasks.expressions.customExpressions.CustomExpression_Net204BiWt;
 import org.cirdles.calamari.tasks.expressions.customExpressions.CustomExpression_Net204cts_sec;
 import org.cirdles.calamari.tasks.expressions.parsing.ExpressionParser;
 import org.cirdles.calamari.tasks.storedTasks.SquidBodorkosTask1;
@@ -100,6 +101,7 @@ public void initialize(URL url, ResourceBundle rb) {
                 CustomExpression_LnPbR_U.EXPRESSION,
                 CustomExpression_LnUO_U.EXPRESSION,
                 CustomExpression_Net204cts_sec.EXPRESSION,
+                CustomExpression_Net204BiWt.EXPRESSION,
                 SquidExpressionMinus1.EXPRESSION,
                 SquidExpressionMinus3.EXPRESSION,
                 SquidExpressionMinus4.EXPRESSION);

diff --git a/...org/cirdles/calamari/tasks/expressions/customExpressions/CustomExpression_Net204BiWt.java b/...org/cirdles/calamari/tasks/expressions/customExpressions/CustomExpression_Net204BiWt.java
@@ -38,7 +38,7 @@ public class CustomExpression_Net204BiWt {
                 .addChild(0, new VariableNode(CustomExpression_Net204cts_sec.EXPRESSION.getName(),
                         "getTaskExpressionsEvaluationsPerSpotByField"));
         ((ExpressionTreeBuilderInterface) EXPRESSION).addChild(new ConstantNode("9", 9));
-        ((ExpressionTreeBuilderInterface) EXPRESSION).setOperation(Function.biWeight());
+        ((ExpressionTreeBuilderInterface) EXPRESSION).setOperation(Function.sqBiweight());
 
         ((ExpressionTree) EXPRESSION).setRootExpressionTree(true);
         ((ExpressionTree) EXPRESSION).setSquidSwitchSCSummaryCalculation(true);

diff --git a/core/src/main/java/org/cirdles/calamari/tasks/expressions/functions/Function.java b/core/src/main/java/org/cirdles/calamari/tasks/expressions/functions/Function.java
@@ -34,9 +34,10 @@ public abstract class Function
     protected String name;
     protected int argumentCount;
     protected int precedence;
-    // establish size of array resullting from evaluation
+    // establish size of array resulting from evaluation
     protected int rowCount;
     protected int colCount;
+    protected String[][] labelsForValues;
 
     @Override
     public void customizeXstream(XStream xstream) {
@@ -61,8 +62,8 @@ public static OperationOrFunctionInterface robReg() {
         return new RobReg();
     }
 
-    public static OperationOrFunctionInterface biWeight() {
-        return new Biweight();
+    public static OperationOrFunctionInterface sqBiweight() {
+        return new SqBiweight();
     }
 
     /**
@@ -162,4 +163,18 @@ public int getColCount() {
     public void setColCount(int colCount) {
         this.colCount = colCount;
     }
+
+    /**
+     * @return the labelsForValues
+     */
+    public String[][] getLabelsForValues() {
+        return labelsForValues;
+    }
+
+    /**
+     * @param labelsForValues the labelsForValues to set
+     */
+    public void setLabelsForValues(String[][] labelsForValues) {
+        this.labelsForValues = labelsForValues;
+    }
 }
diff --git a/...tasks/expressions/functions/Biweight.java → ...sks/expressions/functions/SqBiweight.java b/...tasks/expressions/functions/Biweight.java → ...sks/expressions/functions/SqBiweight.java
@@ -15,7 +15,6 @@
  */
 package org.cirdles.calamari.tasks.expressions.functions;
 
-import java.math.BigDecimal;
 import java.util.List;
 import org.cirdles.calamari.shrimp.ShrimpFractionExpressionInterface;
 import org.cirdles.calamari.tasks.expressions.ExpressionTreeInterface;
@@ -24,36 +23,48 @@
  *
  * @author James F. Bowring
  */
-public class Biweight extends Function {
+public class SqBiweight extends Function {
 
-    public Biweight() {
-        name = "Biweight";
+    /**
+     * Provides the functionality of Squid's sqBiweight and biWt by calculating
+     * TukeysBiweight and returning mean, sigma, and 95% confidence and encoding
+     * the labels for each cell of the values array produced by eval2Array.
+     *
+     * @see
+     * https://raw.githubusercontent.com/CIRDLES/LudwigLibrary/master/vbaCode/squid2.5Basic/Resistant.bas
+     * @see
+     * https://raw.githubusercontent.com/CIRDLES/LudwigLibrary/master/vbaCode/squid2.5Basic/StringUtils.bas
+     */
+    public SqBiweight() {
+        name = "sqBiweight";
         argumentCount = 2;
         precedence = 4;
         rowCount = 1;
-        colCount = 2;
+        colCount = 3;
+        labelsForValues = new String[][]{{"Biwt Mean", "Biwt Sigma", "\u00B195%conf"}};
     }
 
     /**
+     * Requires that child 0 is a VariableNode that evaluates to a double array
+     * with one row and a column for each member of shrimpFractions and that
+     * child 1 is a ConstantNode that evaluates to an integer.
      *
-     * @param childrenET the value of childrenET
-     * @param shrimpFractions the value of shrimpFraction
-     * @return the double[][]
+     * @param childrenET list containing child 0 and child 1
+     * @param shrimpFractions a list of shrimpFractions
+     * @return the double[1][3] array of mean, sigma, 95% confidence
      */
     @Override
     public double[][] eval2Array(
             List<ExpressionTreeInterface> childrenET, List<ShrimpFractionExpressionInterface> shrimpFractions) {
 
         double[][] retVal;
         try {
-            // assume child 0 is a VariableNode
-            // assume child 1 is a number
             double[][] variableValues = childrenET.get(0).eval2Array(shrimpFractions);
-            double [][] tuning = childrenET.get(1).eval2Array(shrimpFractions);
-            BigDecimal[] retValBD = org.cirdles.ludwig.TukeyBiweight.biweightMean(variableValues[0], tuning[0][0]);
-            retVal = new double[][]{{retValBD[0].doubleValue(), retValBD[1].doubleValue()}};
-        } catch (Exception e) {
-            retVal = new double[][]{{0.0, 0.0}};
+            double[][] tuning = childrenET.get(1).eval2Array(shrimpFractions);
+            double[][] tukeysBiweight = org.cirdles.ludwig.SquidMathUtils.tukeysBiweight(variableValues[0], tuning[0][0]);
+            retVal = new double[][]{{tukeysBiweight[0][0], tukeysBiweight[0][1], tukeysBiweight[0][2]}};
+        } catch (ArithmeticException e) {
+            retVal = new double[][]{{0.0, 0.0, 0.0}};
         }
 
         return retVal;
@@ -68,7 +79,7 @@ public double[][] eval2Array(
     public String toStringMathML(List<ExpressionTreeInterface> childrenET) {
         String retVal
                 = "<mrow>"
-                + "<mi>RobReg</mi>"
+                + "<mi>" + name + "</mi>"
                 + "<mfenced>";
 
         for (int i = 0; i < childrenET.size(); i++) {