WM updates (#711)

* Updated gradle

* Fixed issues #706 and #709

* Tweaked WM display

* Handle missing WM

Author: bowring

squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/plots/plotControllers/PlotsController.java

@@ -738,14 +738,19 @@ public void refreshPlot() {
                 plotToolBar.getItems().addAll(plot.toolbarControlsFactory());
 
             } catch (Exception e) {
+                plot = null;
+                removePlotWhenNull();
             }
         } else {
-            plotAndConfigAnchorPane.getChildren().clear();
-            plotToolBar.getItems().clear();
-
-            plotVBox.getChildren().remove(plotToolBar);
+            removePlotWhenNull();
         }
+    }
 
+    private void removePlotWhenNull()
+    {
+        plotAndConfigAnchorPane.getChildren().clear();
+        plotToolBar.getItems().clear();
+        plotVBox.getChildren().remove(plotToolBar);
     }
 
     @Override

squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/plots/plotControllers/RefMatWeightedMeanToolBoxNode.java

@@ -176,6 +176,7 @@ private void displaySample(String newValue) throws SquidException {
 
         // each fraction stores this info, so get from first one
         String selectedAge = shrimpFractions.get(0).getSelectedAgeExpressionName();
+        ((Task) squidProject.getTask()).evaluateUnknownsWithChangedParameters(shrimpFractions);
         SpotSummaryDetails spotSummaryDetailsWM
                 = ((Task) squidProject.getTask()).evaluateSelectedAgeWeightedMeanForUnknownGroup(newValue, shrimpFractions);
         spotSummaryDetailsWM.setManualRejectionEnabled(true);
@@ -458,7 +459,7 @@ public void changed(ObservableValue<? extends SquidReportColumnInterface> observ
                         String selectedExpression = newValue.getExpressionName();
                         sampleNode.getSpotSummaryDetailsWM().setSelectedExpressionName(
                                 selectedExpression);
-                        refreshSampleCheckboxSelectionStatus(sampleNode.getSpotSummaryDetailsWM());
+
                         sortFractionCheckboxesByValue(sampleNode.getSpotSummaryDetailsWM());
                         plotsController.refreshPlot();
                     }
@@ -740,10 +741,17 @@ private void sortFractionCheckboxesByValue(SpotSummaryDetails spotSummaryDetails
         });
     }
 
-    private void refreshSampleCheckboxSelectionStatus(SpotSummaryDetails spotSummaryDetails){
-        for (int i = 0; i < sampleItem.getChildren().size(); i++) {
-            ((CheckBoxTreeItem<SampleTreeNodeInterface>)sampleItem.getChildren().get(i)).setSelected(!spotSummaryDetails
-                    .getRejectedIndices()[i]);
+    private void refreshSampleCheckboxSelectionStatus(SpotSummaryDetails spotSummaryDetails) {
+        if (PlotsController.plot != null) {
+            try {
+                for (TreeItem<SampleTreeNodeInterface> spotCheckBox : PlotsController.spotsTreeViewCheckBox.getRoot().getChildren()) {
+                    int indexOfSpot = ((WeightedMeanSpotNode) spotCheckBox.getValue()).getIndexOfSpot();
+                    ((CheckBoxTreeItem<SampleTreeNodeInterface>) spotCheckBox).setSelected(
+                            !sampleNode.getSpotSummaryDetailsWM().getRejectedIndices()[indexOfSpot]);
+                }
+            } catch (Exception e) {
+                //e.printStackTrace();
+            }
         }
     }
 }

squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/plots/plotControllers/SamplesWeightedMeanToolBoxNode.java

@@ -333,6 +333,7 @@ public void changed(ObservableValue<? extends SquidReportCategoryInterface> obse
             @Override
             public void changed(ObservableValue<? extends SquidReportColumnInterface> observable, SquidReportColumnInterface oldValue, SquidReportColumnInterface newValue) {
                 if (newValue != null) {
+                    PlotsController.spotsTreeViewCheckBox.setRoot(sampleItem);
                     String selectedExpression = newValue.getExpressionName();
                     if (categoryComboBox.getSelectionModel().getSelectedItem().getDisplayName().compareToIgnoreCase("AGES") == 0) {
 
@@ -363,6 +364,8 @@ public void changed(ObservableValue<? extends SquidReportColumnInterface> observ
                                 probabilitySlider.valueProperty().setValue(spotSummaryDetailsWM.getMinProbabilityWM());
                             }
                         } catch (SquidException squidException) {
+                            PlotsController.plot = null;
+                            PlotsController.spotsTreeViewCheckBox.setRoot(null);
                         }
 
                     } else {
@@ -392,15 +395,13 @@ public void changed(ObservableValue<? extends SquidReportColumnInterface> observ
                         PlotsController.plot = myPlot;
                         sampleNode.setSamplePlotWM(myPlot);
 
-//                        updateSampleFromSlider(probabilitySlider.getValue());
                         // if value is unchanged, then we need to force update
                         if (Double.compare(probabilitySlider.getValue(), spotSummaryDetailsWM.getMinProbabilityWM()) == 0) {
                             updateSampleFromSlider(probabilitySlider.getValue());
                         } else {
                             // this also forces an update
                             probabilitySlider.valueProperty().setValue(spotSummaryDetailsWM.getMinProbabilityWM());
                         }
-
                     }
 
                     // sort by selected sort expression