Various (#170)

Evolution plots ready for review.
File I/O speedups.
Generalizes reading of Squid3 csv files to handle any number of ratios / masses.

nb-configuration.xml

@@ -14,6 +14,5 @@ That way multiple projects can share the same settings (useful for formatting ru
 Any value defined here will override the pom.xml file value but is only applicable to the current project.
 -->
         <org-netbeans-modules-javascript2-requirejs.enabled>true</org-netbeans-modules-javascript2-requirejs.enabled>
-        <netbeans.hint.jdkPlatform>JDK_1.8</netbeans.hint.jdkPlatform>
     </properties>
 </project-shared-configuration>

pom.xml

@@ -21,7 +21,7 @@
     <groupId>org.cirdles</groupId>
     <artifactId>ET_Redux</artifactId>
     <name>ET_Redux</name>
-    <version>3.6.71</version>
+    <version>3.6.72</version>
     <description>Successor to U-Pb_Redux</description>
     <url>https://cirdles.org</url>
     <inceptionYear>2006</inceptionYear>

src/main/java/org/earthtime/ETReduxFrame.java

@@ -1603,9 +1603,15 @@ public void updateReportTable(boolean performReduction, boolean inLiveMode, Stri
             ((SampleDateInterpretationsManager) sampleDateInterpDialog).setSample(theSample);
         }
 
-        try {
-            ((SampleDateInterpretationsManager) sampleDateInterpDialog).refreshSampleDateInterpretations(false, inLiveMode);
-        } catch (Exception e) {
+
+        if ((theSample.getSampleAnalysisType().length() == 0)
+                ||theSample.isAnalysisTypeUSERIES()) {
+            // oct 2018 problem of time sink involving setselectedrow of tree
+        } else {
+            try {
+                ((SampleDateInterpretationsManager) sampleDateInterpDialog).refreshSampleDateInterpretations(false, inLiveMode);
+            } catch (Exception e) {
+            }
         }
     }
 
@@ -3660,12 +3666,12 @@ private void manageSampleDateInterpretation(SampleTreeI dateTreeByAliquot, Sampl
             myPlotAnyPanel = new PlotAny2Panel(theSample, this);
             myUseriesIsochronPanel = new IsochronsPanel(theSample, this);
 
-            if (myEvolutionPlotPanel == null) {
+           // if (myEvolutionPlotPanel == null) {
 //                myEvolutionPlotPanel = null;
                 myEvolutionPlotPanel = new EvolutionPlotPanelII(theSample, this);
 //                PlaceHolderForJavaFxThread placeHolderForJavaFXThread = new PlaceHolderForJavaFxThread();
 //                placeHolderForJavaFXThread.runme();
-            }
+           // }
 
             theSample.getSampleDateInterpretationGUISettings().//
                     setConcordiaOptions(((ConcordiaPlotDisplayInterface) myConcordiaGraphPanel).getConcordiaOptions());

src/main/java/org/earthtime/UPb_Redux/dateInterpretation/SampleTreeAnalysisMode.java

@@ -638,7 +638,7 @@ public void actionPerformed(ActionEvent arg0) {
                         }
                     });
                     popup.add(menuItem);
-                    
+
                     if (sample.getIsotopeSystem().compareToIgnoreCase("UTh") == 0) {
                         menuItem = new JMenuItem("Set Isochrons for this model");
                         menuItem.addActionListener((ActionEvent arg0) -> {
@@ -647,7 +647,7 @@ public void actionPerformed(ActionEvent arg0) {
                             myIsochronDialog.setSize(325, 385);
                             myIsochronDialog.setVisible(true);
                             ((SampleDateModel) nodeInfo).setIsochronModels(((IsochronsSelectorDialog) myIsochronDialog).getSelectedIsochrons());
-                            
+
                             getSampleTreeChange().sampleTreeChangeAnalysisMode(node);
                         });
                         popup.add(menuItem);

src/main/java/org/earthtime/UPb_Redux/valueModels/SampleDateModel.java

@@ -170,6 +170,7 @@ public class SampleDateModel extends ValueModel implements
     private transient McLeanRegressionLineInterface mcLeanRegressionLine;
     private static String unitsForYears = "Ma";
     private SortedSet<IsochronModel> isochronModels;
+    private boolean automaticIsochronSelection;
 
     /**
      * creates a new instance of <code>SampleDateModel</code> with all of its
@@ -192,6 +193,7 @@ public SampleDateModel() {
 
         //this.unitsForYears = "Ma";
         this.isochronModels = new TreeSet<>();
+        this.automaticIsochronSelection = true;
     }
 
     /**
@@ -3174,4 +3176,18 @@ public SortedSet<IsochronModel> getIsochronModels() {
     public void setIsochronModels(SortedSet<IsochronModel> isochronModels) {
         this.isochronModels = isochronModels;
     }
+
+    /**
+     * @return the automaticIsochronSelection
+     */
+    public boolean isAutomaticIsochronSelection() {
+        return automaticIsochronSelection;
+    }
+
+    /**
+     * @param automaticIsochronSelection the automaticIsochronSelection to set
+     */
+    public void setAutomaticIsochronSelection(boolean automaticIsochronSelection) {
+        this.automaticIsochronSelection = automaticIsochronSelection;
+    }
 }

src/main/java/org/earthtime/UTh_Redux/samples/SampleUTh.java

@@ -539,7 +539,9 @@ public static ValueModel generateDefaultSampleDateModel(){
         ValueModel defaultSDM = new SampleDateModel();
 
         defaultSDM.setName("DEFAULT");
-        ((SampleDateModel)defaultSDM).setIsochronModels(IsochronModel.generateDefaultEvolutionIsochronModels());
+        ((SampleDateModel)defaultSDM).setIsochronModels(
+                IsochronModel.generateDefaultEvolutionIsochronModels());
+        ((SampleDateModel)defaultSDM).setAutomaticIsochronSelection(true);
 
         return defaultSDM;
     }