Tracer crashes on very small positive values #167

beast-dev · Feb 9, 2022 · afe112b · afe112b
1 parent c249ecc
commit afe112b
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Showing 9 changed files with 28 additions and 24 deletions.
diff --git a/src/tracer/application/TracerApp.java b/src/tracer/application/TracerApp.java
@@ -69,11 +69,12 @@ static public void main(String[] args) {
                     public void run() {
                         try {
                             for (UIManager.LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {
-                                System.out.println(info.getName() + " - " + info.getClassName());
+//                                System.out.println(info.getName() + " - " + info.getClassName());
                                 // Tracer Issue #172 Mac OS X - com.apple.laf.AquaLookAndFeel
                                 if (info.getName().startsWith("Mac")) {
                                     UIManager.setLookAndFeel(info.getClassName());
                                     lafLoaded = true;
+                                    System.out.println("Set look & feel to : " + info.getName() + " - " + info.getClassName());
                                 }
                             }
 //                            UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");

diff --git a/src/tracer/traces/ContinuousDensityPanel.java b/src/tracer/traces/ContinuousDensityPanel.java
@@ -111,17 +111,17 @@ public ContinuousDensityPanel(final JFrame frame) {
 
         setOpaque(false);
 
-        kdeChart = new JChart(new LinearAxis(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis());
+        kdeChart = new JChart(new LinearAxis2(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis2());
         kdeChartPanel = new JChartPanel(kdeChart, "","","");
         kdeToolBar = createToolBar(Type.KDE, currentSettings);
         densityChartSetupDialog = new ChartSetupDialog(frame, true, false, true, false,
                 Axis.AT_MAJOR_TICK, Axis.AT_MAJOR_TICK, Axis.AT_ZERO, Axis.AT_MAJOR_TICK);
 
-        histogramChart = new JChart(new LinearAxis(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis());
+        histogramChart = new JChart(new LinearAxis2(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis2());
         histogramChartPanel = new JChartPanel(histogramChart, "","","");
         histogramToolBar = createToolBar(Type.HISTOGRAM, currentSettings);
 
-        violinChart = new JParallelChart(false, new LinearAxis(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS));
+        violinChart = new JParallelChart(false, new LinearAxis2(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS));
         violinChartPanel = new JChartPanel(violinChart, "","","");
         violinToolBar = createToolBar(Type.VIOLIN, currentSettings);
         violinChartSetupDialog = new ChartSetupDialog(frame, false, true, false, true,

diff --git a/src/tracer/traces/ContinuousJointDensityPanel.java b/src/tracer/traces/ContinuousJointDensityPanel.java
@@ -26,7 +26,8 @@
 package tracer.traces;
 
 import dr.app.gui.chart.*;
-import dr.inference.trace.*;
+import dr.inference.trace.TraceCorrelation;
+import dr.inference.trace.TraceList;
 import dr.stats.Variate;
 
 import javax.swing.*;
@@ -68,7 +69,7 @@ class Settings extends TraceChartPanel.Settings {
     public ContinuousJointDensityPanel(final JFrame frame) {
         super(frame);
 
-        chart = new JChart(new LinearAxis(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS));
+        chart = new JChart(new LinearAxis2(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis2(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS));
         chartPanel = new JChartPanel(chart, "", "", ""); // xAxisTitle, yAxisTitle
 
         toolBar = createSinglePairToolBar(frame);
@@ -235,8 +236,8 @@ private void createContinuousScatterPlot(TraceList traceList1, int traceIndex1,
             k += minCount / sampleSize;
         }
 
-        getChart().setXAxis(new LinearAxis());
-        getChart().setYAxis(new LinearAxis());
+        getChart().setXAxis(new LinearAxis2());
+        getChart().setYAxis(new LinearAxis2());
 
         // add plot
         ScatterPlot plot = new ScatterPlot(samples1, samples2);

diff --git a/src/tracer/traces/DiscreteContinuousJointDensityPanel.java b/src/tracer/traces/DiscreteContinuousJointDensityPanel.java
@@ -63,7 +63,7 @@ public class DiscreteContinuousJointDensityPanel extends TraceChartPanel {
     public DiscreteContinuousJointDensityPanel(final JFrame frame) {
         super(frame);
 
-        parallelChart = new JParallelChart(false, new LinearAxis(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS));
+        parallelChart = new JParallelChart(false, new LinearAxis2(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS));
         chartPanel = new JChartPanel(parallelChart, "", "", ""); // xAxisTitle, yAxisTitle
 
         toolBar = createToolBar(frame);

diff --git a/src/tracer/traces/DiscreteDensityPanel.java b/src/tracer/traces/DiscreteDensityPanel.java
@@ -26,7 +26,9 @@
 package tracer.traces;
 
 import dr.app.gui.chart.*;
-import dr.inference.trace.*;
+import dr.inference.trace.Trace;
+import dr.inference.trace.TraceList;
+import dr.inference.trace.TraceType;
 import dr.stats.Variate;
 
 import javax.swing.*;
@@ -63,7 +65,7 @@ private class Settings extends TraceChartPanel.Settings {
      */
     public DiscreteDensityPanel(final JFrame frame) {
         super(frame);
-        densityChart = new JChart(new LinearAxis(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis(Axis.AT_ZERO, Axis.AT_MAJOR_TICK_PLUS));
+        densityChart = new JChart(new LinearAxis2(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis2(Axis.AT_ZERO, Axis.AT_MAJOR_TICK_PLUS));
         densityChartPanel = new JChartPanel(densityChart, "","","");
         toolBar = createToolBar(currentSettings);
     }

diff --git a/src/tracer/traces/DiscreteJointDensityPanel.java b/src/tracer/traces/DiscreteJointDensityPanel.java
@@ -27,17 +27,12 @@
 
 import dr.app.gui.chart.*;
 import dr.inference.trace.TraceCorrelation;
-import dr.inference.trace.TraceDistribution;
 import dr.inference.trace.TraceList;
-import dr.inference.trace.TraceType;
 import dr.stats.Variate;
 
 import javax.swing.*;
-import java.awt.*;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 /**
  * A panel that displays correlation plots of 2 discrete traces
@@ -66,7 +61,7 @@ public class DiscreteJointDensityPanel extends TraceChartPanel {
     public DiscreteJointDensityPanel(final JFrame frame) {
         super(frame);
 
-        chart = new JChart(new LinearAxis(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS));
+        chart = new JChart(new LinearAxis2(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis2(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS));
         chartPanel = new JChartPanel(chart, "", "", ""); // xAxisTitle, yAxisTitle
 
         toolBar = createSinglePairToolBar(frame);

diff --git a/src/tracer/traces/FrequencyPanel.java b/src/tracer/traces/FrequencyPanel.java
@@ -26,12 +26,15 @@
 package tracer.traces;
 
 import dr.app.gui.chart.*;
-import dr.inference.trace.*;
+import dr.inference.trace.Trace;
+import dr.inference.trace.TraceCorrelation;
+import dr.inference.trace.TraceList;
+import dr.inference.trace.TraceType;
 
 import javax.swing.*;
 import java.awt.*;
 import java.awt.event.ActionEvent;
-import java.util.*;
+import java.util.Set;
 
 
 /**
@@ -60,8 +63,9 @@ public class FrequencyPanel extends TraceChartPanel {
      */
     public FrequencyPanel(final JFrame frame) {
         super(frame);
+        // LinearAxis2 can handle small ranged values (range < 1E-30) correctly, but LinearAxis cannot
         traceChart = new JChart(
-                new LinearAxis(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis());
+                new LinearAxis2(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS), new LinearAxis());
         traceChartPanel = new JChartPanel(traceChart, "","", "Frequency"); // xAxisTitle, yAxisTitle
         toolBar = createToolBar(currentSettings);
     }
@@ -146,7 +150,7 @@ protected void setupTraces() {
                 if (td != null) {
                     histogramPlot.setIntervals(td.getUpperHPD(), td.getLowerHPD());
                 }
-                getChartPanel().getChart().setXAxis(new LinearAxis(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS));
+                getChartPanel().getChart().setXAxis(new LinearAxis2(Axis.AT_MAJOR_TICK_PLUS, Axis.AT_MAJOR_TICK_PLUS));
 
                 plot = histogramPlot;
             } else if (traceType.isDiscrete()) {

diff --git a/src/tracer/traces/IntervalsPanel.java b/src/tracer/traces/IntervalsPanel.java
@@ -65,7 +65,7 @@ public class IntervalsPanel extends TraceChartPanel {
      */
     public IntervalsPanel(final JFrame frame) {
         super(frame);
-        intervalsChart = new JParallelChart(false, new LinearAxis(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS));
+        intervalsChart = new JParallelChart(false, new LinearAxis2(Axis.AT_MAJOR_TICK_MINUS, Axis.AT_MAJOR_TICK_PLUS));
         chartPanel = new JChartPanel(intervalsChart, "", "", ""); // xAxisTitle, yAxisTitle
 
         toolBar = createToolBar();

diff --git a/src/tracer/traces/RawTracePanel.java b/src/tracer/traces/RawTracePanel.java
@@ -71,7 +71,8 @@ public class RawTracePanel extends TraceChartPanel {
      */
     public RawTracePanel(final JFrame frame) {
         super(frame);
-        traceChart = new JTraceChart(new LinearAxis(Axis.AT_ZERO, Axis.AT_DATA), new LinearAxis());
+        // LinearAxis2 can handle small ranged values (range < 1E-30) correctly, but LinearAxis cannot
+        traceChart = new JTraceChart(new LinearAxis(Axis.AT_ZERO, Axis.AT_DATA), new LinearAxis2());
         chartPanel = new JChartPanel(traceChart, "", "", ""); // xAxisTitle, yAxisTitle
         toolBar = createToolBar(currentSettings);
     }
@@ -281,7 +282,7 @@ protected void setupTraces() {
                             getChart().getYAxis().setRange(0.0, 1.0);
                         }
                     } else {
-                        getChart().setYAxis(new LinearAxis(Axis.AT_DATA, Axis.AT_DATA));
+                        getChart().setYAxis(new LinearAxis2(Axis.AT_DATA, Axis.AT_DATA));
                     }
                     int selectedColour = currentSettings.cm.addTraceColour(tl.getFullName(), name, currentSettings.colourBy);
 //                    System.out.println(tl.getName() + " : " + name + " : " + values.size() + "  " + stateStart + "  " + stateStep);