Bug fixing.

danv61 · danv61 · commit 6ef5bfd5e76f · 2026-04-17T17:14:36.000-04:00
diff --git a/vcell-client/src/main/java/cbit/plot/gui/PlotRenderers.java b/vcell-client/src/main/java/cbit/plot/gui/PlotRenderers.java
@@ -239,6 +239,16 @@ public void draw(Graphics2D g2,
                     // vertical segment: (xB, yA) → (xB, yB)
                     step.lineTo(xB, yB);
                 }
+                // VERTICAL SEGMENT from last upper point to first lower point
+                // compute first lower point at the rightmost x
+                double tLast = (time != null ? time[n - 1] : (n - 1) * dt);
+                double vLastLower = lower[n - 1];
+                double normLastLower = (vLastLower - yMinRounded) / (yMaxRounded - yMinRounded);
+                int xLast = x0 + (int)Math.round((tLast / xMaxRounded) * plotWidth);
+                int yLastLower = y0 - (int)Math.round(normLastLower * plotHeight);
+                // vertical segment from last upper point to first lower point
+                step.lineTo(xLast, yLastLower);
+
                 // ---- LOWER BOUNDARY (right → left) ----
                 for (int i = n - 1; i > 0; i--) {
                     // current point
diff --git a/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/ClusterSpecificationPanel.java b/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/ClusterSpecificationPanel.java
@@ -155,7 +155,11 @@ private String buildTooltip(ODESolverResultSetColumnDescription cd, DisplayMode
                         "<html>Number of clusters of size <b>" + name +
                                 "</b> <font color=\"#8B0000\">[molecules]</font></html>";
                 case MEAN, OVERALL -> {
-                    ClusterStatistic stat = ClusterStatistic.valueOf(name);
+                    ClusterStatistic stat = ClusterStatistic.fromString(name);
+                    if(stat == null) {
+                        lg.error("Unknown column name in ClusterYAxisRenderer: " + name);
+                        yield name; // fallback to just showing the name without tooltip
+                    }
                     yield "<html>" + stat.description +
                             "<font color=\"#8B0000\"> [" + stat.unit + "]</font></html>";
                 }
@@ -170,6 +174,10 @@ public void actionPerformed(ActionEvent e) {
             if (e.getSource() instanceof JRadioButton rb && SwingUtilities.isDescendingFrom(rb, ClusterSpecificationPanel.this)) {
                 lg.debug("actionPerformed() called. Source is JRadioButton: {}", rb.getText());
                 DisplayMode mode = DisplayMode.fromActionCommand(cmd);
+                // set property to inform the list about current mode (needed for renderer)
+                // moved here from valueChanged() because the tooltip of the y-axis choices needs to be updated
+                // immediately when the mode changes, even before any selection is made in the list
+                yAxisChoiceList.putClientProperty("ClusterDisplayMode", mode);
                 populateYAxisChoices(mode);
             }
         }
@@ -192,8 +200,9 @@ public void valueChanged(ListSelectionEvent e) {
                 java.util.List<ColumnDescription> selected = getYAxisChoice().getSelectedValuesList();
                 DisplayMode mode = getCurrentDisplayMode();
                 ODESolverResultSet srs = getResultSetForMode(mode);
-                // set property to inform the list about current mode (needed for renderer)
-                yAxisChoiceList.putClientProperty("ClusterDisplayMode", mode);
+                // moved this to actionPerformed() where it belongs, it was being called too late here
+//                // set property to inform the list about current mode (needed for renderer)
+//                yAxisChoiceList.putClientProperty("ClusterDisplayMode", mode);
                 // fire the event upward
                 firePropertyChange("ClusterSelection", null, new ClusterSelection(mode, selected, srs));
             }
diff --git a/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/ClusterVisualizationPanel.java b/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/ClusterVisualizationPanel.java
@@ -84,6 +84,11 @@ public void propertyChange(PropertyChangeEvent evt) {
                     redrawLegend(sel);      // redraw legend (one plot, multiple curves)
                     redrawPlot(sel);        // redraw plot (one plot, multiple curves)
                     redrawDataTable(sel);   // redraw data table
+                    if(sel.mode == ClusterSpecificationPanel.DisplayMode.COUNTS) {
+                        getClusterPlotPanel().setStepAvg(true);
+                    } else {
+                        getClusterPlotPanel().setStepAvg(false);
+                    }
                 } catch (ExpressionException e) {
                     throw new RuntimeException(e);
                 }
@@ -144,8 +149,10 @@ public void componentShown(ComponentEvent e) {
                         lg.debug("componentShown() called, height = " + clusterPlotPanel.getHeight());
                     }
                 });
-                clusterPlotPanel.setStepAvg(false);
-                clusterPlotPanel.setStepBand(true);
+
+                // uncomment these to override the defaulta AbstractPlotPanel renderer options
+//                clusterPlotPanel.setStepAvg(false);
+//                clusterPlotPanel.setStepBand(true);
 
             } catch (java.lang.Throwable ivjExc) {
                 handleException(ivjExc);
diff --git a/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/MoleculeSpecificationPanel.java b/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/MoleculeSpecificationPanel.java
@@ -156,6 +156,9 @@ public void actionPerformed(ActionEvent e) {
 
                 if (DisplayMode.isDisplayModeActionCommand(cmd)) {
                     java.util.List<DisplayMode> displayModes = getSelectedDisplayModes();
+                    // in ClusterSpecificationPanel need the mode for the renderer, so we had to put it in a ClientProperty
+                    // but in MoleculeSpecificationPanel we don't have that requirement
+                    // note that it's bad style to just query the checkboxes directly from within a renderer
                     populateYAxisChoices(displayModes);
                 } else if (StatisticSelection.isStatisticSelectionActionCommand(cmd)) {
                     MoleculeSelection sel = new MoleculeSelection(
diff --git a/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/MoleculeVisualizationPanel.java b/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/MoleculeVisualizationPanel.java
@@ -147,8 +147,10 @@ public void componentShown(ComponentEvent e) {
                         lg.debug("componentShown() called, height = " + moleculePlotPanel.getHeight());
                     }
                 });
-                moleculePlotPanel.setStepAvg(false);
-                moleculePlotPanel.setStepBand(true);
+
+                // uncomment these to override the defaulta AbstractPlotPanel renderer options, feel free to add more
+//                moleculePlotPanel.setStepAvg(true);
+//                moleculePlotPanel.setStepBand(true);
 
             } catch (java.lang.Throwable ivjExc) {
                 handleException(ivjExc);
