mzmine · tomas-pluskal · Apr 1, 2020 · Feb 15, 2020 · Feb 16, 2020 · Feb 16, 2020
diff --git a/src/main/java/io/github/mzmine/datamodel/FeatureStatus.java b/src/main/java/io/github/mzmine/datamodel/FeatureStatus.java
@@ -17,6 +17,8 @@
 
 package io.github.mzmine.datamodel;
 
+import io.github.mzmine.util.color.SimpleColorPalette;
+import io.github.mzmine.util.javafx.FxColorUtil;
 import java.awt.Color;
 import io.github.mzmine.main.MZmineCore;
 import io.github.mzmine.util.color.Colors;
@@ -46,36 +48,37 @@ public enum FeatureStatus {
   MANUAL;
 
   public Color getColor() {
-    Vision vision =
-        MZmineCore.getConfiguration() != null ? MZmineCore.getConfiguration().getColorVision()
-            : Vision.DEUTERANOPIA;
+    SimpleColorPalette palette =
+        (MZmineCore.getConfiguration().getDefaultColorPalette() != null) ? MZmineCore.getConfiguration()
+            .getDefaultColorPalette() : SimpleColorPalette.DEFAULT.get(Vision.DEUTERANOPIA);
     switch (this) {
       case DETECTED:
-        return Colors.getPositiveColor(vision);
+        return palette.getPositiveColorAWT();
       case ESTIMATED:
-        return Colors.getNeutralColor();
+        return palette.getNeutralColorAWT();
       case MANUAL:
         return Color.BLACK;
       case UNKNOWN:
       default:
-        return Colors.getNegativeColor(vision);
+        return palette.getNegativeColorAWT();
     }
   }
 
   public javafx.scene.paint.Color getColorFX() {
-    Vision vision =
-        MZmineCore.getConfiguration() != null ? MZmineCore.getConfiguration().getColorVision()
-            : Vision.DEUTERANOPIA;
+    SimpleColorPalette palette =
+        (MZmineCore.getConfiguration().getDefaultColorPalette() != null) ? MZmineCore.getConfiguration()
+            .getDefaultColorPalette() : SimpleColorPalette.DEFAULT.get(Vision.DEUTERANOPIA);
+
     switch (this) {
       case DETECTED:
-        return ColorsFX.getPositiveColor(vision);
+        return palette.getPositiveColor();
       case ESTIMATED:
-        return ColorsFX.getNeutralColor();
+        return palette.getNeutralColor();
       case MANUAL:
         return javafx.scene.paint.Color.BLACK;
       case UNKNOWN:
       default:
-        return ColorsFX.getNegativeColor(vision);
+        return palette.getNegativeColor();
     }
   }
 }
diff --git a/src/main/java/io/github/mzmine/gui/chartbasics/chartthemes/ChartThemeParameters.java b/src/main/java/io/github/mzmine/gui/chartbasics/chartthemes/ChartThemeParameters.java
@@ -19,10 +19,7 @@
 package io.github.mzmine.gui.chartbasics.chartthemes;
 
 
-import java.util.List;
 import org.jfree.chart.JFreeChart;
-import org.jfree.chart.plot.XYPlot;
-import org.jfree.chart.title.Title;
 import io.github.mzmine.parameters.Parameter;
 import io.github.mzmine.parameters.dialogs.ParameterSetupDialog;
 import io.github.mzmine.parameters.impl.SimpleParameterSet;
@@ -82,7 +79,7 @@ public class ChartThemeParameters extends SimpleParameterSet {
   public static final BooleanParameter showYAxis = new BooleanParameter("Show y axis", "", true);
 
   public ChartThemeParameters() {
-    super(new Parameter[] {showLegends, showTitle, changeTitle, xlabel, ylabel, color, masterFont,
+    super(new Parameter[]{showLegends, showTitle, changeTitle, xlabel, ylabel, color, masterFont,
         titleFont, captionFont, labelFont, xGridPaint, yGridPaint, showXAxis, showYAxis});
     changeTitle.setValue(false);
     xlabel.setValue(false);
@@ -96,13 +93,15 @@ public ExitCode showSetupDialog(boolean valueCheckRequired) {
 
     assert Platform.isFxApplicationThread();
 
-    if ((parameters == null) || (parameters.length == 0))
+    if ((parameters == null) || (parameters.length == 0)) {
       return ExitCode.OK;
+    }
     ParameterSetupDialog dialog = new ChartThemeParametersSetupDialog(valueCheckRequired, this);
     dialog.showAndWait();
     return dialog.getExitCode();
   }
 
+  @Deprecated
   public void applyToChart(JFreeChart chart) {
     // // apply chart settings
     // boolean showTitle = this.getParameter(ChartThemeParameters.showTitle).getValue();
@@ -169,29 +168,29 @@ public void applyToChartTheme(EStandardChartTheme theme) {
     String ylabel =
         this.getParameter(ChartThemeParameters.ylabel).getEmbeddedParameter().getValue();
     FontSpecs master = this.getParameter(ChartThemeParameters.masterFont).getValue();
-    FontSpecs large = this.getParameter(ChartThemeParameters.titleFont).getValue();
-    FontSpecs medium = this.getParameter(ChartThemeParameters.captionFont).getValue();
-    FontSpecs small = this.getParameter(ChartThemeParameters.labelFont).getValue();
+    FontSpecs titleFont = this.getParameter(ChartThemeParameters.titleFont).getValue();
+    FontSpecs captionFont = this.getParameter(ChartThemeParameters.captionFont).getValue();
+    FontSpecs labelFont = this.getParameter(ChartThemeParameters.labelFont).getValue();
     Color bgColor = this.getParameter(ChartThemeParameters.color).getValue();
 
     theme.setShowTitle(showTitle);
-    theme.getShowSubtitles(showLegends);
+    theme.getShowSubtitles(showTitle);
     theme.setChartBackgroundPaint(FxColorUtil.fxColorToAWT(bgColor));
     theme.setPlotBackgroundPaint(FxColorUtil.fxColorToAWT(bgColor));
 
     theme.setMasterFont(FxFontUtil.fxFontToAWT(master.getFont()));
-    theme.setExtraLargeFont(FxFontUtil.fxFontToAWT(large.getFont()));
-    theme.setLargeFont(FxFontUtil.fxFontToAWT(medium.getFont()));
-    theme.setRegularFont(FxFontUtil.fxFontToAWT(small.getFont()));
-    theme.setSmallFont(FxFontUtil.fxFontToAWT(small.getFont()));
+    theme.setExtraLargeFont(FxFontUtil.fxFontToAWT(titleFont.getFont()));
+    theme.setLargeFont(FxFontUtil.fxFontToAWT(captionFont.getFont()));
+    theme.setRegularFont(FxFontUtil.fxFontToAWT(labelFont.getFont()));
+    theme.setSmallFont(FxFontUtil.fxFontToAWT(labelFont.getFont()));
 
     theme.setMasterFontColor(FxColorUtil.fxColorToAWT(master.getColor()));
-    theme.setAxisLabelPaint(FxColorUtil.fxColorToAWT(medium.getColor()));
-    theme.setTickLabelPaint(FxColorUtil.fxColorToAWT(small.getColor()));
-    theme.setTitlePaint(FxColorUtil.fxColorToAWT(large.getColor()));
-    theme.setItemLabelPaint(FxColorUtil.fxColorToAWT(small.getColor()));
-    theme.setLegendItemPaint(FxColorUtil.fxColorToAWT(medium.getColor()));
-    theme.setAxisLinePaint(FxColorUtil.fxColorToAWT(medium.getColor()));
+    theme.setAxisLabelPaint(FxColorUtil.fxColorToAWT(captionFont.getColor()));
+    theme.setTickLabelPaint(FxColorUtil.fxColorToAWT(labelFont.getColor()));
+    theme.setTitlePaint(FxColorUtil.fxColorToAWT(titleFont.getColor()));
+    theme.setItemLabelPaint(FxColorUtil.fxColorToAWT(labelFont.getColor()));
+    theme.setLegendItemPaint(FxColorUtil.fxColorToAWT(captionFont.getColor()));
+    theme.setAxisLinePaint(FxColorUtil.fxColorToAWT(captionFont.getColor()));
 
     theme.setShowXAxis(showXAxis);
     theme.setShowYAxis(showYAxis);

diff --git a/src/main/java/io/github/mzmine/gui/chartbasics/chartthemes/EStandardChartTheme.java b/src/main/java/io/github/mzmine/gui/chartbasics/chartthemes/EStandardChartTheme.java
@@ -18,20 +18,25 @@
 
 package io.github.mzmine.gui.chartbasics.chartthemes;
 
+import java.awt.BasicStroke;
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.Paint;
+import java.awt.Stroke;
+import javax.annotation.Nonnull;
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.StandardChartTheme;
 import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.block.BlockBorder;
 import org.jfree.chart.plot.XYPlot;
 import org.jfree.chart.renderer.category.StandardBarPainter;
 import org.jfree.chart.renderer.xy.StandardXYBarPainter;
 import org.jfree.chart.title.LegendTitle;
 import org.jfree.chart.title.PaintScaleLegend;
+import org.jfree.chart.title.TextTitle;
 import org.jfree.chart.ui.RectangleEdge;
 import io.github.mzmine.gui.chartbasics.chartthemes.ChartThemeFactory.THEME;
-import io.github.mzmine.util.javafx.FxColorUtil;
+import org.jfree.chart.ui.RectangleInsets;
 
 /**
  * More options for the StandardChartTheme
@@ -42,6 +47,14 @@ public class EStandardChartTheme extends StandardChartTheme {
   private static final long serialVersionUID = 1L;
 
   private static final Color DEFAULT_GRID_COLOR = Color.BLACK;
+  private static final Color DEFAULT_CROSS_HAIR_COLOR = Color.BLACK;
+
+  private static final boolean DEFAULT_CROSS_HAIR_VISIBLE = true;
+  private static final Stroke DEFAULT_CROSS_HAIR_STROKE = new BasicStroke(1.0F, BasicStroke.CAP_BUTT,
+      BasicStroke.JOIN_BEVEL, 1.0f, new float[] {5.0F, 3.0F}, 0.0F);
+
+  private static final RectangleInsets DEFAULT_AXIS_OFFSET = new RectangleInsets(5.0, 5.0, 5.0, 5.0);
+  private static final double TITLE_TOP_MARGIN = 5.0;
 
   public static final String XML_DESC = "ChartTheme";
   // master font
@@ -126,9 +139,50 @@ public void setAll(boolean antiAlias, boolean showTitle, boolean noBG, Color cBG
   public void apply(JFreeChart chart) {
     super.apply(chart);
     XYPlot p = chart.getXYPlot();
+
+    // Cross hair and  axis visibility colors
+    applyToCrosshair(chart);
+    applyToAxes(chart);
+
+//    applyToTitles(chart);
+
+    // apply bg
+    chart.setBackgroundPaint(this.getChartBackgroundPaint());
+    chart.getPlot().setBackgroundPaint(this.getPlotBackgroundPaint());
+
     //
-    p.setDomainGridlinesVisible(showXGrid);
-    p.setRangeGridlinesVisible(showYGrid);
+    chart.setAntiAlias(isAntiAliased());
+    p.setBackgroundAlpha(isNoBackground() ? 0 : 1);
+
+    applyToLegend(chart);
+
+  }
+
+
+  public void applyToCrosshair(@Nonnull JFreeChart chart){
+    XYPlot p = chart.getXYPlot();
+    p.setDomainCrosshairPaint(DEFAULT_CROSS_HAIR_COLOR);
+    p.setRangeCrosshairPaint(DEFAULT_CROSS_HAIR_COLOR);
+    p.setDomainCrosshairStroke(DEFAULT_CROSS_HAIR_STROKE);
+    p.setRangeCrosshairStroke(DEFAULT_CROSS_HAIR_STROKE);
+    p.setDomainCrosshairVisible(DEFAULT_CROSS_HAIR_VISIBLE);
+    p.setRangeCrosshairVisible(DEFAULT_CROSS_HAIR_VISIBLE);
+  }
+
+  public void applyToAxes(@Nonnull JFreeChart chart){
+    XYPlot p = chart.getXYPlot();
+    p.getDomainAxis().setVisible(isShowXAxis());
+    p.getRangeAxis().setVisible(isShowYAxis());
+    p.setDomainGridlinesVisible(isShowXGrid());
+    p.setDomainGridlinePaint(getClrXGrid());
+    p.setRangeGridlinesVisible(isShowYGrid());
+    p.setRangeGridlinePaint(getClrYGrid());
+
+    if (isUseXLabel())
+      p.getDomainAxis().setLabel(getXlabel());
+    if (isUseYLabel())
+      p.getRangeAxis().setLabel(getYlabel());
+
     // all axes
     for (int i = 0; i < p.getDomainAxisCount(); i++) {
       NumberAxis a = (NumberAxis) p.getDomainAxis(i);
@@ -144,42 +198,35 @@ public void apply(JFreeChart chart) {
       // visible?
       a.setVisible(showYAxis);
     }
-    // apply bg
-    chart.setBackgroundPaint(this.getChartBackgroundPaint());
-    chart.getPlot().setBackgroundPaint(this.getPlotBackgroundPaint());
 
-    for (int i = 0; i < chart.getSubtitleCount(); i++) {
-      // visible?
-      chart.getSubtitle(i).setVisible(subtitleVisible);
-      //
-      if (PaintScaleLegend.class.isAssignableFrom(chart.getSubtitle(i).getClass()))
-        ((PaintScaleLegend) chart.getSubtitle(i))
-            .setBackgroundPaint(this.getChartBackgroundPaint());
-    }
-    if (chart.getLegend() != null)
-      chart.getLegend().setBackgroundPaint(this.getChartBackgroundPaint());
-
-    if (isUseXLabel())
-      p.getDomainAxis().setLabel(getXlabel());
-    if (isUseYLabel())
-      p.getRangeAxis().setLabel(getYlabel());
-
-    p.getDomainAxis().setVisible(isShowXAxis());
-    p.getRangeAxis().setVisible(isShowYAxis());
+    p.setAxisOffset(DEFAULT_AXIS_OFFSET);
+  }
 
-    p.setDomainGridlinesVisible(isShowXGrid());
-    p.setDomainGridlinePaint(getClrXGrid());
-    p.setRangeGridlinesVisible(isShowYGrid());
-    p.setRangeGridlinePaint(getClrYGrid());
+  public void applyToLegend(@Nonnull JFreeChart chart){
 
-    //
-    chart.setAntiAlias(isAntiAliased());
-    chart.getTitle().setVisible(isShowTitle());
-    p.setBackgroundAlpha(isNoBackground() ? 0 : 1);
+    if (chart.getLegend() != null)
+      chart.getLegend().setBackgroundPaint(this.getChartBackgroundPaint());
 
     fixLegend(chart);
   }
 
+//  public void applyToTitles(@Nonnull JFreeChart chart){
+//    chart.getSubtitles().forEach(s -> {
+//      if(s instanceof TextTitle && s != chart.getTitle()){
+//        ((TextTitle) s).setFont(getRegularFont());
+//        ((TextTitle) s).setMargin(TITLE_TOP_MARGIN, 0d, 0d, 0d);
+//        ((TextTitle) s).setVisible(isShowTitle());
+////        ((TextTitle) s).setPaint(subtitleFontColor); // should be set by the theme itself.
+////        subtitle color is set by the chart theme parameters
+//
+//        if (PaintScaleLegend.class.isAssignableFrom(s.getClass())) {
+//          ((PaintScaleLegend) s)
+//              .setBackgroundPaint(this.getChartBackgroundPaint());
+//        }
+//      }
+//    });
+//  }
+
   public boolean isNoBackground() {
     return ((Color) this.getPlotBackgroundPaint()).getAlpha() == 0;
   }
@@ -194,6 +241,8 @@ public void setNoBackground(boolean state) {
         new Color(cchart.getRed(), cchart.getGreen(), cchart.getBlue(), state ? 0 : 255));
   }
 
+
+
   /**
    * Fixes the legend item's colour after the colours of the datasets/series in the plot were
    * changed.
@@ -211,6 +260,7 @@ public static void fixLegend(JFreeChart chart) {
     newLegend.setItemFont(oldLegend.getItemFont());
     chart.addLegend(newLegend);
     newLegend.setVisible(oldLegend.isVisible());
+    newLegend.setFrame(BlockBorder.NONE);
   }
 
   // GETTERS AND SETTERS
@@ -349,4 +399,5 @@ public Color getClrYGrid() {
   public void setClrYGrid(Color clrYGrid) {
     this.clrYGrid = clrYGrid;
   }
+
 }
diff --git a/src/main/java/io/github/mzmine/gui/chartbasics/graphicsexport/GraphicsExportDialogFX.java b/src/main/java/io/github/mzmine/gui/chartbasics/graphicsexport/GraphicsExportDialogFX.java
@@ -18,6 +18,8 @@
 
 package io.github.mzmine.gui.chartbasics.graphicsexport;
 
+import io.github.mzmine.util.color.SimpleColorPalette;
+import io.github.mzmine.util.javafx.FxColorUtil;
 import java.awt.Color;
 import java.io.File;
 import java.util.logging.Level;
@@ -60,7 +62,7 @@ public class GraphicsExportDialogFX extends ParameterSetupDialog {
   protected JFreeChart chart;
   protected EChartViewer chartPanel;
   protected ChartThemeParameters chartParam;
-  protected Color[] colors;
+  protected SimpleColorPalette colors;
 
   private Button btnRenewPreview;
   private Button btnApply;
@@ -74,7 +76,7 @@ public GraphicsExportDialogFX(boolean valueCheckRequired, ParameterSet parameter
     chartParam = (ChartThemeParameters) parameterSet
         .getParameter(GraphicsExportParameters.chartParameters).getValue();
 
-    colors = Colors.getSevenColorPalette(MZmineCore.getConfiguration().getColorVision(), true);
+    colors = parameterSet.getParameter(GraphicsExportParameters.colorPalette).getValue();
 
     try {
       this.chart = (JFreeChart) chart.clone();
@@ -115,9 +117,11 @@ public GraphicsExportDialogFX(boolean valueCheckRequired, ParameterSet parameter
   protected void applyTheme() {
     // update param
     updateParameterSetFromComponents();
+    chartParam = (ChartThemeParameters) parameterSet
+        .getParameter(GraphicsExportParameters.chartParameters).getValue();
+    colors = parameterSet.getParameter(GraphicsExportParameters.colorPalette).getValue();
     // apply settings
     chartParam.applyToChartTheme(theme);
-    chartParam.applyToChart(chartPanel.getChart());
     setStandardColors();
     theme.apply(chartPanel.getChart());
     disableCrosshair();
@@ -130,7 +134,11 @@ protected void disableCrosshair() {
   }
 
   protected void setStandardColors() {
-    DrawingSupplier ds = new DefaultDrawingSupplier(colors, colors, colors,
+    Color[] clrs = new Color[colors.size()];
+    for(int i = 0; i < colors.size(); i++)
+      clrs[i] = colors.getAWT(i);
+
+    DrawingSupplier ds = new DefaultDrawingSupplier(clrs, clrs, clrs,
         DefaultDrawingSupplier.DEFAULT_STROKE_SEQUENCE,
         DefaultDrawingSupplier.DEFAULT_OUTLINE_STROKE_SEQUENCE,
         DefaultDrawingSupplier.DEFAULT_SHAPE_SEQUENCE);

diff --git a/src/main/java/io/github/mzmine/gui/chartbasics/graphicsexport/GraphicsExportParameters.java b/src/main/java/io/github/mzmine/gui/chartbasics/graphicsexport/GraphicsExportParameters.java
@@ -18,6 +18,7 @@
 
 package io.github.mzmine.gui.chartbasics.graphicsexport;
 
+import io.github.mzmine.parameters.parametertypes.colorpalette.ColorPaletteParameter;
 import java.awt.Dimension;
 import java.io.File;
 import java.text.DecimalFormat;
@@ -82,9 +83,11 @@ public enum FixedSize {
   public static final ParameterSetParameter chartParameters = new ParameterSetParameter(
       "Chart parameters", "Manually set the chart parameters", new ChartThemeParameters());
 
+  public static final ColorPaletteParameter colorPalette = new ColorPaletteParameter("Color palette", "The color palette used for export.");
+
   public GraphicsExportParameters() {
     super(new Parameter[] {path, unit, exportFormat, fixedSize, width, height, dpi, color, alpha,
-        chartParameters});
+        chartParameters, colorPalette});
     height.setValue(true);
   }