X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureTypeSettings.java;h=f59aa59cccf26e217ecdc2cbb8277dd60899a5f6;hb=2bd87d696f010a6364fca99c3137d6a06b9af23b;hp=5169dfbd8d3bb7dd112a7c14a2df854fd616109c;hpb=217274a8e9ea2ae20d5a6d21989b8b16840ca6f0;p=jalview.git

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index 5169dfb..f59aa59 100644
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -62,7 +62,6 @@ import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
 import javax.swing.JSlider;
-import javax.swing.JTabbedPane;
 import javax.swing.JTextField;
 import javax.swing.border.LineBorder;
 import javax.swing.event.ChangeEvent;
@@ -105,14 +104,15 @@ public class FeatureTypeSettings extends JalviewDialog
   /*
    * FeatureRenderer holds colour scheme and filters for feature types
    */
-  private final FeatureRenderer fr; // todo refactor to allow interface type here
+  private final FeatureRenderer fr; // todo refactor to allow interface type
+                                    // here
 
   /*
    * the view panel to update when settings change
    */
   final AlignmentViewPanel ap;
 
-  private final String featureType;
+  final String featureType;
 
   /*
    * the colour and filters to reset to on Cancel
@@ -153,6 +153,10 @@ public class FeatureTypeSettings extends JalviewDialog
 
   JRadioButton graduatedColour = new JRadioButton();
 
+  JPanel coloursPanel;
+  
+  JPanel filtersPanel;
+
   JPanel singleColour = new JPanel();
 
   JPanel minColour = new JPanel();
@@ -197,13 +201,8 @@ public class FeatureTypeSettings extends JalviewDialog
    */
   List<FeatureMatcherI> filters;
 
-  // set white normally, black to debug layout
-  private Color debugBorderColour = Color.white;
-
   private JPanel chooseFiltersPanel;
 
-  private JTabbedPane tabbedPane;
-
   /**
    * Constructor
    * 
@@ -212,28 +211,14 @@ public class FeatureTypeSettings extends JalviewDialog
    */
   public FeatureTypeSettings(FeatureRenderer frender, String theType)
   {
-    this(frender, false, theType);
-  }
-
-  /**
-   * Constructor, with option to make a blocking dialog (has to complete in the
-   * AWT event queue thread). Currently this option is always set to false.
-   * 
-   * @param frender
-   * @param blocking
-   * @param theType
-   */
-  FeatureTypeSettings(FeatureRenderer frender, boolean blocking,
-          String theType)
-  {
     this.fr = frender;
     this.featureType = theType;
     ap = fr.ap;
     originalFilter = fr.getFeatureFilter(theType);
     originalColour = fr.getFeatureColours().get(theType);
-
+    
     adjusting = true;
-
+    
     try
     {
       initialise();
@@ -242,28 +227,27 @@ public class FeatureTypeSettings extends JalviewDialog
       ex.printStackTrace();
       return;
     }
-
-    updateColoursTab();
-
-    updateFiltersTab();
-
+    
+    updateColoursPanel();
+    
+    updateFiltersPanel();
+    
     adjusting = false;
-
+    
     colourChanged(false);
-
+    
     String title = MessageManager
             .formatMessage("label.display_settings_for", new String[]
             { theType });
-    initDialogFrame(this, true, blocking, title, 600, 360);
-
+    initDialogFrame(this, true, false, title, 580, 500);
     waitForInput();
   }
 
   /**
-   * Configures the widgets on the Colours tab according to the current feature
+   * Configures the widgets on the Colours panel according to the current feature
    * colour scheme
    */
-  private void updateColoursTab()
+  private void updateColoursPanel()
   {
     FeatureColourI fc = fr.getFeatureColours().get(featureType);
 
@@ -278,9 +262,9 @@ public class FeatureTypeSettings extends JalviewDialog
        */
       if (fc.isSimpleColour())
       {
-        simpleColour.setSelected(true);
         singleColour.setBackground(fc.getColour());
         singleColour.setForeground(fc.getColour());
+        simpleColour.setSelected(true);
       }
 
       /*
@@ -401,8 +385,6 @@ public class FeatureTypeSettings extends JalviewDialog
   private void initialise()
   {
     this.setLayout(new BorderLayout());
-    tabbedPane = new JTabbedPane();
-    this.add(tabbedPane, BorderLayout.CENTER);
 
     /*
      * an ActionListener that applies colour changes
@@ -417,18 +399,16 @@ public class FeatureTypeSettings extends JalviewDialog
     };
 
     /*
-     * first tab: colour options
+     * first panel: colour options
      */
     JPanel coloursPanel = initialiseColoursPanel();
-    tabbedPane.addTab(MessageManager.getString("action.colour"),
-            coloursPanel);
+    this.add(coloursPanel, BorderLayout.NORTH);
 
     /*
-     * second tab: filter options
+     * second panel: filter options
      */
     JPanel filtersPanel = initialiseFiltersPanel();
-    tabbedPane.addTab(MessageManager.getString("label.filters"),
-            filtersPanel);
+    this.add(filtersPanel, BorderLayout.CENTER);
 
     JPanel okCancelPanel = initialiseOkCancelPanel();
 
@@ -556,7 +536,8 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         if (minColour.isEnabled())
         {
-          showColourChooser(minColour, "label.select_colour_minimum_value");
+          String ttl = MessageManager.getString("label.select_colour_minimum_value");
+          showColourChooser(minColour, ttl);
         }
       }
     });
@@ -572,19 +553,19 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         if (maxColour.isEnabled())
         {
-          showColourChooser(maxColour, "label.select_colour_maximum_value");
+          String ttl = MessageManager.getString("label.select_colour_maximum_value");
+          showColourChooser(maxColour, ttl);
         }
       }
     });
     maxColour.setBorder(new LineBorder(Color.black));
 
     /*
-     * default max colour to current colour (if a plain colour),
-     * or to Black if colour by label;  make min colour a pale
-     * version of max colour
+     * default max colour to last plain colour;
+     * make min colour a pale version of max colour
      */
     FeatureColourI fc = fr.getFeatureColours().get(featureType);
-    Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
+    Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
     maxColour.setBackground(bg);
     minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
 
@@ -734,15 +715,16 @@ public class FeatureTypeSettings extends JalviewDialog
   private JPanel initialiseColoursPanel()
   {
     JPanel colourByPanel = new JPanel();
+    colourByPanel.setBackground(Color.white);
     colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
+    JvSwingUtils.createTitledBorder(colourByPanel,
+            MessageManager.getString("action.colour"), true);
 
     /*
      * simple colour radio button and colour picker
      */
     JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
     simpleColourPanel.setBackground(Color.white);
-    JvSwingUtils.createTitledBorder(simpleColourPanel,
-            MessageManager.getString("label.simple"), true);
     colourByPanel.add(simpleColourPanel);
 
     simpleColour = new JRadioButton(
@@ -755,14 +737,24 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         if (simpleColour.isSelected() && !adjusting)
         {
-          showColourChooser(singleColour, "label.select_colour");
+          colourChanged(true);
         }
       }
     });
-    
+
     singleColour.setFont(JvSwingUtils.getLabelFont());
     singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
     singleColour.setPreferredSize(new Dimension(40, 20));
+    if (originalColour.isGraduatedColour())
+    {
+      singleColour.setBackground(originalColour.getMaxColour());
+      singleColour.setForeground(originalColour.getMaxColour());
+    }
+    else
+    {
+      singleColour.setBackground(originalColour.getColour());
+      singleColour.setForeground(originalColour.getColour());
+    }
     singleColour.addMouseListener(new MouseAdapter()
     {
       @Override
@@ -770,7 +762,8 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         if (simpleColour.isSelected())
         {
-          showColourChooser(singleColour, "label.select_colour");
+          String ttl = MessageManager.formatMessage("label.select_colour_for",  featureType);
+          showColourChooser(singleColour, ttl);
         }
       }
     });
@@ -838,10 +831,9 @@ public class FeatureTypeSettings extends JalviewDialog
    * 
    * @param colourPanel
    *          the panel whose background colour is being picked
-   * @param key
-   *          message bundle key for the dialog title
+   * @param title
    */
-  void showColourChooser(JPanel colourPanel, String key)
+  void showColourChooser(JPanel colourPanel, String title)
   {
     ColourChooserListener listener = new ColourChooserListener()
     {
@@ -854,14 +846,14 @@ public class FeatureTypeSettings extends JalviewDialog
         colourChanged(true);
       }
     };
-    JalviewColourChooser.showColourChooser(this, MessageManager.getString(key),
-            colourPanel.getBackground(), listener);
+	JalviewColourChooser.showColourChooser(this, title, 
+	  colourPanel.getBackground(), listener);
   }
 
   /**
-   * Constructs and sets the selected colour options as the colour for the feature
-   * type, and repaints the alignment, and optionally the Overview and/or
-   * structure viewer if open
+   * Constructs and sets the selected colour options as the colour for the
+   * feature type, and repaints the alignment, and optionally the Overview
+   * and/or structure viewer if open
    * 
    * @param updateStructsAndOverview
    */
@@ -889,7 +881,7 @@ public class FeatureTypeSettings extends JalviewDialog
     fr.setColour(featureType, acg);
     ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
 
-    updateColoursTab();
+    updateColoursPanel();
   }
 
   /**
@@ -912,8 +904,8 @@ public class FeatureTypeSettings extends JalviewDialog
      */
     if (byCategory.isSelected())
     {
-      Color c = this.getBackground();
-      FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
+      Color c = singleColour.getBackground();
+      FeatureColourI fc = new FeatureColour(c);
       fc.setColourByLabel(true);
       String byWhat = (String) colourByTextCombo.getSelectedItem();
       if (!LABEL_18N.equals(byWhat))
@@ -1075,8 +1067,8 @@ public class FeatureTypeSettings extends JalviewDialog
 
   /**
    * Converts the slider value to its absolute value by dividing by the
-   * scaleFactor. Rounding errors are squashed by forcing min/max of slider range
-   * to the actual min/max of feature score range
+   * scaleFactor. Rounding errors are squashed by forcing min/max of slider
+   * range to the actual min/max of feature score range
    * 
    * @return
    */
@@ -1099,11 +1091,11 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
-   * A helper method to build the drop-down choice of attributes for a feature. If
-   * 'withRange' is true, then Score, and any attributes with a min-max range, are
-   * added. If 'withText' is true, Label and any known attributes are added. This
-   * allows 'categorical numerical' attributes e.g. codon position to be coloured
-   * by text.
+   * A helper method to build the drop-down choice of attributes for a feature.
+   * If 'withRange' is true, then Score, and any attributes with a min-max
+   * range, are added. If 'withText' is true, Label and any known attributes are
+   * added. This allows 'categorical numerical' attributes e.g. codon position
+   * to be coloured by text.
    * <p>
    * Where metadata is available with a description for an attribute, that is
    * added as a tooltip.
@@ -1198,7 +1190,6 @@ public class FeatureTypeSettings extends JalviewDialog
   {
     JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
     andOrPanel.setBackground(Color.white);
-    andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour));
     andFilters = new JRadioButton(MessageManager.getString("label.and"));
     orFilters = new JRadioButton(MessageManager.getString("label.or"));
     ActionListener actionListener = new ActionListener()
@@ -1228,7 +1219,7 @@ public class FeatureTypeSettings extends JalviewDialog
    * for adding a condition. This should be called after a filter has been
    * removed, added or amended.
    */
-  private void updateFiltersTab()
+  private void updateFiltersPanel()
   {
     /*
      * clear the panel and list of filter conditions
@@ -1286,7 +1277,6 @@ public class FeatureTypeSettings extends JalviewDialog
     for (FeatureMatcherI filter : filters)
     {
       JPanel row = addFilter(filter, attNames, filterIndex);
-      row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
       chooseFiltersPanel.add(row);
       filterIndex++;
     }
@@ -1298,7 +1288,8 @@ public class FeatureTypeSettings extends JalviewDialog
   /**
    * A helper method that constructs a row (panel) with one filter condition:
    * <ul>
-   * <li>a drop-down list of Label, Score and attribute names to choose from</li>
+   * <li>a drop-down list of Label, Score and attribute names to choose
+   * from</li>
    * <li>a drop-down list of conditions to choose from</li>
    * <li>a text field for input of a match pattern</li>
    * <li>optionally, a 'remove' button</li>
@@ -1335,8 +1326,8 @@ public class FeatureTypeSettings extends JalviewDialog
      * drop-down choice of attribute, with description as a tooltip 
      * if we can obtain it
      */
-    JComboBox<String> attCombo = populateAttributesDropdown(attNames,
-            true, true);
+    JComboBox<String> attCombo = populateAttributesDropdown(attNames, true,
+            true);
     String filterBy = setSelectedAttribute(attCombo, filter);
 
     JComboBox<Condition> condCombo = new JComboBox<>();
@@ -1496,8 +1487,8 @@ public class FeatureTypeSettings extends JalviewDialog
    * @param selectedCondition
    * @param patternField
    */
-  private void setNumericHints(String attName,
-          Condition selectedCondition, JTextField patternField)
+  private void setNumericHints(String attName, Condition selectedCondition,
+          JTextField patternField)
   {
     patternField.setToolTipText("");
 
@@ -1531,11 +1522,11 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
-   * Populates the drop-down list of comparison conditions for the given attribute
-   * name. The conditions added depend on the datatype of the attribute values.
-   * The supplied condition is set as the selected item in the list, provided it
-   * is in the list. If the pattern is now invalid (non-numeric pattern for a
-   * numeric condition), it is cleared.
+   * Populates the drop-down list of comparison conditions for the given
+   * attribute name. The conditions added depend on the datatype of the
+   * attribute values. The supplied condition is set as the selected item in the
+   * list, provided it is in the list. If the pattern is now invalid
+   * (non-numeric pattern for a numeric condition), it is cleared.
    * 
    * @param attName
    * @param cond
@@ -1614,12 +1605,12 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
-   * Answers true unless a numeric condition has been selected with a non-numeric
-   * value. Sets the value field to RED with a tooltip if in error.
+   * Answers true unless a numeric condition has been selected with a
+   * non-numeric value. Sets the value field to RED with a tooltip if in error.
    * <p>
-   * If the pattern is expected but is empty, this method returns false, but does
-   * not mark the field as invalid. This supports selecting an attribute for a new
-   * condition before a match pattern has been entered.
+   * If the pattern is expected but is empty, this method returns false, but
+   * does not mark the field as invalid. This supports selecting an attribute
+   * for a new condition before a match pattern has been entered.
    * 
    * @param value
    * @param condCombo
@@ -1665,14 +1656,15 @@ public class FeatureTypeSettings extends JalviewDialog
 
   /**
    * Constructs a filter condition from the given input fields, and replaces the
-   * condition at filterIndex with the new one. Does nothing if the pattern field
-   * is blank (unless the match condition is one that doesn't require a pattern,
-   * e.g. 'Is present'). Answers true if the filter was updated, else false.
+   * condition at filterIndex with the new one. Does nothing if the pattern
+   * field is blank (unless the match condition is one that doesn't require a
+   * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
+   * false.
    * <p>
    * This method may update the tooltip on the filter value field to show the
-   * value range, if a numeric condition is selected. This ensures the tooltip is
-   * updated when a numeric valued attribute is chosen on the last 'add a filter'
-   * row.
+   * value range, if a numeric condition is selected. This ensures the tooltip
+   * is updated when a numeric valued attribute is chosen on the last 'add a
+   * filter' row.
    * 
    * @param attCombo
    * @param condCombo
@@ -1720,17 +1712,6 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
-   * Makes the dialog visible, at the Feature Colour tab or at the Filters tab
-   * 
-   * @param coloursTab
-   */
-  public void showTab(boolean coloursTab)
-  {
-    setVisible(true);
-    tabbedPane.setSelectedIndex(coloursTab ? 0 : 1);
-  }
-
-  /**
    * Action on any change to feature filtering, namely
    * <ul>
    * <li>change of selected attribute</li>
@@ -1738,8 +1719,8 @@ public class FeatureTypeSettings extends JalviewDialog
    * <li>change of match pattern</li>
    * <li>removal of a condition</li>
    * </ul>
-   * The inputs are parsed into a combined filter and this is set for the feature
-   * type, and the alignment redrawn.
+   * The inputs are parsed into a combined filter and this is set for the
+   * feature type, and the alignment redrawn.
    */
   protected void filtersChanged()
   {
@@ -1773,6 +1754,6 @@ public class FeatureTypeSettings extends JalviewDialog
     fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
     ap.paintAlignment(true, true);
 
-    updateFiltersTab();
+    updateFiltersPanel();
   }
 }