X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureTypeSettings.java;h=c4be1c0d2c369efc5cc7dc18ea6358ea6fc941bb;hb=35f590cdfe3352c8f6a0592a1f1bf64925f21b98;hp=89c693f1352295fa60747ae93767c893a9bdd8d3;hpb=11e8324f332f5648ba0f13b902621dc7a20137e4;p=jalview.git

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index 89c693f..c4be1c0 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.SwingConstants;
 import javax.swing.border.LineBorder;
@@ -107,7 +106,8 @@ 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
@@ -155,7 +155,12 @@ public class FeatureTypeSettings extends JalviewDialog
 
   private JRadioButton graduatedColour = new JRadioButton();
 
-  private JPanel singleColour = new JPanel();
+  /**
+   * colours and filters are shown in tabbed view or single content pane
+   */
+  JPanel coloursPanel, filtersPanel;
+
+  JPanel singleColour = new JPanel();
 
   private JPanel minColour = new JPanel();
 
@@ -199,13 +204,8 @@ public class FeatureTypeSettings extends JalviewDialog
    */
   private List<FeatureMatcherI> filters;
 
-  // set white normally, black to debug layout
-  private Color debugBorderColour = Color.white;
-
   private JPanel chooseFiltersPanel;
 
-  private JTabbedPane tabbedPane;
-
   /**
    * Constructor
    * 
@@ -214,28 +214,14 @@ 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();
@@ -244,20 +230,20 @@ public class FeatureTypeSettings extends JalviewDialog
       ex.printStackTrace();
       return;
     }
-
+    
     updateColoursTab();
-
+    
     updateFiltersTab();
-
+    
     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, 500, 500);
+    
     waitForInput();
   }
 
@@ -280,9 +266,9 @@ public class FeatureTypeSettings extends JalviewDialog
        */
       if (fc.isSimpleColour())
       {
-        simpleColour.setSelected(true);
         singleColour.setBackground(fc.getColour());
         singleColour.setForeground(fc.getColour());
+        simpleColour.setSelected(true);
       }
 
       /*
@@ -380,7 +366,7 @@ public class FeatureTypeSettings extends JalviewDialog
                         : BELOW_THRESHOLD_OPTION);
         slider.setEnabled(true);
         slider.setValue((int) (fc.getThreshold() * scaleFactor));
-        thresholdValue.setText(String.valueOf(getRoundedSliderValue()));
+        thresholdValue.setText(String.valueOf(fc.getThreshold()));
         thresholdValue.setEnabled(true);
         thresholdIsMin.setEnabled(true);
       }
@@ -403,8 +389,6 @@ 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
@@ -419,18 +403,16 @@ public class FeatureTypeSettings extends JalviewDialog
     };
 
     /*
-     * first tab: colour options
+     * first panel/tab: colour options
      */
     JPanel coloursPanel = initialiseColoursPanel();
-    tabbedPane.addTab(MessageManager.getString("action.colour"),
-            coloursPanel);
+    this.add(coloursPanel, BorderLayout.NORTH);
 
     /*
-     * second tab: filter options
+     * second panel/tab: filter options
      */
     JPanel filtersPanel = initialiseFiltersPanel();
-    tabbedPane.addTab(MessageManager.getString("label.filters"),
-            filtersPanel);
+    this.add(filtersPanel, BorderLayout.CENTER);
 
     JPanel okCancelPanel = initialiseOkCancelPanel();
 
@@ -581,12 +563,11 @@ public class FeatureTypeSettings extends JalviewDialog
     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));
 
@@ -671,6 +652,7 @@ public class FeatureTypeSettings extends JalviewDialog
         {
           thresholdValue
                   .setText(String.valueOf(slider.getValue() / scaleFactor));
+          thresholdValue.setBackground(Color.white); // to reset red for invalid
           sliderValueChanged();
         }
       }
@@ -736,15 +718,16 @@ 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(
@@ -757,15 +740,24 @@ 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
@@ -849,9 +841,9 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
-   * 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
    */
@@ -902,8 +894,8 @@ 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))
@@ -1028,21 +1020,23 @@ public class FeatureTypeSettings extends JalviewDialog
   {
     try
     {
+      /*
+       * set 'adjusting' flag while moving the slider, so it 
+       * doesn't then in turn change the value (with rounding)
+       */
       adjusting = true;
       float f = Float.parseFloat(thresholdValue.getText());
+      f = Float.max(f,  this.min);
+      f = Float.min(f, this.max);
+      thresholdValue.setText(String.valueOf(f));
       slider.setValue((int) (f * scaleFactor));
       threshline.value = f;
       thresholdValue.setBackground(Color.white); // ok
-
-      /*
-       * force repaint of any Overview window or structure
-       */
-      ap.paintAlignment(true, true);
+      adjusting = false;
+      colourChanged(true);
     } catch (NumberFormatException ex)
     {
       thresholdValue.setBackground(Color.red); // not ok
-    } finally
-    {
       adjusting = false;
     }
   }
@@ -1065,8 +1059,8 @@ 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
    */
@@ -1089,11 +1083,11 @@ 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.
@@ -1188,7 +1182,6 @@ 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()
@@ -1271,7 +1264,6 @@ public class FeatureTypeSettings extends JalviewDialog
     for (FeatureMatcherI filter : filters)
     {
       JPanel row = addFilter(filter, attNames, filterIndex);
-      row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
       chooseFiltersPanel.add(row);
       filterIndex++;
     }
@@ -1283,7 +1275,8 @@ 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>
@@ -1481,8 +1474,8 @@ 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("");
 
@@ -1516,11 +1509,11 @@ 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
@@ -1551,7 +1544,7 @@ public class FeatureTypeSettings extends JalviewDialog
     condCombo.removeAllItems();
     for (Condition c : Condition.values())
     {
-      if ((c.isNumeric() && type != Datatype.Character)
+      if ((c.isNumeric() && type == Datatype.Number)
               || (!c.isNumeric() && type != Datatype.Number))
       {
         condCombo.addItem(c);
@@ -1599,12 +1592,12 @@ 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
@@ -1650,14 +1643,15 @@ 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
@@ -1705,17 +1699,6 @@ 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>
@@ -1723,8 +1706,8 @@ 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()
   {