X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureTypeSettings.java;h=82e826f05e86d58f6f5bfa5779fa899500ddaf61;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=c784d8d578d7a7ffbcf70da66bf36b68f0756028;hpb=161e8cc8828152180efe8ab861487fea051e4efc;p=jalview.git

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index c784d8d..82e826f 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 +230,19 @@ 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, 580, 500);
     waitForInput();
   }
 
@@ -280,9 +265,9 @@ public class FeatureTypeSettings extends JalviewDialog
        */
       if (fc.isSimpleColour())
       {
-        simpleColour.setSelected(true);
         singleColour.setBackground(fc.getColour());
         singleColour.setForeground(fc.getColour());
+        simpleColour.setSelected(true);
       }
 
       /*
@@ -325,6 +310,7 @@ public class FeatureTypeSettings extends JalviewDialog
        * Graduated colour, by score or attribute value range
        */
       graduatedColour.setSelected(true);
+      updateColourMinMax(); // ensure min, max are set
       colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
       minColour.setEnabled(true);
       maxColour.setEnabled(true);
@@ -379,7 +365,7 @@ 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);
       }
@@ -402,8 +388,6 @@ 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
@@ -418,18 +402,16 @@ 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();
 
@@ -580,14 +562,20 @@ 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
+     * if not set, default max colour to last plain colour,
+     * and make min colour a pale version of max colour
      */
-    FeatureColourI fc = fr.getFeatureColours().get(featureType);
-    Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
-    maxColour.setBackground(bg);
-    minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
+    Color max = originalColour.getMaxColour();
+    if (max == null)
+    {
+      max = originalColour.getColour();
+      minColour.setBackground(ColorUtils.bleachColour(max, 0.9f));
+    }
+    else
+    {
+      maxColour.setBackground(max);
+      minColour.setBackground(originalColour.getMinColour());
+    }
 
     noValueCombo = new JComboBox<>();
     noValueCombo.addItem(MessageManager.getString("label.no_colour"));
@@ -670,6 +658,7 @@ public class FeatureTypeSettings extends JalviewDialog
         {
           thresholdValue
                   .setText(String.valueOf(slider.getValue() / scaleFactor));
+          thresholdValue.setBackground(Color.white); // to reset red for invalid
           sliderValueChanged();
         }
       }
@@ -735,15 +724,16 @@ 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(
@@ -756,15 +746,24 @@ 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
@@ -848,9 +847,9 @@ 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
    */
@@ -889,42 +888,9 @@ public class FeatureTypeSettings extends JalviewDialog
   private FeatureColourI makeColourFromInputs()
   {
     /*
-     * easiest case - a single colour
-     */
-    if (simpleColour.isSelected())
-    {
-      return new FeatureColour(singleColour.getBackground());
-    }
-
-    /*
-     * next easiest case - colour by Label, or attribute text
-     */
-    if (byCategory.isSelected())
-    {
-      Color c = this.getBackground();
-      FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
-      fc.setColourByLabel(true);
-      String byWhat = (String) colourByTextCombo.getSelectedItem();
-      if (!LABEL_18N.equals(byWhat))
-      {
-        fc.setAttributeName(
-                FeatureMatcher.fromAttributeDisplayName(byWhat));
-      }
-      return fc;
-    }
-
-    /*
-     * remaining case - graduated colour by score, or attribute value
+     * min-max range is to (or from) threshold value if 
+     * 'threshold is min/max' is selected 
      */
-    Color noColour = null;
-    if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
-    {
-      noColour = minColour.getBackground();
-    }
-    else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
-    {
-      noColour = maxColour.getBackground();
-    }
 
     float thresh = 0f;
     try
@@ -934,11 +900,6 @@ public class FeatureTypeSettings extends JalviewDialog
     {
       // invalid inputs are already handled on entry
     }
-
-    /*
-     * min-max range is to (or from) threshold value if 
-     * 'threshold is min/max' is selected 
-     */
     float minValue = min;
     float maxValue = max;
     final int thresholdOption = threshold.getSelectedIndex();
@@ -952,14 +913,50 @@ public class FeatureTypeSettings extends JalviewDialog
     {
       maxValue = thresh;
     }
+    Color noColour = null;
+    if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
+    {
+      noColour = minColour.getBackground();
+    }
+    else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
+    {
+      noColour = maxColour.getBackground();
+    }
+
+    /*
+     * construct a colour that 'remembers' all the options, including
+     * those not currently selected
+     */
+    FeatureColourI fc = new FeatureColour(singleColour.getBackground(),
+            minColour.getBackground(), maxColour.getBackground(), noColour,
+            minValue, maxValue);
 
     /*
-     * make the graduated colour
+     * easiest case - a single colour
      */
-    FeatureColourI fc = new FeatureColour(minColour.getBackground(),
-            maxColour.getBackground(), noColour, minValue, maxValue);
+    if (simpleColour.isSelected())
+    {
+      ((FeatureColour) fc).setGraduatedColour(false);
+      return fc;
+    }
 
     /*
+     * next easiest case - colour by Label, or attribute text
+     */
+    if (byCategory.isSelected())
+    {
+      fc.setColourByLabel(true);
+      String byWhat = (String) colourByTextCombo.getSelectedItem();
+      if (!LABEL_18N.equals(byWhat))
+      {
+        fc.setAttributeName(
+                FeatureMatcher.fromAttributeDisplayName(byWhat));
+      }
+      return fc;
+    }
+
+    /*
+     * remaining case - graduated colour by score, or attribute value;
      * set attribute to colour by if selected
      */
     String byWhat = (String) colourByRangeCombo.getSelectedItem();
@@ -1027,21 +1024,23 @@ 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;
     }
   }
@@ -1064,8 +1063,8 @@ 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
    */
@@ -1088,11 +1087,11 @@ 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.
@@ -1187,7 +1186,6 @@ 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()
@@ -1270,7 +1268,6 @@ public class FeatureTypeSettings extends JalviewDialog
     for (FeatureMatcherI filter : filters)
     {
       JPanel row = addFilter(filter, attNames, filterIndex);
-      row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
       chooseFiltersPanel.add(row);
       filterIndex++;
     }
@@ -1282,7 +1279,8 @@ 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>
@@ -1407,16 +1405,13 @@ public class FeatureTypeSettings extends JalviewDialog
      * disable pattern field for condition 'Present / NotPresent'
      */
     Condition selectedCondition = (Condition) condCombo.getSelectedItem();
-    if (!selectedCondition.needsAPattern())
-    {
-      patternField.setEnabled(false);
-    }
+    patternField.setEnabled(selectedCondition.needsAPattern());
 
     /*
      * if a numeric condition is selected, show the value range
      * as a tooltip on the value input field
      */
-    setPatternTooltip(filterBy, selectedCondition, patternField);
+    setNumericHints(filterBy, selectedCondition, patternField);
 
     /*
      * add remove button if filter is populated (non-empty pattern)
@@ -1471,15 +1466,20 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
-   * If a numeric comparison condition is selected, retrieve the min-max range for
-   * the value (score or attribute), and set it as a tooltip on the value file
+   * If a numeric comparison condition is selected, retrieves the min-max range
+   * for the value (score or attribute), and sets it as a tooltip on the value
+   * field. If the field is currently empty, then pre-populates it with
+   * <ul>
+   * <li>the minimum value, if condition is > or >=</li>
+   * <li>the maximum value, if condition is < or <=</li>
+   * </ul>
    * 
    * @param attName
    * @param selectedCondition
    * @param patternField
    */
-  private void setPatternTooltip(String attName,
-          Condition selectedCondition, JTextField patternField)
+  private void setNumericHints(String attName, Condition selectedCondition,
+          JTextField patternField)
   {
     patternField.setToolTipText("");
 
@@ -1488,19 +1488,36 @@ public class FeatureTypeSettings extends JalviewDialog
       float[] minMax = getMinMax(attName);
       if (minMax != null)
       {
-        String tip = String.format("(%s - %s)",
-                DECFMT_2_2.format(minMax[0]), DECFMT_2_2.format(minMax[1]));
+        String minFormatted = DECFMT_2_2.format(minMax[0]);
+        String maxFormatted = DECFMT_2_2.format(minMax[1]);
+        String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
         patternField.setToolTipText(tip);
+        if (patternField.getText().isEmpty())
+        {
+          if (selectedCondition == Condition.GE
+                  || selectedCondition == Condition.GT)
+          {
+            patternField.setText(minFormatted);
+          }
+          else
+          {
+            if (selectedCondition == Condition.LE
+                    || selectedCondition == Condition.LT)
+            {
+              patternField.setText(maxFormatted);
+            }
+          }
+        }
       }
     }
   }
 
   /**
-   * 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
@@ -1527,10 +1544,11 @@ public class FeatureTypeSettings extends JalviewDialog
     ItemListener listener = condCombo.getItemListeners()[0];
     condCombo.removeItemListener(listener);
     boolean condIsValid = false;
+
     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);
@@ -1553,8 +1571,6 @@ public class FeatureTypeSettings extends JalviewDialog
       condCombo.setSelectedIndex(0);
     }
 
-    condCombo.addItemListener(listener);
-
     /*
      * clear pattern if it is now invalid for condition
      */
@@ -1572,15 +1588,20 @@ public class FeatureTypeSettings extends JalviewDialog
         patternField.setText("");
       }
     }
+
+    /*
+     * restore the listener
+     */
+    condCombo.addItemListener(listener);
   }
 
   /**
-   * 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
@@ -1626,14 +1647,15 @@ 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
@@ -1648,10 +1670,11 @@ public class FeatureTypeSettings extends JalviewDialog
     Condition cond = (Condition) condCombo.getSelectedItem();
     String pattern = valueField.getText().trim();
 
-    setPatternTooltip(attName, cond, valueField);
+    setNumericHints(attName, cond, valueField);
 
     if (pattern.length() == 0 && cond.needsAPattern())
     {
+      valueField.setEnabled(true); // ensure pattern field is enabled!
       return false;
     }
 
@@ -1680,17 +1703,6 @@ 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>
@@ -1698,8 +1710,8 @@ 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()
   {