X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureTypeSettings.java;h=c5727989006a100a4ff3c7179a47e83f8e23115a;hb=5b126eb259ecff2dce5c024066ced2528d87d39a;hp=c3567315ab2564ad590d06ae805777f972a527a4;hpb=761ad3f4f8408cee61c932d926532e186d71b95d;p=jalview.git

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index c356731..c572798 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
    * 
@@ -256,7 +256,7 @@ public class FeatureTypeSettings extends JalviewDialog
     String title = MessageManager
             .formatMessage("label.display_settings_for", new String[]
             { theType });
-    initDialogFrame(this, true, blocking, title, 600, 360);
+    initDialogFrame(this, true, blocking, title, 500, 500);
 
     waitForInput();
   }
@@ -295,8 +295,8 @@ public class FeatureTypeSettings extends JalviewDialog
         if (fc.isColourByAttribute())
         {
           String[] attributeName = fc.getAttributeName();
-          colourByTextCombo
-                  .setSelectedItem(toAttributeDisplayName(attributeName));
+          colourByTextCombo.setSelectedItem(
+                  FeatureMatcher.toAttributeDisplayName(attributeName));
         }
         else
         {
@@ -325,6 +325,7 @@ 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);
@@ -336,8 +337,8 @@ public class FeatureTypeSettings extends JalviewDialog
       if (fc.isColourByAttribute())
       {
         String[] attributeName = fc.getAttributeName();
-        colourByRangeCombo
-                .setSelectedItem(toAttributeDisplayName(attributeName));
+        colourByRangeCombo.setSelectedItem(
+                FeatureMatcher.toAttributeDisplayName(attributeName));
       }
       else
       {
@@ -402,8 +403,6 @@ 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 +417,16 @@ 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();
 
@@ -478,7 +475,7 @@ public class FeatureTypeSettings extends JalviewDialog
     {
       // colour by attribute range
       minMax = FeatureAttributes.getInstance().getMinMax(featureType,
-              fromAttributeDisplayName(attName));
+              FeatureMatcher.fromAttributeDisplayName(attName));
     }
     return minMax;
   }
@@ -735,15 +732,18 @@ 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);
+//    JvSwingUtils.createTitledBorder(simpleColourPanel,
+//            MessageManager.getString("label.simple"), true);
     colourByPanel.add(simpleColourPanel);
 
     simpleColour = new JRadioButton(
@@ -761,7 +761,7 @@ public class FeatureTypeSettings extends JalviewDialog
       }
 
     });
-    
+
     singleColour.setFont(JvSwingUtils.getLabelFont());
     singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
     singleColour.setPreferredSize(new Dimension(40, 20));
@@ -848,9 +848,9 @@ 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
    */
@@ -907,7 +907,8 @@ public class FeatureTypeSettings extends JalviewDialog
       String byWhat = (String) colourByTextCombo.getSelectedItem();
       if (!LABEL_18N.equals(byWhat))
       {
-        fc.setAttributeName(fromAttributeDisplayName(byWhat));
+        fc.setAttributeName(
+                FeatureMatcher.fromAttributeDisplayName(byWhat));
       }
       return fc;
     }
@@ -964,7 +965,7 @@ public class FeatureTypeSettings extends JalviewDialog
     String byWhat = (String) colourByRangeCombo.getSelectedItem();
     if (!SCORE_18N.equals(byWhat))
     {
-      fc.setAttributeName(fromAttributeDisplayName(byWhat));
+      fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
     }
 
     /*
@@ -989,30 +990,6 @@ public class FeatureTypeSettings extends JalviewDialog
     return fc;
   }
 
-  /**
-   * A helper method that converts a 'compound' attribute name from its display
-   * form, e.g. CSQ:PolyPhen to array form, e.g. { "CSQ", "PolyPhen" }
-   * 
-   * @param attribute
-   * @return
-   */
-  private String[] fromAttributeDisplayName(String attribute)
-  {
-    return attribute == null ? null : attribute.split(COLON);
-  }
-
-  /**
-   * A helper method that converts a 'compound' attribute name to its display
-   * form, e.g. CSQ:PolyPhen from its array form, e.g. { "CSQ", "PolyPhen" }
-   * 
-   * @param attName
-   * @return
-   */
-  private String toAttributeDisplayName(String[] attName)
-  {
-    return attName == null ? "" : String.join(COLON, attName);
-  }
-
   @Override
   protected void raiseClosed()
   {
@@ -1087,8 +1064,8 @@ 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
    */
@@ -1111,11 +1088,11 @@ 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.
@@ -1159,7 +1136,7 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         continue;
       }
-      displayAtts.add(toAttributeDisplayName(attName));
+      displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
       String desc = fa.getDescription(featureType, attName);
       if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
       {
@@ -1210,7 +1187,6 @@ 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()
@@ -1293,7 +1269,6 @@ public class FeatureTypeSettings extends JalviewDialog
     for (FeatureMatcherI filter : filters)
     {
       JPanel row = addFilter(filter, attNames, filterIndex);
-      row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
       chooseFiltersPanel.add(row);
       filterIndex++;
     }
@@ -1305,7 +1280,8 @@ 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>
@@ -1383,7 +1359,8 @@ public class FeatureTypeSettings extends JalviewDialog
     }
     else
     {
-      attCombo.setSelectedItem(toAttributeDisplayName(attName));
+      attCombo.setSelectedItem(
+              FeatureMatcher.toAttributeDisplayName(attName));
     }
     attCombo.addItemListener(new ItemListener()
     {
@@ -1429,16 +1406,13 @@ 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)
@@ -1486,22 +1460,27 @@ public class FeatureTypeSettings extends JalviewDialog
     }
     else
     {
-      item = toAttributeDisplayName(filter.getAttribute());
+      item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
     }
     attCombo.setSelectedItem(item);
     return item;
   }
 
   /**
-   * 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("");
 
@@ -1510,19 +1489,36 @@ 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
@@ -1533,7 +1529,7 @@ public class FeatureTypeSettings extends JalviewDialog
           JComboBox<Condition> condCombo, JTextField patternField)
   {
     Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
-            fromAttributeDisplayName(attName));
+            FeatureMatcher.fromAttributeDisplayName(attName));
     if (LABEL_18N.equals(attName))
     {
       type = Datatype.Character;
@@ -1549,10 +1545,11 @@ 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);
@@ -1575,8 +1572,6 @@ public class FeatureTypeSettings extends JalviewDialog
       condCombo.setSelectedIndex(0);
     }
 
-    condCombo.addItemListener(listener);
-
     /*
      * clear pattern if it is now invalid for condition
      */
@@ -1594,15 +1589,20 @@ 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
@@ -1648,14 +1648,15 @@ 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
@@ -1670,10 +1671,11 @@ 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;
     }
 
@@ -1693,7 +1695,7 @@ public class FeatureTypeSettings extends JalviewDialog
     else
     {
       km = FeatureMatcher.byAttribute(cond, pattern,
-              fromAttributeDisplayName(attName));
+              FeatureMatcher.fromAttributeDisplayName(attName));
     }
 
     filters.set(filterIndex, km);
@@ -1702,17 +1704,6 @@ 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>
@@ -1720,8 +1711,8 @@ 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()
   {