X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=44a16683651634b54ca39a690c364318f91c1bea;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=1b036c16a8bced406812b2dcc722ff3a947846ac;hpb=c5cece0a9d56e59293c8e6497b5afa6e26842646;p=jalview.git

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 1b036c1..44a1668 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -22,14 +22,23 @@ package jalview.gui;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
 import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.math.BigDecimal;
+import java.math.MathContext;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.JButton;
@@ -37,7 +46,6 @@ import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
-import javax.swing.JSlider;
 import javax.swing.JTextField;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
@@ -45,29 +53,23 @@ import javax.swing.event.ChangeListener;
 @SuppressWarnings("serial")
 public abstract class AnnotationRowFilter extends JPanel
 {
+  private static final String TWO_DP = "%.2f";
+
+  private final static MathContext FOUR_SIG_FIG = new MathContext(4);
+
   protected AlignViewport av;
 
   protected AlignmentPanel ap;
 
   protected int[] annmap;
 
-  protected boolean enableSeqAss = false;
-
-  private AlignmentAnnotation currentAnnotation;
-
   protected boolean adjusting = false;
 
-  protected JCheckBox currentColours = new JCheckBox();
-
-  protected JPanel minColour = new JPanel();
-
-  protected JPanel maxColour = new JPanel();
-
   protected JCheckBox seqAssociated = new JCheckBox();
 
-  protected JCheckBox thresholdIsMin = new JCheckBox();
+  protected JCheckBox percentThreshold = new JCheckBox();
 
-  protected JSlider slider = new JSlider();
+  protected Slider slider;
 
   protected JTextField thresholdValue = new JTextField(20);
 
@@ -83,6 +85,41 @@ public abstract class AnnotationRowFilter extends JPanel
    */
   protected boolean sliderDragging = false;
 
+  protected JComboBox<String> threshold = new JComboBox<>();
+
+  protected JComboBox<String> annotations;
+
+  /*
+   * map from annotation to its menu item display label
+   * - so we know which item to pre-select on restore
+   */
+  private Map<AlignmentAnnotation, String> annotationLabels;
+
+  private AlignmentAnnotation currentAnnotation;
+
+  /**
+   * Constructor
+   * 
+   * @param viewport
+   * @param alignPanel
+   */
+  public AnnotationRowFilter(AlignViewport viewport,
+          final AlignmentPanel alignPanel)
+  {
+    this.av = viewport;
+    this.ap = alignPanel;
+    this.slider = new Slider(0f, 100f, 50f);
+
+    thresholdValue.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
+  }
+
   protected void addSliderChangeListener()
   {
 
@@ -93,13 +130,80 @@ public abstract class AnnotationRowFilter extends JPanel
       {
         if (!adjusting)
         {
-          thresholdValue.setText((slider.getValue() / 1000f) + "");
+          setThresholdValueText();
           valueChanged(!sliderDragging);
         }
       }
     });
   }
 
+  /**
+   * update the text field from the threshold slider. preserves state of
+   * 'adjusting' so safe to call in init.
+   */
+  protected void setThresholdValueText()
+  {
+    boolean oldadj = adjusting;
+    adjusting = true;
+    if (percentThreshold.isSelected())
+    {
+      thresholdValue
+              .setText(String.format(TWO_DP, getSliderPercentageValue()));
+    }
+    else
+    {
+      /*
+       * round to 4 significant digits without trailing zeroes
+       */
+      float f = getSliderValue();
+      BigDecimal formatted = new BigDecimal(f).round(FOUR_SIG_FIG)
+              .stripTrailingZeros();
+      thresholdValue.setText(formatted.toPlainString());
+    }
+    adjusting = oldadj;
+  }
+
+  /**
+   * Answers the value of the slider position (descaled to 'true' value)
+   * 
+   * @return
+   */
+  protected float getSliderValue()
+  {
+    return slider.getSliderValue();
+  }
+
+  /**
+   * Sets the slider value (scaled from the true value to the slider range)
+   * 
+   * @param value
+   */
+  protected void setSliderValue(float value)
+  {
+    slider.setSliderValue(value);
+  }
+
+  /**
+   * Answers the value of the slider position as a percentage between minimum
+   * and maximum of its range
+   * 
+   * @return
+   */
+  protected float getSliderPercentageValue()
+  {
+    return slider.getSliderPercentageValue();
+  }
+
+  /**
+   * Sets the slider position for a given percentage value of its min-max range
+   * 
+   * @param pct
+   */
+  protected void setSliderPercentageValue(float pct)
+  {
+    slider.setSliderPercentageValue(pct);
+  }
+
   protected void addSliderMouseListeners()
   {
 
@@ -122,43 +226,34 @@ public abstract class AnnotationRowFilter extends JPanel
       @Override
       public void mouseReleased(MouseEvent evt)
       {
-        if (sliderDragging)
-        {
-          sliderDragging = false;
-          valueChanged(true);
-        }
-        ap.paintAlignment(true);
-      }
-    });
-  }
-
-  public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
-  {
-    this.av = av;
-    this.ap = ap;
-    thresholdValue.addFocusListener(new FocusAdapter()
-    {
-      @Override
-      public void focusLost(FocusEvent e)
-      {
-        thresholdValue_actionPerformed();
+        sliderDragReleased();
       }
     });
   }
 
-  public AnnotationRowFilter()
-  {
-
-  }
-
+  /**
+   * Builds and returns a list of menu items (display text) for choice of
+   * annotation. Also builds maps between annotations, their positions in the
+   * list, and their display labels in the list.
+   * 
+   * @param isSeqAssociated
+   * @return
+   */
   public Vector<String> getAnnotationItems(boolean isSeqAssociated)
   {
-    Vector<String> list = new Vector<String>();
+    annotationLabels = new HashMap<>();
+
+    Vector<String> list = new Vector<>();
     int index = 1;
-    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    int[] anmap = new int[av.getAlignment()
+            .getAlignmentAnnotation().length];
+    seqAssociated.setEnabled(false);
+    for (int i = 0; i < av.getAlignment()
+            .getAlignmentAnnotation().length; i++)
     {
-      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
+      AlignmentAnnotation annotation = av.getAlignment()
+              .getAlignmentAnnotation()[i];
+      if (annotation.sequenceRef == null)
       {
         if (isSeqAssociated)
         {
@@ -167,30 +262,29 @@ public abstract class AnnotationRowFilter extends JPanel
       }
       else
       {
-        enableSeqAss = true;
+        seqAssociated.setEnabled(true);
       }
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      String label = annotation.label;
       // add associated sequence ID if available
-      if (!isSeqAssociated
-              && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+      if (!isSeqAssociated && annotation.sequenceRef != null)
       {
-        label = label
-                + "_"
-                + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
-                        .getName();
+        label = label + "_" + annotation.sequenceRef.getName();
       }
       // make label unique
       if (!list.contains(label))
       {
         anmap[list.size()] = i;
         list.add(label);
+        annotationLabels.put(annotation, label);
       }
       else
       {
         if (!isSeqAssociated)
         {
           anmap[list.size()] = i;
-          list.add(label + "_" + (index++));
+          label = label + "_" + (index++);
+          list.add(label);
+          annotationLabels.put(annotation, label);
         }
       }
     }
@@ -213,11 +307,6 @@ public abstract class AnnotationRowFilter extends JPanel
     return selectedThresholdItem;
   }
 
-  public void modelChanged()
-  {
-    seqAssociated.setEnabled(enableSeqAss);
-  }
-
   public void ok_actionPerformed()
   {
     try
@@ -231,7 +320,7 @@ public abstract class AnnotationRowFilter extends JPanel
   public void cancel_actionPerformed()
   {
     reset();
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
     try
     {
       frame.setClosed(true);
@@ -240,54 +329,77 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void thresholdCheck_actionPerformed()
+  protected void thresholdCheck_actionPerformed()
   {
     updateView();
   }
 
-  public void annotations_actionPerformed()
+  protected void selectedAnnotationChanged()
   {
     updateView();
   }
 
-  public void threshold_actionPerformed()
+  protected void threshold_actionPerformed()
   {
     updateView();
   }
 
-  public void thresholdValue_actionPerformed()
+  /**
+   * Updates the slider position, and the display, for an update in the slider's
+   * text input field
+   */
+  protected void thresholdValue_actionPerformed()
   {
     try
     {
       float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue((int) (f * 1000));
+      if (percentThreshold.isSelected())
+      {
+        setSliderPercentageValue(f);
+      }
+      else
+      {
+        setSliderValue(f);
+      }
       updateView();
     } catch (NumberFormatException ex)
     {
     }
   }
 
-  public void thresholdIsMin_actionPerformed()
+  protected void percentageValue_actionPerformed()
+  {
+    setThresholdValueText();
+  }
+
+  protected void thresholdIsMin_actionPerformed()
   {
     updateView();
   }
 
-  protected void populateThresholdComboBox(JComboBox<String> threshold)
+  protected void populateThresholdComboBox(JComboBox<String> thresh)
   {
-    threshold.addItem(MessageManager
+    thresh.addItem(MessageManager
             .getString("label.threshold_feature_no_threshold"));
-    threshold.addItem(MessageManager
+    thresh.addItem(MessageManager
             .getString("label.threshold_feature_above_threshold"));
-    threshold.addItem(MessageManager
+    thresh.addItem(MessageManager
             .getString("label.threshold_feature_below_threshold"));
   }
 
-  protected void seqAssociated_actionPerformed(JComboBox<String> annotations)
+  /**
+   * Rebuilds the drop-down list of annotations to choose from when the 'per
+   * sequence only' checkbox is checked or unchecked.
+   * 
+   * @param anns
+   */
+  protected void seqAssociated_actionPerformed(JComboBox<String> anns)
   {
     adjusting = true;
-    String cursel = (String) annotations.getSelectedItem();
-    boolean isvalid = false, isseqs = seqAssociated.isSelected();
-    annotations.removeAllItems();
+    String cursel = (String) anns.getSelectedItem();
+    boolean isvalid = false;
+    boolean isseqs = seqAssociated.isSelected();
+    anns.removeAllItems();
     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
     {
       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
@@ -295,20 +407,22 @@ public abstract class AnnotationRowFilter extends JPanel
         isvalid = true;
         cursel = anitem;
       }
-      annotations.addItem(anitem);
+      anns.addItem(anitem);
     }
-    adjusting = false;
     if (isvalid)
     {
-      annotations.setSelectedItem(cursel);
+      anns.setSelectedItem(cursel);
     }
     else
     {
-      if (annotations.getItemCount() > 0)
+      if (anns.getItemCount() > 0)
       {
-        annotations.setSelectedIndex(0);
+        anns.setSelectedIndex(0);
       }
     }
+    adjusting = false;
+
+    updateView();
   }
 
   protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
@@ -320,9 +434,11 @@ public abstract class AnnotationRowFilter extends JPanel
     }
 
     float thr = annotation.threshold.value;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < av.getAlignment()
+            .getAlignmentAnnotation().length; i++)
     {
-      AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+      AlignmentAnnotation aa = av.getAlignment()
+              .getAlignmentAnnotation()[i];
       if (aa.label.equals(annotation.label)
               && (annotation.getCalcId() == null ? aa.getCalcId() == null
                       : annotation.getCalcId().equals(aa.getCalcId())))
@@ -339,79 +455,153 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  protected boolean colorAlignmContaining(AlignmentAnnotation currentAnn,
-          int selectedThresholdOption)
+  public AlignmentAnnotation getCurrentAnnotation()
   {
+    return currentAnnotation;
+  }
 
-    AnnotationColourGradient acg = null;
-    if (currentColours.isSelected())
-    {
-      acg = new AnnotationColourGradient(currentAnn,
-              av.getGlobalColourScheme(), selectedThresholdOption);
-    }
-    else
+  protected void setCurrentAnnotation(AlignmentAnnotation annotation)
+  {
+    this.currentAnnotation = annotation;
+  }
+
+  /**
+   * update associated view model and trigger any necessary repaints.
+   * 
+   * @param updateAllAnnotation
+   */
+  protected abstract void valueChanged(boolean updateAllAnnotation);
+
+  protected abstract void updateView();
+
+  protected abstract void reset();
+
+  protected String getAnnotationMenuLabel(AlignmentAnnotation ann)
+  {
+    return annotationLabels.get(ann);
+  }
+
+  protected void jbInit()
+  {
+    ok.setOpaque(false);
+    ok.setText(MessageManager.getString("action.ok"));
+    ok.addActionListener(new ActionListener()
     {
-      acg = new AnnotationColourGradient(currentAnn,
-              minColour.getBackground(), maxColour.getBackground(),
-              selectedThresholdOption);
-    }
-    acg.setSeqAssociated(seqAssociated.isSelected());
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed();
+      }
+    });
 
-    if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+    cancel.setOpaque(false);
+    cancel.setText(MessageManager.getString("action.cancel"));
+    cancel.addActionListener(new ActionListener()
     {
-      acg.setPredefinedColours(true);
-    }
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed();
+      }
+    });
 
-    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+    annotations.addItemListener(new ItemListener()
+    {
+      @Override
+      public void itemStateChanged(ItemEvent e)
+      {
+        selectedAnnotationChanged();
+      }
+    });
+    annotations.setToolTipText(
+            MessageManager.getString("info.select_annotation_row"));
 
-    av.setGlobalColourScheme(acg);
+    threshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed();
+      }
+    });
 
-    if (av.getAlignment().getGroups() != null)
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(7);
+    thresholdValue.addActionListener(new ActionListener()
     {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
 
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+    percentThreshold
+            .setText(MessageManager.getString("label.as_percentage"));
+    percentThreshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
-        if (sg.cs == null)
+        if (!adjusting)
         {
-          continue;
+          percentageValue_actionPerformed();
         }
+      }
+    });
+    slider.setPaintLabels(false);
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setOpaque(false);
+    slider.setPreferredSize(new Dimension(100, 32));
+  }
 
-        if (currentColours.isSelected())
-        {
-          sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
-                  selectedThresholdOption);
-          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
-                  .isSelected());
-
-        }
-        else
-        {
-          sg.cs = new AnnotationColourGradient(currentAnn,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdOption);
-          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
-                  .isSelected());
-        }
+  public JComboBox<String> getThreshold()
+  {
+    return threshold;
+  }
 
-      }
-    }
-    return false;
+  public void setThreshold(JComboBox<String> thresh)
+  {
+    this.threshold = thresh;
   }
 
-  public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+  public JComboBox<String> getAnnotations()
   {
-    return currentAnnotation;
+    return annotations;
   }
 
-  public void setCurrentAnnotation(
-          jalview.datamodel.AlignmentAnnotation currentAnnotation)
+  public void setAnnotations(JComboBox<String> anns)
   {
-    this.currentAnnotation = currentAnnotation;
+    this.annotations = anns;
   }
 
-  public abstract void valueChanged(boolean updateAllAnnotation);
+  protected void sliderDragReleased()
+  {
+    if (sliderDragging)
+    {
+      sliderDragging = false;
+      valueChanged(true);
+    }
+  }
 
-  public abstract void updateView();
+  /**
+   * Sets the min-max range and current value of the slider, with rescaling from
+   * true values to slider range as required
+   * 
+   * @param min
+   * @param max
+   * @param value
+   */
+  protected void setSliderModel(float min, float max, float value)
+  {
+    slider.setSliderModel(min, max, value);
 
-  public abstract void reset();
+    /*
+     * tick mark every 10th position
+     */
+    slider.setMajorTickSpacing(
+            (slider.getMaximum() - slider.getMinimum()) / 10);
+  }
 }