X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=1035a6c72e6f44ded96ec678e74eed295a240967;hb=ad69997e7967bae13b30470ca6d1ab74e0bb3046;hp=37f1e554fc31983e48321f28434638142ff970e3;hpb=a49b953d151391cd9526a7655997c6409f20306c;p=jalview.git

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 37f1e55..1035a6c 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -22,12 +22,21 @@ 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.util.HashMap;
+import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.JButton;
@@ -49,21 +58,11 @@ public abstract class AnnotationRowFilter extends JPanel
 
   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();
 
@@ -81,6 +80,38 @@ public abstract class AnnotationRowFilter extends JPanel
    */
   protected boolean sliderDragging = false;
 
+  protected JComboBox<String> threshold = new JComboBox<String>();
+
+  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;
+    thresholdValue.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
+  }
+
   protected void addSliderChangeListener()
   {
 
@@ -91,13 +122,27 @@ public abstract class AnnotationRowFilter extends JPanel
       {
         if (!adjusting)
         {
-          thresholdValue.setText((slider.getValue() / 1000f) + "");
+          setThresholdValueText();
           valueChanged(!sliderDragging);
         }
       }
     });
   }
 
+  protected void setThresholdValueText()
+  {
+    adjusting = true;
+    if (percentThreshold.isSelected())
+    {
+      thresholdValue.setText("" + (slider.getValue() - slider.getMinimum())
+              * 100f / (slider.getMaximum() - slider.getMinimum()));
+    }
+    else
+    {
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
+    }
+    adjusting = false;
+  }
   protected void addSliderMouseListeners()
   {
 
@@ -130,25 +175,27 @@ public abstract class AnnotationRowFilter extends JPanel
     });
   }
 
-  public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
-  {
-    this.av = av;
-    this.ap = ap;
-  }
-
-  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)
   {
+    annotationLabels = new HashMap<AlignmentAnnotation, String>();
+
     Vector<String> list = new Vector<String>();
     int index = 1;
     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)
         {
@@ -157,30 +204,29 @@ 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);
         }
       }
     }
@@ -203,11 +249,6 @@ public abstract class AnnotationRowFilter extends JPanel
     return selectedThresholdItem;
   }
 
-  public void modelChanged()
-  {
-    seqAssociated.setEnabled(enableSeqAss);
-  }
-
   public void ok_actionPerformed()
   {
     try
@@ -230,54 +271,75 @@ 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()
+  protected void thresholdValue_actionPerformed()
   {
     try
     {
       float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue((int) (f * 1000));
+      if (percentThreshold.isEnabled())
+      {
+        slider.setValue(slider.getMinimum()
+                + ((int) ((f / 100f) * (slider.getMaximum() - slider
+                        .getMinimum()))));
+      }
+      else
+      {
+        slider.setValue((int) (f * 1000));
+      }
       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)))
@@ -285,20 +347,22 @@ 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,
@@ -329,80 +393,119 @@ 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
-    {
-      acg = new AnnotationColourGradient(currentAnn,
-              minColour.getBackground(), maxColour.getBackground(),
-              selectedThresholdOption);
-    }
-    acg.setSeqAssociated(seqAssociated.isSelected());
+  protected void setCurrentAnnotation(AlignmentAnnotation annotation)
+  {
+    this.currentAnnotation = annotation;
+  }
 
-    if (currentAnn.graphMin == 0f
-            && currentAnn.graphMax == 0f)
-    {
-      acg.setPredefinedColours(true);
-    }
+  protected abstract void valueChanged(boolean updateAllAnnotation);
 
-    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+  protected abstract void updateView();
 
-    av.setGlobalColourScheme(acg);
+  protected abstract void reset();
 
-    if (av.getAlignment().getGroups() != null)
+  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()
     {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed();
+      }
+    });
 
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+    cancel.setOpaque(false);
+    cancel.setText(MessageManager.getString("action.cancel"));
+    cancel.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
-        if (sg.cs == null)
-        {
-          continue;
-        }
+        cancel_actionPerformed();
+      }
+    });
 
-        if (currentColours.isSelected())
-        {
-          sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
-                  selectedThresholdOption);
-          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
-                  .isSelected());
+    annotations.addItemListener(new ItemListener()
+    {
+      @Override
+      public void itemStateChanged(ItemEvent e)
+      {
+        selectedAnnotationChanged();
+      }
+    });
+    annotations.setToolTipText(MessageManager
+            .getString("info.select_annotation_row"));
 
-        }
-        else
+    threshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed();
+      }
+    });
+
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(7);
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
+
+    percentThreshold.setText(MessageManager.getString("label.as_percentage"));
+    percentThreshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (!adjusting)
         {
-          sg.cs = new AnnotationColourGradient(currentAnn,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdOption);
-          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
-                  .isSelected());
+          percentageValue_actionPerformed();
         }
-
       }
-    }
-    return false;
+    });
+    slider.setPaintLabels(false);
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setOpaque(false);
+    slider.setPreferredSize(new Dimension(100, 32));
   }
 
-  public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+  public JComboBox<String> getThreshold()
   {
-    return currentAnnotation;
+    return threshold;
   }
 
-  public void setCurrentAnnotation(
-          jalview.datamodel.AlignmentAnnotation currentAnnotation)
+  public void setThreshold(JComboBox<String> thresh)
   {
-    this.currentAnnotation = currentAnnotation;
+    this.threshold = thresh;
   }
 
-  public abstract void valueChanged(boolean updateAllAnnotation);
-
-  public abstract void updateView();
+  public JComboBox<String> getAnnotations()
+  {
+    return annotations;
+  }
 
-  public abstract void reset();
+  public void setAnnotations(JComboBox<String> anns)
+  {
+    this.annotations = anns;
+  }
 }