X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=f13cb10579c79b4690885d4000b059e23723ca7c;hb=1cec732f963ab102c9d8381203df8c8cba2a9ee4;hp=722ecdc6b13a3fe106654a7d70ef82b437ba3295;hpb=ca5a59c203b85a6c0f26c3d52d7827c5fa9fa4c5;p=jalview.git

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 722ecdc..f13cb10 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -1,21 +1,45 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
-import jalview.api.analysis.AnnotationFilterParameter;
-import jalview.api.analysis.AnnotationFilterParameter.SearchableAnnotationField;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
 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.List;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Vector;
 
+import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
@@ -34,33 +58,61 @@ public abstract class AnnotationRowFilter extends JPanel
 
   protected int[] annmap;
 
-  protected boolean enableSeqAss = false;
-
-  private jalview.datamodel.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 JTextField thresholdValue = new JTextField(20);
 
   protected JInternalFrame frame;
+
+  protected JButton ok = new JButton();
+
+  protected JButton cancel = new JButton();
+
   /**
    * enabled if the user is dragging the slider - try to keep updates to a
    * minimun
    */
   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;
+    thresholdValue.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
+  }
+
   protected void addSliderChangeListener()
   {
 
@@ -71,13 +123,33 @@ 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("" + (slider.getValue() - slider.getMinimum())
+              * 100f / (slider.getMaximum() - slider.getMinimum()));
+    }
+    else
+    {
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
+    }
+    adjusting = oldadj;
+  }
+
   protected void addSliderMouseListeners()
   {
 
@@ -100,36 +172,34 @@ public abstract class AnnotationRowFilter extends JPanel
       @Override
       public void mouseReleased(MouseEvent evt)
       {
-        if (sliderDragging)
-        {
-          sliderDragging = false;
-          valueChanged(true);
-        }
-        ap.paintAlignment(true);
+        sliderDragReleased();
       }
     });
   }
 
-
-  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)
   {
-    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)
         {
@@ -138,21 +208,29 @@ 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 && annotation.sequenceRef != null)
+      {
+        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);
         }
       }
     }
@@ -175,14 +253,8 @@ public abstract class AnnotationRowFilter extends JPanel
     return selectedThresholdItem;
   }
 
-  public void modelChanged()
-  {
-    seqAssociated.setEnabled(enableSeqAss);
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
+  public void ok_actionPerformed()
   {
-    updateView();
     try
     {
       frame.setClosed(true);
@@ -191,10 +263,10 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void cancel_actionPerformed(ActionEvent e)
+  public void cancel_actionPerformed()
   {
     reset();
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
     try
     {
       frame.setClosed(true);
@@ -203,55 +275,74 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void thresholdCheck_actionPerformed(ActionEvent e)
+  protected void thresholdCheck_actionPerformed()
   {
     updateView();
   }
 
-  public void annotations_actionPerformed(ActionEvent e)
+  protected void selectedAnnotationChanged()
   {
     updateView();
   }
 
-  public void threshold_actionPerformed(ActionEvent e)
+  protected void threshold_actionPerformed()
   {
     updateView();
   }
 
-  public void thresholdValue_actionPerformed(ActionEvent e)
+  protected void thresholdValue_actionPerformed()
   {
     try
     {
       float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue((int) (f * 1000));
+      if (percentThreshold.isSelected())
+      {
+        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(ActionEvent actionEvent)
+  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
-            .getString("label.threshold_feature_no_thereshold"));
-    threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold"));
-    threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold"));
+    thresh.addItem(MessageManager
+            .getString("label.threshold_feature_no_threshold"));
+    thresh.addItem(MessageManager
+            .getString("label.threshold_feature_above_threshold"));
+    thresh.addItem(MessageManager
+            .getString("label.threshold_feature_below_threshold"));
   }
 
-  protected void seqAssociated_actionPerformed(ActionEvent arg0,
-          JComboBox<String> annotations, JCheckBox seqAssociated)
+  /**
+   * 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)))
@@ -259,20 +350,22 @@ 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,
@@ -284,9 +377,11 @@ 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())))
@@ -303,163 +398,134 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  protected boolean colorAlignmContaining(
-          AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
+  public AlignmentAnnotation getCurrentAnnotation()
   {
+    return currentAnnotation;
+  }
 
-    AnnotationColourGradient acg = null;
-    if (currentColours.isSelected())
-    {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              av.getGlobalColourScheme(), selectedThresholdItem);
-    }
-    else
-    {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              minColour.getBackground(), maxColour.getBackground(),
-              selectedThresholdItem);
-    }
-    acg.setSeqAssociated(seqAssociated.isSelected());
-
-    if (currentAnnotation.graphMin == 0f
-            && currentAnnotation.graphMax == 0f)
-    {
-      acg.setPredefinedColours(true);
-    }
-
-    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+  protected void setCurrentAnnotation(AlignmentAnnotation annotation)
+  {
+    this.currentAnnotation = annotation;
+  }
 
-    av.setGlobalColourScheme(acg);
+  /**
+   * update associated view model and trigger any necessary repaints.
+   * 
+   * @param updateAllAnnotation
+   */
+  protected abstract void valueChanged(boolean updateAllAnnotation);
 
-    if (av.getAlignment().getGroups() != null)
-    {
+  protected abstract void updateView();
 
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
-      {
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        if (currentColours.isSelected())
-        {
-          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
-                  selectedThresholdItem);
-          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
-                  .isSelected());
+  protected abstract void reset();
 
-        }
-        else
-        {
-          sg.cs = new AnnotationColourGradient(currentAnnotation,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdItem);
-          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
-                  .isSelected());
-        }
-
-      }
-    }
-    return false;
+  protected String getAnnotationMenuLabel(AlignmentAnnotation ann)
+  {
+    return annotationLabels.get(ann);
   }
 
-  protected boolean filterAnnotations(Annotation[] annotations,
-          AnnotationFilterParameter filterParams, ColumnSelection cs)
+  protected void jbInit()
   {
-    av.showAllHiddenColumns();
-    cs.clear();
-    int count = 0;
-    do
+    ok.setOpaque(false);
+    ok.setText(MessageManager.getString("action.ok"));
+    ok.addActionListener(new ActionListener()
     {
-      if (annotations[count] != null)
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
+        ok_actionPerformed();
+      }
+    });
 
-        boolean itemMatched = false;
-
-        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
-                && annotations[count].value > currentAnnotation.threshold.value)
-        {
-          itemMatched = true;
-        }
-        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
-                && annotations[count].value < currentAnnotation.threshold.value)
-        {
-          itemMatched = true;
-        }
-
-        if (filterParams.isFilterAlphaHelix()
-                && annotations[count].secondaryStructure == 'H')
-        {
-          itemMatched = true;
-        }
+    cancel.setOpaque(false);
+    cancel.setText(MessageManager.getString("action.cancel"));
+    cancel.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed();
+      }
+    });
 
-        if (filterParams.isFilterBetaSheet()
-                && annotations[count].secondaryStructure == 'E')
-        {
-          itemMatched = true;
-        }
+    annotations.addItemListener(new ItemListener()
+    {
+      @Override
+      public void itemStateChanged(ItemEvent e)
+      {
+        selectedAnnotationChanged();
+      }
+    });
+    annotations.setToolTipText(
+            MessageManager.getString("info.select_annotation_row"));
 
-        if (filterParams.isFilterTurn()
-                && annotations[count].secondaryStructure == 'S')
-        {
-          itemMatched = true;
-        }
+    threshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed();
+      }
+    });
 
-        String regexSearchString = filterParams.getRegexString();
-        if (regexSearchString != null
-                && !filterParams.getRegexSearchFields().isEmpty())
-        {
-          List<SearchableAnnotationField> fields = filterParams
-                  .getRegexSearchFields();
-          try
-          {
-            if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
-                    && annotations[count].displayCharacter
-                            .matches(regexSearchString))
-            {
-              itemMatched = true;
-            }
-          } catch (java.util.regex.PatternSyntaxException pse)
-          {
-            if (annotations[count].displayCharacter
-                    .equals(regexSearchString))
-            {
-              itemMatched = true;
-            }
-          }
-          if (fields.contains(SearchableAnnotationField.DESCRIPTION)
-                  && annotations[count].description != null
-                  && annotations[count].description
-                          .matches(regexSearchString))
-          {
-            itemMatched = true;
-          }
-        }
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(7);
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
 
-        if (itemMatched)
+    percentThreshold
+            .setText(MessageManager.getString("label.as_percentage"));
+    percentThreshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (!adjusting)
         {
-          cs.addElement(count);
+          percentageValue_actionPerformed();
         }
       }
-      count++;
-    } while (count < annotations.length);
-    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 JComboBox<String> getAnnotations()
+  {
+    return annotations;
+  }
 
-  public abstract void updateView();
+  public void setAnnotations(JComboBox<String> anns)
+  {
+    this.annotations = anns;
+  }
 
-  public abstract void reset();
+  protected void sliderDragReleased()
+  {
+    if (sliderDragging)
+    {
+      sliderDragging = false;
+      valueChanged(true);
+    }
+  }
 }