From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 30 Mar 2017 10:01:08 +0000 (+0100)
Subject: Merge branch 'develop' into bug/JAL-2346annotationChoice
X-Git-Tag: Release_2_10_3b1~336^2~2^2~1^2~2^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d5bcc3830eab04e6db816e1c2ad8fce1dc189612;p=jalview.git

Merge branch 'develop' into bug/JAL-2346annotationChoice

Conflicts:
	src/jalview/gui/AnnotationRowFilter.java
---

d5bcc3830eab04e6db816e1c2ad8fce1dc189612
diff --cc src/jalview/gui/AnnotationRowFilter.java
index bc5bc54,7705bc3..c2bf41b
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@@ -78,38 -83,6 +78,38 @@@ public abstract class AnnotationRowFilt
     */
    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 av
-    * @param ap
++   * @param viewport
++   * @param alignPanel
 +   */
-   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
++  public AnnotationRowFilter(AlignViewport viewport, final AlignmentPanel alignPanel)
 +  {
-     this.av = av;
-     this.ap = ap;
++    this.av = viewport;
++    this.ap = alignPanel;
 +    thresholdValue.addFocusListener(new FocusAdapter()
 +    {
 +      @Override
 +      public void focusLost(FocusEvent e)
 +      {
 +        thresholdValue_actionPerformed();
 +      }
 +    });
 +  }
 +
    protected void addSliderChangeListener()
    {
  
@@@ -159,18 -132,27 +159,18 @@@
      });
    }
  
-   /**
-    * 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 AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
 -  {
 -    this.av = av;
 -    this.ap = ap;
 -    thresholdValue.addFocusListener(new FocusAdapter()
 -    {
 -      @Override
 -      public void focusLost(FocusEvent e)
 -      {
 -        thresholdValue_actionPerformed();
 -      }
 -    });
 -  }
 -
 -  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];
@@@ -363,107 -339,76 +363,107 @@@
      }
    }
  
 -  protected boolean colorAlignmContaining(AlignmentAnnotation currentAnn,
 -          int selectedThresholdOption)
 +  public AlignmentAnnotation getCurrentAnnotation()
    {
 +    return currentAnnotation;
 +  }
  
-   protected void setCurrentAnnotation(AlignmentAnnotation 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 = currentAnnotation;
++    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();
 +      }
 +    });
  
 -        AnnotationColourGradient scheme = null;
 -        if (currentColours.isSelected())
 -        {
 -          scheme = new AnnotationColourGradient(currentAnn,
 -                  sg.getColourScheme(), selectedThresholdOption);
 -        }
 -        else
 -        {
 -          scheme = new AnnotationColourGradient(currentAnn,
 -                  minColour.getBackground(), maxColour.getBackground(),
 -                  selectedThresholdOption);
 -        }
 -        scheme.setSeqAssociated(seqAssociated.isSelected());
 -        sg.setColourScheme(scheme);
 +    annotations.addItemListener(new ItemListener()
 +    {
 +      @Override
 +      public void itemStateChanged(ItemEvent e)
 +      {
 +        selectedAnnotationChanged();
        }
 -    }
 -    return false;
 +    });
 +    annotations.setToolTipText(MessageManager
 +            .getString("info.select_annotation_row"));
 +
 +    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();
 +      }
 +    });
 +
 +    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;
 +  }
  }