+/*
+ * 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.AnnotationRowFilterI;
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.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;
import javax.swing.event.ChangeListener;
@SuppressWarnings("serial")
-public abstract class AnnotationRowFilter extends JPanel implements
- AnnotationRowFilterI
+public abstract class AnnotationRowFilter extends JPanel
{
protected AlignViewport av;
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 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<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
+ */
+ 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();
+ }
+ });
+ }
+
protected void addSliderChangeListener()
{
});
}
-
- public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
- {
- this.av = av;
- this.ap = ap;
- }
-
- public AnnotationRowFilter()
- {
-
- }
-
- @Override
+ /**
+ * 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)
{
}
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);
}
}
}
- // seqAssociated.setEnabled(enableSeqAss);
this.annmap = new int[list.size()];
System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
return list;
return selectedThresholdItem;
}
- public void modelChanged()
+ public void ok_actionPerformed()
{
- seqAssociated.setEnabled(enableSeqAss);
- }
-
- public void ok_actionPerformed(ActionEvent e)
- {
- updateView();
try
{
frame.setClosed(true);
}
}
- public void cancel_actionPerformed(ActionEvent e)
+ public void cancel_actionPerformed()
{
reset();
ap.paintAlignment(true);
}
}
- 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
{
}
}
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ 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)))
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,
}
}
- 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());
+ protected void setCurrentAnnotation(AlignmentAnnotation currentAnnotation)
+ {
+ this.currentAnnotation = currentAnnotation;
+ }
- if (currentAnnotation.graphMin == 0f
- && currentAnnotation.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);
+ }
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ protected void jbInit()
+ {
+ ok.setOpaque(false);
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- if (sg.cs == null)
- {
- continue;
- }
-
- if (currentColours.isSelected())
- {
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- selectedThresholdItem);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
+ ok_actionPerformed();
+ }
+ });
- }
- else
- {
- sg.cs = new AnnotationColourGradient(currentAnnotation,
- minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdItem);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
- }
+ cancel.setOpaque(false);
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed();
+ }
+ });
+ annotations.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ selectedAnnotationChanged();
}
- }
- return false;
- }
+ });
+ annotations.setToolTipText(MessageManager
+ .getString("info.select_annotation_row"));
- protected boolean markColumnsContaining(
- AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
- {
- try
+ threshold.addActionListener(new ActionListener()
{
- if (currentAnnotation != null)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- Annotation[] annotations = currentAnnotation.annotations;
- ColumnSelection cs = av.getColumnSelection();
- cs.clear();
- if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
- {
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
- if (currentAnnotation.label.equals("Secondary Structure")
- && annotations[count].secondaryStructure != ' ')
- {
- cs.addElement(count);
- }
- else if (currentAnnotation.label
- .equals("Iron Sulphur Contacts"))
- {
- cs.addElement(count);
- }
- else if (annotations[count].value != 0.0)
- {
- cs.addElement(count);
- }
-
- }
- count++;
- } while (count < annotations.length);
- }
- else
- {
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
- if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- if (annotations[count].value > currentAnnotation.threshold.value)
- {
- cs.addElement(count);
- }
- }
- else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- if (annotations[count].value < currentAnnotation.threshold.value)
- {
- cs.addElement(count);
- }
- }
-
- }
- count++;
- } while (count < annotations.length);
- }
+ threshold_actionPerformed();
}
+ });
- return true;
- } catch (Exception e)
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
+ thresholdValue.addActionListener(new ActionListener()
{
- e.printStackTrace();
- return false;
- }
+ @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 JComboBox<String> getAnnotations()
+ {
+ return annotations;
+ }
+
+ public void setAnnotations(JComboBox<String> anns)
+ {
+ this.annotations = anns;
+ }
}
git://source.jalview.org / jalview.git / blobdiff