--- /dev/null
+package jalview.api;
+
+import java.util.Vector;
+
+public interface AnnotationRowFilterI
+{
+ public Vector<String> getAnnotationItems(boolean isSeqAssociated);
+
+ public void modelChanged();
+
+ public void valueChanged(boolean updateAllAnnotation);
+
+ public void updateView();
+
+ public void reset();
+}
@Override
public void annotationColumn_actionPerformed(ActionEvent e)
{
- new AnnotationColumnSelection(viewport, alignPanel);
+ new AnnotationColumnChooser(viewport, alignPanel);
}
@Override
private boolean rightAlignIds = false;
- private AnnotationColumnSelection currentAnnotationColumnSelectionState;
+ private AnnotationColumnChooser currentAnnotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
*
this.rightAlignIds = rightAlignIds;
}
- public AnnotationColumnSelection getCurrentAnnotationColumnSelectionState()
+ public AnnotationColumnChooser getCurrentAnnotationColumnSelectionState()
{
return currentAnnotationColumnSelectionState;
}
public void setCurrentAnnotationColumnSelectionState(
- AnnotationColumnSelection currentAnnotationColumnSelectionState)
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
{
this.currentAnnotationColumnSelectionState = currentAnnotationColumnSelectionState;
}
package jalview.gui;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Hashtable;
-import java.util.Vector;
import javax.swing.BorderFactory;
import javax.swing.JButton;
-import javax.swing.JCheckBox;
import javax.swing.JColorChooser;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
-import javax.swing.JSlider;
-import javax.swing.JTextField;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
import net.miginfocom.swing.MigLayout;
-public class AnnotationColourChooser extends JPanel
+@SuppressWarnings("serial")
+public class AnnotationColourChooser extends AnnotationRowFilter
{
- JInternalFrame frame;
-
- AlignViewport av;
-
- AlignmentPanel ap;
ColourSchemeI oldcs;
- Hashtable oldgroupColours;
-
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
-
- boolean adjusting = false;
+ Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
/**
* enabled if the user is dragging the slider - try to keep updates to a
* minimun
*/
- boolean sliderDragging = false;
+
+ JComboBox<String> annotations;
+
+ JButton defColours = new JButton();
+
+ JButton ok = new JButton();
+
+ JButton cancel = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JPanel jPanel2 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ private JComboBox<String> threshold = new JComboBox<String>();
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
+ super(av, ap);
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
+ oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.cs != null)
}
}
}
- this.av = av;
- this.ap = ap;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
MessageManager.getString("label.colour_by_annotation"), 520,
215);
- slider.addChangeListener(new ChangeListener()
- {
- @Override
- public void stateChanged(ChangeEvent evt)
- {
- if (!adjusting)
- {
- thresholdValue.setText((slider.getValue() / 1000f) + "");
- valueChanged(!sliderDragging);
- }
- }
- });
- slider.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent e)
- {
- sliderDragging = true;
- super.mousePressed(e);
- }
-
- @Override
- public void mouseDragged(MouseEvent e)
- {
- sliderDragging = true;
- super.mouseDragged(e);
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (sliderDragging)
- {
- sliderDragging = false;
- valueChanged(true);
- }
- ap.paintAlignment(true);
- }
- });
+ addSliderChangeListener();
+ addSliderMouseListeners();
if (av.getAlignment().getAlignmentAnnotation() == null)
{
seqAssociated.setSelected(acg.isSeqAssociated());
}
- annotations = new JComboBox(
+ annotations = new JComboBox<String>(
getAnnotationItems(seqAssociated.isSelected()));
- 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"));
+ populateThresholdComboBox(threshold);
if (oldcs instanceof AnnotationColourGradient)
{
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.setSelectedIndex(0);
+ getThreshold().setSelectedIndex(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.setSelectedIndex(1);
+ getThreshold().setSelectedIndex(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.setSelectedIndex(2);
+ getThreshold().setSelectedIndex(2);
break;
default:
throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
} catch (Exception ex)
{
}
-
adjusting = false;
- changeColour();
+ updateView();
frame.invalidate();
frame.pack();
-
- }
-
- private Vector<String> getAnnotationItems(boolean isSeqAssociated)
- {
- Vector<String> list = new Vector<String>();
- int index = 1;
- int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
- boolean enableSeqAss = false;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
- {
- if (isSeqAssociated)
- {
- continue;
- }
- }
- else
- {
- enableSeqAss = true;
- }
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- {
- anmap[list.size()] = i;
- list.add(label);
-
- }
- else
- {
- if (!isSeqAssociated)
- {
- anmap[list.size()] = i;
- list.add(label + "_" + (index++));
- }
- }
- }
- seqAssociated.setEnabled(enableSeqAss);
- this.annmap = new int[list.size()];
- System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
- return list;
- }
-
- private void setDefaultMinMax()
- {
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
}
public AnnotationColourChooser()
annotations_actionPerformed(e);
}
});
- threshold.addActionListener(new ActionListener()
+ getThreshold().addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@Override
public void actionPerformed(ActionEvent arg0)
{
- seqAssociated_actionPerformed(arg0);
+ seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
}
});
colpanel.add(minColour);
colpanel.add(maxColour);
jPanel2.add(colpanel, "wrap");
- jPanel2.add(threshold);
+ jPanel2.add(getThreshold());
jPanel2.add(defColours, "skip 1, wrap");
jPanel2.add(thresholdIsMin);
jPanel2.add(slider, "grow");
this.validate();
}
- protected void seqAssociated_actionPerformed(ActionEvent arg0)
- {
- adjusting = true;
- String cursel = (String) annotations.getSelectedItem();
- boolean isvalid = false, isseqs = seqAssociated.isSelected();
- this.annotations.removeAllItems();
- for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
- {
- if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
- {
- isvalid = true;
- cursel = anitem;
- }
- this.annotations.addItem(anitem);
- }
- adjusting = false;
- if (isvalid)
- {
- this.annotations.setSelectedItem(cursel);
- }
- else
- {
- if (annotations.getItemCount() > 0)
- {
- annotations.setSelectedIndex(0);
- }
- }
- }
-
protected void resetColours_actionPerformed(ActionEvent arg0)
{
setDefaultMinMax();
- changeColour();
+ updateView();
}
- JComboBox annotations;
-
- int[] annmap;
-
- JPanel minColour = new JPanel();
-
- JPanel maxColour = new JPanel();
-
- JButton defColours = new JButton();
-
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- JComboBox threshold = new JComboBox();
-
- JSlider slider = new JSlider();
-
- JTextField thresholdValue = new JTextField(20);
-
- JCheckBox currentColours = new JCheckBox();
-
- JCheckBox thresholdIsMin = new JCheckBox();
-
- JCheckBox seqAssociated = new JCheckBox();
+ private void setDefaultMinMax()
+ {
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
+ }
public void minColour_actionPerformed()
{
minColour.setBackground(col);
}
minColour.repaint();
- changeColour();
+ updateView();
}
public void maxColour_actionPerformed()
maxColour.setBackground(col);
}
maxColour.repaint();
- changeColour();
+ updateView();
}
- void changeColour()
+ public void reset()
{
- // Check if combobox is still adjusting
- if (adjusting)
- {
- return;
- }
-
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
- .getSelectedIndex()]];
-
- int aboveThreshold = -1;
- if (threshold.getSelectedIndex() == 1)
- {
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
- }
- else if (threshold.getSelectedIndex() == 2)
- {
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
- }
-
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(true);
-
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
- {
- slider.setEnabled(false);
- thresholdValue.setEnabled(false);
- thresholdValue.setText("");
- thresholdIsMin.setEnabled(false);
- }
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
- && currentAnnotation.threshold == null)
- {
- currentAnnotation
- .setThreshold(new jalview.datamodel.GraphLine(
- (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
- "Threshold", Color.black));
- }
-
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
- {
- adjusting = true;
- float range = currentAnnotation.graphMax * 1000
- - currentAnnotation.graphMin * 1000;
-
- slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
- slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
- slider.setValue((int) (currentAnnotation.threshold.value * 1000));
- thresholdValue.setText(currentAnnotation.threshold.value + "");
- slider.setMajorTickSpacing((int) (range / 10f));
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- adjusting = false;
- }
-
- AnnotationColourGradient acg = null;
- if (currentColours.isSelected())
- {
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
- }
- else
- {
- acg = new AnnotationColourGradient(currentAnnotation,
- minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
- }
- acg.setSeqAssociated(seqAssociated.isSelected());
-
- if (currentAnnotation.graphMin == 0f
- && currentAnnotation.graphMax == 0f)
- {
- acg.setPredefinedColours(true);
- }
-
- acg.thresholdIsMinMax = thresholdIsMin.isSelected();
-
- av.setGlobalColourScheme(acg);
-
+ av.setGlobalColourScheme(oldcs);
if (av.getAlignment().getGroups() != null)
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs == null)
- {
- continue;
- }
-
- if (currentColours.isSelected())
- {
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- aboveThreshold);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
-
- }
- else
- {
- sg.cs = new AnnotationColourGradient(currentAnnotation,
- minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
- }
-
+ sg.cs = oldgroupColours.get(sg);
}
}
- ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of
- // updated colours.
- ap.paintAlignment(true);
- }
-
- public void ok_actionPerformed(ActionEvent e)
- {
- changeColour();
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
}
- public void cancel_actionPerformed(ActionEvent e)
+ public void valueChanged(boolean updateAllAnnotation)
{
- reset();
- // ensure all original colouring is propagated to listeners.
- ap.paintAlignment(true);
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
+ if (currentColours.isSelected()
+ && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
+ updateView();
}
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false);
}
- void reset()
- {
- av.setGlobalColourScheme(oldcs);
- if (av.getAlignment().getGroups() != null)
- {
-
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
- {
- sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
- }
- }
- }
-
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
+ public JComboBox<String> getThreshold()
{
- changeColour();
+ return threshold;
}
- public void threshold_actionPerformed(ActionEvent e)
+ public void setThreshold(JComboBox<String> threshold)
{
- changeColour();
+ this.threshold = threshold;
}
- public void thresholdValue_actionPerformed(ActionEvent e)
+ public void currentColours_actionPerformed(ActionEvent e)
{
- try
- {
- float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
- } catch (NumberFormatException ex)
+ if (currentColours.isSelected())
{
+ reset();
}
+ maxColour.setEnabled(!currentColours.isSelected());
+ minColour.setEnabled(!currentColours.isSelected());
+ updateView();
}
- public void valueChanged(boolean updateAllAnnotation)
+ @Override
+ public void updateView()
{
- if (currentColours.isSelected()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
- {
- changeColour();
- }
- currentAnnotation.threshold.value = slider.getValue() / 1000f;
- propagateSeqAssociatedThreshold(updateAllAnnotation);
- ap.paintAlignment(false);
+ changeColour();
}
-
- private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+ void changeColour()
{
- if (currentAnnotation.sequenceRef == null
- || currentAnnotation.threshold == null)
+ // Check if combobox is still adjusting
+ if (adjusting)
{
return;
}
- // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation
- // is false, since we only need to provide a quick visual indicator
- float thr = currentAnnotation.threshold.value;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]]);
+
+ int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
+ .getSelectedIndex());
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(true);
+
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
- AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
- if (aa.label.equals(currentAnnotation.label)
- && (currentAnnotation.getCalcId() == null ? aa.getCalcId() == null
- : currentAnnotation.getCalcId()
- .equals(aa.getCalcId())))
- {
- if (aa.threshold == null)
- {
- aa.threshold = new GraphLine(currentAnnotation.threshold);
- }
- else
- {
- aa.threshold.value = thr;
- }
- }
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ thresholdIsMin.setEnabled(false);
}
- }
-
- public void currentColours_actionPerformed(ActionEvent e)
- {
- if (currentColours.isSelected())
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
+ && getCurrentAnnotation().threshold == null)
{
- reset();
+ getCurrentAnnotation()
+ .setThreshold(new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
+ if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ adjusting = true;
+ float range = getCurrentAnnotation().graphMax * 1000
+ - getCurrentAnnotation().graphMin * 1000;
- changeColour();
- }
+ slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
+ slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
+ slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+ thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+ slider.setMajorTickSpacing((int) (range / 10f));
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ adjusting = false;
+ }
+ colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
- {
- changeColour();
+ ap.alignmentChanged();
+ // ensure all associated views (overviews, structures, etc) are notified of
+ // updated colours.
+ ap.paintAlignment(true);
}
}
--- /dev/null
+package jalview.gui;
+
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+
+import net.miginfocom.swing.MigLayout;
+
+@SuppressWarnings("serial")
+public class AnnotationColumnChooser extends AnnotationRowFilter
+{
+
+ private JComboBox<String> annotations;
+
+ JButton ok = new JButton();
+
+ JButton cancel = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JPanel jPanel2 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ private JComboBox<String> threshold = new JComboBox<String>();
+
+
+ public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
+ {
+ super(av, ap);
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
+
+ addSliderChangeListener();
+ addSliderMouseListeners();
+
+ if (av.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+
+ adjusting = true;
+
+ setAnnotations(new JComboBox<String>(
+ getAnnotationItems(seqAssociated.isSelected())));
+ populateThresholdComboBox(threshold);
+
+ if (av.getCurrentAnnotationColumnSelectionState() != null)
+ {
+ annotations.setSelectedIndex(av
+ .getCurrentAnnotationColumnSelectionState().getAnnotations()
+ .getSelectedIndex());
+ threshold.setSelectedIndex(av
+ .getCurrentAnnotationColumnSelectionState().getThreshold()
+ .getSelectedIndex());
+ }
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ }
+ adjusting = false;
+
+ updateView();
+ frame.invalidate();
+ frame.pack();
+ }
+
+
+ public AnnotationColumnChooser()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ ok.setOpaque(false);
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ cancel.setOpaque(false);
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+
+ getAnnotations().addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ getThreshold().addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ threshold_actionPerformed(e);
+ }
+ });
+ thresholdValue.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ thresholdValue_actionPerformed(e);
+ }
+ });
+ slider.setPaintLabels(false);
+ slider.setPaintTicks(true);
+ slider.setBackground(Color.white);
+ slider.setEnabled(false);
+ slider.setOpaque(false);
+ slider.setPreferredSize(new Dimension(100, 32));
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
+ thresholdIsMin.setBackground(Color.white);
+ thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
+ thresholdIsMin.setText(MessageManager
+ .getString("label.threshold_minmax"));
+ thresholdIsMin.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ thresholdIsMin_actionPerformed(actionEvent);
+ }
+ });
+ seqAssociated.setBackground(Color.white);
+ seqAssociated.setFont(JvSwingUtils.getLabelFont());
+ seqAssociated.setText(MessageManager
+ .getString("label.per_sequence_only"));
+ seqAssociated.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+ }
+ });
+
+ this.setLayout(borderLayout1);
+ jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
+ jPanel1.setBackground(Color.white);
+ jPanel2.setBackground(Color.white);
+
+ jPanel1.add(ok);
+ jPanel1.add(cancel);
+ jPanel2.add(getAnnotations(), "grow, wrap");
+ jPanel2.add(seqAssociated, "wrap");
+ jPanel2.add(getThreshold(), "grow, wrap");
+ jPanel2.add(thresholdIsMin, "wrap");
+ jPanel2.add(slider, "grow");
+ jPanel2.add(thresholdValue, "grow");
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ this.add(jPanel2, java.awt.BorderLayout.CENTER);
+ this.validate();
+ }
+
+
+ public void reset()
+ {
+ av.getColumnSelection().clear();
+ }
+
+ public void valueChanged(boolean updateAllAnnotation)
+ {
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ updateView();
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false);
+ }
+
+ public JComboBox<String> getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold(JComboBox<String> threshold)
+ {
+ this.threshold = threshold;
+ }
+
+ public JComboBox<String> getAnnotations()
+ {
+ return annotations;
+ }
+
+ public void setAnnotations(JComboBox<String> annotations)
+ {
+ this.annotations = annotations;
+ }
+
+ @Override
+ public void updateView()
+ {
+ changeColumnSelection();
+ }
+ void changeColumnSelection()
+ {
+ // Check if combobox is still adjusting
+ if (adjusting)
+ {
+ return;
+ }
+
+ setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]]);
+
+
+ int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
+ .getSelectedIndex());
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(true);
+
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ thresholdIsMin.setEnabled(false);
+ }
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
+ && getCurrentAnnotation().threshold == null)
+ {
+ getCurrentAnnotation()
+ .setThreshold(new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
+ }
+
+ if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ adjusting = true;
+ float range = getCurrentAnnotation().graphMax * 1000
+ - getCurrentAnnotation().graphMin * 1000;
+
+ slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
+ slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
+ slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+ thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+ slider.setMajorTickSpacing((int) (range / 10f));
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ adjusting = false;
+ }
+
+ markColumnsContaining(getCurrentAnnotation(), selectedThresholdItem);
+ av.setCurrentAnnotationColumnSelectionState(this);
+ ap.alignmentChanged();
+ ap.paintAlignment(true);
+ }
+}
+++ /dev/null
-package jalview.gui;
-
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.GraphLine;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JPanel;
-import javax.swing.JSlider;
-import javax.swing.JTextField;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-
-import net.miginfocom.swing.MigLayout;
-
-public class AnnotationColumnSelection extends JPanel
-{
- JInternalFrame frame;
-
- AlignViewport av;
-
- AlignmentPanel ap;
-
- ColourSchemeI oldcs;
-
- Hashtable oldgroupColours;
-
- private JComboBox annotations;
-
- int[] annmap;
-
- JPanel minColour = new JPanel();
-
- JPanel maxColour = new JPanel();
-
- JButton defColours = new JButton();
-
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- private JComboBox threshold = new JComboBox();
-
- JSlider slider = new JSlider();
-
- JTextField thresholdValue = new JTextField(20);
-
- JCheckBox currentColours = new JCheckBox();
-
- JCheckBox thresholdIsMin = new JCheckBox();
-
- JCheckBox seqAssociated = new JCheckBox();
-
- private jalview.datamodel.AlignmentAnnotation currentAnnotation;
-
- boolean adjusting = false;
-
- /**
- * enabled if the user is dragging the slider - try to keep updates to a
- * minimun
- */
- boolean sliderDragging = false;
-
- public AnnotationColumnSelection(AlignViewport av, final AlignmentPanel ap)
- {
-
- this.av = av;
- this.ap = ap;
- frame = new JInternalFrame();
- frame.setContentPane(this);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
-
- slider.addChangeListener(new ChangeListener()
- {
- @Override
- public void stateChanged(ChangeEvent evt)
- {
- if (!adjusting)
- {
- thresholdValue.setText((slider.getValue() / 1000f) + "");
- valueChanged(!sliderDragging);
- }
- }
- });
- slider.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent e)
- {
- sliderDragging = true;
- super.mousePressed(e);
- }
-
- @Override
- public void mouseDragged(MouseEvent e)
- {
- sliderDragging = true;
- super.mouseDragged(e);
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (sliderDragging)
- {
- sliderDragging = false;
- valueChanged(true);
- }
- ap.paintAlignment(true);
- }
- });
-
- if (av.getAlignment().getAlignmentAnnotation() == null)
- {
- return;
- }
-
- // Always get default shading from preferences.
- setDefaultMinMax();
-
- adjusting = true;
-
- setAnnotations(new JComboBox(
- getAnnotationItems(seqAssociated.isSelected())));
-
- 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"));
-
- if (av.getCurrentAnnotationColumnSelectionState() != null)
- {
- annotations.setSelectedIndex(av
- .getCurrentAnnotationColumnSelectionState().getAnnotations()
- .getSelectedIndex());
- threshold.setSelectedIndex(av
- .getCurrentAnnotationColumnSelectionState().getThreshold()
- .getSelectedIndex());
- System.out.println("selected annotation : "
- + av.getCurrentAnnotationColumnSelectionState()
- .getAnnotations().getSelectedIndex());
- System.out.println("selected threshold : "
- + av.getCurrentAnnotationColumnSelectionState()
- .getThreshold().getSelectedIndex());
- }
-
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- }
-
- adjusting = false;
-
- changeColumnSelection();
- frame.invalidate();
- frame.pack();
-
- }
-
- private Vector<String> getAnnotationItems(boolean isSeqAssociated)
- {
- Vector<String> list = new Vector<String>();
- int index = 1;
- int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
- boolean enableSeqAss = false;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
- {
- if (isSeqAssociated)
- {
- continue;
- }
- }
- else
- {
- enableSeqAss = true;
- }
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- {
- anmap[list.size()] = i;
- list.add(label);
-
- }
- else
- {
- if (!isSeqAssociated)
- {
- anmap[list.size()] = i;
- list.add(label + "_" + (index++));
- }
- }
- }
- seqAssociated.setEnabled(enableSeqAss);
- this.annmap = new int[list.size()];
- System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
- return list;
- }
-
- private void setDefaultMinMax()
- {
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
- }
-
- public AnnotationColumnSelection()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- private void jbInit() throws Exception
- {
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
-
- getAnnotations().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- getThreshold().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed(e);
- }
- });
- thresholdValue.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- thresholdValue_actionPerformed(e);
- }
- });
- slider.setPaintLabels(false);
- slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setEnabled(false);
- slider.setOpaque(false);
- slider.setPreferredSize(new Dimension(100, 32));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
- thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager
- .getString("label.threshold_minmax"));
- thresholdIsMin.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- thresholdIsMin_actionPerformed(actionEvent);
- }
- });
- seqAssociated.setBackground(Color.white);
- seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager
- .getString("label.per_sequence_only"));
- seqAssociated.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- seqAssociated_actionPerformed(arg0);
- }
- });
-
- this.setLayout(borderLayout1);
- jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
- jPanel1.setBackground(Color.white);
- jPanel2.setBackground(Color.white);
-
- jPanel1.add(ok);
- jPanel1.add(cancel);
- jPanel2.add(getAnnotations(), "grow, wrap");
- jPanel2.add(seqAssociated, "wrap");
- jPanel2.add(getThreshold(), "grow, wrap");
- jPanel2.add(thresholdIsMin, "wrap");
- jPanel2.add(slider, "grow");
- jPanel2.add(thresholdValue, "grow");
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel2, java.awt.BorderLayout.CENTER);
- this.validate();
- }
-
- protected void seqAssociated_actionPerformed(ActionEvent arg0)
- {
- adjusting = true;
- String cursel = (String) getAnnotations().getSelectedItem();
- boolean isvalid = false, isseqs = seqAssociated.isSelected();
- this.getAnnotations().removeAllItems();
- for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
- {
- if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
- {
- isvalid = true;
- cursel = anitem;
- }
- this.getAnnotations().addItem(anitem);
- }
- adjusting = false;
- if (isvalid)
- {
- this.getAnnotations().setSelectedItem(cursel);
- }
- else
- {
- if (getAnnotations().getItemCount() > 0)
- {
- getAnnotations().setSelectedIndex(0);
- }
- }
- }
-
-
- void changeColumnSelection()
- {
- // Check if combobox is still adjusting
- if (adjusting)
- {
- return;
- }
-
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
- .getSelectedIndex()]]);
-
- int aboveThreshold = -1;
- if (getThreshold().getSelectedIndex() == 1)
- {
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
- }
- else if (getThreshold().getSelectedIndex() == 2)
- {
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
- }
-
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(true);
-
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
- {
- slider.setEnabled(false);
- thresholdValue.setEnabled(false);
- thresholdValue.setText("");
- thresholdIsMin.setEnabled(false);
- }
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
- && getCurrentAnnotation().threshold == null)
- {
- getCurrentAnnotation()
- .setThreshold(new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
- }
-
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
- {
- adjusting = true;
- float range = getCurrentAnnotation().graphMax * 1000
- - getCurrentAnnotation().graphMin * 1000;
-
- slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
- slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
- thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
- slider.setMajorTickSpacing((int) (range / 10f));
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- adjusting = false;
- }
-
- markColumnsContaining(getCurrentAnnotation(), aboveThreshold);
- av.setCurrentAnnotationColumnSelectionState(this);
- ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of
- // updated colours.
- ap.paintAlignment(true);
- }
-
- public boolean markColumnsContaining(
- AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
- {
- try
- {
- if (currentAnnotation != null)
- {
- 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);
- }
- }
-
- return true;
- } catch (Exception e)
- {
- e.printStackTrace();
- return false;
- }
- }
-
- public void ok_actionPerformed(ActionEvent e)
- {
- changeColumnSelection();
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
-
- public void cancel_actionPerformed(ActionEvent e)
- {
- reset();
- // ensure all original colouring is propagated to listeners.
- ap.paintAlignment(true);
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
-
- void reset()
- {
- av.getColumnSelection().clear();
- }
-
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColumnSelection();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColumnSelection();
- }
-
- public void threshold_actionPerformed(ActionEvent e)
- {
- changeColumnSelection();
- }
-
- public void thresholdValue_actionPerformed(ActionEvent e)
- {
- try
- {
- float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
- changeColumnSelection();
- } catch (NumberFormatException ex)
- {
- }
- }
-
- public void valueChanged(boolean updateAllAnnotation)
- {
- getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
- changeColumnSelection();
- // propagateSeqAssociatedThreshold(updateAllAnnotation);
- ap.paintAlignment(false);
- }
-
- private void propagateSeqAssociatedThreshold(boolean allAnnotation)
- {
- if (getCurrentAnnotation().sequenceRef == null
- || getCurrentAnnotation().threshold == null)
- {
- return;
- }
-
-
- float thr = getCurrentAnnotation().threshold.value;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
- if (aa.label.equals(getCurrentAnnotation().label)
- && (getCurrentAnnotation().getCalcId() == null ? aa
- .getCalcId() == null : getCurrentAnnotation()
- .getCalcId()
- .equals(aa.getCalcId())))
- {
- if (aa.threshold == null)
- {
- aa.threshold = new GraphLine(getCurrentAnnotation().threshold);
- }
- else
- {
- aa.threshold.value = thr;
- }
- }
- }
- }
-
- public void currentColours_actionPerformed(ActionEvent e)
- {
- if (currentColours.isSelected())
- {
- reset();
- }
-
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
-
- changeColumnSelection();
- }
-
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
- {
- changeColumnSelection();
- }
-
- public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
- {
- return currentAnnotation;
- }
-
- public void setCurrentAnnotation(
- jalview.datamodel.AlignmentAnnotation currentAnnotation)
- {
- this.currentAnnotation = currentAnnotation;
- }
-
- public JComboBox getThreshold()
- {
- return threshold;
- }
-
- public void setThreshold(JComboBox threshold)
- {
- this.threshold = threshold;
- }
-
- public JComboBox getAnnotations()
- {
- return annotations;
- }
-
- public void setAnnotations(JComboBox annotations)
- {
- this.annotations = annotations;
- }
-
-}
--- /dev/null
+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.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Vector;
+
+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;
+
+@SuppressWarnings("serial")
+public abstract class AnnotationRowFilter extends JPanel implements
+ AnnotationRowFilterI
+{
+ protected AlignViewport av;
+
+ protected AlignmentPanel ap;
+
+ 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;
+ /**
+ * enabled if the user is dragging the slider - try to keep updates to a
+ * minimun
+ */
+ protected boolean sliderDragging = false;
+
+ protected void addSliderChangeListener()
+ {
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ if (!adjusting)
+ {
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
+ valueChanged(!sliderDragging);
+ }
+ }
+ });
+ }
+
+ protected void addSliderMouseListeners()
+ {
+
+ slider.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ sliderDragging = true;
+ super.mousePressed(e);
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent e)
+ {
+ sliderDragging = true;
+ super.mouseDragged(e);
+ }
+
+ @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;
+ }
+
+ public AnnotationRowFilter()
+ {
+
+ }
+
+ @Override
+ public Vector<String> getAnnotationItems(boolean isSeqAssociated)
+ {
+ Vector<String> list = new Vector<String>();
+ int index = 1;
+ int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
+ {
+ if (isSeqAssociated)
+ {
+ continue;
+ }
+ }
+ else
+ {
+ enableSeqAss = true;
+ }
+ String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ if (!list.contains(label))
+ {
+ anmap[list.size()] = i;
+ list.add(label);
+
+ }
+ else
+ {
+ if (!isSeqAssociated)
+ {
+ anmap[list.size()] = i;
+ list.add(label + "_" + (index++));
+ }
+ }
+ }
+ // seqAssociated.setEnabled(enableSeqAss);
+ this.annmap = new int[list.size()];
+ System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
+ return list;
+ }
+
+ protected int getSelectedThresholdItem(int indexValue)
+ {
+ int selectedThresholdItem = -1;
+ if (indexValue == 1)
+ {
+ selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
+ }
+ else if (indexValue == 2)
+ {
+ selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
+ }
+ return selectedThresholdItem;
+ }
+
+ public void modelChanged()
+ {
+ seqAssociated.setEnabled(enableSeqAss);
+ }
+
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ updateView();
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ reset();
+ ap.paintAlignment(true);
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void thresholdCheck_actionPerformed(ActionEvent e)
+ {
+ updateView();
+ }
+
+ public void annotations_actionPerformed(ActionEvent e)
+ {
+ updateView();
+ }
+
+ public void threshold_actionPerformed(ActionEvent e)
+ {
+ updateView();
+ }
+
+ public void thresholdValue_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ float f = Float.parseFloat(thresholdValue.getText());
+ slider.setValue((int) (f * 1000));
+ updateView();
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+
+ public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ {
+ updateView();
+ }
+
+ protected void populateThresholdComboBox(JComboBox<String> threshold)
+ {
+ 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"));
+ }
+
+ protected void seqAssociated_actionPerformed(ActionEvent arg0,
+ JComboBox<String> annotations, JCheckBox seqAssociated)
+ {
+ adjusting = true;
+ String cursel = (String) annotations.getSelectedItem();
+ boolean isvalid = false, isseqs = seqAssociated.isSelected();
+ annotations.removeAllItems();
+ for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
+ {
+ if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
+ {
+ isvalid = true;
+ cursel = anitem;
+ }
+ annotations.addItem(anitem);
+ }
+ adjusting = false;
+ if (isvalid)
+ {
+ annotations.setSelectedItem(cursel);
+ }
+ else
+ {
+ if (annotations.getItemCount() > 0)
+ {
+ annotations.setSelectedIndex(0);
+ }
+ }
+ }
+
+ protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
+ AlignmentAnnotation annotation)
+ {
+ if (annotation.sequenceRef == null || annotation.threshold == null)
+ {
+ return;
+ }
+
+ float thr = annotation.threshold.value;
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+ if (aa.label.equals(annotation.label)
+ && (annotation.getCalcId() == null ? aa.getCalcId() == null
+ : annotation.getCalcId().equals(aa.getCalcId())))
+ {
+ if (aa.threshold == null)
+ {
+ aa.threshold = new GraphLine(annotation.threshold);
+ }
+ else
+ {
+ aa.threshold.value = thr;
+ }
+ }
+ }
+ }
+
+ protected boolean colorAlignmContaining(
+ AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
+ {
+
+ 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();
+
+ av.setGlobalColourScheme(acg);
+
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ 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());
+
+ }
+ else
+ {
+ sg.cs = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdItem);
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+ }
+
+ }
+ }
+ return false;
+ }
+
+ protected boolean markColumnsContaining(
+ AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
+ {
+ try
+ {
+ if (currentAnnotation != null)
+ {
+ 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);
+ }
+ }
+
+ return true;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ return false;
+ }
+ }
+
+ public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+ {
+ return currentAnnotation;
+ }
+
+ public void setCurrentAnnotation(
+ jalview.datamodel.AlignmentAnnotation currentAnnotation)
+ {
+ this.currentAnnotation = currentAnnotation;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff