*/
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 jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.util.Hashtable;
import java.util.Vector;
-import jalview.bin.Cache;
-import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
import javax.swing.BorderFactory;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JColorChooser;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
@SuppressWarnings("serial")
public class AnnotationColourChooser extends AnnotationRowFilter
{
+ private static final int ONETHOUSAND = 1000;
- ColourSchemeI oldcs;
-
- Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
-
- /**
- * enabled if the user is dragging the slider - try to keep updates to a
- * minimun
- */
+ private ColourSchemeI oldcs;
- JComboBox<String> annotations;
+ private JButton defColours;
- JButton defColours = new JButton();
+ private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
- JPanel jPanel1 = new JPanel();
+ private JCheckBox currentColours = new JCheckBox();
- JPanel jPanel2 = new JPanel();
+ private JPanel minColour = new JPanel();
- BorderLayout borderLayout1 = new BorderLayout();
+ private JPanel maxColour = new JPanel();
- private JComboBox<String> threshold = new JComboBox<String>();
+ private JCheckBox thresholdIsMin = new JCheckBox();
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
thresholdValue.setText("" + acg.getAnnotationThreshold());
}
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- }
+ jbInit();
adjusting = false;
updateView();
frame.pack();
}
- public AnnotationColourChooser()
+ @Override
+ protected void jbInit()
{
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ super.jbInit();
- private void jbInit() throws Exception
- {
minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
}
}
});
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed();
- }
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed();
- }
- });
+
+ defColours = new JButton();
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
defColours.setToolTipText(MessageManager
}
});
- annotations.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed();
- }
- });
- getThreshold().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed();
- }
- });
- 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));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
currentColours.setFont(JvSwingUtils.getLabelFont());
currentColours.setOpaque(false);
currentColours.setText(MessageManager
}
});
- this.setLayout(borderLayout1);
+ this.setLayout(new BorderLayout());
+ JPanel jPanel1 = new JPanel();
+ JPanel jPanel2 = new JPanel();
jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
}
}
- public JComboBox<String> getThreshold()
- {
- return threshold;
- }
-
- public void setThreshold(JComboBox<String> threshold)
- {
- this.threshold = threshold;
- }
-
public void currentColours_actionPerformed()
{
if (currentColours.isSelected())
if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
{
adjusting = true;
- float range = getCurrentAnnotation().graphMax * 1000
- - getCurrentAnnotation().graphMin * 1000;
+ float range = getCurrentAnnotation().graphMax * ONETHOUSAND
+ - getCurrentAnnotation().graphMin * ONETHOUSAND;
- slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
- slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+ slider.setMinimum((int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
+ slider.setMaximum((int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
+ slider.setValue((int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
ap.paintAlignment(true);
}
+ protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption)
+ {
+
+ 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());
+
+ if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+ {
+ acg.setPredefinedColours(true);
+ }
+
+ acg.setThresholdIsMinMax(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(currentAnn, sg.cs,
+ selectedThresholdOption);
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+ }
+ else
+ {
+ sg.cs = new AnnotationColourGradient(currentAnn,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdOption);
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+ }
+ }
+ }
+ return false;
+ }
+
}
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Color;
-import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
public class AnnotationColumnChooser extends AnnotationRowFilter implements
ItemListener
{
-
- private JComboBox<String> annotations;
-
- private JPanel actionPanel = new JPanel();
-
- private JPanel thresholdPanel = new JPanel();
-
private JPanel switchableViewsPanel = new JPanel(new CardLayout());
- private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
- .getLayout());
-
- private JPanel noGraphFilterView = new JPanel();
-
- private JPanel graphFilterView = new JPanel();
-
private JPanel annotationComboBoxPanel = new JPanel();
- private BorderLayout borderLayout1 = new BorderLayout();
-
- private JComboBox<String> threshold = new JComboBox<String>();
-
private StructureFilterPanel gStructureFilterPanel;
private StructureFilterPanel ngStructureFilterPanel;
private ColumnSelection oldColumnSelection;
- public AnnotationColumnChooser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
super(av, ap);
frame.pack();
}
- private void jbInit() throws Exception
+ @Override
+ protected void jbInit()
{
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed();
- }
- });
-
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed();
- }
- });
-
- annotations.addItemListener(this);
- 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));
+ super.jbInit();
+ JPanel thresholdPanel = new JPanel();
thresholdPanel.setBorder(new TitledBorder(MessageManager
.getString("label.threshold_filter")));
thresholdPanel.setBackground(Color.white);
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ JPanel actionPanel = new JPanel();
actionPanel.setBackground(Color.white);
actionPanel.setFont(JvSwingUtils.getLabelFont());
+ JPanel graphFilterView = new JPanel();
graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
graphFilterView.setBackground(Color.white);
+ JPanel noGraphFilterView = new JPanel();
noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
noGraphFilterView.setBackground(Color.white);
switchableViewsPanel.add(graphFilterView,
AnnotationColumnChooser.GRAPH_VIEW);
- this.setLayout(borderLayout1);
+ this.setLayout(new BorderLayout());
this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
this.add(actionPanel, java.awt.BorderLayout.SOUTH);
this.validate();
}
- public void updateThresholdPanelToolTip()
+ protected void updateThresholdPanelToolTip()
{
thresholdValue.setToolTipText("");
slider.setToolTipText("");
}
@Override
- public void reset()
+ protected void reset()
{
if (this.getOldColumnSelection() != null)
{
}
}
- 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()
{
selectedAnnotationChanged();
}
+ @Override
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
ngFurtherActionPanel.syncState();
ngStructureFilterPanel.syncState();
+ CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
+ .getLayout();
switchableViewsLayout.show(switchableViewsPanel, currentView);
updateView();
}
*/
package jalview.gui;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+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 jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.util.MessageManager;
-
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
protected int[] annmap;
- /*
- * map from annotation to its menu item display label
- * - so we know which item to pre-select on restore
- */
- private Map<AlignmentAnnotation, String> annotationLabels;
-
- 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 JSlider slider = new JSlider();
protected JTextField thresholdValue = new JTextField(20);
*/
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 boolean enableSeqAss = false;
+
+ 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()
- {
-
- }
-
/**
* Builds and returns a list of menu items (display text) for choice of
* annotation. Also builds maps between annotations, their positions in the
}
}
- 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
{
}
}
- public void thresholdIsMin_actionPerformed()
+ 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"));
}
* Rebuilds the drop-down list of annotations to choose from when the 'per
* sequence only' checkbox is checked or unchecked.
*
- * @param annotations
+ * @param anns
*/
- protected void seqAssociated_actionPerformed(JComboBox<String> annotations)
+ protected void seqAssociated_actionPerformed(JComboBox<String> anns)
{
adjusting = true;
- String cursel = (String) annotations.getSelectedItem();
+ String cursel = (String) anns.getSelectedItem();
boolean isvalid = false, isseqs = seqAssociated.isSelected();
- annotations.removeAllItems();
+ 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);
}
}
}
}
}
- protected boolean colorAlignmentContaining(
- AlignmentAnnotation currentAnn, int selectedThresholdOption)
+ protected AlignmentAnnotation getCurrentAnnotation()
+ {
+ return currentAnnotation;
+ }
+
+ protected void setCurrentAnnotation(AlignmentAnnotation currentAnnotation)
{
+ this.currentAnnotation = 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 abstract void valueChanged(boolean updateAllAnnotation);
- if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
- {
- acg.setPredefinedColours(true);
- }
+ protected abstract void updateView();
- acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+ protected abstract void reset();
- av.setGlobalColourScheme(acg);
+ protected String getAnnotationMenuLabel(AlignmentAnnotation ann)
+ {
+ return annotationLabels.get(ann);
+ }
- if (av.getAlignment().getGroups() != null)
+ 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());
- }
- else
- {
- sg.cs = new AnnotationColourGradient(currentAnn,
- minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdOption);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
- }
+ 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 AlignmentAnnotation getCurrentAnnotation()
+ public JComboBox<String> getThreshold()
{
- return currentAnnotation;
+ return threshold;
}
- public void setCurrentAnnotation(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 abstract void reset();
+ public JComboBox<String> getAnnotations()
+ {
+ return annotations;
+ }
- protected String getAnnotationMenuLabel(AlignmentAnnotation ann)
+ public void setAnnotations(JComboBox<String> anns)
{
- return annotationLabels.get(ann);
+ this.annotations = anns;
}
}
git://source.jalview.org / jalview.git / commitdiff