label.normalise_logo = Normalise Logo
label.no_colour_selection_in_scheme = Please, make a colour selection before to apply colour scheme
label.no_colour_selection_warn = Error saving colour scheme
+label.select_by_annotation = Select By Annotation
+action.select_by_annotation = Select by annotation...
+label.threshold_filter = Threshold Filter
+action.hide = Hide
+action.select = Select
+label.alpha_helix = Alpha Helix
+label.beta_strand = Beta Strand
+label.turn = Turn
+label.select_all = Select All
+label.structures_filter = Structures Filter
+label.search_filter = Search Filter
+label.display_name = Display Label
+label.description = Description
*/
package jalview.controller;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.List;
-
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureRenderer;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
public class AlignViewController implements AlignViewControllerI
{
(int) (Math.random() * 255), (int) (Math.random() * 255));
col = col.brighter();
for (SequenceI sq : gps[g].getSequences(null))
+ {
viewport.setSequenceColour(sq, col);
+ }
}
return true;
}
}
}
+ public static boolean filterAnnotations(Annotation[] annotations,
+ AnnotationFilterParameter filterParams, ColumnSelection cs)
+ {
+ cs.revealAllHiddenColumns();
+ cs.clear();
+ int count = 0;
+ do
+ {
+ if (annotations[count] != null)
+ {
+
+ boolean itemMatched = false;
+
+ if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+ && annotations[count].value > filterParams
+ .getThresholdValue())
+ {
+ itemMatched = true;
+ }
+ if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+ && annotations[count].value < filterParams
+ .getThresholdValue())
+ {
+ itemMatched = true;
+ }
+
+ if (filterParams.isFilterAlphaHelix()
+ && annotations[count].secondaryStructure == 'H')
+ {
+ itemMatched = true;
+ }
+
+ if (filterParams.isFilterBetaSheet()
+ && annotations[count].secondaryStructure == 'E')
+ {
+ itemMatched = true;
+ }
+
+ if (filterParams.isFilterTurn()
+ && annotations[count].secondaryStructure == 'S')
+ {
+ itemMatched = true;
+ }
+
+ 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;
+ }
+ }
+
+ if (itemMatched)
+ {
+ cs.addElement(count);
+ }
+ }
+ count++;
+ } while (count < annotations.length);
+ return false;
+ }
+
@Override
public void sortAlignmentByFeatureDensity(String[] typ)
{
}
@Override
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColumnChooser(viewport, alignPanel);
+ }
+
+ @Override
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
new RNAHelicesColourChooser(viewport, alignPanel);
Color textColour = Color.black;
Color textColour2 = Color.white;
+ private boolean rightAlignIds = false;
+
+ private AnnotationColumnChooser annotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
*
{
this.showAutocalculatedAbove = showAutocalculatedAbove;
}
+
+
+ public boolean isShowAnnotation()
+ {
+ return super.isShowAnnotation();
+ }
+
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
+
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
+ {
+ return annotationColumnSelectionState;
+ }
+
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = 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)
- {
- reset();
- // ensure all original colouring is propagated to listeners.
- ap.paintAlignment(true);
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
}
- void reset()
+ public void valueChanged(boolean updateAllAnnotation)
{
- av.setGlobalColourScheme(oldcs);
- if (av.getAlignment().getGroups() != null)
+ if (slider.isEnabled())
{
-
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ if (currentColours.isSelected()
+ && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
- sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
+ updateView();
}
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false);
}
}
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void threshold_actionPerformed(ActionEvent e)
+ public JComboBox<String> getThreshold()
{
- changeColour();
+ return threshold;
}
- public void thresholdValue_actionPerformed(ActionEvent e)
+ public void setThreshold(JComboBox<String> threshold)
{
- try
- {
- float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
- } catch (NumberFormatException ex)
- {
- }
+ this.threshold = threshold;
}
- public void valueChanged(boolean updateAllAnnotation)
+ public void currentColours_actionPerformed(ActionEvent e)
{
- if (currentColours.isSelected()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ if (currentColours.isSelected())
{
- changeColour();
+ reset();
}
- currentAnnotation.threshold.value = slider.getValue() / 1000f;
- propagateSeqAssociatedThreshold(updateAllAnnotation);
- ap.paintAlignment(false);
+ maxColour.setEnabled(!currentColours.isSelected());
+ minColour.setEnabled(!currentColours.isSelected());
+ updateView();
}
- private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+ @Override
+ public void updateView()
{
- 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.controller.AlignViewController;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+
+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;
+import java.awt.event.ItemListener;
+import java.util.Iterator;
+
+import javax.swing.ButtonGroup;
+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.JRadioButton;
+import javax.swing.JTextField;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+
+import net.miginfocom.swing.MigLayout;
+
+@SuppressWarnings("serial")
+public class AnnotationColumnChooser extends AnnotationRowFilter implements
+ ItemListener
+{
+
+ private JComboBox<String> annotations;
+
+ private JButton ok = new JButton();
+
+ private JButton cancel = new JButton();
+
+ 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 StructureFilterPanel currentStructureFilterPanel;
+
+ private SearchPanel currentSearchPanel;
+
+ private SearchPanel gSearchPanel;
+
+ private SearchPanel ngSearchPanel;
+
+ private FurtherActionPanel currentFurtherActionPanel;
+
+ private FurtherActionPanel gFurtherActionPanel;
+
+ private FurtherActionPanel ngFurtherActionPanel;
+
+ public static final int ACTION_OPTION_SELECT = 1;
+
+ public static int ACTION_OPTION_HIDE = 2;
+
+ public static String NO_GRAPH_VIEW = "0";
+
+ public static String GRAPH_VIEW = "1";
+
+ private int actionOption = ACTION_OPTION_SELECT;
+
+ private ColumnSelection oldColumnSelection;
+
+ public AnnotationColumnChooser()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
+ {
+ super(av, ap);
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.select_by_annotation"), 520,
+ 215);
+
+ addSliderChangeListener();
+ addSliderMouseListeners();
+
+ if (av.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+ setOldColumnSelection(av.getColumnSelection());
+ adjusting = true;
+
+ setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
+ populateThresholdComboBox(threshold);
+
+ // restore Object state from the previous session if one exists
+ if (av.getAnnotationColumnSelectionState() != null)
+ {
+ currentSearchPanel = av.getAnnotationColumnSelectionState()
+ .getCurrentSearchPanel();
+ currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+ .getCurrentStructureFilterPanel();
+ annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
+ .getAnnotations().getSelectedIndex());
+ threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
+ .getThreshold().getSelectedIndex());
+ actionOption = av.getAnnotationColumnSelectionState()
+ .getActionOption();
+ }
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ }
+ adjusting = false;
+
+ updateView();
+ frame.invalidate();
+ frame.pack();
+ }
+
+ 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);
+ }
+ });
+
+ annotations.addItemListener(this);
+ threshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ threshold_actionPerformed(e);
+ }
+ });
+
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
+ 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));
+
+ thresholdPanel.setBorder(new TitledBorder(MessageManager
+ .getString("label.threshold_filter")));
+ thresholdPanel.setBackground(Color.white);
+ thresholdPanel.setFont(JvSwingUtils.getLabelFont());
+ thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+
+ actionPanel.setBackground(Color.white);
+ actionPanel.setFont(JvSwingUtils.getLabelFont());
+
+ graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ graphFilterView.setBackground(Color.white);
+
+ noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ noGraphFilterView.setBackground(Color.white);
+
+ annotationComboBoxPanel.setBackground(Color.white);
+ annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
+
+ gSearchPanel = new SearchPanel(this);
+ ngSearchPanel = new SearchPanel(this);
+ gFurtherActionPanel = new FurtherActionPanel(this);
+ ngFurtherActionPanel = new FurtherActionPanel(this);
+ gStructureFilterPanel = new StructureFilterPanel(this);
+ ngStructureFilterPanel = new StructureFilterPanel(this);
+
+ thresholdPanel.add(getThreshold());
+ thresholdPanel.add(thresholdValue, "wrap");
+ thresholdPanel.add(slider, "grow, span, wrap");
+
+ actionPanel.add(ok);
+ actionPanel.add(cancel);
+
+ graphFilterView.add(gSearchPanel, "grow, span, wrap");
+ graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
+ graphFilterView.add(thresholdPanel, "grow, span, wrap");
+ graphFilterView.add(gFurtherActionPanel);
+
+ noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
+ noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
+ noGraphFilterView.add(ngFurtherActionPanel);
+
+ annotationComboBoxPanel.add(getAnnotations());
+ switchableViewsPanel.add(noGraphFilterView,
+ AnnotationColumnChooser.NO_GRAPH_VIEW);
+ switchableViewsPanel.add(graphFilterView,
+ AnnotationColumnChooser.GRAPH_VIEW);
+
+ this.setLayout(borderLayout1);
+ this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
+ this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
+ this.add(actionPanel, java.awt.BorderLayout.SOUTH);
+
+ selectedAnnotationChanged();
+ this.validate();
+ }
+
+ @SuppressWarnings("unchecked")
+ public void reset()
+ {
+ if (this.getOldColumnSelection() != null)
+ {
+ av.getColumnSelection().clear();
+
+ if (av.getAnnotationColumnSelectionState() != null)
+ {
+ ColumnSelection oldSelection = av
+ .getAnnotationColumnSelectionState()
+ .getOldColumnSelection();
+ if (oldSelection != null && oldSelection.getHiddenColumns() != null
+ && !oldSelection.getHiddenColumns().isEmpty())
+ {
+ for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
+ .iterator(); itr.hasNext();)
+ {
+ int positions[] = itr.next();
+ av.hideColumns(positions[0], positions[1]);
+ }
+ }
+ av.setColumnSelection(oldSelection);
+ }
+ ap.paintAlignment(true);
+ }
+
+ }
+
+ public void valueChanged(boolean updateAllAnnotation)
+ {
+ if (slider.isEnabled())
+ {
+ 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()
+ {
+ // Check if combobox is still adjusting
+ if (adjusting)
+ {
+ return;
+ }
+
+ AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
+
+ setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]]);
+
+ int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
+ .getSelectedIndex());
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ // build filter params
+ }
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ if (getCurrentAnnotation().threshold == null)
+ {
+ getCurrentAnnotation()
+ .setThreshold(
+ new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
+ }
+
+ 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;
+
+ // build filter params
+ filterParams
+ .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
+ if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+ {
+ filterParams
+ .setThresholdValue(getCurrentAnnotation().threshold.value);
+
+ if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
+ {
+ filterParams
+ .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
+ }
+ else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
+ {
+ filterParams
+ .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
+ }
+ }
+ }
+
+ if (currentStructureFilterPanel != null)
+ {
+ if (currentStructureFilterPanel.alphaHelix.isSelected())
+ {
+ filterParams.setFilterAlphaHelix(true);
+ }
+ if (currentStructureFilterPanel.betaStrand.isSelected())
+ {
+ filterParams.setFilterBetaSheet(true);
+ }
+ if (currentStructureFilterPanel.turn.isSelected())
+ {
+ filterParams.setFilterTurn(true);
+ }
+ }
+
+ if (currentSearchPanel != null)
+ {
+
+ if (!currentSearchPanel.searchBox.getText().isEmpty())
+ {
+ currentSearchPanel.description.setEnabled(true);
+ currentSearchPanel.displayName.setEnabled(true);
+ filterParams.setRegexString(currentSearchPanel.searchBox.getText());
+ if (currentSearchPanel.displayName.isSelected())
+ {
+ filterParams
+ .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+ }
+ if (currentSearchPanel.description.isSelected())
+ {
+ filterParams
+ .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+ }
+ }
+ else
+ {
+ currentSearchPanel.description.setEnabled(false);
+ currentSearchPanel.displayName.setEnabled(false);
+ }
+ }
+
+ AlignViewController.filterAnnotations(
+ getCurrentAnnotation().annotations, filterParams,
+ av.getColumnSelection());
+
+ av.showAllHiddenColumns();
+ if (getActionOption() == ACTION_OPTION_HIDE)
+ {
+ av.hideSelectedColumns();
+ }
+
+ filterParams = null;
+ av.setAnnotationColumnSelectionState(this);
+ ap.paintAlignment(true);
+ }
+
+ public ColumnSelection getOldColumnSelection()
+ {
+ return oldColumnSelection;
+ }
+
+ public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+ {
+ if (currentColumnSelection != null)
+ {
+ this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+ }
+ }
+
+ public FurtherActionPanel getCurrentFutherActionPanel()
+ {
+ return currentFurtherActionPanel;
+ }
+
+ public void setCurrentFutherActionPanel(
+ FurtherActionPanel currentFutherActionPanel)
+ {
+ this.currentFurtherActionPanel = currentFutherActionPanel;
+ }
+
+ public SearchPanel getCurrentSearchPanel()
+ {
+ return currentSearchPanel;
+ }
+
+ public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
+ {
+ this.currentSearchPanel = currentSearchPanel;
+ }
+
+ public int getActionOption()
+ {
+ return actionOption;
+ }
+
+ public void setActionOption(int actionOption)
+ {
+ this.actionOption = actionOption;
+ }
+
+ public StructureFilterPanel getCurrentStructureFilterPanel()
+ {
+ return currentStructureFilterPanel;
+ }
+
+ public void setCurrentStructureFilterPanel(
+ StructureFilterPanel currentStructureFilterPanel)
+ {
+ this.currentStructureFilterPanel = currentStructureFilterPanel;
+ }
+
+ public void select_action(ActionEvent actionEvent)
+ {
+ JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
+ if (radioButton.isSelected())
+ {
+ setActionOption(ACTION_OPTION_SELECT);
+ updateView();
+ }
+ }
+
+ public void hide_action(ActionEvent actionEvent)
+ {
+ JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
+ if (radioButton.isSelected())
+ {
+ setActionOption(ACTION_OPTION_HIDE);
+ updateView();
+ }
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ selectedAnnotationChanged();
+ }
+
+ public void selectedAnnotationChanged()
+ {
+ String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
+ if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
+ {
+ currentView = AnnotationColumnChooser.GRAPH_VIEW;
+ }
+
+ gSearchPanel.syncState();
+ gFurtherActionPanel.syncState();
+ gStructureFilterPanel.syncState();
+
+ ngSearchPanel.syncState();
+ ngFurtherActionPanel.syncState();
+ ngStructureFilterPanel.syncState();
+
+ switchableViewsLayout.show(switchableViewsPanel, currentView);
+ updateView();
+ }
+
+
+ public class FurtherActionPanel extends JPanel
+ {
+ private AnnotationColumnChooser aColChooser;
+
+ private JRadioButton hideOption = new JRadioButton();
+
+ private JRadioButton selectOption = new JRadioButton();
+
+ private ButtonGroup optionsGroup = new ButtonGroup();
+
+ public FurtherActionPanel(AnnotationColumnChooser aColChooser)
+ {
+ this.aColChooser = aColChooser;
+ JvSwingUtils.jvInitComponent(selectOption, "action.select");
+ selectOption.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ selectRadioAction(actionEvent);
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(hideOption, "action.hide");
+ hideOption.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ hideRadioAction(actionEvent);
+ }
+ });
+
+ optionsGroup.add(selectOption);
+ optionsGroup.add(hideOption);
+ optionsGroup.setSelected(selectOption.getModel(), true);
+
+ JvSwingUtils.jvInitComponent(this);
+ syncState();
+
+ this.add(selectOption);
+ this.add(hideOption);
+ }
+
+ public void selectRadioAction(ActionEvent actionEvent)
+ {
+ aColChooser.setCurrentFutherActionPanel(this);
+ aColChooser.select_action(actionEvent);
+ }
+
+ public void hideRadioAction(ActionEvent actionEvent)
+ {
+ aColChooser.setCurrentFutherActionPanel(this);
+ aColChooser.hide_action(actionEvent);
+ }
+
+ public void syncState()
+ {
+ if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
+ {
+ this.optionsGroup.setSelected(this.hideOption.getModel(),
+ true);
+ }
+ else
+ {
+ this.optionsGroup.setSelected(this.selectOption.getModel(), true);
+ }
+ }
+ }
+
+ public class StructureFilterPanel extends JPanel
+ {
+ private AnnotationColumnChooser aColChooser;
+
+ private JCheckBox alphaHelix = new JCheckBox();
+
+ private JCheckBox betaStrand = new JCheckBox();
+
+ private JCheckBox turn = new JCheckBox();
+
+ private JCheckBox all = new JCheckBox();
+
+ public StructureFilterPanel(AnnotationColumnChooser aColChooser)
+ {
+ this.aColChooser = aColChooser;
+
+ JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
+ alphaHelix.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ alphaHelix_actionPerformed();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
+ betaStrand.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ betaStrand_actionPerformed();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(turn, "label.turn");
+ turn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ turn_actionPerformed();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(all, "label.select_all");
+ all.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ all_actionPerformed();
+ }
+ });
+
+ this.setBorder(new TitledBorder(MessageManager
+ .getString("label.structures_filter")));
+ JvSwingUtils.jvInitComponent(this);
+
+ this.add(all);
+ this.add(alphaHelix);
+ this.add(betaStrand);
+ this.add(turn);
+ }
+
+ public void alphaHelix_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void betaStrand_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void turn_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void all_actionPerformed()
+ {
+ if (all.isSelected())
+ {
+ alphaHelix.setSelected(true);
+ betaStrand.setSelected(true);
+ turn.setSelected(true);
+ }
+ else
+ {
+ alphaHelix.setSelected(false);
+ betaStrand.setSelected(false);
+ turn.setSelected(false);
+ }
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void updateSelectAllState()
+ {
+ if (alphaHelix.isSelected() && betaStrand.isSelected()
+ && turn.isSelected())
+ {
+ all.setSelected(true);
+ }
+ else
+ {
+ all.setSelected(false);
+ }
+ }
+
+ public void syncState()
+ {
+ StructureFilterPanel sfp = aColChooser
+ .getCurrentStructureFilterPanel();
+ if (sfp != null)
+ {
+ alphaHelix.setSelected(sfp.alphaHelix.isSelected());
+ betaStrand.setSelected(sfp.betaStrand.isSelected());
+ turn.setSelected(sfp.turn.isSelected());
+ if (sfp.all.isSelected())
+ {
+ all.setSelected(true);
+ alphaHelix.setSelected(true);
+ betaStrand.setSelected(true);
+ turn.setSelected(true);
+ }
+ }
+
+ }
+ }
+
+ public class SearchPanel extends JPanel
+ {
+ private AnnotationColumnChooser aColChooser;
+
+ private JCheckBox displayName = new JCheckBox();
+
+ private JCheckBox description = new JCheckBox();
+
+ private JTextField searchBox = new JTextField(10);
+
+ public SearchPanel(AnnotationColumnChooser aColChooser)
+ {
+
+ this.aColChooser = aColChooser;
+ JvSwingUtils.jvInitComponent(this);
+ this.setBorder(new TitledBorder(MessageManager
+ .getString("label.search_filter")));
+
+ JvSwingUtils.jvInitComponent(searchBox);
+ searchBox.getDocument().addDocumentListener(
+ new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(displayName, "label.display_name");
+ displayName.setEnabled(false);
+ displayName.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ displayNameCheckboxAction();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(description, "label.description");
+ description.setEnabled(false);
+ description.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ discriptionCheckboxAction();
+ }
+ });
+
+ syncState();
+ this.add(searchBox);
+ this.add(displayName);
+ this.add(description);
+ }
+
+ public void displayNameCheckboxAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void discriptionCheckboxAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void searchStringAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void syncState()
+ {
+ SearchPanel sp = aColChooser.getCurrentSearchPanel();
+ if (sp != null)
+ {
+ description.setEnabled(sp.description.isEnabled());
+ description.setSelected(sp.description.isSelected());
+
+ displayName.setEnabled(sp.displayName.isEnabled());
+ displayName.setSelected(sp.displayName.isSelected());
+
+ searchBox.setText(sp.searchBox.getText());
+ }
+ }
+ }
+
+}
--- /dev/null
+package jalview.gui;
+
+import jalview.datamodel.AlignmentAnnotation;
+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
+{
+ 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()
+ {
+
+ }
+
+ 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++));
+ }
+ }
+ }
+ 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;
+ }
+
+
+ public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+ {
+ return currentAnnotation;
+ }
+
+ public void setCurrentAnnotation(
+ jalview.datamodel.AlignmentAnnotation currentAnnotation)
+ {
+ this.currentAnnotation = currentAnnotation;
+ }
+
+ public abstract void valueChanged(boolean updateAllAnnotation);
+
+ public abstract void updateView();
+
+ public abstract void reset();
+}
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.Color;
import java.awt.Font;
import java.awt.Rectangle;
import java.awt.event.ActionListener;
+import javax.swing.AbstractButton;
import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JLabel;
}
}
+ public static void jvInitComponent(AbstractButton comp, String i18nString)
+ {
+ setColorAndFont(comp);
+ if (i18nString != null && !i18nString.isEmpty())
+ {
+ comp.setText(MessageManager.getString(i18nString));
+ }
+ }
+
+ public static void jvInitComponent(JComponent comp)
+ {
+ setColorAndFont(comp);
+ }
+
+ // public static void jvInitComponent(JComponent comp, String name){
+ // setColorAndFont(comp);
+ // comp.setText(MessageManager.getString("label.select_all"));
+ // }
+
+ private static void setColorAndFont(JComponent comp)
+ {
+ comp.setBackground(Color.white);
+ comp.setFont(JvSwingUtils.getLabelFont());
+ }
}
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
/**
* DOCUMENT ME!
*
res = av.getColumnSelection().adjustForHiddenColumns(res);
reveal = null;
+ if (av.getColumnSelection().getHiddenColumns() != null)
+ {
for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
{
int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
}
}
-
+ }
repaint();
}
}
gg.drawLine(
- (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
y + 2,
- (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
y + (fm.getDescent() * 2));
}
else
{
gg.drawLine(
- (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
y + fm.getDescent(),
- (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
y + (fm.getDescent() * 2));
}
}
{
gg.setColor(Color.blue);
int res;
- if (av.getShowHiddenMarkers())
+ if (av.getShowHiddenMarkers()
+ && av.getColumnSelection().getHiddenColumns() != null)
{
for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
.size(); i++)
* that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "jvp", "sto,stk", "jar", PhylipFile.FILE_EXT };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "sto,stk", PhylipFile.FILE_EXT, "jvp" };
/**
* List of writable formats by the application. Order must correspond with the
* WRITABLE_EXTENSIONS list of formats.
*/
public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "STH", "Jalview", PhylipFile.FILE_DESC };
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+ PhylipFile.FILE_DESC, "Jalview" };
/**
* List of readable format file extensions by application in order
JMenuItem annotationColour = new JMenuItem();
+ JMenuItem annotationColumn = new JMenuItem();
+
protected JMenuItem rnahelicesColour = new JMenuItem();
JMenuItem associatedData = new JMenuItem();
}
});
+ annotationColumn.setText(MessageManager
+ .getString("action.select_by_annotation"));
+ annotationColumn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColumn_actionPerformed(e);
+ }
+ });
+
rnahelicesColour.setText(MessageManager
.getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
calculateMenu.add(expandAlignment);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
}
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
--- /dev/null
+package jalview.viewmodel.annotationfilter;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class AnnotationFilterParameter
+{
+ public enum ThresholdType
+ {
+ NO_THRESHOLD, BELOW_THRESHOLD, ABOVE_THRESHOLD;
+ }
+
+ public enum SearchableAnnotationField
+ {
+ DISPLAY_STRING, DESCRIPTION;
+ }
+ private ThresholdType thresholdType;
+
+ private float thresholdValue;
+
+ private boolean filterAlphaHelix = false;
+
+ private boolean filterBetaSheet = false;
+
+ private boolean filterTurn = false;
+
+ private String regexString;
+
+ private List<SearchableAnnotationField> regexSearchFields = new ArrayList<SearchableAnnotationField>();
+
+ public ThresholdType getThresholdType()
+ {
+ return thresholdType;
+ }
+
+ public void setThresholdType(ThresholdType thresholdType)
+ {
+ this.thresholdType = thresholdType;
+ }
+
+ public float getThresholdValue()
+ {
+ return thresholdValue;
+ }
+
+ public void setThresholdValue(float thresholdValue)
+ {
+ this.thresholdValue = thresholdValue;
+ }
+
+ public String getRegexString()
+ {
+ return regexString;
+ }
+
+ public void setRegexString(String regexString)
+ {
+ this.regexString = regexString;
+ }
+
+ public List<SearchableAnnotationField> getRegexSearchFields()
+ {
+ return regexSearchFields;
+ }
+
+ public void addRegexSearchField(SearchableAnnotationField regexSearchField)
+ {
+ this.regexSearchFields.add(regexSearchField);
+ }
+
+ public boolean isFilterAlphaHelix()
+ {
+ return filterAlphaHelix;
+ }
+
+ public void setFilterAlphaHelix(boolean alphaHelix)
+ {
+ this.filterAlphaHelix = alphaHelix;
+ }
+
+ public boolean isFilterBetaSheet()
+ {
+ return filterBetaSheet;
+ }
+
+ public void setFilterBetaSheet(boolean betaSheet)
+ {
+ this.filterBetaSheet = betaSheet;
+ }
+
+ public boolean isFilterTurn()
+ {
+ return filterTurn;
+ }
+
+ public void setFilterTurn(boolean turn)
+ {
+ this.filterTurn = turn;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff