X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=d5bc7d10dfa739c6f7d10ccfd3f8eacc6dbc2584;hb=7362a6f5c2b2c02b14042a9c0a060e399429f6d9;hp=87e2d7869558147a7b91ba6389bb2a658b33cf94;hpb=f73031db2e38bfe6e3f1cd42f91b0f9b0130071a;p=jalview.git
diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 87e2d78..d5bc7d1 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -1,43 +1,92 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.gui;
+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.JButton;
+import javax.swing.ButtonGroup;
+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
+public class AnnotationColumnChooser extends AnnotationRowFilter implements
+ ItemListener
{
+ private JPanel switchableViewsPanel = new JPanel(new CardLayout());
- private ColumnSelection oldColumnSelection;
+ private JPanel annotationComboBoxPanel = new JPanel();
+
+ private StructureFilterPanel gStructureFilterPanel;
+
+ private StructureFilterPanel ngStructureFilterPanel;
+
+ private StructureFilterPanel currentStructureFilterPanel;
+
+ private SearchPanel currentSearchPanel;
+
+ private SearchPanel gSearchPanel;
+
+ private SearchPanel ngSearchPanel;
- private JComboBox annotations;
+ private FurtherActionPanel currentFurtherActionPanel;
- JButton ok = new JButton();
+ private FurtherActionPanel gFurtherActionPanel;
- JButton cancel = new JButton();
+ private FurtherActionPanel ngFurtherActionPanel;
- JPanel jPanel1 = new JPanel();
+ public static final int ACTION_OPTION_SELECT = 1;
- JPanel jPanel2 = new JPanel();
+ public static int ACTION_OPTION_HIDE = 2;
- BorderLayout borderLayout1 = new BorderLayout();
+ public static String NO_GRAPH_VIEW = "0";
- private JComboBox threshold = new JComboBox();
+ public static String GRAPH_VIEW = "1";
+ private int actionOption = ACTION_OPTION_SELECT;
+
+ private ColumnSelection oldColumnSelection;
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
@@ -45,7 +94,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.select_by_annotation"), 520,
+ 215);
addSliderChangeListener();
addSliderMouseListeners();
@@ -57,18 +108,25 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
setOldColumnSelection(av.getColumnSelection());
adjusting = true;
- setAnnotations(new JComboBox(
- getAnnotationItems(seqAssociated.isSelected())));
+ setAnnotations(new JComboBox(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
-
- if (av.getCurrentAnnotationColumnSelectionState() != null)
+ AnnotationColumnChooser lastChooser = av
+ .getAnnotationColumnSelectionState();
+ // restore Object state from the previous session if one exists
+ if (lastChooser != null)
{
- annotations.setSelectedIndex(av
- .getCurrentAnnotationColumnSelectionState().getAnnotations()
- .getSelectedIndex());
- threshold.setSelectedIndex(av
- .getCurrentAnnotationColumnSelectionState().getThreshold()
- .getSelectedIndex());
+ currentSearchPanel = lastChooser
+ .getCurrentSearchPanel();
+ currentStructureFilterPanel = lastChooser
+ .getCurrentStructureFilterPanel();
+ annotations.setSelectedIndex(lastChooser
+ .getAnnotations().getSelectedIndex());
+ threshold.setSelectedIndex(lastChooser
+ .getThreshold().getSelectedIndex());
+ actionOption = lastChooser
+ .getActionOption();
+ percentThreshold.setSelected(lastChooser.percentThreshold
+ .isSelected());
}
try
@@ -84,226 +142,701 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
frame.pack();
}
+ @Override
+ protected void jbInit()
+ {
+ 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]", "[][]"));
+
+ percentThreshold.setBackground(Color.white);
+ percentThreshold.setFont(JvSwingUtils.getLabelFont());
+
+ 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);
+
+ 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(percentThreshold, "wrap");
+ thresholdPanel.add(slider, "grow");
+ thresholdPanel.add(thresholdValue, "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(new BorderLayout());
+ this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
+ this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
+ this.add(actionPanel, java.awt.BorderLayout.SOUTH);
+
+ selectedAnnotationChanged();
+ updateThresholdPanelToolTip();
+ this.validate();
+ }
- public AnnotationColumnChooser()
+ protected void updateThresholdPanelToolTip()
{
- try
- {
- jbInit();
- } catch (Exception ex)
+ thresholdValue.setToolTipText("");
+ slider.setToolTipText("");
+
+ String defaultTtip = MessageManager
+ .getString("info.change_threshold_mode_to_enable");
+
+ String thresh = getThreshold().getSelectedItem().toString();
+ if (thresh.equalsIgnoreCase("No Threshold"))
{
- ex.printStackTrace();
+ thresholdValue.setToolTipText(defaultTtip);
+ slider.setToolTipText(defaultTtip);
}
}
- private void jbInit() throws Exception
+ @Override
+ protected void reset()
{
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
+ if (this.getOldColumnSelection() != null)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ av.getColumnSelection().clear();
+
+ if (av.getAnnotationColumnSelectionState() != null)
{
- ok_actionPerformed(e);
+ ColumnSelection oldSelection = av
+ .getAnnotationColumnSelectionState()
+ .getOldColumnSelection();
+ if (oldSelection != null && oldSelection.getHiddenColumns() != null
+ && !oldSelection.getHiddenColumns().isEmpty())
+ {
+ for (Iterator itr = oldSelection.getHiddenColumns()
+ .iterator(); itr.hasNext();)
+ {
+ int positions[] = itr.next();
+ av.hideColumns(positions[0], positions[1]);
+ }
+ }
+ av.setColumnSelection(oldSelection);
}
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
+ ap.paintAlignment(true);
+ }
+
+ }
+
+ @Override
+ public void valueChanged(boolean updateAllAnnotation)
+ {
+ if (slider.isEnabled())
+ {
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ updateView();
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false);
+ }
+ }
+
+ @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);
+ percentThreshold.setEnabled(true);
+
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ percentThreshold.setEnabled(false);
+ // build filter params
+ }
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ if (getCurrentAnnotation().threshold == null)
{
- cancel_actionPerformed(e);
+ getCurrentAnnotation()
+ .setThreshold(
+ new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
- });
- getAnnotations().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
+ 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));
+
+ setThresholdValueText();
+
+ 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)
{
- annotations_actionPerformed(e);
+ 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);
+ }
}
- });
- getThreshold().addActionListener(new ActionListener()
+ }
+
+ updateThresholdPanelToolTip();
+ if (currentStructureFilterPanel != null)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ if (currentStructureFilterPanel.alphaHelix.isSelected())
{
- threshold_actionPerformed(e);
+ filterParams.setFilterAlphaHelix(true);
}
- });
- thresholdValue.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
+ if (currentStructureFilterPanel.betaStrand.isSelected())
{
- thresholdValue_actionPerformed(e);
+ filterParams.setFilterBetaSheet(true);
}
- });
- 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)
+ if (currentStructureFilterPanel.turn.isSelected())
{
- thresholdIsMin_actionPerformed(actionEvent);
+ filterParams.setFilterTurn(true);
}
- });
- seqAssociated.setBackground(Color.white);
- seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager
- .getString("label.per_sequence_only"));
- seqAssociated.addActionListener(new ActionListener()
+ }
+
+ if (currentSearchPanel != null)
{
- @Override
- public void actionPerformed(ActionEvent arg0)
+ if (!currentSearchPanel.searchBox.getText().isEmpty())
{
- seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+ 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);
+ }
}
- });
-
- 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();
+ else
+ {
+ currentSearchPanel.description.setEnabled(false);
+ currentSearchPanel.displayName.setEnabled(false);
+ }
+ }
+
+ av.getColumnSelection().filterAnnotations(
+ getCurrentAnnotation().annotations, filterParams);
+
+ av.showAllHiddenColumns();
+ if (getActionOption() == ACTION_OPTION_HIDE)
+ {
+ av.hideSelectedColumns();
+ }
+
+ filterParams = null;
+ av.setAnnotationColumnSelectionState(this);
+ ap.paintAlignment(true);
}
- public void reset()
+ public ColumnSelection getOldColumnSelection()
{
- av.getColumnSelection().clear();
- av.setColumnSelection(this.getOldColumnSelection());
+ return oldColumnSelection;
}
- public void valueChanged(boolean updateAllAnnotation)
+ public void setOldColumnSelection(ColumnSelection currentColumnSelection)
{
- getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
- updateView();
- propagateSeqAssociatedThreshold(updateAllAnnotation,
- getCurrentAnnotation());
- ap.paintAlignment(false);
+ if (currentColumnSelection != null)
+ {
+ this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+ }
}
- public JComboBox getThreshold()
+ public FurtherActionPanel getCurrentFutherActionPanel()
{
- return threshold;
+ return currentFurtherActionPanel;
}
- public void setThreshold(JComboBox threshold)
+ public void setCurrentFutherActionPanel(
+ FurtherActionPanel currentFutherActionPanel)
{
- this.threshold = threshold;
+ this.currentFurtherActionPanel = currentFutherActionPanel;
}
- public JComboBox getAnnotations()
+ public SearchPanel getCurrentSearchPanel()
{
- return annotations;
+ return currentSearchPanel;
}
- public void setAnnotations(JComboBox annotations)
+ public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
{
- this.annotations = annotations;
+ 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 updateView()
+ public void itemStateChanged(ItemEvent e)
{
- changeColumnSelection();
+ selectedAnnotationChanged();
}
- void changeColumnSelection()
+
+ @Override
+ public void selectedAnnotationChanged()
{
- // Check if combobox is still adjusting
- if (adjusting)
+ String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
+ if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
{
- return;
+ currentView = AnnotationColumnChooser.GRAPH_VIEW;
}
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
- .getSelectedIndex()]]);
+ gSearchPanel.syncState();
+ gFurtherActionPanel.syncState();
+ gStructureFilterPanel.syncState();
+ ngSearchPanel.syncState();
+ ngFurtherActionPanel.syncState();
+ ngStructureFilterPanel.syncState();
- int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
- .getSelectedIndex());
+ CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
+ .getLayout();
+ switchableViewsLayout.show(switchableViewsPanel, currentView);
+ updateView();
+ }
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(true);
+ public class FurtherActionPanel extends JPanel
+ {
+ private AnnotationColumnChooser aColChooser;
- if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
+ private JRadioButton hideOption = new JRadioButton();
+
+ private JRadioButton selectOption = new JRadioButton();
+
+ private ButtonGroup optionsGroup = new ButtonGroup();
+
+ public FurtherActionPanel(AnnotationColumnChooser aColChooser)
{
- slider.setEnabled(false);
- thresholdValue.setEnabled(false);
- thresholdValue.setText("");
- thresholdIsMin.setEnabled(false);
+ 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);
}
- else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
- && getCurrentAnnotation().threshold == null)
+
+ public void selectRadioAction(ActionEvent actionEvent)
{
- getCurrentAnnotation()
- .setThreshold(new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ aColChooser.setCurrentFutherActionPanel(this);
+ aColChooser.select_action(actionEvent);
}
- if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+ public void hideRadioAction(ActionEvent actionEvent)
{
- 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;
+ aColChooser.setCurrentFutherActionPanel(this);
+ aColChooser.hide_action(actionEvent);
}
- markColumnsContaining(getCurrentAnnotation(), selectedThresholdItem);
- av.setCurrentAnnotationColumnSelectionState(this);
- ap.alignmentChanged();
- ap.paintAlignment(true);
+ 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 ColumnSelection getOldColumnSelection()
+ public class StructureFilterPanel extends JPanel
{
- return oldColumnSelection;
+ 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 void setOldColumnSelection(ColumnSelection currentColumnSelection)
+ public class SearchPanel extends JPanel
{
- if (currentColumnSelection != null)
+ 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.setToolTipText(MessageManager
+ .getString("info.enter_search_text_here"));
+ 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.label");
+ 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()
{
- this.oldColumnSelection = new ColumnSelection();
- this.oldColumnSelection.setElementsFrom(currentColumnSelection);
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void searchStringAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ updateSearchPanelToolTips();
+ }
+
+ 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());
+ }
+ updateSearchPanelToolTips();
+ }
+
+ public void updateSearchPanelToolTips()
+ {
+ String defaultTtip = MessageManager
+ .getString("info.enter_search_text_to_enable");
+ String labelTtip = MessageManager.formatMessage(
+ "info.search_in_annotation_label", annotations
+ .getSelectedItem().toString());
+ String descTtip = MessageManager.formatMessage(
+ "info.search_in_annotation_description", annotations
+ .getSelectedItem().toString());
+ displayName.setToolTipText(displayName.isEnabled() ? labelTtip
+ : defaultTtip);
+ description.setToolTipText(description.isEnabled() ? descTtip
+ : defaultTtip);
}
}
+
}