/* * 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.jbgui; import jalview.datamodel.SequenceI; import jalview.fts.api.FTSDataColumnI; import jalview.fts.core.FTSDataColumnPreferences; import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource; import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; import jalview.gui.JvSwingUtils; import jalview.gui.StructureViewer; import jalview.util.MessageManager; import java.awt.BorderLayout; import java.awt.CardLayout; import java.awt.Component; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.Font; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.Arrays; import java.util.HashMap; import java.util.Map; import javax.swing.ImageIcon; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JList; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JSeparator; import javax.swing.JTabbedPane; import javax.swing.JTable; import javax.swing.JTextField; import javax.swing.ListCellRenderer; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; import javax.swing.event.InternalFrameEvent; import javax.swing.table.TableColumn; import net.miginfocom.swing.MigLayout; @SuppressWarnings("serial") /** * GUI layout for structure chooser * * @author tcnofoegbu * */ public abstract class GStructureChooser extends JPanel implements ItemListener { private static final Font VERDANA_12 = new Font("Verdana", 0, 12); protected static final String VIEWS_FILTER = "VIEWS_FILTER"; protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE"; protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID"; /* * 'cached' structure view */ protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB"; protected JPanel statusPanel = new JPanel(); public JLabel statusBar = new JLabel(); protected String frameTitle = MessageManager .getString("label.structure_chooser"); protected JInternalFrame mainFrame = new JInternalFrame(frameTitle); protected JComboBox cmb_filterOption = new JComboBox<>(); protected AlignmentPanel ap; protected StringBuilder errorWarning = new StringBuilder(); protected JButton btn_add; protected JButton btn_newView; protected JButton btn_pdbFromFile = new JButton(); protected JCheckBox chk_superpose = new JCheckBox( MessageManager.getString("label.superpose_structures")); protected JTextField txt_search = new JTextField(14); protected JPanel pnl_switchableViews = new JPanel(new CardLayout()); protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews .getLayout()); protected JCheckBox chk_invertFilter = new JCheckBox( MessageManager.getString("label.invert")); protected ImageIcon loadingImage = new ImageIcon( getClass().getResource("/images/loading.gif")); protected ImageIcon goodImage = new ImageIcon( getClass().getResource("/images/good.png")); protected ImageIcon errorImage = new ImageIcon( getClass().getResource("/images/error.png")); protected ImageIcon warningImage = new ImageIcon( getClass().getResource("/images/warning.gif")); protected JLabel lbl_loading = new JLabel(loadingImage); protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage); protected JLabel lbl_fromFileStatus = new JLabel(errorImage); protected AssociateSeqPanel idInputAssSeqPanel = new AssociateSeqPanel(); protected AssociateSeqPanel fileChooserAssSeqPanel = new AssociateSeqPanel(); protected JComboBox targetView = new JComboBox<>(); protected JTable tbl_local_pdb = new JTable(); protected JTabbedPane pnl_filter = new JTabbedPane(); protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences( PreferenceSource.STRUCTURE_CHOOSER, PDBFTSRestClient.getInstance()); protected FTSDataColumnI[] previousWantedFields; protected static Map tempUserPrefs = new HashMap<>(); private JTable tbl_summary = new JTable() { private boolean inLayout; @Override public boolean getScrollableTracksViewportWidth() { return hasExcessWidth(); } @Override public void doLayout() { if (hasExcessWidth()) { autoResizeMode = AUTO_RESIZE_SUBSEQUENT_COLUMNS; } inLayout = true; super.doLayout(); inLayout = false; autoResizeMode = AUTO_RESIZE_OFF; } protected boolean hasExcessWidth() { return getPreferredSize().width < getParent().getWidth(); } @Override public void columnMarginChanged(ChangeEvent e) { if (isEditing()) { removeEditor(); } TableColumn resizingColumn = getTableHeader().getResizingColumn(); // Need to do this here, before the parent's // layout manager calls getPreferredSize(). if (resizingColumn != null && autoResizeMode == AUTO_RESIZE_OFF && !inLayout) { resizingColumn.setPreferredWidth(resizingColumn.getWidth()); String colHeader = resizingColumn.getHeaderValue().toString(); tempUserPrefs.put(colHeader, resizingColumn.getWidth()); } resizeAndRepaint(); } @Override public String getToolTipText(MouseEvent evt) { String toolTipText = null; java.awt.Point pnt = evt.getPoint(); int rowIndex = rowAtPoint(pnt); int colIndex = columnAtPoint(pnt); try { if (getValueAt(rowIndex, colIndex) == null) { return null; } toolTipText = getValueAt(rowIndex, colIndex).toString(); } catch (Exception e) { // e.printStackTrace(); } toolTipText = (toolTipText == null ? null : (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(true, "\"" + toolTipText.subSequence(0, 500) + "...\"") : JvSwingUtils.wrapTooltip(true, toolTipText))); return toolTipText; } }; public GStructureChooser() { try { jbInit(); mainFrame.setVisible(false); mainFrame.invalidate(); mainFrame.pack(); } catch (Exception e) { e.printStackTrace(); } } /** * Initializes the GUI default properties * * @throws Exception */ private void jbInit() throws Exception { Integer width = tempUserPrefs.get("structureChooser.width") == null ? 800 : tempUserPrefs.get("structureChooser.width"); Integer height = tempUserPrefs.get("structureChooser.height") == null ? 400 : tempUserPrefs.get("structureChooser.height"); tbl_summary.setAutoCreateRowSorter(true); tbl_summary.getTableHeader().setReorderingAllowed(false); tbl_summary.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { validateSelections(); } @Override public void mouseReleased(MouseEvent e) { validateSelections(); } }); tbl_summary.addKeyListener(new KeyAdapter() { @Override public void keyPressed(KeyEvent evt) { validateSelections(); switch (evt.getKeyCode()) { case KeyEvent.VK_ESCAPE: // escape key mainFrame.dispose(); break; case KeyEvent.VK_ENTER: // enter key if (btn_add.isEnabled()) { add_ActionPerformed(); } break; case KeyEvent.VK_TAB: // tab key if (evt.isShiftDown()) { pnl_filter.requestFocus(); } else { btn_add.requestFocus(); } evt.consume(); break; default: return; } } }); JButton btn_cancel = new JButton( MessageManager.getString("action.cancel")); btn_cancel.setFont(VERDANA_12); btn_cancel.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { closeAction(pnl_filter.getHeight()); } }); btn_cancel.addKeyListener(new KeyAdapter() { @Override public void keyPressed(KeyEvent evt) { if (evt.getKeyCode() == KeyEvent.VK_ENTER) { closeAction(pnl_filter.getHeight()); } } }); tbl_local_pdb.setAutoCreateRowSorter(true); tbl_local_pdb.getTableHeader().setReorderingAllowed(false); tbl_local_pdb.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { validateSelections(); } @Override public void mouseReleased(MouseEvent e) { validateSelections(); } }); tbl_local_pdb.addKeyListener(new KeyAdapter() { @Override public void keyPressed(KeyEvent evt) { validateSelections(); switch (evt.getKeyCode()) { case KeyEvent.VK_ESCAPE: // escape key mainFrame.dispose(); break; case KeyEvent.VK_ENTER: // enter key if (btn_add.isEnabled()) { add_ActionPerformed(); } break; case KeyEvent.VK_TAB: // tab key if (evt.isShiftDown()) { cmb_filterOption.requestFocus(); } else { if (btn_add.isEnabled()) { btn_add.requestFocus(); } else { btn_cancel.requestFocus(); } } evt.consume(); break; default: return; } } }); btn_newView = new JButton(MessageManager.getString("action.new_view")); btn_newView.setFont(VERDANA_12); btn_newView.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { newView_ActionPerformed(); } }); btn_newView.addKeyListener(new KeyAdapter() { @Override public void keyPressed(KeyEvent evt) { if (evt.getKeyCode() == KeyEvent.VK_ENTER) { newView_ActionPerformed(); } } }); btn_add = new JButton(MessageManager.getString("action.add")); btn_add.setFont(VERDANA_12); btn_add.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { add_ActionPerformed(); } }); btn_add.addKeyListener(new KeyAdapter() { @Override public void keyPressed(KeyEvent evt) { if (evt.getKeyCode() == KeyEvent.VK_ENTER) { add_ActionPerformed(); } } }); btn_pdbFromFile.setFont(VERDANA_12); String btn_title = MessageManager.getString("label.select_pdb_file"); btn_pdbFromFile.setText(btn_title + " "); btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { pdbFromFile_actionPerformed(); } }); btn_pdbFromFile.addKeyListener(new KeyAdapter() { @Override public void keyPressed(KeyEvent evt) { if (evt.getKeyCode() == KeyEvent.VK_ENTER) { pdbFromFile_actionPerformed(); } } }); JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary); scrl_foundStructures.setPreferredSize(new Dimension(width, height)); JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb); scrl_localPDB.setPreferredSize(new Dimension(width, height)); scrl_localPDB.setHorizontalScrollBarPolicy( JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); chk_invertFilter.setFont(VERDANA_12); txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.enter_pdb_id_tip"))); txt_search.getDocument().addDocumentListener(new DocumentListener() { @Override public void insertUpdate(DocumentEvent e) { txt_search_ActionPerformed(); } @Override public void removeUpdate(DocumentEvent e) { txt_search_ActionPerformed(); } @Override public void changedUpdate(DocumentEvent e) { txt_search_ActionPerformed(); } }); cmb_filterOption.setFont(VERDANA_12); cmb_filterOption.setToolTipText( MessageManager.getString("info.select_filter_option")); cmb_filterOption.addItemListener(this); // add CustomComboSeparatorsRenderer to filter option combo-box cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer( (ListCellRenderer) cmb_filterOption.getRenderer()) { @Override protected boolean addSeparatorAfter(JList list, FilterOption value, int index) { return value.isAddSeparatorAfter(); } }); chk_invertFilter.addItemListener(this); targetView.setVisible(false); JPanel actionsPanel = new JPanel(new MigLayout()); actionsPanel.add(targetView, "left"); actionsPanel.add(btn_add, "wrap"); actionsPanel.add(chk_superpose, "left"); actionsPanel.add(btn_newView); actionsPanel.add(btn_cancel, "right"); JPanel pnl_main = new JPanel(); pnl_main.add(cmb_filterOption); pnl_main.add(lbl_loading); pnl_main.add(chk_invertFilter); lbl_loading.setVisible(false); JPanel pnl_fileChooser = new JPanel(new FlowLayout()); pnl_fileChooser.add(btn_pdbFromFile); pnl_fileChooser.add(lbl_fromFileStatus); JPanel pnl_fileChooserBL = new JPanel(new BorderLayout()); pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH); pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER); JPanel pnl_idInput = new JPanel(new FlowLayout()); pnl_idInput.add(txt_search); pnl_idInput.add(lbl_pdbManualFetchStatus); JPanel pnl_idInputBL = new JPanel(new BorderLayout()); pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH); pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER); final String foundStructureSummary = MessageManager .getString("label.found_structures_summary"); final String configureCols = MessageManager .getString("label.configure_displayed_columns"); ChangeListener changeListener = new ChangeListener() { @Override public void stateChanged(ChangeEvent changeEvent) { JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent .getSource(); int index = sourceTabbedPane.getSelectedIndex(); btn_add.setVisible(targetView.isVisible()); btn_newView.setVisible(true); btn_cancel.setVisible(true); if (sourceTabbedPane.getTitleAt(index).equals(configureCols)) { btn_add.setEnabled(false); btn_cancel.setEnabled(false); btn_add.setVisible(false); btn_newView.setEnabled(false); btn_cancel.setVisible(false); previousWantedFields = pdbDocFieldPrefs .getStructureSummaryFields() .toArray(new FTSDataColumnI[0]); } if (sourceTabbedPane.getTitleAt(index) .equals(foundStructureSummary)) { btn_cancel.setEnabled(true); if (wantedFieldsUpdated()) { tabRefresh(); } else { validateSelections(); } } } }; pnl_filter.addChangeListener(changeListener); pnl_filter.setPreferredSize(new Dimension(width, height)); pnl_filter.add(foundStructureSummary, scrl_foundStructures); pnl_filter.add(configureCols, pdbDocFieldPrefs); JPanel pnl_locPDB = new JPanel(new BorderLayout()); pnl_locPDB.add(scrl_localPDB); pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE); pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID); pnl_switchableViews.add(pnl_filter, VIEWS_FILTER); pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB); this.setLayout(new BorderLayout()); this.add(pnl_main, java.awt.BorderLayout.NORTH); this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER); // this.add(pnl_actions, java.awt.BorderLayout.SOUTH); statusPanel.setLayout(new GridLayout()); JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout()); pnl_actionsAndStatus.add(actionsPanel, BorderLayout.CENTER); pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH); statusPanel.add(statusBar, null); this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH); mainFrame.addInternalFrameListener( new javax.swing.event.InternalFrameAdapter() { @Override public void internalFrameClosing(InternalFrameEvent e) { closeAction(pnl_filter.getHeight()); } }); mainFrame.setVisible(true); mainFrame.setContentPane(this); mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Integer x = tempUserPrefs.get("structureChooser.x"); Integer y = tempUserPrefs.get("structureChooser.y"); if (x != null && y != null) { mainFrame.setLocation(x, y); } Desktop.addInternalFrame(mainFrame, frameTitle, width, height); } protected void closeAction(int preferredHeight) { // System.out.println(">>>>>>>>>> closing internal frame!!!"); // System.out.println("width : " + mainFrame.getWidth()); // System.out.println("heigh : " + mainFrame.getHeight()); // System.out.println("x : " + mainFrame.getX()); // System.out.println("y : " + mainFrame.getY()); tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth()); tempUserPrefs.put("structureChooser.height", preferredHeight); tempUserPrefs.put("structureChooser.x", mainFrame.getX()); tempUserPrefs.put("structureChooser.y", mainFrame.getY()); mainFrame.dispose(); } public boolean wantedFieldsUpdated() { if (previousWantedFields == null) { return true; } FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs .getStructureSummaryFields().toArray(new FTSDataColumnI[0]); return Arrays.equals(currentWantedFields, previousWantedFields) ? false : true; } @Override /** * Event listener for the 'filter' combo-box and 'invert' check-box */ public void itemStateChanged(ItemEvent e) { stateChanged(e); } /** * This inner class provides the data model for the structure filter combo-box * * @author tcnofoegbu * */ public class FilterOption { private String name; private String value; private String view; private boolean addSeparatorAfter; /** * Model for structure filter option * * @param name * - the name of the Option * @param value * - the value of the option * @param view * - the category of the filter option * @param addSeparatorAfter * - if true, a horizontal separator is rendered immediately after * this filter option, otherwise */ public FilterOption(String name, String value, String view, boolean addSeparatorAfter) { this.name = name; this.value = value; this.view = view; this.addSeparatorAfter = addSeparatorAfter; } public String getName() { return name; } public void setName(String name) { this.name = name; } public String getValue() { return value; } public void setValue(String value) { this.value = value; } public String getView() { return view; } public void setView(String view) { this.view = view; } @Override public String toString() { return this.name; } public boolean isAddSeparatorAfter() { return addSeparatorAfter; } public void setAddSeparatorAfter(boolean addSeparatorAfter) { this.addSeparatorAfter = addSeparatorAfter; } } /** * This inner class provides the provides the data model for associate * sequence combo-box - cmb_assSeq * * @author tcnofoegbu * */ public class AssociateSeqOptions { private SequenceI sequence; private String name; public AssociateSeqOptions(SequenceI seq) { this.sequence = seq; this.name = (seq.getName().length() >= 23) ? seq.getName().substring(0, 23) : seq.getName(); } public AssociateSeqOptions(String name, SequenceI seq) { this.name = name; this.sequence = seq; } @Override public String toString() { return name; } public String getName() { return name; } public void setName(String name) { this.name = name; } public SequenceI getSequence() { return sequence; } public void setSequence(SequenceI sequence) { this.sequence = sequence; } } /** * This inner class holds the Layout and configuration of the panel which * handles association of manually fetched structures to a unique sequence * when more than one sequence selection is made * * @author tcnofoegbu * */ public class AssociateSeqPanel extends JPanel implements ItemListener { private JComboBox cmb_assSeq = new JComboBox<>(); private JLabel lbl_associateSeq = new JLabel(); public AssociateSeqPanel() { this.setLayout(new FlowLayout()); this.add(cmb_assSeq); this.add(lbl_associateSeq); cmb_assSeq.setToolTipText( MessageManager.getString("info.associate_wit_sequence")); cmb_assSeq.addItemListener(this); } public void loadCmbAssSeq() { populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq); } public JComboBox getCmb_assSeq() { return cmb_assSeq; } public void setCmb_assSeq(JComboBox cmb_assSeq) { this.cmb_assSeq = cmb_assSeq; } @Override public void itemStateChanged(ItemEvent e) { if (e.getStateChange() == ItemEvent.SELECTED) { cmbAssSeqStateChanged(); } } } public JTable getResultTable() { return tbl_summary; } public JComboBox getCmbFilterOption() { return cmb_filterOption; } /** * Custom ListCellRenderer for adding a separator between different categories * of structure chooser filter option drop-down. * * @author tcnofoegbu * */ public abstract class CustomComboSeparatorsRenderer implements ListCellRenderer { private ListCellRenderer regent; private JPanel separatorPanel = new JPanel(new BorderLayout()); private JSeparator jSeparator = new JSeparator(); public CustomComboSeparatorsRenderer( ListCellRenderer listCellRenderer) { this.regent = listCellRenderer; } @Override public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) { Component comp = regent.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus); if (index != -1 && addSeparatorAfter(list, (FilterOption) value, index)) { separatorPanel.removeAll(); separatorPanel.add(comp, BorderLayout.CENTER); separatorPanel.add(jSeparator, BorderLayout.SOUTH); return separatorPanel; } else { return comp; } } protected abstract boolean addSeparatorAfter(JList list, FilterOption value, int index); } protected abstract void stateChanged(ItemEvent e); protected abstract void add_ActionPerformed(); protected abstract void newView_ActionPerformed(); protected abstract void pdbFromFile_actionPerformed(); protected abstract void txt_search_ActionPerformed(); protected abstract void populateCmbAssociateSeqOptions( JComboBox cmb_assSeq, JLabel lbl_associateSeq); protected abstract void cmbAssSeqStateChanged(); protected abstract void tabRefresh(); protected abstract void validateSelections(); }