X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGStructureChooser.java;h=e4e73d18f4038f857af017e5f8f11a3141c73155;hb=6849cc1cb983a45b4b8fd840f5ffc7d31ca80f33;hp=efc3062a6c7f3291ba52fc12bf31a9c5b416334b;hpb=3bbaa9775e08ab53f42fc4589935ab63bd05d388;p=jalview.git diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java index efc3062..e4e73d1 100644 --- a/src/jalview/jbgui/GStructureChooser.java +++ b/src/jalview/jbgui/GStructureChooser.java @@ -22,16 +22,19 @@ 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.JvSummaryTable; import jalview.gui.JvSwingUtils; -import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource; import jalview.util.MessageManager; -import jalview.ws.dbsources.PDBRestClient; -import jalview.ws.dbsources.PDBRestClient.PDBDocField; import java.awt.BorderLayout; import java.awt.CardLayout; +import java.awt.Component; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.GridLayout; @@ -43,6 +46,8 @@ 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; @@ -51,15 +56,19 @@ 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; @SuppressWarnings("serial") /** @@ -96,6 +105,8 @@ public abstract class GStructureChooser extends JPanel implements protected JButton btn_pdbFromFile = new JButton(); + protected JButton btn_runPhyre2Prediction = new JButton(); + protected JTextField txt_search = new JTextField(14); private JPanel pnl_actions = new JPanel(); @@ -106,6 +117,10 @@ public abstract class GStructureChooser extends JPanel implements private JPanel pnl_fileChooser = new JPanel(new FlowLayout()); + private JPanel pnl_phyre2Prediction = new JPanel(new FlowLayout()); + + private JPanel pnl_phyre2PredictionBL = new JPanel(new BorderLayout()); + private JPanel pnl_idInputBL = new JPanel(new BorderLayout()); private JPanel pnl_fileChooserBL = new JPanel(new BorderLayout()); @@ -145,6 +160,8 @@ public abstract class GStructureChooser extends JPanel implements protected JLabel lbl_fromFileStatus = new JLabel(errorImage); + protected AssciateSeqPanel phyre2InputAssSeqPanel = new AssciateSeqPanel(); + protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel(); protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel(); @@ -157,44 +174,35 @@ public abstract class GStructureChooser extends JPanel implements protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB"; - protected JTable tbl_summary = new JTable() - { - @Override - public String getToolTipText(MouseEvent evt) - { - String toolTipText = null; - java.awt.Point pnt = evt.getPoint(); - int rowIndex = rowAtPoint(pnt); - int colIndex = columnAtPoint(pnt); - - try - { - 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; - } - }; - - protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary); + protected static final String VIEWS_PHYRE2_PREDICTION = "VIEWS_PHYRE2_PREDICTION"; protected JTable tbl_local_pdb = new JTable(); protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb); - private JTabbedPane pnl_filter = new JTabbedPane(); + protected JTabbedPane pnl_filter = new JTabbedPane(); - private PDBDocFieldPreferences pdbDocFieldPrefs = new PDBDocFieldPreferences( - PreferenceSource.STRUCTURE_CHOOSER); + protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences( + PreferenceSource.STRUCTURE_CHOOSER, + PDBFTSRestClient.getInstance()); - protected PDBDocField[] previousWantedFields; + protected FTSDataColumnI[] previousWantedFields; + + protected static Map tempUserPrefs = new HashMap(); + + private JTable tbl_summary = new JvSummaryTable(tempUserPrefs); + + + protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary); + + JPanel phyreResultPanel = new JPanel(new BorderLayout()); + + protected static Map tempPrefsForPhyre = new HashMap(); + + private JTable tbl_phyre2_summary = new JvSummaryTable(tempPrefsForPhyre); + + protected JScrollPane scrl_phyre2Summary = new JScrollPane( + tbl_phyre2_summary); public GStructureChooser() { @@ -215,8 +223,13 @@ public abstract class GStructureChooser extends JPanel implements * * @throws Exception */ + @SuppressWarnings("unchecked") 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() @@ -316,6 +329,7 @@ public abstract class GStructureChooser extends JPanel implements } } evt.consume(); + break; default: return; } @@ -350,7 +364,7 @@ public abstract class GStructureChooser extends JPanel implements @Override public void actionPerformed(ActionEvent e) { - mainFrame.dispose(); + closeAction(pnl_filter.getHeight()); } }); btn_cancel.addKeyListener(new KeyAdapter() @@ -360,7 +374,7 @@ public abstract class GStructureChooser extends JPanel implements { if (evt.getKeyCode() == KeyEvent.VK_ENTER) { - mainFrame.dispose(); + closeAction(pnl_filter.getHeight()); } } }); @@ -388,11 +402,93 @@ public abstract class GStructureChooser extends JPanel implements } }); - scrl_foundStructures.setPreferredSize(new Dimension(500, 300)); - scrl_foundStructures - .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); + btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12)); + tbl_phyre2_summary.setAutoCreateRowSorter(true); + tbl_phyre2_summary.getTableHeader().setReorderingAllowed(false); + + tbl_phyre2_summary.addMouseListener(new MouseAdapter() + { + @Override + public void mouseClicked(MouseEvent e) + { + validateSelections(); + } + + @Override + public void mouseReleased(MouseEvent e) + { + validateSelections(); + } + }); + tbl_phyre2_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_view.isEnabled()) + { + ok_ActionPerformed(); + } + break; + case KeyEvent.VK_TAB: // tab key + if (evt.isShiftDown()) + { + cmb_filterOption.requestFocus(); + } + else + { + if (btn_view.isEnabled()) + { + btn_view.requestFocus(); + } + else + { + btn_cancel.requestFocus(); + } + } + evt.consume(); + break; + default: + return; + } + } + }); - scrl_localPDB.setPreferredSize(new Dimension(500, 300)); + String btn_runPhyre2Prediction_title = MessageManager + .getString("label.run_phyre2_prediction"); + btn_runPhyre2Prediction + .setText(btn_runPhyre2Prediction_title + " "); + btn_runPhyre2Prediction + .addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + predict3DModelWithPhyre2(); + } + }); + btn_runPhyre2Prediction.addKeyListener(new KeyAdapter() + { + @Override + public void keyPressed(KeyEvent evt) + { + if (evt.getKeyCode() == KeyEvent.VK_ENTER) + { + predict3DModelWithPhyre2(); + } + } + }); + + scrl_foundStructures.setPreferredSize(new Dimension(width, height)); + + scrl_localPDB.setPreferredSize(new Dimension(width, height)); scrl_localPDB .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); @@ -400,9 +496,8 @@ public abstract class GStructureChooser extends JPanel implements chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12)); chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12)); chk_rememberSettings.setVisible(false); - - txt_search.setToolTipText(MessageManager - .getString("label.enter_pdb_id")); + txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.enter_pdb_id"))); cmb_filterOption.setToolTipText(MessageManager .getString("info.select_filter_option")); txt_search.getDocument().addDocumentListener(new DocumentListener() @@ -427,6 +522,19 @@ public abstract class GStructureChooser extends JPanel implements }); 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); pnl_actions.add(chk_rememberSettings); @@ -444,6 +552,17 @@ public abstract class GStructureChooser extends JPanel implements pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH); pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER); + scrl_phyre2Summary.setPreferredSize(new Dimension(width, height)); + scrl_phyre2Summary + .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); + + phyreResultPanel.add(pnl_phyre2Prediction, BorderLayout.NORTH); + phyreResultPanel.add(scrl_phyre2Summary, BorderLayout.CENTER); + + pnl_phyre2Prediction.add(btn_runPhyre2Prediction); + pnl_phyre2PredictionBL.add(phyre2InputAssSeqPanel, BorderLayout.NORTH); + pnl_phyre2PredictionBL.add(phyreResultPanel, BorderLayout.CENTER); + pnl_idInput.add(txt_search); pnl_idInput.add(lbl_pdbManualFetchStatus); pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH); @@ -469,9 +588,9 @@ public abstract class GStructureChooser extends JPanel implements btn_cancel.setEnabled(false); btn_view.setVisible(false); btn_cancel.setVisible(false); - previousWantedFields = PDBDocFieldPreferences + previousWantedFields = pdbDocFieldPrefs .getStructureSummaryFields().toArray( - new PDBRestClient.PDBDocField[0]); + new FTSDataColumnI[0]); } if (sourceTabbedPane.getTitleAt(index) .equals(foundStructureSummary)) @@ -489,7 +608,7 @@ public abstract class GStructureChooser extends JPanel implements } }; pnl_filter.addChangeListener(changeListener); - pnl_filter.setPreferredSize(new Dimension(500, 300)); + pnl_filter.setPreferredSize(new Dimension(width, height)); pnl_filter.add(foundStructureSummary, scrl_foundStructures); pnl_filter.add(configureCols, pdbDocFieldPrefs); @@ -499,6 +618,8 @@ public abstract class GStructureChooser extends JPanel implements pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID); pnl_switchableViews.add(pnl_filter, VIEWS_FILTER); pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB); + pnl_switchableViews + .add(pnl_phyre2PredictionBL, VIEWS_PHYRE2_PREDICTION); this.setLayout(mainLayout); this.add(pnl_main, java.awt.BorderLayout.NORTH); @@ -510,10 +631,35 @@ public abstract class GStructureChooser extends JPanel implements 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); - Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400); + 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) + { + tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth()); + tempUserPrefs.put("structureChooser.height", + pnl_filter.getHeight() - 76); + tempUserPrefs.put("structureChooser.x", mainFrame.getX()); + tempUserPrefs.put("structureChooser.y", mainFrame.getY()); + mainFrame.dispose(); } public boolean wantedFieldsUpdated() @@ -523,9 +669,10 @@ public abstract class GStructureChooser extends JPanel implements return true; } - return Arrays.equals(PDBDocFieldPreferences.getStructureSummaryFields() - .toArray(new PDBRestClient.PDBDocField[0]), - previousWantedFields) ? false : true; + FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs + .getStructureSummaryFields().toArray(new FTSDataColumnI[0]); + return Arrays.equals(currentWantedFields, previousWantedFields) ? false + : true; } @@ -552,11 +699,15 @@ public abstract class GStructureChooser extends JPanel implements private String view; - public FilterOption(String name, String value, String view) + private boolean addSeparatorAfter; + + 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() @@ -594,6 +745,16 @@ public abstract class GStructureChooser extends JPanel implements { return this.name; } + + public boolean isAddSeparatorAfter() + { + return addSeparatorAfter; + } + + public void setAddSeparatorAfter(boolean addSeparatorAfter) + { + this.addSeparatorAfter = addSeparatorAfter; + } } /** @@ -699,16 +860,64 @@ public abstract class GStructureChooser extends JPanel implements } } + public JTable getResultTable() + { + return tbl_summary; + } + public JComboBox getCmbFilterOption() { return cmb_filterOption; } - protected abstract void stateChanged(ItemEvent e); - protected abstract void updateCurrentView(); + public JTable getPhyreResultTable() + { + return tbl_phyre2_summary; + } - protected abstract void populateFilterComboBox(); + 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 ok_ActionPerformed(); @@ -724,4 +933,7 @@ public abstract class GStructureChooser extends JPanel implements public abstract void tabRefresh(); public abstract void validateSelections(); -} + + public abstract void predict3DModelWithPhyre2(); + +} \ No newline at end of file