X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=6ca0769f867fe0ffdd45b105f8a6661160a58afd;hb=364f1cf36d12a069be963ec0166c9170e8b6f365;hp=dc0a127a716fedcc899ae4a1b9644dee65c787cd;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index dc0a127..6ca0769 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; @@ -28,6 +29,7 @@ import jalview.io.JalviewFileChooser; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import jalview.ws.dbsources.das.api.jalviewSourceI; import java.awt.BorderLayout; @@ -52,6 +54,7 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; +import java.util.Arrays; import java.util.Hashtable; import java.util.Iterator; import java.util.List; @@ -87,7 +90,8 @@ import javax.swing.table.AbstractTableModel; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; -public class FeatureSettings extends JPanel +public class FeatureSettings extends JPanel implements + FeatureSettingsControllerI { DasSourceBrowser dassourceBrowser; @@ -122,7 +126,8 @@ public class FeatureSettings extends JPanel this.af = af; fr = af.getFeatureRenderer(); // allow transparency to be recovered - transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100)); + transparency.setMaximum(100 - (int) ((originalTransparency = fr + .getTransparency()) * 100)); try { @@ -132,15 +137,18 @@ public class FeatureSettings extends JPanel ex.printStackTrace(); } - table = new JTable() { + table = new JTable() + { @Override - public String getToolTipText(MouseEvent e) { - if (table.columnAtPoint(e.getPoint()) == 0) { + public String getToolTipText(MouseEvent e) + { + if (table.columnAtPoint(e.getPoint()) == 0) + { /* * Tooltip for feature name only */ - return JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.feature_settings_click_drag")); + return JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.feature_settings_click_drag")); } return null; } @@ -157,6 +165,7 @@ public class FeatureSettings extends JPanel table.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); @@ -184,38 +193,32 @@ public class FeatureSettings extends JPanel { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), table.getValueAt(selectedRow, 1), fr.getMinMax(), - evt.getX(), - evt.getY()); + evt.getX(), evt.getY()); } } }); table.addMouseMotionListener(new MouseMotionAdapter() { + @Override public void mouseDragged(MouseEvent evt) { int newRow = table.rowAtPoint(evt.getPoint()); if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { - Object[] temp = new Object[3]; - temp[0] = table.getValueAt(selectedRow, 0); - temp[1] = table.getValueAt(selectedRow, 1); - temp[2] = table.getValueAt(selectedRow, 2); - - table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); - table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); - table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); - - table.setValueAt(temp[0], newRow, 0); - table.setValueAt(temp[1], newRow, 1); - table.setValueAt(temp[2], newRow, 2); - + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + Object[] temp = data[selectedRow]; + data[selectedRow] = data[newRow]; + data[newRow] = temp; + updateFeatureRenderer(data); + table.repaint(); selectedRow = newRow; } } }); -// table.setToolTipText(JvSwingUtils.wrapTooltip(true, -// MessageManager.getString("label.feature_settings_click_drag"))); + // table.setToolTipText(JvSwingUtils.wrapTooltip(true, + // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); dassourceBrowser = new DasSourceBrowser(this); @@ -226,11 +229,12 @@ public class FeatureSettings extends JPanel fr.findAllFeatures(true); // display everything! } - setTableData(); + discoverAllFeatureData(); final PropertyChangeListener change; final FeatureSettings fs = this; fr.addPropertyChangeListener(change = new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (!fs.resettingTable && !fs.handlingUpdate) @@ -261,6 +265,7 @@ public class FeatureSettings extends JPanel frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -275,8 +280,7 @@ public class FeatureSettings extends JPanel final Object typeCol, final Hashtable minmax, int x, int y) { JPopupMenu men = new JPopupMenu(MessageManager.formatMessage( - "label.settings_for_param", new String[] - { type })); + "label.settings_for_param", new String[] { type })); JMenuItem scr = new JMenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); @@ -284,10 +288,11 @@ public class FeatureSettings extends JPanel scr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.af.avc.sortAlignmentByFeatureScore(new String[] - { type }); + me.af.avc.sortAlignmentByFeatureScore(Arrays + .asList(new String[] { type })); } }); @@ -296,10 +301,11 @@ public class FeatureSettings extends JPanel dens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.af.avc.sortAlignmentByFeatureDensity(new String[] - { type }); + me.af.avc.sortAlignmentByFeatureDensity(Arrays + .asList(new String[] { type })); } }); @@ -334,6 +340,7 @@ public class FeatureSettings extends JPanel { JColorChooser colorChooser; + @Override public void actionPerformed(ActionEvent e) { if (e.getSource() == mxcol) @@ -420,7 +427,8 @@ public class FeatureSettings extends JPanel */ Hashtable typeWidth = null; - synchronized public void setTableData() + @Override + synchronized public void discoverAllFeatureData() { Vector allFeatures = new Vector(); Vector allGroups = new Vector(); @@ -428,15 +436,13 @@ public class FeatureSettings extends JPanel String group; for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { - if (af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures() == null) + tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) + .getSequenceFeatures(); + if (tmpfeatures == null) { continue; } - tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); - int index = 0; while (index < tmpfeatures.length) { @@ -505,6 +511,7 @@ public class FeatureSettings extends JPanel check.setFont(new Font("Serif", Font.BOLD, 12)); check.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent evt) { fr.setGroupVisibility(check.getText(), check.isSelected()); @@ -514,8 +521,7 @@ public class FeatureSettings extends JPanel af.alignPanel.overviewPanel.updateOverviewImage(); } - resetTable(new String[] - { grp }); + resetTable(new String[] { grp }); } }); groupPanel.add(check); @@ -546,7 +552,7 @@ public class FeatureSettings extends JPanel { tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); + .getSequenceFeatures(); if (tmpfeatures == null) { continue; @@ -703,11 +709,13 @@ public class FeatureSettings extends JPanel void load() { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "fc" }, + new String[] { "Sequence Feature Colours" }, + "Sequence Feature Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.load_feature_colours")); + chooser.setDialogTitle(MessageManager + .getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); @@ -722,8 +730,7 @@ public class FeatureSettings extends JPanel file), "UTF-8"); jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours(); - jucs = jucs - .unmarshal(in); + jucs = jucs.unmarshal(in); for (int i = jucs.getColourCount() - 1; i >= 0; i--) { @@ -801,11 +808,13 @@ public class FeatureSettings extends JPanel void save() { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "fc" }, + new String[] { "Sequence Feature Colours" }, + "Sequence Feature Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_feature_colours")); + chooser.setDialogTitle(MessageManager + .getString("label.save_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -940,9 +949,9 @@ public class FeatureSettings extends JPanel } } if (sort) - { + { jalview.util.QuickSort.sort(width, data); - // update global priority order + // update global priority order } updateFeatureRenderer(data, false); @@ -965,10 +974,19 @@ public class FeatureSettings extends JPanel updateFeatureRenderer(data, true); } + /** + * Update the priority order of features; only repaint if this changed the + * order of visible features + * + * @param data + * @param visibleNew + */ private void updateFeatureRenderer(Object[][] data, boolean visibleNew) { - fr.setFeaturePriority(data, visibleNew); - af.alignPanel.paintAlignment(true); + if (fr.setFeaturePriority(data, visibleNew)) + { + af.alignPanel.paintAlignment(true); + } } int selectedRow = -1; @@ -1025,6 +1043,7 @@ public class FeatureSettings extends JPanel invert.setText(MessageManager.getString("label.invert_selection")); invert.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { invertSelection(); @@ -1034,6 +1053,7 @@ public class FeatureSettings extends JPanel optimizeOrder.setText(MessageManager.getString("label.optimise_order")); optimizeOrder.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { orderByAvWidth(); @@ -1044,6 +1064,7 @@ public class FeatureSettings extends JPanel .setText(MessageManager.getString("label.seq_sort_by_score")); sortByScore.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { af.avc.sortAlignmentByFeatureScore(null); @@ -1054,6 +1075,7 @@ public class FeatureSettings extends JPanel .getString("label.sequence_sort_by_density")); sortByDens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { af.avc.sortAlignmentByFeatureDensity(null); @@ -1063,6 +1085,23 @@ public class FeatureSettings extends JPanel help.setText(MessageManager.getString("action.help")); help.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + Help.showHelpWindow(HelpId.SequenceFeatureSettings); + } catch (HelpSetException e1) + { + e1.printStackTrace(); + } + } + }); + help.setFont(JvSwingUtils.getLabelFont()); + help.setText(MessageManager.getString("action.help")); + help.addActionListener(new ActionListener() + { + @Override public void actionPerformed(ActionEvent e) { try @@ -1078,6 +1117,7 @@ public class FeatureSettings extends JPanel cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fr.setTransparency(originalTransparency); @@ -1089,6 +1129,7 @@ public class FeatureSettings extends JPanel ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { close(); @@ -1098,6 +1139,7 @@ public class FeatureSettings extends JPanel loadColours.setText(MessageManager.getString("label.load_colours")); loadColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { load(); @@ -1107,6 +1149,7 @@ public class FeatureSettings extends JPanel saveColours.setText(MessageManager.getString("label.save_colours")); saveColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { save(); @@ -1114,6 +1157,7 @@ public class FeatureSettings extends JPanel }); transparency.addChangeListener(new ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { fr.setTransparency((100 - transparency.getValue()) / 100f); @@ -1127,6 +1171,7 @@ public class FeatureSettings extends JPanel fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); fetchDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fetchDAS_actionPerformed(e); @@ -1135,6 +1180,7 @@ public class FeatureSettings extends JPanel saveDAS.setText(MessageManager.getString("action.save_as_default")); saveDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { saveDAS_actionPerformed(e); @@ -1146,14 +1192,17 @@ public class FeatureSettings extends JPanel cancelDAS.setText(MessageManager.getString("action.cancel_fetch")); cancelDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cancelDAS_actionPerformed(e); } }); this.add(tabbedPane, java.awt.BorderLayout.CENTER); - tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane); - tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane); + tabbedPane.addTab(MessageManager.getString("label.feature_settings"), + settingsPane); + tabbedPane.addTab(MessageManager.getString("label.das_settings"), + dasSettingsPane); bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); transbuttons.add(optimizeOrder); transbuttons.add(invert); @@ -1198,7 +1247,7 @@ public class FeatureSettings extends JPanel { SequenceI[] dataset, seqs; int iSize; - AlignViewport vp = af.getViewport(); + AlignmentViewport vp = af.getViewport(); if (vp.getSelectionGroup() != null && vp.getSelectionGroup().getSize() > 0) { @@ -1283,6 +1332,7 @@ public class FeatureSettings extends JPanel Runnable fetcher = new Runnable() { + @Override public void run() { doDasFeatureFetch(dassources, true, false); @@ -1347,8 +1397,10 @@ public class FeatureSettings extends JPanel this.data = data; } - private String[] columnNames = - { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") }; + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.display") }; private Object[][] data; @@ -1362,6 +1414,7 @@ public class FeatureSettings extends JPanel this.data = data; } + @Override public int getColumnCount() { return columnNames.length; @@ -1372,31 +1425,37 @@ public class FeatureSettings extends JPanel return data[row]; } + @Override public int getRowCount() { return data.length; } + @Override public String getColumnName(int col) { return columnNames[col]; } + @Override public Object getValueAt(int row, int col) { return data[row][col]; } + @Override public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } + @Override public boolean isCellEditable(int row, int col) { return col == 0 ? false : true; } + @Override public void setValueAt(Object value, int row, int col) { data[row][col] = value; @@ -1421,6 +1480,7 @@ public class FeatureSettings extends JPanel setVerticalTextPosition(SwingConstants.CENTER); } + @Override public Component getTableCellRendererComponent(JTable table, Object color, boolean isSelected, boolean hasFocus, int row, int column) @@ -1586,16 +1646,19 @@ class FeatureIcon implements Icon } } + @Override public int getIconWidth() { return width; } + @Override public int getIconHeight() { return height; } + @Override public void paintIcon(Component c, Graphics g, int x, int y) { @@ -1676,6 +1739,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, /** * Handles events from the editor button and from the dialog's OK button. */ + @Override public void actionPerformed(ActionEvent e) { @@ -1721,6 +1785,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, } // Implement the one CellEditor method that AbstractCellEditor doesn't. + @Override public Object getCellEditorValue() { if (currentColor == null) @@ -1731,6 +1796,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, } // Implement the one method defined by TableCellEditor. + @Override public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column) {