X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=935d9c673836a6d16236cb5a7a3ceb227fb70f06;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=d30f5a066721148ae3827d51fd06deaa94eb3aa6;hpb=72b3f05a1157da32ada5aea139139996dddea219;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index d30f5a0..935d9c6 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 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,30 +20,77 @@ */ package jalview.gui; -import java.io.*; -import java.util.*; -import java.util.List; -import java.awt.*; -import java.awt.event.*; -import java.beans.PropertyChangeEvent; -import java.beans.PropertyChangeListener; - -import javax.swing.*; -import javax.swing.event.*; -import javax.swing.table.*; - -import jalview.analysis.AlignmentSorter; -import jalview.api.FeaturesDisplayedI; +import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; -import jalview.commands.OrderCommand; -import jalview.datamodel.*; -import jalview.io.*; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.gui.Help.HelpId; +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; -public class FeatureSettings extends JPanel +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Rectangle; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.event.MouseMotionAdapter; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +import java.util.Set; +import java.util.Vector; + +import javax.help.HelpSetException; +import javax.swing.AbstractCellEditor; +import javax.swing.BorderFactory; +import javax.swing.Icon; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JDialog; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.JScrollPane; +import javax.swing.JSlider; +import javax.swing.JTabbedPane; +import javax.swing.JTable; +import javax.swing.ListSelectionModel; +import javax.swing.SwingConstants; +import javax.swing.SwingUtilities; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; +import javax.swing.table.AbstractTableModel; +import javax.swing.table.TableCellEditor; +import javax.swing.table.TableCellRenderer; + +public class FeatureSettings extends JPanel implements + FeatureSettingsControllerI { DasSourceBrowser dassourceBrowser; @@ -78,7 +125,8 @@ 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 { @@ -88,7 +136,22 @@ 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) + { + /* + * Tooltip for feature name only + */ + return JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.feature_settings_click_drag")); + } + return null; + } + }; table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); table.setFont(new Font("Verdana", Font.PLAIN, 12)); table.setDefaultRenderer(Color.class, new ColorRenderer()); @@ -104,7 +167,7 @@ public class FeatureSettings extends JPanel public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); - if (evt.isPopupTrigger()) + if (SwingUtilities.isRightMouseButton(evt)) { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), table.getValueAt(selectedRow, 1), fr.getMinMax(), @@ -118,6 +181,19 @@ public class FeatureSettings extends JPanel (String) table.getValueAt(selectedRow, 0)); } } + + // isPopupTrigger fires on mouseReleased on Mac + @Override + public void mouseReleased(MouseEvent evt) + { + selectedRow = table.rowAtPoint(evt.getPoint()); + if (evt.isPopupTrigger()) + { + popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), + table.getValueAt(selectedRow, 1), fr.getMinMax(), + evt.getX(), evt.getY()); + } + } }); table.addMouseMotionListener(new MouseMotionAdapter() @@ -144,10 +220,8 @@ public class FeatureSettings extends JPanel } } }); - table.setToolTipText("" - + JvSwingUtils - .wrapTooltip("Click/drag feature types up or down to change render order.
Double click to select columns containing feature in alignment/current selection
Pressing Alt will select columns outside features rather than inside
Pressing Shift to modify current selection (rather than clear current selection)
Press CTRL or Command/Meta to toggle columns in/outside features
") - + ""); + // table.setToolTipText(JvSwingUtils.wrapTooltip(true, + // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); dassourceBrowser = new DasSourceBrowser(this); @@ -158,7 +232,7 @@ public class FeatureSettings extends JPanel fr.findAllFeatures(true); // display everything! } - setTableData(); + discoverAllFeatureData(); final PropertyChangeListener change; final FeatureSettings fs = this; fr.addPropertyChangeListener(change = new PropertyChangeListener() @@ -207,8 +281,7 @@ 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); @@ -218,8 +291,7 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent e) { - me.af.avc.sortAlignmentByFeatureScore(new String[] - { type }); + me.af.avc.sortAlignmentByFeatureScore(new String[] { type }); } }); @@ -230,8 +302,7 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent e) { - me.af.avc.sortAlignmentByFeatureDensity(new String[] - { type }); + me.af.avc.sortAlignmentByFeatureDensity(new String[] { type }); } }); @@ -352,7 +423,8 @@ 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(); @@ -360,15 +432,13 @@ 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) { @@ -440,14 +510,13 @@ public class FeatureSettings extends JPanel public void itemStateChanged(ItemEvent evt) { fr.setGroupVisibility(check.getText(), check.isSelected()); - af.alignPanel.seqPanel.seqCanvas.repaint(); + af.alignPanel.getSeqPanel().seqCanvas.repaint(); if (af.alignPanel.overviewPanel != null) { af.alignPanel.overviewPanel.updateOverviewImage(); } - resetTable(new String[] - { grp }); + resetTable(new String[] { grp }); } }); groupPanel.add(check); @@ -478,7 +547,7 @@ public class FeatureSettings extends JPanel { tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); + .getSequenceFeatures(); if (tmpfeatures == null) { continue; @@ -618,22 +687,30 @@ public class FeatureSettings extends JPanel { order[i] = fr.getOrder(data[i][0].toString()); if (order[i] < 0) + { order[i] = fr.setOrder(data[i][0].toString(), i / order.length); + } if (i > 1) + { sort = sort || order[i - 1] > order[i]; + } } if (sort) + { jalview.util.QuickSort.sort(order, data); + } } 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("Load Feature Colours"); + chooser.setDialogTitle(MessageManager + .getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); @@ -648,8 +725,7 @@ public class FeatureSettings extends JPanel file), "UTF-8"); jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours(); - jucs = (jalview.schemabinding.version2.JalviewUserColours) jucs - .unmarshal(in); + jucs = jucs.unmarshal(in); for (int i = jucs.getColourCount() - 1; i >= 0; i--) { @@ -727,11 +803,13 @@ 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("Save Feature Colour Scheme"); + chooser.setDialogTitle(MessageManager + .getString("label.save_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -815,7 +893,9 @@ public class FeatureSettings extends JPanel public void orderByAvWidth() { if (table == null || table.getModel() == null) + { return; + } Object[][] data = ((FeatureTableModel) table.getModel()).getData(); float[] width = new float[data.length]; float[] awidth; @@ -837,7 +917,9 @@ public class FeatureSettings extends JPanel width[i] = 0; } if (max < width[i]) + { max = width[i]; + } } boolean sort = false; for (int i = 0; i < width.length; i++) @@ -857,11 +939,15 @@ public class FeatureSettings extends JPanel fr.setOrder(data[i][0].toString(), width[i]); // store for later } if (i > 0) + { sort = sort || width[i - 1] > width[i]; + } } if (sort) + { jalview.util.QuickSort.sort(width, data); - // update global priority order + // update global priority order + } updateFeatureRenderer(data, false); table.repaint(); @@ -929,7 +1015,9 @@ public class FeatureSettings extends JPanel JButton sortByDens = new JButton(); - JPanel transbuttons = new JPanel(new GridLayout(4, 1)); + JButton help = new JButton(); + + JPanel transbuttons = new JPanel(new GridLayout(5, 1)); private void jbInit() throws Exception { @@ -975,6 +1063,36 @@ public class FeatureSettings extends JPanel af.avc.sortAlignmentByFeatureDensity(null); } }); + help.setFont(JvSwingUtils.getLabelFont()); + help.setText(MessageManager.getString("action.help")); + help.addActionListener(new ActionListener() + { + 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() + { + public void actionPerformed(ActionEvent e) + { + try + { + Help.showHelpWindow(HelpId.SequenceFeatureSettings); + } catch (HelpSetException e1) + { + e1.printStackTrace(); + } + } + }); cancel.setFont(JvSwingUtils.getLabelFont()); cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() @@ -1017,12 +1135,14 @@ public class FeatureSettings extends JPanel { public void stateChanged(ChangeEvent evt) { - fr.setTransparency((float) (100 - transparency.getValue()) / 100f); + fr.setTransparency((100 - transparency.getValue()) / 100f); af.alignPanel.paintAlignment(true); } }); transparency.setMaximum(70); + transparency.setToolTipText(MessageManager + .getString("label.transparency_tip")); fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); fetchDAS.addActionListener(new ActionListener() { @@ -1051,13 +1171,18 @@ public class FeatureSettings extends JPanel } }); this.add(tabbedPane, java.awt.BorderLayout.CENTER); - tabbedPane.addTab("Feature Settings", settingsPane); - tabbedPane.addTab("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); transbuttons.add(sortByScore); transbuttons.add(sortByDens); + transbuttons.add(help); + JPanel sliderPanel = new JPanel(); + sliderPanel.add(transparency); transPanel.add(transparency); transPanel.add(transbuttons); buttonPanel.add(ok); @@ -1094,7 +1219,7 @@ 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) { @@ -1243,8 +1368,10 @@ public class FeatureSettings extends JPanel this.data = data; } - private String[] columnNames = - { "Feature Type", "Colour", "Display" }; + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.display") }; private Object[][] data;