X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=a3921f6ccfbbb7c7743ab076640734b8f4e425f1;hb=f37c3fd4fe12799de498de5f397252e9f457fee9;hp=93442b2faa3dfab1c0ade95be8f5d9ff17388263;hpb=81c9c8d460d5e2261111f7bdced2a75f1af64f9a;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 93442b2..a3921f6 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -26,6 +26,7 @@ import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.gui.JvSwingUtils; import jalview.gui.StructureViewer.ViewerType; import jalview.util.MessageManager; +import jalview.util.Platform; import java.awt.BorderLayout; import java.awt.Color; @@ -47,11 +48,13 @@ import java.awt.event.MouseEvent; import javax.swing.AbstractButton; import javax.swing.AbstractCellEditor; import javax.swing.BorderFactory; +import javax.swing.BoxLayout; import javax.swing.ButtonGroup; import javax.swing.DefaultListCellRenderer; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JComboBox; +import javax.swing.JComponent; import javax.swing.JFileChooser; import javax.swing.JLabel; import javax.swing.JPanel; @@ -71,6 +74,8 @@ import javax.swing.event.ChangeListener; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; +import net.miginfocom.swing.MigLayout; + /** * Base class for the Preferences panel. * @@ -186,6 +191,19 @@ public class GPreferences extends JPanel protected JComboBox nucColour = new JComboBox<>(); /* + * Overview tab components + */ + protected JPanel gapColour = new JPanel(); + + protected JPanel hiddenColour = new JPanel(); + + protected JCheckBox useLegacyGap; + + protected JCheckBox showHiddenAtStart; + + protected JLabel gapLabel; + + /* * Connections tab components */ protected JTable linkUrlTable = new JTable(); @@ -259,17 +277,19 @@ public class GPreferences extends JPanel /* * hmmer tab and components */ - protected JPanel hmmerTab = new JPanel(); + protected JPanel hmmerTab; + + protected JCheckBox hmmrTrimTermini; - protected JCheckBox hmmrTrimTermini = new JCheckBox(); + protected AbstractButton hmmerBackgroundUniprot; - protected AbstractButton hmmerBackgroundUniprot = new JCheckBox(); + protected AbstractButton hmmerBackgroundAlignment; - protected AbstractButton hmmerBackgroundAlignment = new JCheckBox(); + protected JTextField hmmerSequenceCount; - protected JTextField hmmerSequenceCount = new JTextField(); + protected JTextField hmmerPath; - protected JTextField hmmerPath = new JTextField(); + protected JTextField cygwinPath; /* * DAS Settings tab @@ -316,6 +336,9 @@ public class GPreferences extends JPanel tabbedPane.add(initColoursTab(), MessageManager.getString("label.colours")); + tabbedPane.add(initOverviewTab(), + MessageManager.getString("label.overview")); + tabbedPane.add(initStructureTab(), MessageManager.getString("label.structure")); @@ -407,13 +430,23 @@ public class GPreferences extends JPanel */ private JPanel initHMMERTab() { - hmmerTab.setLayout(null); + hmmerTab = new JPanel(); + hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS)); + hmmerTab.setLayout(new MigLayout("flowy")); - JLabel installationLocation = new JLabel( + /* + * path to hmmer binaries folder + */ + JPanel installationPanel = new JPanel(new MigLayout("flowy")); + // new FlowLayout(FlowLayout.LEFT)); + JvSwingUtils.createTitledBorder(installationPanel, + MessageManager.getString("label.installation"), true); + hmmerTab.add(installationPanel); + JLabel hmmerLocation = new JLabel( MessageManager.getString("label.hmmer_location")); - installationLocation.setFont(LABEL_FONT); - installationLocation.setBounds(new Rectangle(22, 10, 250, 23)); - hmmerPath.setBounds(new Rectangle(22, 30, 300, 23)); + hmmerLocation.setFont(LABEL_FONT); + final int pathFieldLength = 40; + hmmerPath = new JTextField(pathFieldLength); hmmerPath.addMouseListener(new MouseAdapter() { @Override @@ -425,54 +458,95 @@ public class GPreferences extends JPanel if (chosen != null) { hmmerPath.setText(chosen); + validateHmmerPath(); } } } }); + installationPanel.add(hmmerLocation); + installationPanel.add(hmmerPath); - JLabel hmmalign = new JLabel( - MessageManager.getString("label.hmmalign_label")); - hmmalign.setFont(LABEL_FONT); - hmmalign.setBounds(new Rectangle(22, 50, 200, 23)); + /* + * path to Cygwin binaries folder (for Windows) + */ + if (Platform.isWindows()) + { + JLabel cygwinLocation = new JLabel( + MessageManager.getString("label.cygwin_location")); + cygwinLocation.setFont(LABEL_FONT); + cygwinPath = new JTextField(pathFieldLength); + cygwinPath.addMouseListener(new MouseAdapter() + { + @Override + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() == 2) + { + String chosen = openFileChooser(true); + if (chosen != null) + { + cygwinPath.setText(chosen); + validateCygwinPath(); + } + } + } + }); + installationPanel.add(cygwinLocation); + installationPanel.add(cygwinPath); + } + /* + * preferences for hmmalign + */ + JPanel alignOptionsPanel = new JPanel(new MigLayout()); + // new FlowLayout(FlowLayout.LEFT)); + JvSwingUtils.createTitledBorder(alignOptionsPanel, + MessageManager.getString("label.hmmalign_options"), true); + hmmerTab.add(alignOptionsPanel); + hmmrTrimTermini = new JCheckBox(); hmmrTrimTermini.setFont(LABEL_FONT); hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini")); - hmmrTrimTermini.setBounds(new Rectangle(22, 70, 200, 23)); - - JLabel hmmsearch = new JLabel( - MessageManager.getString("label.hmmsearch_label")); - hmmsearch.setFont(LABEL_FONT); - hmmsearch.setBounds(new Rectangle(22, 90, 200, 23)); + alignOptionsPanel.add(hmmrTrimTermini); + /* + * preferences for hmmsearch + */ + JPanel searchOptions = new JPanel(new MigLayout()); + // FlowLayout(FlowLayout.LEFT)); + JvSwingUtils.createTitledBorder(searchOptions, + MessageManager.getString("label.hmmsearch_options"), true); + hmmerTab.add(searchOptions); JLabel sequencesToKeep = new JLabel( MessageManager.getString("label.no_of_sequences")); sequencesToKeep.setFont(LABEL_FONT); - sequencesToKeep.setBounds(new Rectangle(22, 110, 125, 23)); - hmmerSequenceCount.setBounds(new Rectangle(150, 110, 40, 23)); + searchOptions.add(sequencesToKeep); + hmmerSequenceCount = new JTextField(5); + searchOptions.add(hmmerSequenceCount); - ButtonGroup backgroundFreqSource = new ButtonGroup(); - backgroundFreqSource.add(hmmerBackgroundUniprot); - backgroundFreqSource.add(hmmerBackgroundAlignment); - backgroundFreqSource.setSelected(hmmerBackgroundUniprot.getModel(), true); - - hmmerBackgroundUniprot.setText(MessageManager.getString("label.freq_uniprot")); + /* + * preferences for Information Content annotation + */ + // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT)); + JPanel annotationOptions = new JPanel(new MigLayout("left")); + JvSwingUtils.createTitledBorder(annotationOptions, + MessageManager.getString("label.information_annotation"), true); + // dummy.add(annotationOptions); + hmmerTab.add(annotationOptions); + ButtonGroup backgroundOptions = new ButtonGroup(); + hmmerBackgroundUniprot = new JRadioButton( + MessageManager.getString("label.freq_uniprot")); hmmerBackgroundUniprot.setFont(LABEL_FONT); - hmmerBackgroundUniprot.setBounds(new Rectangle(22, 130, 255, 23)); - - hmmerBackgroundAlignment.setText(MessageManager.getString("label.freq_alignment")); + hmmerBackgroundAlignment = new JRadioButton( + MessageManager.getString("label.freq_alignment")); hmmerBackgroundAlignment.setFont(LABEL_FONT); - hmmerBackgroundAlignment.setBounds(new Rectangle(22, 150, 300, 23)); - - hmmerTab.add(hmmerBackgroundUniprot); - hmmerTab.add(hmmerBackgroundAlignment); - hmmerTab.add(hmmalign); - hmmerTab.add(hmmsearch); - hmmerTab.add(installationLocation); - hmmerTab.add(hmmerPath); - hmmerTab.add(hmmrTrimTermini); - hmmerTab.add(sequencesToKeep); - hmmerTab.add(sequencesToKeep); - hmmerTab.add(hmmerSequenceCount); + backgroundOptions.add(hmmerBackgroundUniprot); + backgroundOptions.add(hmmerBackgroundAlignment); + backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true); + // disable buttons for now as annotation only uses Uniprot background + hmmerBackgroundAlignment.setEnabled(false); + hmmerBackgroundUniprot.setEnabled(false); + annotationOptions.add(hmmerBackgroundUniprot, "wrap"); + annotationOptions.add(hmmerBackgroundAlignment); return hmmerTab; } @@ -609,7 +683,9 @@ public class GPreferences extends JPanel MessageManager.getString("label.default_browser_unix")); defaultBrowser.setFont(LABEL_FONT); defaultBrowser.setText(""); - + final String tooltip = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.double_click_to_browse")); + defaultBrowser.setToolTipText(tooltip); defaultBrowser.addMouseListener(new MouseAdapter() { @Override @@ -1030,7 +1106,7 @@ public class GPreferences extends JPanel protColourLabel.setHorizontalAlignment(SwingConstants.LEFT); protColourLabel.setText( MessageManager.getString("label.prot_alignment_colour") + " "); - JvSwingUtils.addtoLayout(coloursTab, + GPreferences.addtoLayout(coloursTab, MessageManager .getString("label.default_colour_scheme_for_alignment"), protColourLabel, protColour); @@ -1042,7 +1118,7 @@ public class GPreferences extends JPanel nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT); nucColourLabel.setText( MessageManager.getString("label.nuc_alignment_colour") + " "); - JvSwingUtils.addtoLayout(coloursTab, + GPreferences.addtoLayout(coloursTab, MessageManager .getString("label.default_colour_scheme_for_alignment"), nucColourLabel, nucColour); @@ -1051,11 +1127,11 @@ public class GPreferences extends JPanel annotationShding.setBorder(new TitledBorder( MessageManager.getString("label.annotation_shading_default"))); annotationShding.setLayout(new GridLayout(1, 2)); - JvSwingUtils.addtoLayout(annotationShding, + GPreferences.addtoLayout(annotationShding, MessageManager.getString( "label.default_minimum_colour_annotation_shading"), mincolourLabel, minColour); - JvSwingUtils.addtoLayout(annotationShding, + GPreferences.addtoLayout(annotationShding, MessageManager.getString( "label.default_maximum_colour_annotation_shading"), maxcolourLabel, maxColour); @@ -1064,6 +1140,151 @@ public class GPreferences extends JPanel } /** + * Initialises the Overview tabbed panel. + * + * @return + */ + private JPanel initOverviewTab() + { + JPanel overviewPanel = new JPanel(); + overviewPanel.setBorder(new TitledBorder( + MessageManager.getString("label.overview_settings"))); + + gapColour.setFont(LABEL_FONT); + // fixing the border colours stops apparent colour bleed from the panel + gapColour.setBorder( + BorderFactory.createEtchedBorder(Color.white, Color.lightGray)); + gapColour.setPreferredSize(new Dimension(40, 20)); + gapColour.addMouseListener(new MouseAdapter() + { + @Override + public void mousePressed(MouseEvent e) + { + gapColour_actionPerformed(gapColour); + } + }); + + hiddenColour.setFont(LABEL_FONT); + // fixing the border colours stops apparent colour bleed from the panel + hiddenColour.setBorder( + BorderFactory.createEtchedBorder(Color.white, Color.lightGray)); + hiddenColour.setPreferredSize(new Dimension(40, 20)); + hiddenColour.addMouseListener(new MouseAdapter() + { + @Override + public void mousePressed(MouseEvent e) + { + hiddenColour_actionPerformed(hiddenColour); + } + }); + + useLegacyGap = new JCheckBox( + MessageManager.getString("label.ov_legacy_gap")); + useLegacyGap.setFont(LABEL_FONT); + useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT); + useLegacyGap.setVerticalTextPosition(SwingConstants.TOP); + gapLabel = new JLabel( + MessageManager.getString("label.gap_colour")); + gapLabel.setFont(LABEL_FONT); + gapLabel.setHorizontalAlignment(SwingConstants.LEFT); + gapLabel.setVerticalTextPosition(SwingConstants.TOP); + showHiddenAtStart = new JCheckBox( + MessageManager.getString("label.ov_show_hide_default")); + showHiddenAtStart.setFont(LABEL_FONT); + showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT); + showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP); + JLabel hiddenLabel = new JLabel( + MessageManager.getString("label.hidden_colour")); + hiddenLabel.setFont(LABEL_FONT); + hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT); + hiddenLabel.setVerticalTextPosition(SwingConstants.TOP); + + useLegacyGap.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + useLegacyGaps_actionPerformed(e); + } + }); + + overviewPanel.setLayout(new GridBagLayout()); + GridBagConstraints c1 = new GridBagConstraints(); + + c1.fill = GridBagConstraints.HORIZONTAL; + c1.gridx = 0; + c1.gridy = 0; + c1.weightx = 1; + c1.ipady = 20; + c1.anchor = GridBagConstraints.FIRST_LINE_START; + overviewPanel.add(useLegacyGap, c1); + + GridBagConstraints c2 = new GridBagConstraints(); + c2.fill = GridBagConstraints.HORIZONTAL; + c2.gridx = 1; + c2.gridy = 0; + c2.insets = new Insets(0, 15, 0, 10); + overviewPanel.add(gapLabel, c2); + + GridBagConstraints c3 = new GridBagConstraints(); + c3.fill = GridBagConstraints.HORIZONTAL; + c3.gridx = 2; + c3.gridy = 0; + c3.insets = new Insets(0, 0, 0, 15); + overviewPanel.add(gapColour, c3); + + GridBagConstraints c4 = new GridBagConstraints(); + c4.fill = GridBagConstraints.HORIZONTAL; + c4.gridx = 0; + c4.gridy = 1; + c4.weightx = 1; + overviewPanel.add(showHiddenAtStart, c4); + + GridBagConstraints c5 = new GridBagConstraints(); + c5.fill = GridBagConstraints.HORIZONTAL; + c5.gridx = 1; + c5.gridy = 1; + c5.insets = new Insets(0, 15, 0, 10); + overviewPanel.add(hiddenLabel, c5); + + GridBagConstraints c6 = new GridBagConstraints(); + c6.fill = GridBagConstraints.HORIZONTAL; + c6.gridx = 2; + c6.gridy = 1; + c6.insets = new Insets(0, 0, 0, 15); + overviewPanel.add(hiddenColour, c6); + + JButton resetButton = new JButton( + MessageManager.getString("label.reset_to_defaults")); + + resetButton.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + resetOvDefaults_actionPerformed(e); + } + }); + + GridBagConstraints c7 = new GridBagConstraints(); + c7.fill = GridBagConstraints.NONE; + c7.gridx = 0; + c7.gridy = 2; + c7.insets = new Insets(10, 0, 0, 0); + c7.anchor = GridBagConstraints.WEST; + overviewPanel.add(resetButton, c7); + + // Add padding so the panel doesn't look ridiculous + JPanel spacePanel = new JPanel(); + overviewPanel.add(spacePanel, + new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0, + GridBagConstraints.WEST, GridBagConstraints.BOTH, + new Insets(0, 0, 0, 5), 0, 0)); + + return overviewPanel; + } + + /** * Initialises the Structure tabbed panel. * * @return @@ -1146,14 +1367,14 @@ public class GPreferences extends JPanel pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); pathLabel.setHorizontalAlignment(SwingConstants.LEFT); pathLabel.setText(MessageManager.getString("label.chimera_path")); - final String tooltip = JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.chimera_path_tip")); - pathLabel.setToolTipText(tooltip); pathLabel.setBounds(new Rectangle(10, ypos, 140, height)); structureTab.add(pathLabel); chimeraPath.setFont(LABEL_FONT); chimeraPath.setText(""); + final String tooltip = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.chimera_path_tip")); + chimeraPath.setToolTipText(tooltip); chimeraPath.setBounds(new Rectangle(160, ypos, 300, height)); chimeraPath.addMouseListener(new MouseAdapter() { @@ -1245,11 +1466,6 @@ public class GPreferences extends JPanel return false; } - protected boolean validateHMMERPath(boolean showWarning) - { - return false; - } - /** * Initialises the Visual tabbed panel. * @@ -1446,6 +1662,9 @@ public class GPreferences extends JPanel startupCheckbox.setSelected(true); startupFileTextfield.setFont(LABEL_FONT); startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20)); + final String tooltip = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.double_click_to_browse")); + startupFileTextfield.setToolTipText(tooltip); startupFileTextfield.addMouseListener(new MouseAdapter() { @Override @@ -1589,12 +1808,28 @@ public class GPreferences extends JPanel { } + protected void gapColour_actionPerformed(JPanel panel) + { + } + + protected void hiddenColour_actionPerformed(JPanel panel) + { + } + protected void showunconserved_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } + protected void useLegacyGaps_actionPerformed(ActionEvent e) + { + } + + protected void resetOvDefaults_actionPerformed(ActionEvent e) + { + } + /** * DOCUMENT ME! * @@ -1738,8 +1973,39 @@ public class GPreferences extends JPanel } - public void hmmerPath_actionPerformed(ActionEvent e) + protected void validateHmmerPath() + { + } + + protected void validateCygwinPath() { + } + /** + * A helper method to add a panel containing a label and a component to a + * panel + * + * @param panel + * @param tooltip + * @param label + * @param valBox + */ + protected static void addtoLayout(JPanel panel, String tooltip, + JComponent label, JComponent valBox) + { + JPanel laypanel = new JPanel(new GridLayout(1, 2)); + JPanel labPanel = new JPanel(new BorderLayout()); + JPanel valPanel = new JPanel(); + labPanel.setBounds(new Rectangle(7, 7, 158, 23)); + valPanel.setBounds(new Rectangle(172, 7, 270, 23)); + labPanel.add(label, BorderLayout.WEST); + valPanel.add(valBox); + laypanel.add(labPanel); + laypanel.add(valPanel); + valPanel.setToolTipText(tooltip); + labPanel.setToolTipText(tooltip); + valBox.setToolTipText(tooltip); + panel.add(laypanel); + panel.validate(); } }