X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;fp=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=4e909f1812268b2a9ea232aeccca74cf6cc89932;hb=7692386ccfe778075dd83a753d30a7a27fe507be;hp=68073828a3565566836834c5decae22f72fde59b;hpb=97264690f394f98cf13cd1d834a53e8956fb1b0e;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 6807382..4e909f1 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; @@ -40,18 +41,20 @@ import java.awt.Insets; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.awt.event.FocusEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; 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. * @@ -142,10 +147,15 @@ public class GPreferences extends JPanel protected JCheckBox showConsensLogo = new JCheckBox(); + protected JCheckBox showInformationHistogram = new JCheckBox(); + + protected JCheckBox showHMMLogo = new JCheckBox(); + protected JCheckBox showDbRefTooltip = new JCheckBox(); protected JCheckBox showNpTooltip = new JCheckBox(); + /* * Structure tab and components */ @@ -264,12 +274,30 @@ public class GPreferences extends JPanel protected JCheckBox sortByTree = new JCheckBox(); + /* + * hmmer tab and components + */ + protected JPanel hmmerTab; + + protected JCheckBox hmmrTrimTermini; + + protected AbstractButton hmmerBackgroundUniprot; + + protected AbstractButton hmmerBackgroundAlignment; + + protected JTextField hmmerSequenceCount; + + protected JTextField hmmerPath; + + protected JTextField cygwinPath; /* * Web Services tab */ protected JPanel wsTab = new JPanel(); + + /** * Creates a new GPreferences object. */ @@ -321,6 +349,8 @@ public class GPreferences extends JPanel tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing")); + tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer")); + /* * See WsPreferences for the real work of configuring this tab. */ @@ -329,7 +359,7 @@ public class GPreferences extends JPanel /* * Handler to validate a tab before leaving it - currently only for - * Structure. + * Structure */ tabbedPane.addChangeListener(new ChangeListener() { @@ -383,6 +413,134 @@ public class GPreferences extends JPanel } /** + * Initialises the hmmer tabbed panel + * + * @return + */ + private JPanel initHMMERTab() + { + hmmerTab = new JPanel(); + hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS)); + hmmerTab.setLayout(new MigLayout("flowy")); + + /* + * 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")); + hmmerLocation.setFont(LABEL_FONT); + final int pathFieldLength = 40; + hmmerPath = new JTextField(pathFieldLength); + hmmerPath.addMouseListener(new MouseAdapter() + { + @Override + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() == 2) + { + String chosen = openFileChooser(true); + if (chosen != null) + { + hmmerPath.setText(chosen); + validateHmmerPath(); + } + } + } + }); + installationPanel.add(hmmerLocation); + installationPanel.add(hmmerPath); + + /* + * 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")); + 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); + searchOptions.add(sequencesToKeep); + hmmerSequenceCount = new JTextField(5); + searchOptions.add(hmmerSequenceCount); + + /* + * 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); + hmmerBackgroundAlignment = new JRadioButton( + MessageManager.getString("label.freq_alignment")); + hmmerBackgroundAlignment.setFont(LABEL_FONT); + 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; + } + + /** * Initialises the Output tabbed panel. * * @return @@ -937,7 +1095,7 @@ 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); @@ -949,7 +1107,7 @@ 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); @@ -958,11 +1116,11 @@ 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); @@ -1214,7 +1372,7 @@ public class GPreferences extends JPanel { if (e.getClickCount() == 2) { - String chosen = openFileChooser(); + String chosen = openFileChooser(false); if (chosen != null) { chimeraPath.setText(chosen); @@ -1269,10 +1427,14 @@ public class GPreferences extends JPanel * * @return */ - protected String openFileChooser() + protected String openFileChooser(boolean forFolder) { String choice = null; JFileChooser chooser = new JFileChooser(); + if (forFolder) + { + chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); + } // chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( @@ -1288,21 +1450,6 @@ public class GPreferences extends JPanel return choice; } - /** - * Validate the structure tab preferences; if invalid, set focus on this tab. - * - * @param e - */ - protected boolean validateStructure(FocusEvent e) - { - if (!validateStructure()) - { - e.getComponent().requestFocusInWindow(); - return false; - } - return true; - } - protected boolean validateStructure() { return false; @@ -1814,4 +1961,40 @@ public class GPreferences extends JPanel } } + + 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(); + } }