import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.gui.StructureViewer.Viewer;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GPreferences;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
import javax.swing.JOptionPane;
+import javax.swing.JPanel;
/**
* DOCUMENT ME!
public class Preferences extends GPreferences
{
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ private static final int MIN_FONT_SIZE = 1;
+
+ private static final int MAX_FONT_SIZE = 30;
+
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
public Preferences()
{
-
+ super();
frame = new JInternalFrame();
frame.setContentPane(this);
dasSource = new DasSourceBrowser();
- dasPanel.add(dasSource, BorderLayout.CENTER);
+ dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
- wsPanel.add(wsPrefs, BorderLayout.CENTER);
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
int width = 500, height = 420;
if (new jalview.util.Platform().isAMac())
{
MessageManager.getString("label.preferences"), width, height);
frame.setMinimumSize(new Dimension(width, height));
+ /*
+ * Set Visual tab defaults
+ */
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
showUnconserved
.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
+ false));
+ showGroupConservation.setSelected(Cache.getDefault(
+ "SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(Cache.getDefault(
+ "SHOW_CONSENSUS_HISTOGRAM", true));
+ showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
+ false));
showNpTooltip.setSelected(Cache
.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
true));
- sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
- for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
- {
- colour.addItem(ColourSchemeProperty.getColourName(i));
- }
-
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");
-
- colour.setSelectedItem(string);
-
- /**
- * default min-max colours for annotation shading
- */
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-
for (int i = 0; i < fonts.length; i++)
{
fontNameCB.addItem(fonts[i]);
}
- for (int i = 1; i < 31; i++)
+ for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
{
fontSizeCB.addItem(i + "");
}
gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
- startupCheckbox
- .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
- startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_3.jar"));
-
sortby.addItem("No sort");
sortby.addItem("Id");
sortby.addItem("Pairwise Identity");
sortAnnBy
.addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
- .valueOf(Cache.getDefault(Cache.SORT_ANNOTATIONS,
+ .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name()));
sortAnnBy.setSelectedItem(savedSort.toString());
sortAutocalc.addItem("Autocalculated first");
sortAutocalc.addItem("Autocalculated last");
-
- final boolean showAbove = Cache.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
true);
sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
: sortAutocalc.getItemAt(1));
+ startupCheckbox
+ .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+ startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
- epsRendering.addItem(MessageManager.getString("label.prompt_each_time"));
- epsRendering.addItem(MessageManager.getString("label.lineart"));
- epsRendering.addItem(MessageManager.getString("action.text"));
- epsRendering.setSelectedIndex(0);
- autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
- userIdWidth.setEnabled(autoIdWidth.isSelected());
- userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
- Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
- userIdWidth.setText(wi == null ? "" : wi.toString());
- blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
- clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
- fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
- msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
- pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
- pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
- pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
-
- modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
-
- autoCalculateConsCheck.setSelected(Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
- showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
- false));
- showGroupConservation.setSelected(Cache.getDefault(
- "SHOW_GROUP_CONSERVATION", false));
- showConsensHistogram.setSelected(Cache.getDefault(
- "SHOW_CONSENSUS_HISTOGRAM", true));
- showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
- false));
-
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ /*
+ * Set Colours tab defaults
+ */
+ for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ {
+ colour.addItem(ColourSchemeProperty.getColourName(i));
+ }
+ String string = Cache.getDefault("DEFAULT_COLOUR", "None");
+ colour.setSelectedItem(string);
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
- /***************************************************************************
- * Set up Connections
+ /*
+ * Set Structure tab defaults.
+ */
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ structFromPdb.setSelected(structSelected);
+ useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+ useRnaView.setEnabled(structSelected);
+ addSecondaryStructure
+ .setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setEnabled(structSelected);
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setEnabled(structSelected);
+ structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
+ Viewer.JMOL.name()));
+
+ /*
+ * Set Connections tab defaults
*/
nameLinks = new Vector();
urlLinks = new Vector();
defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+ // note antisense here: default is true
questionnaire
- .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
- // antisense
- // here
- versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
- // is
- // true
+ .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
+ versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
+
+ /*
+ * Set Output tab defaults
+ */
+ epsRendering
+ .addItem(MessageManager.getString("label.prompt_each_time"));
+ epsRendering.addItem(MessageManager.getString("label.lineart"));
+ epsRendering.addItem(MessageManager.getString("action.text"));
+ epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
+ "Prompt each time"));
+ autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ userIdWidth.setEnabled(autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
+ Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+ userIdWidth.setText(wi == null ? "" : wi.toString());
+ blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
+ clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+ fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
+ msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
+ pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
+ pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
+ pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
+ modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+
+ /*
+ * Set Editing tab defaults
+ */
+ autoCalculateConsCheck.setSelected(Cache.getDefault(
+ "AUTO_CALC_CONSENSUS", true));
+ padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+
annotations_actionPerformed(null); // update the display of the annotation
// settings
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
}
/**
- * DOCUMENT ME!
+ * Save user selections on the Preferences tabs to the Cache and write out to
+ * file.
*
* @param e
- * DOCUMENT ME!
*/
public void ok_actionPerformed(ActionEvent e)
{
-
+ /*
+ * Save Visual settings
+ */
Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
Boolean.toString(seqLimit.isSelected()));
Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
- .getSelectedItem().toString());
Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
.getSelectedItem().toString());
.forDescription(sortAnnBy.getSelectedItem().toString());
if (annSortOrder != null)
{
- Cache.applicationProperties.setProperty(Cache.SORT_ANNOTATIONS,
+ Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
annSortOrder.name());
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(Cache.SHOW_AUTOCALC_ABOVE,
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
Boolean.valueOf(showAutocalcFirst).toString());
+ /*
+ * Save Colours settings
+ */
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
+ .getSelectedItem().toString());
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
maxColour.getBackground());
+ /*
+ * Save Structure settings
+ */
+ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Boolean.toString(addTempFactor.isSelected()));
+ Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Boolean.toString(addSecondaryStructure.isSelected()));
+ Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Boolean.toString(useRnaView.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Boolean.toString(structFromPdb.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
+ .getSelectedItem().toString());
+
+ /*
+ * Save Output settings
+ */
if (epsRendering.getSelectedItem().equals("Prompt each time"))
{
Cache.applicationProperties.remove("EPS_RENDERING");
.getSelectedItem().toString());
}
+ /*
+ * Save Connections settings
+ */
if (defaultBrowser.getText().trim().length() < 1)
{
Cache.applicationProperties.remove("DEFAULT_BROWSER");
// by just adding the given line
Cache.removeProperty("NOQUESTIONNAIRES");
}
+
+ /*
+ * Save Output settings
+ */
Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
Boolean.toString(blcjv.isSelected()));
Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
userIdWidth.getText());
+ /*
+ * Save Editing settings
+ */
Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
Cache.applicationProperties.setProperty("SORT_BY_TREE",
dasSource.saveProperties(Cache.applicationProperties);
wsPrefs.updateAndRefreshWsMenuConfig(false);
+
Cache.saveProperties();
+
try
{
frame.setClosed(true);
super.showunconserved_actionPerformed(e);
}
- private void jbInit() throws Exception
- {
- }
-
public static Collection getGroupURLLinks()
{
return groupURLLinks;
}
- public void minColour_actionPerformed()
+ @Override
+ public void minColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
if (col != null)
{
- minColour.setBackground(col);
+ panel.setBackground(col);
}
- minColour.repaint();
+ panel.repaint();
}
- public void maxColour_actionPerformed()
+ @Override
+ public void maxColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
if (col != null)
{
- maxColour.setBackground(col);
+ panel.setBackground(col);
}
- maxColour.repaint();
+ panel.repaint();
}
@Override
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.gui.StructureViewer.Viewer;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import javax.swing.event.ListSelectionListener;
/**
- * DOCUMENT ME!
+ * Base class for the Preferences panel.
*
* @author $author$
* @version $Revision$
*/
public class GPreferences extends JPanel
{
- JTabbedPane tabbedPane = new JTabbedPane();
-
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JPanel okCancelPanel = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- protected JCheckBox quality = new JCheckBox();
-
- JPanel visualTab = new JPanel();
-
- JPanel visual2Tab = new JPanel();
+ private static final Font verdana11 = JvSwingUtils.getLabelFont();
+ /*
+ * Visual tab components
+ */
protected JCheckBox fullScreen = new JCheckBox();
- protected JCheckBox conservation = new JCheckBox();
-
- protected JCheckBox identity = new JCheckBox();
-
- protected JCheckBox annotations = new JCheckBox();
-
- protected JPanel minColour = new JPanel();
-
- JLabel mincolourLabel = new JLabel();
-
- protected JPanel maxColour = new JPanel();
-
- JLabel maxcolourLabel = new JLabel();
-
- JLabel gapLabel = new JLabel();
-
- protected JComboBox<String> colour = new JComboBox<String>();
+ protected JCheckBox openoverv = new JCheckBox();
- JLabel colourLabel = new JLabel();
+ protected JCheckBox seqLimit = new JCheckBox();
- JLabel fontLabel = new JLabel();
+ protected JCheckBox rightAlign = new JCheckBox();
protected JComboBox<String> fontSizeCB = new JComboBox<String>();
protected JComboBox<String> fontNameCB = new JComboBox<String>();
- protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
-
- protected JCheckBox startupCheckbox = new JCheckBox();
-
- protected JTextField startupFileTextfield = new JTextField();
-
- JPanel connectTab = new JPanel();
-
- JLabel serverLabel = new JLabel();
-
- protected JList linkURLList = new JList();
-
- protected JTextField proxyServerTB = new JTextField();
-
- protected JTextField proxyPortTB = new JTextField();
+ protected JCheckBox showUnconserved = new JCheckBox();
- JLabel portLabel = new JLabel();
+ protected JCheckBox idItalics = new JCheckBox();
- JLabel browserLabel = new JLabel();
+ protected JCheckBox smoothFont = new JCheckBox();
- protected JTextField defaultBrowser = new JTextField();
+ protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
- JButton newLink = new JButton();
+ protected JCheckBox wrap = new JCheckBox();
- JButton editLink = new JButton();
+ protected JComboBox<String> sortby = new JComboBox<String>();
- JButton deleteLink = new JButton();
+ protected JComboBox<String> sortAnnBy = new JComboBox<String>();
- JScrollPane linkScrollPane = new JScrollPane();
+ protected JComboBox<String> sortAutocalc = new JComboBox<String>();
- JPanel linkPanel = new JPanel();
+ protected JCheckBox startupCheckbox = new JCheckBox();
- BorderLayout borderLayout2 = new BorderLayout();
+ protected JTextField startupFileTextfield = new JTextField();
- JPanel editLinkButtons = new JPanel();
+ // below are in the 'second column'
+ protected JCheckBox annotations = new JCheckBox();
- GridLayout gridLayout1 = new GridLayout();
+ protected JCheckBox quality = new JCheckBox();
- protected JList linkNameList = new JList();
+ protected JCheckBox conservation = new JCheckBox();
- JPanel linkPanel2 = new JPanel();
+ protected JCheckBox identity = new JCheckBox();
- BorderLayout borderLayout3 = new BorderLayout();
+ protected JCheckBox showGroupConsensus = new JCheckBox();
- protected JCheckBox useProxy = new JCheckBox();
+ protected JCheckBox showGroupConservation = new JCheckBox();
- JPanel jPanel1 = new JPanel();
+ protected JCheckBox showConsensHistogram = new JCheckBox();
- TitledBorder titledBorder1 = new TitledBorder(
- MessageManager.getString("label.proxy_server"));
+ protected JCheckBox showConsensLogo = new JCheckBox();
- TitledBorder titledBorder2 = new TitledBorder(
- MessageManager.getString("label.file_output"));
+ protected JCheckBox showDbRefTooltip = new JCheckBox();
- GridBagLayout gridBagLayout2 = new GridBagLayout();
+ protected JCheckBox showNpTooltip = new JCheckBox();
- GridBagLayout gridBagLayout1 = new GridBagLayout();
+ /*
+ * Annotations tab components
+ */
+ protected JCheckBox structFromPdb = new JCheckBox();
- GridBagLayout gridBagLayout3 = new GridBagLayout();
+ protected JCheckBox useRnaView = new JCheckBox();
- protected JComboBox<String> sortby = new JComboBox<String>();
+ protected JCheckBox addSecondaryStructure = new JCheckBox();
- JLabel sortLabel = new JLabel();
+ protected JCheckBox addTempFactor = new JCheckBox();
- protected JComboBox<String> sortAnnBy = new JComboBox<String>();
+ protected JComboBox<String> structViewer = new JComboBox<String>();
- protected JComboBox<String> sortAutocalc = new JComboBox<String>();
+ /*
+ * Colours tab components
+ */
+ protected JPanel minColour = new JPanel();
- JLabel sortAnnLabel = new JLabel();
+ protected JPanel maxColour = new JPanel();
- JPanel jPanel2 = new JPanel();
+ protected JComboBox<String> colour = new JComboBox<String>();
- JPanel visual2panel = new JPanel();
+ /*
+ * Connections tab components
+ */
+ protected JList linkURLList = new JList();
- GridLayout gridLayout2 = new GridLayout();
+ protected JTextField proxyServerTB = new JTextField();
- GridLayout gridLayout4 = new GridLayout();
+ protected JTextField proxyPortTB = new JTextField();
- JPanel annsettingsPanel = new JPanel();
+ protected JTextField defaultBrowser = new JTextField();
- JPanel autoAnnotSettings1 = new JPanel();
+ protected JList linkNameList = new JList();
- JPanel autoAnnotSettings2 = new JPanel();
+ protected JCheckBox useProxy = new JCheckBox();
- JPanel autoAnnotSettings3 = new JPanel();
+ protected JCheckBox usagestats = new JCheckBox();
- JPanel exportTab = new JPanel();
+ protected JCheckBox questionnaire = new JCheckBox();
- JLabel epsLabel = new JLabel();
+ protected JCheckBox versioncheck = new JCheckBox();
+ /*
+ * Output tab components
+ */
protected JComboBox<String> epsRendering = new JComboBox<String>();
protected JLabel userIdWidthlabel = new JLabel();
protected JTextField userIdWidth = new JTextField();
- JLabel jLabel1 = new JLabel();
-
protected JCheckBox blcjv = new JCheckBox();
protected JCheckBox pileupjv = new JCheckBox();
protected JCheckBox pfamjv = new JCheckBox();
- FlowLayout flowLayout1 = new FlowLayout();
-
protected JCheckBox pirjv = new JCheckBox();
- JPanel jPanel11 = new JPanel();
-
- Font verdana11 = JvSwingUtils.getLabelFont();
-
- protected JCheckBox seqLimit = new JCheckBox();
-
- GridLayout gridLayout3 = new GridLayout();
-
- protected JCheckBox smoothFont = new JCheckBox();
-
- JPanel calcTab = new JPanel();
+ protected JCheckBox modellerOutput = new JCheckBox();
+ /*
+ * Editing tab components
+ */
protected JCheckBox autoCalculateConsCheck = new JCheckBox();
protected JCheckBox padGaps = new JCheckBox();
- protected JCheckBox modellerOutput = new JCheckBox();
-
- protected JPanel dasPanel = new JPanel();
-
- BorderLayout borderLayout4 = new BorderLayout();
-
- protected JPanel wsPanel = new JPanel();
-
- BorderLayout borderLayout5 = new BorderLayout();
-
- protected JCheckBox wrap = new JCheckBox();
-
- protected JCheckBox rightAlign = new JCheckBox();
-
- protected JCheckBox showUnconserved = new JCheckBox();
-
- protected JCheckBox showDbRefTooltip = new JCheckBox();
-
- protected JCheckBox showNpTooltip = new JCheckBox();
-
- protected JCheckBox idItalics = new JCheckBox();
-
- protected JCheckBox openoverv = new JCheckBox();
-
- protected JCheckBox usagestats = new JCheckBox();
-
- protected JCheckBox questionnaire = new JCheckBox();
-
- protected JCheckBox versioncheck = new JCheckBox();
-
- protected JLabel showGroupbits = new JLabel();
-
- protected JLabel showConsensbits = new JLabel();
-
- protected JCheckBox showConsensLogo = new JCheckBox();
-
- protected JCheckBox showConsensHistogram = new JCheckBox();
-
- protected JCheckBox showGroupConsensus = new JCheckBox();
-
- protected JCheckBox showGroupConservation = new JCheckBox();
-
- protected JCheckBox shareSelections = new JCheckBox();
+ protected JCheckBox sortByTree = new JCheckBox();
- protected JCheckBox followHighlight = new JCheckBox();
+ /*
+ * DAS Settings tab
+ */
+ protected JPanel dasTab = new JPanel();
- protected JCheckBox sortByTree = new JCheckBox();
+ /*
+ * Web Services tab
+ */
+ protected JPanel wsTab = new JPanel();
/**
* Creates a new GPreferences object.
}
/**
- * DOCUMENT ME!
+ * Construct the panel and its tabbed sub-panels.
*
* @throws Exception
- * DOCUMENT ME!
*/
private void jbInit() throws Exception
{
- this.setLayout(borderLayout1);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
+ JTabbedPane tabbedPane = new JTabbedPane();
+ this.setLayout(new BorderLayout());
+ JPanel okCancelPanel = initOkCancelPanel();
+ this.add(tabbedPane, BorderLayout.CENTER);
+ this.add(okCancelPanel, BorderLayout.SOUTH);
+
+ tabbedPane.add(initVisualTab(),
+ MessageManager.getString("label.visual"));
+
+ tabbedPane.add(initColoursTab(),
+ MessageManager.getString("label.colours"));
+
+ tabbedPane.add(initStructureTab(),
+ MessageManager.getString("label.structure"));
+
+ tabbedPane.add(initConnectionsTab(),
+ MessageManager.getString("label.connections"));
+
+ tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
+
+ tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
+
+ /*
+ * See DasSourceBrowser for the real work of configuring this tab.
+ */
+ dasTab.setLayout(new BorderLayout());
+ tabbedPane
+ .add(dasTab, MessageManager.getString("label.das_settings"));
+
+ /*
+ * See WsPreferences for the real work of configuring this tab.
+ */
+ wsTab.setLayout(new BorderLayout());
+ tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+ }
+
+ /**
+ * Initialises the Editing tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initEditingTab()
+ {
+ JPanel editingTab = new JPanel();
+ editingTab.setLayout(null);
+ autoCalculateConsCheck.setFont(verdana11);
+ autoCalculateConsCheck.setText(MessageManager
+ .getString("label.autocalculate_consensus"));
+ autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
+ padGaps.setFont(verdana11);
+ padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
+ padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+ sortByTree.setFont(verdana11);
+ sortByTree
+ .setText(MessageManager.getString("label.sort_with_new_tree"));
+ sortByTree
+ .setToolTipText(MessageManager
+ .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
+ sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+ editingTab.add(autoCalculateConsCheck);
+ editingTab.add(padGaps);
+ editingTab.add(sortByTree);
+ return editingTab;
+ }
+
+ /**
+ * Initialises the Output tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initOutputTab()
+ {
+ JPanel outputTab = new JPanel();
+ outputTab.setLayout(null);
+ JLabel epsLabel = new JLabel();
+ epsLabel.setFont(verdana11);
+ epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
+ epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+ epsRendering.setFont(verdana11);
+ epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+ JLabel jLabel1 = new JLabel();
+ jLabel1.setFont(verdana11);
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText(MessageManager.getString("label.append_start_end"));
+ jLabel1.setFont(verdana11);
+ fastajv.setFont(verdana11);
+ fastajv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setText(MessageManager.getString("label.clustal") + " ");
+ blcjv.setText(MessageManager.getString("label.blc") + " ");
+ fastajv.setText(MessageManager.getString("label.fasta") + " ");
+ msfjv.setText(MessageManager.getString("label.msf") + " ");
+ pfamjv.setText(MessageManager.getString("label.pfam") + " ");
+ pileupjv.setText(MessageManager.getString("label.pileup") + " ");
+ msfjv.setFont(verdana11);
+ msfjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setText(MessageManager.getString("label.pir") + " ");
+ JPanel jPanel11 = new JPanel();
+ jPanel11.setFont(verdana11);
+ TitledBorder titledBorder2 = new TitledBorder(
+ MessageManager.getString("label.file_output"));
+ jPanel11.setBorder(titledBorder2);
+ jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+ GridLayout gridLayout3 = new GridLayout();
+ jPanel11.setLayout(gridLayout3);
+ gridLayout3.setRows(8);
+ blcjv.setFont(verdana11);
+ blcjv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setFont(verdana11);
+ clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
+ pfamjv.setFont(verdana11);
+ pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pileupjv.setFont(verdana11);
+ pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setFont(verdana11);
+ pirjv.setHorizontalAlignment(SwingConstants.LEFT);
+ autoIdWidth.setFont(verdana11);
+ autoIdWidth.setText(MessageManager
+ .getString("label.automatically_set_id_width"));
+ autoIdWidth
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
+ autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
+ autoIdWidth.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- ok_actionPerformed(e);
+ autoIdWidth_actionPerformed();
}
});
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
+ userIdWidthlabel.setFont(verdana11);
+ userIdWidthlabel.setText(MessageManager
+ .getString("label.figure_id_column_width"));
+ userIdWidth
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
+ userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
+ userIdWidth.setText("");
+ userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
+ userIdWidth.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- cancel_actionPerformed(e);
- }
- });
- quality.setEnabled(false);
- quality.setFont(verdana11);
- quality.setHorizontalAlignment(SwingConstants.RIGHT);
- quality.setHorizontalTextPosition(SwingConstants.LEFT);
- quality.setSelected(true);
- quality.setText(MessageManager.getString("label.quality"));
- visualTab.setBorder(new TitledBorder(MessageManager
- .getString("action.open_new_aligmnent")));
- visualTab.setLayout(null);
- visual2Tab.setBorder(new TitledBorder(MessageManager
- .getString("action.open_new_aligmnent")));
- visual2Tab.setLayout(new FlowLayout());
- fullScreen.setFont(verdana11);
- fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
- fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
- fullScreen.setText(MessageManager.getString("label.maximize_window"));
- conservation.setEnabled(false);
- conservation.setFont(verdana11);
- conservation.setHorizontalAlignment(SwingConstants.RIGHT);
- conservation.setHorizontalTextPosition(SwingConstants.LEFT);
- conservation.setSelected(true);
- conservation.setText(MessageManager.getString("label.conservation"));
- identity.setEnabled(false);
- identity.setFont(verdana11);
- identity.setHorizontalAlignment(SwingConstants.RIGHT);
- identity.setHorizontalTextPosition(SwingConstants.LEFT);
- identity.setSelected(true);
- identity.setText(MessageManager.getString("label.consensus"));
- showGroupbits.setFont(verdana11);
- showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText(MessageManager.getString("action.show_group")
- + ":");
- showConsensbits.setFont(verdana11);
- showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText(MessageManager.getString("label.consensus")
- + ":");
- showConsensHistogram.setEnabled(false);
- showConsensHistogram.setFont(verdana11);
- showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensHistogram.setSelected(true);
- showConsensHistogram.setText(MessageManager
- .getString("label.histogram"));
- showConsensLogo.setEnabled(false);
- showConsensLogo.setFont(verdana11);
- showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensLogo.setSelected(true);
- showConsensLogo.setText(MessageManager.getString("label.logo"));
- showGroupConsensus.setEnabled(false);
- showGroupConsensus.setFont(verdana11);
- showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupConsensus.setSelected(true);
- showGroupConsensus.setText(MessageManager.getString("label.consensus"));
- showGroupConservation.setEnabled(false);
- showGroupConservation.setFont(verdana11);
- showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupConservation.setSelected(true);
- showGroupConservation.setText(MessageManager
- .getString("label.conservation"));
- showNpTooltip.setEnabled(true);
- showNpTooltip.setFont(verdana11);
- showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
- showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
- showNpTooltip.setSelected(true);
- showNpTooltip.setText(MessageManager
- .getString("label.non_positional_features"));
- showDbRefTooltip.setEnabled(true);
- showDbRefTooltip.setFont(verdana11);
- showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
- showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
- showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText(MessageManager
- .getString("label.database_references"));
- annotations.setFont(verdana11);
- annotations.setHorizontalAlignment(SwingConstants.RIGHT);
- annotations.setHorizontalTextPosition(SwingConstants.LEADING);
- annotations.setSelected(true);
- annotations.setText(MessageManager.getString("label.show_annotations"));
- annotations.setBounds(new Rectangle(169, 12, 200, 23));
- annotations.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- identity.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- showGroupConsensus.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- showUnconserved.setFont(verdana11);
- showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
- showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
- showUnconserved.setSelected(true);
- showUnconserved.setText(MessageManager
- .getString("action.show_unconserved"));
- showUnconserved.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showunconserved_actionPerformed(e);
- }
- });
- // / TODO: fit these in to preferences panel!!!!!
- shareSelections.setFont(verdana11);
- shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
- shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
- shareSelections.setSelected(true);
- shareSelections.setText(MessageManager
- .getString("label.share_selection_across_views"));
- followHighlight.setFont(verdana11);
- followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
- followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
- // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
- followHighlight.setSelected(true);
- followHighlight.setText(MessageManager
- .getString("label.scroll_highlighted_regions"));
-
- gapLabel.setFont(verdana11);
- gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
- colour.setFont(verdana11);
- colour.setBounds(new Rectangle(172, 225, 155, 21));
- colourLabel.setFont(verdana11);
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText(MessageManager.getString("label.alignment_colour")
- + " ");
- fontLabel.setFont(verdana11);
- fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- fontLabel.setText(MessageManager.getString("label.font"));
- fontSizeCB.setFont(verdana11);
- fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
- fontStyleCB.setFont(verdana11);
- fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
- fontNameCB.setFont(verdana11);
- fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
- gapSymbolCB.setFont(verdana11);
- gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
- mincolourLabel.setFont(verdana11);
- mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- mincolourLabel.setText(MessageManager.getString("label.min_colour"));
- minColour.setFont(verdana11);
- minColour.setBorder(BorderFactory.createEtchedBorder());
- minColour.setPreferredSize(new Dimension(40, 20));
- minColour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent e)
- {
- minColour_actionPerformed();
- }
- });
- maxcolourLabel.setFont(verdana11);
- maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
- maxColour.setFont(verdana11);
- maxColour.setBorder(BorderFactory.createEtchedBorder());
- maxColour.setPreferredSize(new Dimension(40, 20));
- maxColour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent e)
- {
- maxColour_actionPerformed();
- }
- });
-
- startupCheckbox.setText(MessageManager.getString("action.open_file"));
- startupCheckbox.setFont(verdana11);
- startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
- startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
- startupCheckbox.setSelected(true);
- startupFileTextfield.setFont(verdana11);
- startupFileTextfield.setBounds(new Rectangle(172, 287, 270, 20));
- startupFileTextfield.addMouseListener(new MouseAdapter()
- {
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- startupFileTextfield_mouseClicked();
- }
+ userIdWidth_actionPerformed();
}
});
+ jPanel11.add(jLabel1);
+ jPanel11.add(blcjv);
+ jPanel11.add(clustaljv);
+ jPanel11.add(fastajv);
+ jPanel11.add(msfjv);
+ jPanel11.add(pfamjv);
+ jPanel11.add(pileupjv);
+ jPanel11.add(pirjv);
+ outputTab.add(autoIdWidth);
+ outputTab.add(userIdWidth);
+ outputTab.add(userIdWidthlabel);
+ outputTab.add(modellerOutput);
+ outputTab.add(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(jPanel11);
+ modellerOutput.setFont(verdana11);
+ modellerOutput.setText(MessageManager
+ .getString("label.use_modeller_output"));
+ modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ return outputTab;
+ }
- connectTab.setLayout(gridBagLayout3);
+ /**
+ * Initialises the Connections tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initConnectionsTab()
+ {
+ JPanel connectTab = new JPanel();
+ connectTab.setLayout(new GridBagLayout());
+ JLabel serverLabel = new JLabel();
serverLabel.setText(MessageManager.getString("label.address"));
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
serverLabel.setFont(verdana11);
proxyServerTB.setFont(verdana11);
proxyPortTB.setFont(verdana11);
+ JLabel portLabel = new JLabel();
portLabel.setFont(verdana11);
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
portLabel.setText(MessageManager.getString("label.port"));
+ JLabel browserLabel = new JLabel();
browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
browserLabel.setText(MessageManager
versioncheck.setFont(verdana11);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
+ JButton newLink = new JButton();
newLink.setText(MessageManager.getString("action.new"));
newLink.addActionListener(new java.awt.event.ActionListener()
{
newLink_actionPerformed(e);
}
});
+ JButton editLink = new JButton();
editLink.setText(MessageManager.getString("action.edit"));
editLink.addActionListener(new java.awt.event.ActionListener()
{
editLink_actionPerformed(e);
}
});
+ JButton deleteLink = new JButton();
deleteLink.setText(MessageManager.getString("action.delete"));
deleteLink.addActionListener(new java.awt.event.ActionListener()
{
}
});
+ JScrollPane linkScrollPane = new JScrollPane();
linkScrollPane.setBorder(null);
+ JPanel linkPanel = new JPanel();
linkPanel.setBorder(new TitledBorder(MessageManager
.getString("label.url_linkfrom_sequence_id")));
- linkPanel.setLayout(borderLayout2);
+ linkPanel.setLayout(new BorderLayout());
+ GridLayout gridLayout1 = new GridLayout();
+ JPanel editLinkButtons = new JPanel();
editLinkButtons.setLayout(gridLayout1);
gridLayout1.setRows(3);
linkNameList.setFont(verdana11);
linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ BorderLayout borderLayout3 = new BorderLayout();
+ JPanel linkPanel2 = new JPanel();
linkPanel2.setLayout(borderLayout3);
linkURLList.setFont(verdana11);
linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
useProxy_actionPerformed();
}
});
+ linkPanel.add(editLinkButtons, BorderLayout.EAST);
+ editLinkButtons.add(newLink, null);
+ editLinkButtons.add(editLink, null);
+ editLinkButtons.add(deleteLink, null);
+ linkPanel.add(linkScrollPane, BorderLayout.CENTER);
+ linkScrollPane.getViewport().add(linkPanel2, null);
+ linkPanel2.add(linkURLList, BorderLayout.CENTER);
+ linkPanel2.add(linkNameList, BorderLayout.WEST);
+ JPanel jPanel1 = new JPanel();
+ TitledBorder titledBorder1 = new TitledBorder(
+ MessageManager.getString("label.proxy_server"));
jPanel1.setBorder(titledBorder1);
- jPanel1.setLayout(gridBagLayout1);
- sortby.setFont(verdana11);
- sortby.setBounds(new Rectangle(172, 240, 155, 21));
- sortLabel.setFont(verdana11);
- sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- sortLabel.setText(MessageManager.getString("label.sort_by"));
- sortAnnBy.setFont(verdana11);
- sortAnnBy.setBounds(new Rectangle(172, 264, 120, 21));
- sortAnnLabel.setFont(verdana11);
- sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
- sortAutocalc.setFont(verdana11);
- sortAutocalc.setBounds(new Rectangle(300, 264, 185, 21));
- jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
- jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(13);
- exportTab.setLayout(null);
- epsLabel.setFont(verdana11);
- epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
- epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
- epsRendering.setFont(verdana11);
- epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
- jLabel1.setFont(verdana11);
- jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText(MessageManager.getString("label.append_start_end"));
- jLabel1.setFont(verdana11);
- fastajv.setFont(verdana11);
- fastajv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setText(MessageManager.getString("label.clustal") + " ");
- blcjv.setText(MessageManager.getString("label.blc") + " ");
- fastajv.setText(MessageManager.getString("label.fasta") + " ");
- msfjv.setText(MessageManager.getString("label.msf") + " ");
- pfamjv.setText(MessageManager.getString("label.pfam") + " ");
- pileupjv.setText(MessageManager.getString("label.pileup") + " ");
- msfjv.setFont(verdana11);
- msfjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setText(MessageManager.getString("label.pir") + " ");
- jPanel11.setFont(verdana11);
- jPanel11.setBorder(titledBorder2);
- jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
- jPanel11.setLayout(gridLayout3);
- blcjv.setFont(verdana11);
- blcjv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setFont(verdana11);
- clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
- pfamjv.setFont(verdana11);
- pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
- pileupjv.setFont(verdana11);
- pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setFont(verdana11);
- pirjv.setHorizontalAlignment(SwingConstants.LEFT);
- seqLimit.setFont(verdana11);
- seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
- seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
- seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
- gridLayout3.setRows(8);
- smoothFont.setFont(verdana11);
- smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
- smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
- smoothFont.setText(MessageManager.getString("label.smooth_font"));
- calcTab.setLayout(null);
- autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
- autoCalculateConsCheck.setText(MessageManager
- .getString("label.autocalculate_consensus"));
- autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(JvSwingUtils.getLabelFont());
- padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
- padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- sortByTree.setFont(JvSwingUtils.getLabelFont());
- sortByTree
- .setText(MessageManager.getString("label.sort_with_new_tree"));
- sortByTree
- .setToolTipText(MessageManager
- .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
- sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
-
- autoIdWidth.setFont(JvSwingUtils.getLabelFont());
- autoIdWidth.setText(MessageManager
- .getString("label.automatically_set_id_width"));
- autoIdWidth
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
- autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
- autoIdWidth.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- autoIdWidth_actionPerformed();
+ jPanel1.setLayout(new GridBagLayout());
+ jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 2, 4, 0), 5, 0));
+ jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 0, 4, 0), 11, 6));
+ connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+ 16, 0, 0, 12), 359, -17));
+ connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+ 21, 0, 35, 12), 4, 6));
+ connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(16, 0, 0, 0), 5, 1));
+ jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 2, 5, 185), 2, -4));
+ jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 54, 1));
+ jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 0), 263, 1));
+ connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(15, 0, 0, 15), 307, 1));
+ connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 70, 1));
+ connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 70, 1));
+ connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 70, 1));
+ return connectTab;
+ }
+
+ /**
+ * Initialises the parent panel which contains the tabbed sections.
+ *
+ * @return
+ */
+ private JPanel initOkCancelPanel()
+ {
+ JButton ok = new JButton();
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
}
});
- userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
- userIdWidthlabel.setText(MessageManager
- .getString("label.figure_id_column_width"));
- userIdWidth
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
- userIdWidthlabel
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
- userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
- userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
- userIdWidth.setText("");
- userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
- userIdWidth.addActionListener(new ActionListener()
+ JButton cancel = new JButton();
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+ JPanel okCancelPanel = new JPanel();
+ okCancelPanel.add(ok);
+ okCancelPanel.add(cancel);
+ return okCancelPanel;
+ }
+
+ /**
+ * Initialises the Colours tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initColoursTab()
+ {
+ JPanel coloursTab = new JPanel();
+ coloursTab.setBorder(new TitledBorder(MessageManager
+ .getString("action.open_new_alignment")));
+ coloursTab.setLayout(new FlowLayout());
+ JLabel mincolourLabel = new JLabel();
+ mincolourLabel.setFont(verdana11);
+ mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ mincolourLabel.setText(MessageManager.getString("label.min_colour"));
+ minColour.setFont(verdana11);
+ minColour.setBorder(BorderFactory.createEtchedBorder());
+ minColour.setPreferredSize(new Dimension(40, 20));
+ minColour.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ minColour_actionPerformed(minColour);
+ }
+ });
+ JLabel maxcolourLabel = new JLabel();
+ maxcolourLabel.setFont(verdana11);
+ maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
+ maxColour.setFont(verdana11);
+ maxColour.setBorder(BorderFactory.createEtchedBorder());
+ maxColour.setPreferredSize(new Dimension(40, 20));
+ maxColour.addMouseListener(new MouseAdapter()
{
+ public void mousePressed(MouseEvent e)
+ {
+ maxColour_actionPerformed(maxColour);
+ }
+ });
+ colour.setFont(verdana11);
+ colour.setBounds(new Rectangle(172, 225, 155, 21));
+ JLabel colourLabel = new JLabel();
+ colourLabel.setFont(verdana11);
+ colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ colourLabel.setText(MessageManager.getString("label.alignment_colour")
+ + " ");
+ JvSwingUtils.addtoLayout(coloursTab, MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ colourLabel, colour);
+ JPanel annotationShding = new JPanel();
+ annotationShding.setBorder(new TitledBorder(MessageManager
+ .getString("label.annotation_shading_default")));
+ annotationShding.setLayout(new GridLayout(1, 2));
+ JvSwingUtils.addtoLayout(annotationShding, MessageManager
+ .getString("label.default_minimum_colour_annotation_shading"),
+ mincolourLabel, minColour);
+ JvSwingUtils.addtoLayout(annotationShding, MessageManager
+ .getString("label.default_maximum_colour_annotation_shading"),
+ maxcolourLabel, maxColour);
+ coloursTab.add(annotationShding); // , FlowLayout.LEFT);
+ return coloursTab;
+ }
+ /**
+ * Initialises the Structure tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initStructureTab()
+ {
+ JPanel structureTab = new JPanel();
+ structureTab.setBorder(new TitledBorder(MessageManager
+ .getString("label.structure_options")));
+ structureTab.setLayout(null);
+ final int width = 400;
+ final int height = 23;
+ final int lineSpacing = 30;
+ int ypos = 30;
+
+ structFromPdb.setFont(verdana11);
+ structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
+ structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
+ structFromPdb.addActionListener(new ActionListener()
+ {
@Override
public void actionPerformed(ActionEvent e)
{
- userIdWidth_actionPerformed();
+ boolean selected = structFromPdb.isSelected();
+ // enable other options only when the first is checked
+ useRnaView.setEnabled(selected);
+ addSecondaryStructure.setEnabled(selected);
+ addTempFactor.setEnabled(selected);
}
});
- modellerOutput.setFont(JvSwingUtils.getLabelFont());
- modellerOutput.setText(MessageManager
- .getString("label.use_modeller_output"));
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ structureTab.add(structFromPdb);
+
+ // indent checkboxes that are conditional on the first one
+ ypos += lineSpacing;
+ useRnaView.setFont(verdana11);
+ useRnaView.setText(MessageManager.getString("label.use_rnaview"));
+ useRnaView.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(useRnaView);
+
+ ypos += lineSpacing;
+ addSecondaryStructure.setFont(verdana11);
+ addSecondaryStructure.setText(MessageManager
+ .getString("label.autoadd_secstr"));
+ addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addSecondaryStructure);
+
+ ypos += lineSpacing;
+ addTempFactor.setFont(verdana11);
+ addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
+ addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addTempFactor);
+
+ ypos += lineSpacing;
+ JLabel viewerLabel = new JLabel();
+ viewerLabel.setFont(verdana11);
+ viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
+ viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
+ structureTab.add(viewerLabel);
+
+ structViewer.setFont(verdana11);
+ structViewer.setBounds(new Rectangle(150, ypos, 120, height));
+ structViewer.addItem(Viewer.JMOL.name());
+ structViewer.addItem(Viewer.CHIMERA.name());
+ structureTab.add(structViewer);
+
+ return structureTab;
+ }
- dasPanel.setLayout(borderLayout4);
- wsPanel.setLayout(borderLayout5);
- wrap.setFont(JvSwingUtils.getLabelFont());
+ /**
+ * Initialises the Visual tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initVisualTab()
+ {
+ JPanel visualTab = new JPanel();
+ visualTab.setBorder(new TitledBorder(MessageManager
+ .getString("action.open_new_alignment")));
+ visualTab.setLayout(null);
+ fullScreen.setFont(verdana11);
+ fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+ fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+ fullScreen.setText(MessageManager.getString("label.maximize_window"));
+ quality.setEnabled(false);
+ quality.setFont(verdana11);
+ quality.setHorizontalAlignment(SwingConstants.RIGHT);
+ quality.setHorizontalTextPosition(SwingConstants.LEFT);
+ quality.setSelected(true);
+ quality.setText(MessageManager.getString("label.quality"));
+ conservation.setEnabled(false);
+ conservation.setFont(verdana11);
+ conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ conservation.setSelected(true);
+ conservation.setText(MessageManager.getString("label.conservation"));
+ identity.setEnabled(false);
+ identity.setFont(verdana11);
+ identity.setHorizontalAlignment(SwingConstants.RIGHT);
+ identity.setHorizontalTextPosition(SwingConstants.LEFT);
+ identity.setSelected(true);
+ identity.setText(MessageManager.getString("label.consensus"));
+ JLabel showGroupbits = new JLabel();
+ showGroupbits.setFont(verdana11);
+ showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupbits.setText(MessageManager.getString("action.show_group")
+ + ":");
+ JLabel showConsensbits = new JLabel();
+ showConsensbits.setFont(verdana11);
+ showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensbits.setText(MessageManager.getString("label.consensus")
+ + ":");
+ showConsensHistogram.setEnabled(false);
+ showConsensHistogram.setFont(verdana11);
+ showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensHistogram.setSelected(true);
+ showConsensHistogram.setText(MessageManager
+ .getString("label.histogram"));
+ showConsensLogo.setEnabled(false);
+ showConsensLogo.setFont(verdana11);
+ showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensLogo.setSelected(true);
+ showConsensLogo.setText(MessageManager.getString("label.logo"));
+ showGroupConsensus.setEnabled(false);
+ showGroupConsensus.setFont(verdana11);
+ showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConsensus.setSelected(true);
+ showGroupConsensus.setText(MessageManager.getString("label.consensus"));
+ showGroupConservation.setEnabled(false);
+ showGroupConservation.setFont(verdana11);
+ showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConservation.setSelected(true);
+ showGroupConservation.setText(MessageManager
+ .getString("label.conservation"));
+ showNpTooltip.setEnabled(true);
+ showNpTooltip.setFont(verdana11);
+ showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showNpTooltip.setSelected(true);
+ showNpTooltip.setText(MessageManager
+ .getString("label.non_positional_features"));
+ showDbRefTooltip.setEnabled(true);
+ showDbRefTooltip.setFont(verdana11);
+ showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showDbRefTooltip.setSelected(true);
+ showDbRefTooltip.setText(MessageManager
+ .getString("label.database_references"));
+ annotations.setFont(verdana11);
+ annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+ annotations.setHorizontalTextPosition(SwingConstants.LEADING);
+ annotations.setSelected(true);
+ annotations.setText(MessageManager.getString("label.show_annotations"));
+ annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ annotations.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ identity.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showUnconserved.setFont(verdana11);
+ showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
+ showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
+ showUnconserved.setSelected(true);
+ showUnconserved.setText(MessageManager
+ .getString("action.show_unconserved"));
+ showUnconserved.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showunconserved_actionPerformed(e);
+ }
+ });
+
+ // TODO these are not yet added to / action from Preferences
+ // JCheckBox shareSelections = new JCheckBox();
+ // shareSelections.setFont(verdana11);
+ // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
+ // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
+ // shareSelections.setSelected(true);
+ // shareSelections.setText(MessageManager
+ // .getString("label.share_selection_across_views"));
+ // JCheckBox followHighlight = new JCheckBox();
+ // followHighlight.setFont(verdana11);
+ // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+ // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+ // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ // followHighlight.setSelected(true);
+ // followHighlight.setText(MessageManager
+ // .getString("label.scroll_highlighted_regions"));
+
+ seqLimit.setFont(verdana11);
+ seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
+ seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
+ seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
+ smoothFont.setFont(verdana11);
+ smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
+ smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
+ smoothFont.setText(MessageManager.getString("label.smooth_font"));
+ JLabel gapLabel = new JLabel();
+ gapLabel.setFont(verdana11);
+ gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
+ JLabel fontLabel = new JLabel();
+ fontLabel.setFont(verdana11);
+ fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ fontLabel.setText(MessageManager.getString("label.font"));
+ fontSizeCB.setFont(verdana11);
+ fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
+ fontStyleCB.setFont(verdana11);
+ fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
+ fontNameCB.setFont(verdana11);
+ fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
+ gapSymbolCB.setFont(verdana11);
+ gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
+ DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+ gapSymbolCB.setRenderer(dlcr);
+
+ startupCheckbox.setText(MessageManager.getString("action.open_file"));
+ startupCheckbox.setFont(verdana11);
+ startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
+ startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
+ startupCheckbox.setSelected(true);
+ startupFileTextfield.setFont(verdana11);
+ startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
+ startupFileTextfield.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ startupFileTextfield_mouseClicked();
+ }
+ }
+ });
+
+ sortby.setFont(verdana11);
+ sortby.setBounds(new Rectangle(172, 240, 155, 21));
+ JLabel sortLabel = new JLabel();
+ sortLabel.setFont(verdana11);
+ sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortLabel.setText(MessageManager.getString("label.sort_by"));
+ sortAnnBy.setFont(verdana11);
+ sortAnnBy.setBounds(new Rectangle(172, 265, 120, 21));
+ JLabel sortAnnLabel = new JLabel();
+ sortAnnLabel.setFont(verdana11);
+ sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
+ sortAutocalc.setFont(verdana11);
+ sortAutocalc.setBounds(new Rectangle(300, 265, 185, 21));
+ JPanel annsettingsPanel = new JPanel();
+ annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
+ annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
+ JPanel autoAnnotSettings1 = new JPanel();
+ autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
+ annsettingsPanel.add(autoAnnotSettings1);
+ JPanel autoAnnotSettings2 = new JPanel();
+ autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
+ annsettingsPanel.add(autoAnnotSettings2);
+ JPanel autoAnnotSettings3 = new JPanel();
+ autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
+ annsettingsPanel.add(autoAnnotSettings3);
+ visualTab.add(annsettingsPanel);
+ Border jb = new EmptyBorder(1, 1, 4, 5);
+ quality.setBorder(jb);
+ conservation.setBorder(jb);
+ identity.setBorder(jb);
+ showConsensbits.setBorder(jb);
+ showGroupbits.setBorder(jb);
+ showGroupConsensus.setBorder(jb);
+ showGroupConservation.setBorder(jb);
+ showConsensHistogram.setBorder(jb);
+ showConsensLogo.setBorder(jb);
+
+ autoAnnotSettings2.add(conservation);
+ autoAnnotSettings1.add(quality);
+ autoAnnotSettings3.add(identity);
+ autoAnnotSettings1.add(showGroupbits);
+ autoAnnotSettings3.add(showGroupConsensus);
+ autoAnnotSettings2.add(showGroupConservation);
+ autoAnnotSettings1.add(showConsensbits);
+ autoAnnotSettings2.add(showConsensHistogram);
+ autoAnnotSettings3.add(showConsensLogo);
+
+ JPanel tooltipSettings = new JPanel();
+ tooltipSettings.setBorder(new TitledBorder(MessageManager
+ .getString("label.sequence_id_tooltip")));
+ tooltipSettings.setBounds(173, 130, 200, 62);
+ tooltipSettings.setLayout(new GridLayout(2, 1));
+ tooltipSettings.add(showDbRefTooltip);
+ tooltipSettings.add(showNpTooltip);
+ visualTab.add(tooltipSettings);
+
+ wrap.setFont(verdana11);
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText(MessageManager.getString("label.wrap_alignment"));
- rightAlign.setFont(JvSwingUtils.getLabelFont());
+ rightAlign.setFont(verdana11);
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
rightAlign.setText(MessageManager.getString("label.right_align_ids"));
- idItalics.setFont(JvSwingUtils.getLabelFont());
+ idItalics.setFont(verdana11);
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
idItalics.setText(MessageManager
.getString("label.sequence_name_italics"));
- openoverv.setFont(JvSwingUtils.getLabelFont());
+ openoverv.setFont(verdana11);
openoverv.setActionCommand(MessageManager
.getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
openoverv.setText(MessageManager.getString(("label.open_overview")));
+ JPanel jPanel2 = new JPanel();
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
+ GridLayout gridLayout2 = new GridLayout();
+ jPanel2.setLayout(gridLayout2);
+ gridLayout2.setRows(13);
jPanel2.add(fullScreen);
jPanel2.add(openoverv);
jPanel2.add(seqLimit);
jPanel2.add(sortLabel);
jPanel2.add(sortAnnLabel);
jPanel2.add(startupCheckbox);
+ visualTab.add(jPanel2);
visualTab.add(annotations);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
- annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
- annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
- annsettingsPanel.add(autoAnnotSettings1);
- annsettingsPanel.add(autoAnnotSettings2);
- annsettingsPanel.add(autoAnnotSettings3);
- autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
- autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
- autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
- visualTab.add(annsettingsPanel);
- Border jb = new EmptyBorder(1, 1, 4, 5);
- quality.setBorder(jb);
- conservation.setBorder(jb);
- identity.setBorder(jb);
- showConsensbits.setBorder(jb);
- showGroupbits.setBorder(jb);
- showGroupConsensus.setBorder(jb);
- showGroupConservation.setBorder(jb);
- showConsensHistogram.setBorder(jb);
- showConsensLogo.setBorder(jb);
-
- autoAnnotSettings2.add(conservation);
- autoAnnotSettings1.add(quality);
- autoAnnotSettings3.add(identity);
- autoAnnotSettings1.add(showGroupbits);
- autoAnnotSettings3.add(showGroupConsensus);
- autoAnnotSettings2.add(showGroupConservation);
- autoAnnotSettings1.add(showConsensbits);
- autoAnnotSettings2.add(showConsensHistogram);
- autoAnnotSettings3.add(showConsensLogo);
-
- JPanel tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder(MessageManager
- .getString("label.sequence_id_tooltip")));
- tooltipSettings.setBounds(173, 130, 200, 62);
- tooltipSettings.setLayout(new GridLayout(2, 1));
- tooltipSettings.add(showDbRefTooltip);
- tooltipSettings.add(showNpTooltip);
- visualTab.add(tooltipSettings);
- visualTab.add(jPanel2);
- JvSwingUtils.addtoLayout(visual2Tab, MessageManager
- .getString("label.default_colour_scheme_for_alignment"),
- colourLabel, colour);
- JPanel annotationShding = new JPanel();
- annotationShding.setBorder(new TitledBorder(MessageManager
- .getString("label.annotation_shading_default")));
- annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding, MessageManager
- .getString("label.default_minimum_colour_annotation_shading"),
- mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding, MessageManager
- .getString("label.default_maximum_colour_annotation_shading"),
- maxcolourLabel, maxColour);
- visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
-
- // visual2panel.add(minColour);
- // visual2panel.add(maxColour);
- // visual2Tab.add(visual2panel);
-
- linkPanel.add(editLinkButtons, BorderLayout.EAST);
- editLinkButtons.add(newLink, null);
- editLinkButtons.add(editLink, null);
- editLinkButtons.add(deleteLink, null);
- linkPanel.add(linkScrollPane, BorderLayout.CENTER);
- linkScrollPane.getViewport().add(linkPanel2, null);
- linkPanel2.add(linkURLList, BorderLayout.CENTER);
- linkPanel2.add(linkNameList, BorderLayout.WEST);
- okCancelPanel.add(ok);
- okCancelPanel.add(cancel);
- this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-
- this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
- jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 4, 0), 5, 0));
- jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 0, 4, 0), 11, 6));
- connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 16, 0, 0, 12), 359, -17));
- connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 21, 0, 35, 12), 4, 6));
- connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(16, 0, 0, 0), 5, 1));
- jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 54, 1));
- jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 0), 263, 1));
- connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(15, 0, 0, 15), 307, 1));
- connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
-
- jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 5, 185), 2, -4));
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
- gapSymbolCB.setRenderer(dlcr);
-
- tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
- tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
- tabbedPane.add(connectTab,
- MessageManager.getString("label.connections"));
- tabbedPane.add(exportTab, MessageManager.getString("label.output"));
- jPanel11.add(jLabel1);
- jPanel11.add(blcjv);
- jPanel11.add(clustaljv);
- jPanel11.add(fastajv);
- jPanel11.add(msfjv);
- jPanel11.add(pfamjv);
- jPanel11.add(pileupjv);
- jPanel11.add(pirjv);
- exportTab.add(autoIdWidth);
- exportTab.add(userIdWidth);
- exportTab.add(userIdWidthlabel);
- exportTab.add(modellerOutput);
- tabbedPane.add(calcTab, MessageManager.getString("label.editing"));
- calcTab.add(autoCalculateConsCheck);
- calcTab.add(padGaps);
- calcTab.add(sortByTree);
-
- tabbedPane
- .add(dasPanel, MessageManager.getString("label.das_settings"));
- tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
-
- exportTab.add(epsLabel);
- exportTab.add(epsRendering);
- exportTab.add(jPanel11);
+ return visualTab;
}
protected void autoIdWidth_actionPerformed()
}
- protected void maxColour_actionPerformed()
+ protected void maxColour_actionPerformed(JPanel panel)
{
- // TODO Auto-generated method stub
-
}
- protected void minColour_actionPerformed()
+ protected void minColour_actionPerformed(JPanel panel)
{
- // TODO Auto-generated method stub
-
}
protected void showunconserved_actionPerformed(ActionEvent e)
git://source.jalview.org / jalview.git / commitdiff