/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.jbgui;
GridLayout gridLayout2 = new GridLayout();
-
JPanel annsettingsPanel = new JPanel();
+
JPanel autoAnnotSettings1 = new JPanel();
+
JPanel autoAnnotSettings2 = new JPanel();
+
JPanel autoAnnotSettings3 = new JPanel();
JPanel exportTab = 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 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 followHighlight = new JCheckBox();
-
/**
* Creates a new GPreferences object.
* DOCUMENT ME!
*
* @throws Exception
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
private void jbInit() throws Exception
{
showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConservation.setSelected(true);
showGroupConservation.setText("Conservation");
+ showNpTooltip.setEnabled(true);
+ showNpTooltip.setFont(verdana11);
+ showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showNpTooltip.setSelected(true);
+ showNpTooltip.setText("Non-positional Features");
+ showDbRefTooltip.setEnabled(true);
+ showDbRefTooltip.setFont(verdana11);
+ showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showDbRefTooltip.setSelected(true);
+ showDbRefTooltip.setText("Database References");
annotations.setFont(verdana11);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
annotations.setHorizontalTextPosition(SwingConstants.LEADING);
annotations.setSelected(true);
annotations.setText("Show Annotations");
- annotations.setBounds(new Rectangle(169, 16, 200, 23));
+ annotations.setBounds(new Rectangle(169, 12, 200, 23));
annotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
identity.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
{
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
+ annotations_actionPerformed(e);
+ }
+ });
showGroupConsensus.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
{
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
+ annotations_actionPerformed(e);
+ }
+ });
showUnconserved.setFont(verdana11);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
- //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
showUnconserved.setSelected(true);
showUnconserved.setText("Show Unconserved");
showUnconserved.addActionListener(new ActionListener()
showunconserved_actionPerformed(e);
}
});
+ // / TODO: fit these in to preferences panel!!!!!
shareSelections.setFont(verdana11);
shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
- //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
shareSelections.setSelected(true);
shareSelections.setText("Share selection across views");
followHighlight.setFont(verdana11);
followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
- //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
followHighlight.setSelected(true);
followHighlight.setText("Scroll to highlighted regions");
-
+
gapLabel.setFont(verdana11);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
gapLabel.setText("Gap Symbol ");
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
fontLabel.setText("Font ");
fontSizeCB.setFont(verdana11);
- fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
+ fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
fontStyleCB.setFont(verdana11);
- fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
+ fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
fontNameCB.setFont(verdana11);
- fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
+ fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
gapSymbolCB.setFont(verdana11);
- gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
+ gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
startupCheckbox.setText("Open file");
startupCheckbox.setFont(verdana11);
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
jPanel2.setLayout(gridLayout2);
gridLayout2.setRows(13);
- // jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
- //jPanel3.setBounds(new Rectangle(173, 35, 274, 78));
- //jPanel3.setLayout(new GridLayout(3,3));
-// autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
-// autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
exportTab.setLayout(null);
epsLabel.setFont(verdana11);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
modellerOutput.setText("Use Modeller Output");
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
dasPanel.setLayout(borderLayout4);
+ wsPanel.setLayout(borderLayout5);
wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
- annsettingsPanel.setBounds(new Rectangle(173,39,300,62));
- annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
+ 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));
-// autoAnnotSettings1.setPreferredSize(new Dimensions())
- autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
- autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
+ 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);
- //visualTab.add(autoAnnotSettings1);
- //visualTab.add(autoAnnotSettings2);
- Border jb = new EmptyBorder(1,1,4,5);
+ Border jb = new EmptyBorder(1, 1, 4, 5);
quality.setBorder(jb);
conservation.setBorder(jb);
identity.setBorder(jb);
showGroupConservation.setBorder(jb);
showConsensHistogram.setBorder(jb);
showConsensLogo.setBorder(jb);
-
+
autoAnnotSettings2.add(conservation);
autoAnnotSettings1.add(quality);
autoAnnotSettings3.add(identity);
-
- /*FlowLayout fl = new FlowLayout();
- fl.setAlignment(FlowLayout.LEFT);
- autoAnnotSettings1.setLayout(fl);
- fl = new FlowLayout();
- fl.setAlignment(FlowLayout.LEFT);
- autoAnnotSettings2.setLayout(fl); */
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("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);
linkPanel.add(editLinkButtons, BorderLayout.EAST);
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(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));
+ 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));
-
+ 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));
calcTab.add(autoCalculateConsCheck);
calcTab.add(padGaps);
tabbedPane.add(dasPanel, "DAS Settings");
+ tabbedPane.add(wsPanel, "Web Services");
exportTab.add(epsLabel);
exportTab.add(epsRendering);
protected void showunconserved_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void ok_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void cancel_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void annotations_actionPerformed(ActionEvent e)
{
git://source.jalview.org / jalview.git / blobdiff