/*
- * 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 2.7)
+ * Copyright (C) 2011 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;
+import jalview.gui.JvSwingUtils;
+
import java.awt.*;
import java.awt.event.*;
protected JCheckBox quality = new JCheckBox();
JPanel visualTab = new JPanel();
+ JPanel visual2Tab = new JPanel();
protected JCheckBox fullScreen = 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 colour = new JComboBox();
JLabel sortLabel = new JLabel();
JPanel jPanel2 = new JPanel();
+ JPanel visual2panel = new JPanel();
GridLayout gridLayout2 = new GridLayout();
+ GridLayout gridLayout4 = new GridLayout();
JPanel annsettingsPanel = new JPanel();
+
JPanel autoAnnotSettings1 = new JPanel();
+
JPanel autoAnnotSettings2 = new JPanel();
+
JPanel autoAnnotSettings3 = new JPanel();
JPanel exportTab = new JPanel();
JLabel epsLabel = new JLabel();
protected JComboBox epsRendering = new JComboBox();
+
+ protected JLabel userIdWidthlabel = new JLabel();
+ protected JCheckBox autoIdWidth = new JCheckBox();
+ protected JTextField userIdWidth = new JTextField();
+
JLabel jLabel1 = new JLabel();
JPanel jPanel11 = new JPanel();
- Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
+ Font verdana11 = JvSwingUtils.getLabelFont();
protected JCheckBox seqLimit = new JCheckBox();
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();
-
+
+ protected JCheckBox sortByTree= new JCheckBox();
/**
* Creates a new GPreferences object.
* DOCUMENT ME!
*
* @throws Exception
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
private void jbInit() throws Exception
{
quality.setText("Quality");
visualTab.setBorder(new TitledBorder("Open new alignment"));
visualTab.setLayout(null);
+ visual2Tab.setBorder(new TitledBorder("Open new alignment"));
+ visual2Tab.setLayout(new FlowLayout());
fullScreen.setFont(verdana11);
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
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_actionPerformed(e);
}
});
- /// TODO: fit these in to preferences panel!!!!!
+ // / TODO: fit these in to preferences panel!!!!!
shareSelections.setFont(verdana11);
shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
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 ");
colour.setBounds(new Rectangle(172, 225, 155, 21));
colourLabel.setFont(verdana11);
colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText("Colour ");
+ colourLabel.setText("Alignment Colour ");
fontLabel.setFont(verdana11);
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));
+ mincolourLabel.setFont(verdana11);
+ mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ mincolourLabel.setText("Minimum 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("Maximum 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("Open file");
startupCheckbox.setFont(verdana11);
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
sortLabel.setText("Sort by ");
jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(13);
+ gridLayout2.setRows(12);
exportTab.setLayout(null);
epsLabel.setFont(verdana11);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
smoothFont.setText("Smooth Font");
calcTab.setLayout(null);
- autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
- 11));
+ autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
autoCalculateConsCheck.setText("AutoCalculate Consensus");
autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- padGaps.setText("Pad gaps when editing");
+ padGaps.setFont(JvSwingUtils.getLabelFont());
+ padGaps.setText("Pad Gaps When Editing");
padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ sortByTree.setFont(JvSwingUtils.getLabelFont());
+ sortByTree.setText("Sort With New Tree");
+ sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
+ sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+
+ autoIdWidth.setFont(JvSwingUtils.getLabelFont());
+ autoIdWidth.setText("Automatically set ID width");
+ autoIdWidth.setToolTipText("<html>"+JvSwingUtils.wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")+"</html>");
+ autoIdWidth.setBounds(new Rectangle(228, 96,188,23));
+ autoIdWidth.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ autoIdWidth_actionPerformed();
+ }
+ });
+ userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
+ userIdWidthlabel.setText("Figure ID column width");
+ userIdWidth
+ .setToolTipText("<html>"+JvSwingUtils
+ .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")+"</html>");
+ userIdWidthlabel
+ .setToolTipText("<html>"+JvSwingUtils
+ .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")+"</html>");
+ 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)
+ {
+ userIdWidth_actionPerformed();
+ }
+ });
+ modellerOutput.setFont(JvSwingUtils.getLabelFont());
modellerOutput.setText("Use Modeller Output");
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+
dasPanel.setLayout(borderLayout4);
- wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ wsPanel.setLayout(borderLayout5);
+ wrap.setFont(JvSwingUtils.getLabelFont());
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText("Wrap Alignment");
- rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ rightAlign.setFont(JvSwingUtils.getLabelFont());
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
rightAlign.setText("Right Align Ids");
- idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ idItalics.setFont(JvSwingUtils.getLabelFont());
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
idItalics.setText("Sequence Name Italics");
- openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ openoverv.setFont(JvSwingUtils.getLabelFont());
openoverv.setActionCommand("Open Overview");
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
jPanel2.add(showUnconserved);
jPanel2.add(idItalics);
jPanel2.add(smoothFont);
- jPanel2.add(wrap);
jPanel2.add(gapLabel);
- jPanel2.add(colourLabel);
+ jPanel2.add(wrap);
jPanel2.add(sortLabel);
jPanel2.add(startupCheckbox);
visualTab.add(annotations);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
- visualTab.add(colour);
visualTab.add(gapSymbolCB);
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
- annsettingsPanel.setBounds(new Rectangle(173,37,300,62));
- 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));
- 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);
- 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);
-autoAnnotSettings1.add(showGroupbits);
+ autoAnnotSettings1.add(showGroupbits);
autoAnnotSettings3.add(showGroupConsensus);
autoAnnotSettings2.add(showGroupConservation);
autoAnnotSettings1.add(showConsensbits);
JPanel tooltipSettings = new JPanel();
tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
- tooltipSettings.setBounds(173, 130, 200,62);
- tooltipSettings.setLayout(new GridLayout(2,1));
+ 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, "Default Colourscheme for alignment", colourLabel, colour);
+ JPanel annotationShding=new JPanel();
+ annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
+ annotationShding.setLayout(new GridLayout(1,2));
+ JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
+ JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for 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);
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));
gapSymbolCB.setRenderer(dlcr);
tabbedPane.add(visualTab, "Visual");
+ tabbedPane.add(visual2Tab,"Colours");
tabbedPane.add(connectTab, "Connections");
tabbedPane.add(exportTab, "Output");
jPanel11.add(jLabel1);
jPanel11.add(pfamjv);
jPanel11.add(pileupjv);
jPanel11.add(pirjv);
+ exportTab.add(autoIdWidth);
+ exportTab.add(userIdWidth);
+ exportTab.add(userIdWidthlabel);
exportTab.add(modellerOutput);
tabbedPane.add(calcTab, "Editing");
calcTab.add(autoCalculateConsCheck);
calcTab.add(padGaps);
+ calcTab.add(sortByTree);
+
tabbedPane.add(dasPanel, "DAS Settings");
+ tabbedPane.add(wsPanel, "Web Services");
exportTab.add(epsLabel);
exportTab.add(epsRendering);
exportTab.add(jPanel11);
}
- protected void showunconserved_actionPerformed(ActionEvent e)
+ protected void autoIdWidth_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void userIdWidth_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void maxColour_actionPerformed()
{
// TODO Auto-generated method stub
}
+ protected void minColour_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ 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