X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=aaa73a14d56ccdb63443f8a00e64d8b1a19d5df8;hb=966aac0d41c1ce4c3e1ef24a2d1b174752d40f83;hp=6b2c0f4b7f2d7e7a225aafa614fe397b21937069;hpb=be5a6a44e9eb355110f3b414d6b0fd5419f5936c;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 6b2c0f4..aaa73a1 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,20 +1,19 @@ /* - * 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 . */ package jalview.jbgui; @@ -136,12 +135,14 @@ public class GPreferences extends JPanel GridLayout gridLayout2 = new GridLayout(); - JPanel jPanel3 = new JPanel(); + JPanel annsettingsPanel = new JPanel(); JPanel autoAnnotSettings1 = new JPanel(); JPanel autoAnnotSettings2 = new JPanel(); + JPanel autoAnnotSettings3 = new JPanel(); + JPanel exportTab = new JPanel(); JLabel epsLabel = new JLabel(); @@ -188,25 +189,46 @@ public class GPreferences extends 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 showConsensProfile = new JCheckBox(); + + 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. */ @@ -225,7 +247,7 @@ public class GPreferences extends JPanel * DOCUMENT ME! * * @throws Exception - * DOCUMENT ME! + * DOCUMENT ME! */ private void jbInit() throws Exception { @@ -273,7 +295,7 @@ public class GPreferences extends JPanel showGroupbits.setFont(verdana11); showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT); showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT); - showGroupbits.setText("Group:"); + showGroupbits.setText("Show group:"); showConsensbits.setFont(verdana11); showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT); showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT); @@ -284,12 +306,12 @@ public class GPreferences extends JPanel showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT); showConsensHistogram.setSelected(true); showConsensHistogram.setText("Histogram"); - showConsensProfile.setEnabled(false); - showConsensProfile.setFont(verdana11); - showConsensProfile.setHorizontalAlignment(SwingConstants.RIGHT); - showConsensProfile.setHorizontalTextPosition(SwingConstants.LEFT); - showConsensProfile.setSelected(true); - showConsensProfile.setText("Profile"); + showConsensLogo.setEnabled(false); + showConsensLogo.setFont(verdana11); + showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT); + showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT); + showConsensLogo.setSelected(true); + showConsensLogo.setText("Logo"); showGroupConsensus.setEnabled(false); showGroupConsensus.setFont(verdana11); showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT); @@ -302,11 +324,24 @@ public class GPreferences extends JPanel 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.LEFT); + annotations.setHorizontalTextPosition(SwingConstants.LEADING); annotations.setSelected(true); annotations.setText("Show Annotations"); + annotations.setBounds(new Rectangle(169, 12, 200, 23)); annotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -314,10 +349,23 @@ public class GPreferences extends JPanel 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.setBounds(new Rectangle(169, 40, 200, 23)); showUnconserved.setSelected(true); showUnconserved.setText("Show Unconserved"); showUnconserved.addActionListener(new ActionListener() @@ -327,7 +375,19 @@ public class GPreferences extends JPanel 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("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("Scroll to highlighted regions"); + gapLabel.setFont(verdana11); gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); gapLabel.setText("Gap Symbol "); @@ -340,13 +400,13 @@ public class GPreferences extends JPanel 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); @@ -476,9 +536,6 @@ public class GPreferences extends JPanel jPanel2.setBounds(new Rectangle(7, 17, 158, 278)); jPanel2.setLayout(gridLayout2); gridLayout2.setRows(13); - jPanel3.setBounds(new Rectangle(173, 35, 274, 26)); - 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); @@ -536,6 +593,7 @@ public class GPreferences extends JPanel 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); @@ -552,11 +610,10 @@ public class GPreferences extends JPanel openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); openoverv.setActionCommand("Open Overview"); openoverv.setHorizontalAlignment(SwingConstants.RIGHT); - openoverv.setHorizontalTextPosition(SwingConstants.LEADING); - openoverv.setText("Open Overview Window"); - openoverv.setBounds(new Rectangle(169, 17, 200, 23)); + openoverv.setHorizontalTextPosition(SwingConstants.LEFT); + openoverv.setText("Open Overview"); jPanel2.add(fullScreen); - jPanel2.add(annotations); + jPanel2.add(openoverv); jPanel2.add(seqLimit); jPanel2.add(rightAlign); jPanel2.add(fontLabel); @@ -568,28 +625,51 @@ public class GPreferences extends JPanel jPanel2.add(colourLabel); jPanel2.add(sortLabel); jPanel2.add(startupCheckbox); - visualTab.add(openoverv); + visualTab.add(annotations); visualTab.add(startupFileTextfield); visualTab.add(sortby); visualTab.add(colour); visualTab.add(gapSymbolCB); - visualTab.add(jPanel3); visualTab.add(fontNameCB); visualTab.add(fontSizeCB); visualTab.add(fontStyleCB); - visualTab.add(autoAnnotSettings1); - visualTab.add(autoAnnotSettings2); - jPanel3.add(conservation); - jPanel3.add(identity); - jPanel3.add(quality); - autoAnnotSettings1.setLayout(new FlowLayout()); - autoAnnotSettings2.setLayout(new FlowLayout()); - autoAnnotSettings1.add(showConsensbits); - autoAnnotSettings1.add(showConsensHistogram); - autoAnnotSettings1.add(showConsensProfile); - autoAnnotSettings2.add(showGroupbits); - autoAnnotSettings2.add(showGroupConsensus); + 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("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); @@ -629,16 +709,16 @@ public class GPreferences extends JPanel 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)); @@ -662,6 +742,7 @@ public class GPreferences extends JPanel calcTab.add(autoCalculateConsCheck); calcTab.add(padGaps); tabbedPane.add(dasPanel, "DAS Settings"); + tabbedPane.add(wsPanel, "Web Services"); exportTab.add(epsLabel); exportTab.add(epsRendering); @@ -671,14 +752,14 @@ public class GPreferences extends JPanel 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) { @@ -688,7 +769,7 @@ public class GPreferences extends JPanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void cancel_actionPerformed(ActionEvent e) { @@ -698,7 +779,7 @@ public class GPreferences extends JPanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void annotations_actionPerformed(ActionEvent e) {