X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=3458347978e96ac2125f6e896b6492faccffef1f;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9d691caa8067f49bd6bacb17c2127ca1622dfd0e;hpb=1aa21d01e983854e9dbb1628350ac6976c52430a;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 9d691ca..3458347 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -21,7 +21,8 @@ package jalview.jbgui; import jalview.gui.JvSwingUtils; -import jalview.gui.StructureViewer.Viewer; +import jalview.gui.StructureViewer.ViewerType; +import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -37,7 +38,6 @@ import java.awt.Insets; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; @@ -59,6 +59,7 @@ import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; import javax.swing.border.Border; import javax.swing.border.EmptyBorder; +import javax.swing.border.EtchedBorder; import javax.swing.border.TitledBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; @@ -73,7 +74,10 @@ import javax.swing.event.ListSelectionListener; */ public class GPreferences extends JPanel { - private static final Font verdana11 = JvSwingUtils.getLabelFont(); + private static final Font LABEL_FONT = JvSwingUtils.getLabelFont(); + + private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont( + false, true); /* * Visual tab components @@ -98,6 +102,8 @@ public class GPreferences extends JPanel protected JCheckBox smoothFont = new JCheckBox(); + protected JCheckBox scaleProteinToCdna = new JCheckBox(); + protected JComboBox gapSymbolCB = new JComboBox(); protected JCheckBox wrap = new JCheckBox(); @@ -157,7 +163,9 @@ public class GPreferences extends JPanel protected JPanel maxColour = new JPanel(); - protected JComboBox colour = new JComboBox(); + protected JComboBox protColour = new JComboBox(); + + protected JComboBox nucColour = new JComboBox(); /* * Connections tab components @@ -207,6 +215,8 @@ public class GPreferences extends JPanel protected JCheckBox modellerOutput = new JCheckBox(); + protected JCheckBox embbedBioJSON = new JCheckBox(); + /* * Editing tab components */ @@ -265,16 +275,17 @@ public class GPreferences extends JPanel tabbedPane.add(initConnectionsTab(), MessageManager.getString("label.connections")); - tabbedPane.add(initOutputTab(), MessageManager.getString("label.output")); + tabbedPane.add(initOutputTab(), + MessageManager.getString("label.output")); - tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing")); + 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")); + tabbedPane.add(dasTab, MessageManager.getString("label.das_settings")); /* * See WsPreferences for the real work of configuring this tab. @@ -317,14 +328,14 @@ public class GPreferences extends JPanel { JPanel editingTab = new JPanel(); editingTab.setLayout(null); - autoCalculateConsCheck.setFont(verdana11); + autoCalculateConsCheck.setFont(LABEL_FONT); autoCalculateConsCheck.setText(MessageManager .getString("label.autocalculate_consensus")); autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23)); - padGaps.setFont(verdana11); + padGaps.setFont(LABEL_FONT); padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing")); padGaps.setBounds(new Rectangle(22, 94, 168, 23)); - sortByTree.setFont(verdana11); + sortByTree.setFont(LABEL_FONT); sortByTree .setText(MessageManager.getString("label.sort_with_new_tree")); sortByTree @@ -347,18 +358,18 @@ public class GPreferences extends JPanel JPanel outputTab = new JPanel(); outputTab.setLayout(null); JLabel epsLabel = new JLabel(); - epsLabel.setFont(verdana11); + epsLabel.setFont(LABEL_FONT); epsLabel.setHorizontalAlignment(SwingConstants.RIGHT); epsLabel.setText(MessageManager.getString("label.eps_rendering_style")); epsLabel.setBounds(new Rectangle(9, 31, 140, 24)); - epsRendering.setFont(verdana11); + epsRendering.setFont(LABEL_FONT); epsRendering.setBounds(new Rectangle(154, 34, 187, 21)); JLabel jLabel1 = new JLabel(); - jLabel1.setFont(verdana11); + jLabel1.setFont(LABEL_FONT); jLabel1.setHorizontalAlignment(SwingConstants.CENTER); jLabel1.setText(MessageManager.getString("label.append_start_end")); - jLabel1.setFont(verdana11); - fastajv.setFont(verdana11); + jLabel1.setFont(LABEL_FONT); + fastajv.setFont(LABEL_FONT); fastajv.setHorizontalAlignment(SwingConstants.LEFT); clustaljv.setText(MessageManager.getString("label.clustal") + " "); blcjv.setText(MessageManager.getString("label.blc") + " "); @@ -366,11 +377,11 @@ public class GPreferences extends JPanel msfjv.setText(MessageManager.getString("label.msf") + " "); pfamjv.setText(MessageManager.getString("label.pfam") + " "); pileupjv.setText(MessageManager.getString("label.pileup") + " "); - msfjv.setFont(verdana11); + msfjv.setFont(LABEL_FONT); msfjv.setHorizontalAlignment(SwingConstants.LEFT); pirjv.setText(MessageManager.getString("label.pir") + " "); JPanel jPanel11 = new JPanel(); - jPanel11.setFont(verdana11); + jPanel11.setFont(LABEL_FONT); TitledBorder titledBorder2 = new TitledBorder( MessageManager.getString("label.file_output")); jPanel11.setBorder(titledBorder2); @@ -378,21 +389,22 @@ public class GPreferences extends JPanel GridLayout gridLayout3 = new GridLayout(); jPanel11.setLayout(gridLayout3); gridLayout3.setRows(8); - blcjv.setFont(verdana11); + blcjv.setFont(LABEL_FONT); blcjv.setHorizontalAlignment(SwingConstants.LEFT); - clustaljv.setFont(verdana11); + clustaljv.setFont(LABEL_FONT); clustaljv.setHorizontalAlignment(SwingConstants.LEFT); - pfamjv.setFont(verdana11); + pfamjv.setFont(LABEL_FONT); pfamjv.setHorizontalAlignment(SwingConstants.LEFT); - pileupjv.setFont(verdana11); + pileupjv.setFont(LABEL_FONT); pileupjv.setHorizontalAlignment(SwingConstants.LEFT); - pirjv.setFont(verdana11); + pirjv.setFont(LABEL_FONT); pirjv.setHorizontalAlignment(SwingConstants.LEFT); - autoIdWidth.setFont(verdana11); + autoIdWidth.setFont(LABEL_FONT); autoIdWidth.setText(MessageManager .getString("label.automatically_set_id_width")); - autoIdWidth - .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png"))); + 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() { @@ -403,13 +415,15 @@ public class GPreferences extends JPanel autoIdWidth_actionPerformed(); } }); - userIdWidthlabel.setFont(verdana11); + userIdWidthlabel.setFont(LABEL_FONT); userIdWidthlabel.setText(MessageManager .getString("label.figure_id_column_width")); userIdWidth - .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column"))); + .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"))); + .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(""); @@ -423,6 +437,14 @@ public class GPreferences extends JPanel userIdWidth_actionPerformed(); } }); + modellerOutput.setFont(LABEL_FONT); + modellerOutput.setText(MessageManager + .getString("label.use_modeller_output")); + modellerOutput.setBounds(new Rectangle(228, 226, 168, 23)); + embbedBioJSON.setFont(LABEL_FONT); + embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson")); + embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23)); + jPanel11.add(jLabel1); jPanel11.add(blcjv); jPanel11.add(clustaljv); @@ -435,13 +457,10 @@ public class GPreferences extends JPanel outputTab.add(userIdWidth); outputTab.add(userIdWidthlabel); outputTab.add(modellerOutput); + outputTab.add(embbedBioJSON); 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; } @@ -457,11 +476,11 @@ public class GPreferences extends JPanel JLabel serverLabel = new JLabel(); serverLabel.setText(MessageManager.getString("label.address")); serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); - serverLabel.setFont(verdana11); - proxyServerTB.setFont(verdana11); - proxyPortTB.setFont(verdana11); + serverLabel.setFont(LABEL_FONT); + proxyServerTB.setFont(LABEL_FONT); + proxyPortTB.setFont(LABEL_FONT); JLabel portLabel = new JLabel(); - portLabel.setFont(verdana11); + portLabel.setFont(LABEL_FONT); portLabel.setHorizontalAlignment(SwingConstants.RIGHT); portLabel.setText(MessageManager.getString("label.port")); JLabel browserLabel = new JLabel(); @@ -469,21 +488,21 @@ public class GPreferences extends JPanel browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); browserLabel.setText(MessageManager .getString("label.default_browser_unix")); - defaultBrowser.setFont(verdana11); + defaultBrowser.setFont(LABEL_FONT); defaultBrowser.setText(""); usagestats.setText(MessageManager .getString("label.send_usage_statistics")); - usagestats.setFont(verdana11); + usagestats.setFont(LABEL_FONT); usagestats.setHorizontalAlignment(SwingConstants.RIGHT); usagestats.setHorizontalTextPosition(SwingConstants.LEADING); questionnaire.setText(MessageManager .getString("label.check_for_questionnaires")); - questionnaire.setFont(verdana11); + questionnaire.setFont(LABEL_FONT); questionnaire.setHorizontalAlignment(SwingConstants.RIGHT); questionnaire.setHorizontalTextPosition(SwingConstants.LEADING); versioncheck.setText(MessageManager .getString("label.check_for_latest_version")); - versioncheck.setFont(verdana11); + versioncheck.setFont(LABEL_FONT); versioncheck.setHorizontalAlignment(SwingConstants.RIGHT); versioncheck.setHorizontalTextPosition(SwingConstants.LEADING); JButton newLink = new JButton(); @@ -542,12 +561,12 @@ public class GPreferences extends JPanel JPanel editLinkButtons = new JPanel(); editLinkButtons.setLayout(gridLayout1); gridLayout1.setRows(3); - linkNameList.setFont(verdana11); + linkNameList.setFont(LABEL_FONT); linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); BorderLayout borderLayout3 = new BorderLayout(); JPanel linkPanel2 = new JPanel(); linkPanel2.setLayout(borderLayout3); - linkURLList.setFont(verdana11); + linkURLList.setFont(LABEL_FONT); linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); defaultBrowser.addMouseListener(new MouseAdapter() @@ -560,7 +579,7 @@ public class GPreferences extends JPanel } } }); - useProxy.setFont(verdana11); + useProxy.setFont(LABEL_FONT); useProxy.setHorizontalAlignment(SwingConstants.RIGHT); useProxy.setHorizontalTextPosition(SwingConstants.LEADING); useProxy.setText(MessageManager.getString("label.use_proxy_server")); @@ -666,10 +685,10 @@ public class GPreferences extends JPanel .getString("action.open_new_alignment"))); coloursTab.setLayout(new FlowLayout()); JLabel mincolourLabel = new JLabel(); - mincolourLabel.setFont(verdana11); + mincolourLabel.setFont(LABEL_FONT); mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT); mincolourLabel.setText(MessageManager.getString("label.min_colour")); - minColour.setFont(verdana11); + minColour.setFont(LABEL_FONT); minColour.setBorder(BorderFactory.createEtchedBorder()); minColour.setPreferredSize(new Dimension(40, 20)); minColour.addMouseListener(new MouseAdapter() @@ -680,10 +699,10 @@ public class GPreferences extends JPanel } }); JLabel maxcolourLabel = new JLabel(); - maxcolourLabel.setFont(verdana11); + maxcolourLabel.setFont(LABEL_FONT); maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT); maxcolourLabel.setText(MessageManager.getString("label.max_colour")); - maxColour.setFont(verdana11); + maxColour.setFont(LABEL_FONT); maxColour.setBorder(BorderFactory.createEtchedBorder()); maxColour.setPreferredSize(new Dimension(40, 20)); maxColour.addMouseListener(new MouseAdapter() @@ -693,16 +712,29 @@ public class GPreferences extends JPanel 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") - + " "); + + protColour.setFont(LABEL_FONT); + protColour.setBounds(new Rectangle(172, 225, 155, 21)); + JLabel protColourLabel = new JLabel(); + protColourLabel.setFont(LABEL_FONT); + protColourLabel.setHorizontalAlignment(SwingConstants.LEFT); + protColourLabel.setText(MessageManager + .getString("label.prot_alignment_colour") + " "); + JvSwingUtils.addtoLayout(coloursTab, MessageManager + .getString("label.default_colour_scheme_for_alignment"), + protColourLabel, protColour); + + nucColour.setFont(LABEL_FONT); + nucColour.setBounds(new Rectangle(172, 240, 155, 21)); + JLabel nucColourLabel = new JLabel(); + nucColourLabel.setFont(LABEL_FONT); + nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT); + nucColourLabel.setText(MessageManager + .getString("label.nuc_alignment_colour") + " "); JvSwingUtils.addtoLayout(coloursTab, MessageManager .getString("label.default_colour_scheme_for_alignment"), - colourLabel, colour); + nucColourLabel, nucColour); + JPanel annotationShding = new JPanel(); annotationShding.setBorder(new TitledBorder(MessageManager .getString("label.annotation_shading_default"))); @@ -730,12 +762,13 @@ public class GPreferences extends JPanel .getString("label.structure_options"))); structureTab.setLayout(null); final int width = 400; - final int height = 23; - final int lineSpacing = 30; + final int height = 22; + final int lineSpacing = 25; int ypos = 30; - structFromPdb.setFont(verdana11); - structFromPdb.setText(MessageManager.getString("label.struct_from_pdb")); + structFromPdb.setFont(LABEL_FONT); + structFromPdb + .setText(MessageManager.getString("label.struct_from_pdb")); structFromPdb.setBounds(new Rectangle(5, ypos, width, height)); structFromPdb.addActionListener(new ActionListener() { @@ -753,36 +786,45 @@ public class GPreferences extends JPanel // indent checkboxes that are conditional on the first one ypos += lineSpacing; - useRnaView.setFont(verdana11); + useRnaView.setFont(LABEL_FONT); useRnaView.setText(MessageManager.getString("label.use_rnaview")); useRnaView.setBounds(new Rectangle(25, ypos, width, height)); structureTab.add(useRnaView); ypos += lineSpacing; - addSecondaryStructure.setFont(verdana11); + addSecondaryStructure.setFont(LABEL_FONT); addSecondaryStructure.setText(MessageManager .getString("label.autoadd_secstr")); addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height)); structureTab.add(addSecondaryStructure); ypos += lineSpacing; - addTempFactor.setFont(verdana11); + addTempFactor.setFont(LABEL_FONT); 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.setFont(LABEL_FONT); 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.setFont(LABEL_FONT); structViewer.setBounds(new Rectangle(160, ypos, 120, height)); - structViewer.addItem(Viewer.JMOL.name()); - structViewer.addItem(Viewer.CHIMERA.name()); + structViewer.addItem(ViewerType.JMOL.name()); + structViewer.addItem(ViewerType.CHIMERA.name()); + structViewer.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + structureViewer_actionPerformed((String) structViewer + .getSelectedItem()); + } + }); structureTab.add(structViewer); ypos += lineSpacing; @@ -790,12 +832,13 @@ public class GPreferences extends JPanel pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); pathLabel.setHorizontalAlignment(SwingConstants.LEFT); pathLabel.setText(MessageManager.getString("label.chimera_path")); - pathLabel.setToolTipText(MessageManager - .getString("label.chimera_path_tip")); + final String tooltip = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.chimera_path_tip")); + pathLabel.setToolTipText(tooltip); pathLabel.setBounds(new Rectangle(10, ypos, 140, height)); structureTab.add(pathLabel); - chimeraPath.setFont(verdana11); + chimeraPath.setFont(LABEL_FONT); chimeraPath.setText(""); chimeraPath.setBounds(new Rectangle(160, ypos, 300, height)); chimeraPath.addMouseListener(new MouseAdapter() @@ -815,19 +858,29 @@ public class GPreferences extends JPanel }); structureTab.add(chimeraPath); - structureTab.addFocusListener(new FocusAdapter() - { - @Override - public void focusLost(FocusEvent e) - { - validateStructure(e); - } + ypos += lineSpacing; + // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100)); + // scrl_pdbDocFieldConfig + // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); + // scrl_pdbDocFieldConfig.setBounds(); + PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences( + PreferenceSource.PREFERENCES); + docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120)); + structureTab.add(docFieldPref); - }); return structureTab; } /** + * Action on choosing a structure viewer from combobox options. + * + * @param selectedItem + */ + protected void structureViewer_actionPerformed(String selectedItem) + { + } + + /** * Show a dialog for the user to choose a file. Returns the chosen path, or * null on Cancel. * @@ -883,81 +936,81 @@ public class GPreferences extends JPanel visualTab.setBorder(new TitledBorder(MessageManager .getString("action.open_new_alignment"))); visualTab.setLayout(null); - fullScreen.setFont(verdana11); + fullScreen.setFont(LABEL_FONT); fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); fullScreen.setText(MessageManager.getString("label.maximize_window")); quality.setEnabled(false); - quality.setFont(verdana11); + quality.setFont(LABEL_FONT); quality.setHorizontalAlignment(SwingConstants.RIGHT); quality.setHorizontalTextPosition(SwingConstants.LEFT); quality.setSelected(true); quality.setText(MessageManager.getString("label.quality")); conservation.setEnabled(false); - conservation.setFont(verdana11); + conservation.setFont(LABEL_FONT); conservation.setHorizontalAlignment(SwingConstants.RIGHT); conservation.setHorizontalTextPosition(SwingConstants.LEFT); conservation.setSelected(true); conservation.setText(MessageManager.getString("label.conservation")); identity.setEnabled(false); - identity.setFont(verdana11); + identity.setFont(LABEL_FONT); 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.setFont(LABEL_FONT); showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT); showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT); showGroupbits.setText(MessageManager.getString("action.show_group") + ":"); JLabel showConsensbits = new JLabel(); - showConsensbits.setFont(verdana11); + showConsensbits.setFont(LABEL_FONT); showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT); showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT); showConsensbits.setText(MessageManager.getString("label.consensus") + ":"); showConsensHistogram.setEnabled(false); - showConsensHistogram.setFont(verdana11); + showConsensHistogram.setFont(LABEL_FONT); showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT); showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT); showConsensHistogram.setSelected(true); showConsensHistogram.setText(MessageManager .getString("label.histogram")); showConsensLogo.setEnabled(false); - showConsensLogo.setFont(verdana11); + showConsensLogo.setFont(LABEL_FONT); showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT); showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT); showConsensLogo.setSelected(true); showConsensLogo.setText(MessageManager.getString("label.logo")); showGroupConsensus.setEnabled(false); - showGroupConsensus.setFont(verdana11); + showGroupConsensus.setFont(LABEL_FONT); showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT); showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT); showGroupConsensus.setSelected(true); showGroupConsensus.setText(MessageManager.getString("label.consensus")); showGroupConservation.setEnabled(false); - showGroupConservation.setFont(verdana11); + showGroupConservation.setFont(LABEL_FONT); showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT); showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT); showGroupConservation.setSelected(true); showGroupConservation.setText(MessageManager .getString("label.conservation")); showNpTooltip.setEnabled(true); - showNpTooltip.setFont(verdana11); + showNpTooltip.setFont(LABEL_FONT); 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.setFont(LABEL_FONT); showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT); showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT); showDbRefTooltip.setSelected(true); showDbRefTooltip.setText(MessageManager .getString("label.database_references")); - annotations.setFont(verdana11); + annotations.setFont(LABEL_FONT); annotations.setHorizontalAlignment(SwingConstants.RIGHT); annotations.setHorizontalTextPosition(SwingConstants.LEADING); annotations.setSelected(true); @@ -984,7 +1037,7 @@ public class GPreferences extends JPanel annotations_actionPerformed(e); } }); - showUnconserved.setFont(verdana11); + showUnconserved.setFont(LABEL_FONT); showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT); showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT); showUnconserved.setSelected(true); @@ -1015,41 +1068,48 @@ public class GPreferences extends JPanel // followHighlight.setText(MessageManager // .getString("label.scroll_highlighted_regions")); - seqLimit.setFont(verdana11); + seqLimit.setFont(LABEL_FONT); seqLimit.setHorizontalAlignment(SwingConstants.RIGHT); seqLimit.setHorizontalTextPosition(SwingConstants.LEFT); seqLimit.setText(MessageManager.getString("label.full_sequence_id")); - smoothFont.setFont(verdana11); + smoothFont.setFont(LABEL_FONT); smoothFont.setHorizontalAlignment(SwingConstants.RIGHT); smoothFont.setHorizontalTextPosition(SwingConstants.LEADING); smoothFont.setText(MessageManager.getString("label.smooth_font")); + scaleProteinToCdna.setFont(LABEL_FONT); + scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT); + scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING); + scaleProteinToCdna.setText(MessageManager + .getString("label.scale_protein_to_cdna")); + scaleProteinToCdna.setToolTipText(MessageManager + .getString("label.scale_protein_to_cdna_tip")); JLabel gapLabel = new JLabel(); - gapLabel.setFont(verdana11); + gapLabel.setFont(LABEL_FONT); gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); gapLabel.setText(MessageManager.getString("label.gap_symbol") + " "); JLabel fontLabel = new JLabel(); - fontLabel.setFont(verdana11); + fontLabel.setFont(LABEL_FONT); fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); fontLabel.setText(MessageManager.getString("label.font")); - fontSizeCB.setFont(verdana11); - fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23)); - fontStyleCB.setFont(verdana11); - fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23)); - fontNameCB.setFont(verdana11); - fontNameCB.setBounds(new Rectangle(172, 104, 147, 23)); - gapSymbolCB.setFont(verdana11); - gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23)); + fontSizeCB.setFont(LABEL_FONT); + fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23)); + fontStyleCB.setFont(LABEL_FONT); + fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23)); + fontNameCB.setFont(LABEL_FONT); + fontNameCB.setBounds(new Rectangle(172, 112, 147, 23)); + gapSymbolCB.setFont(LABEL_FONT); + gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23)); DefaultListCellRenderer dlcr = new DefaultListCellRenderer(); dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER); gapSymbolCB.setRenderer(dlcr); startupCheckbox.setText(MessageManager.getString("action.open_file")); - startupCheckbox.setFont(verdana11); + startupCheckbox.setFont(LABEL_FONT); startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT); startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT); startupCheckbox.setSelected(true); - startupFileTextfield.setFont(verdana11); - startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20)); + startupFileTextfield.setFont(LABEL_FONT); + startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20)); startupFileTextfield.addMouseListener(new MouseAdapter() { public void mouseClicked(MouseEvent e) @@ -1060,33 +1120,26 @@ public class GPreferences extends JPanel } } }); - - sortby.setFont(verdana11); - sortby.setBounds(new Rectangle(172, 240, 155, 21)); + + sortby.setFont(LABEL_FONT); + sortby.setBounds(new Rectangle(172, 260, 155, 21)); JLabel sortLabel = new JLabel(); - sortLabel.setFont(verdana11); + sortLabel.setFont(LABEL_FONT); sortLabel.setHorizontalAlignment(SwingConstants.RIGHT); sortLabel.setText(MessageManager.getString("label.sort_by")); - sortAnnBy.setFont(verdana11); - sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21)); + sortAnnBy.setFont(LABEL_FONT); + sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21)); JLabel sortAnnLabel = new JLabel(); - sortAnnLabel.setFont(verdana11); + sortAnnLabel.setFont(LABEL_FONT); sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT); sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by")); - sortAutocalc.setFont(verdana11); - sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21)); + sortAutocalc.setFont(LABEL_FONT); + sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21)); + JPanel annsettingsPanel = new JPanel(); - annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61)); + annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75)); 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); + annsettingsPanel.setBorder(new EtchedBorder()); visualTab.add(annsettingsPanel); Border jb = new EmptyBorder(1, 1, 4, 5); quality.setBorder(jb); @@ -1099,50 +1152,51 @@ public class GPreferences extends JPanel 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 autoAnnotSettings = new JPanel(); + autoAnnotSettings.setLayout(new GridLayout(3, 3)); + annsettingsPanel.add(autoAnnotSettings); + autoAnnotSettings.add(quality); + autoAnnotSettings.add(conservation); + autoAnnotSettings.add(identity); + autoAnnotSettings.add(showGroupbits); + autoAnnotSettings.add(showGroupConservation); + autoAnnotSettings.add(showGroupConsensus); + autoAnnotSettings.add(showConsensbits); + autoAnnotSettings.add(showConsensHistogram); + autoAnnotSettings.add(showConsensLogo); JPanel tooltipSettings = new JPanel(); tooltipSettings.setBorder(new TitledBorder(MessageManager .getString("label.sequence_id_tooltip"))); - tooltipSettings.setBounds(173, 130, 200, 62); + tooltipSettings.setBounds(173, 140, 220, 62); tooltipSettings.setLayout(new GridLayout(2, 1)); tooltipSettings.add(showDbRefTooltip); tooltipSettings.add(showNpTooltip); visualTab.add(tooltipSettings); - wrap.setFont(verdana11); + wrap.setFont(LABEL_FONT); wrap.setHorizontalAlignment(SwingConstants.TRAILING); wrap.setHorizontalTextPosition(SwingConstants.LEADING); wrap.setText(MessageManager.getString("label.wrap_alignment")); - rightAlign.setFont(verdana11); + rightAlign.setFont(LABEL_FONT); rightAlign.setForeground(Color.black); rightAlign.setHorizontalAlignment(SwingConstants.RIGHT); rightAlign.setHorizontalTextPosition(SwingConstants.LEFT); rightAlign.setText(MessageManager.getString("label.right_align_ids")); - idItalics.setFont(verdana11); + idItalics.setFont(LABEL_FONT_ITALIC); idItalics.setHorizontalAlignment(SwingConstants.RIGHT); idItalics.setHorizontalTextPosition(SwingConstants.LEADING); idItalics.setText(MessageManager .getString("label.sequence_name_italics")); - openoverv.setFont(verdana11); + openoverv.setFont(LABEL_FONT); 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.setBounds(new Rectangle(7, 17, 158, 310)); + jPanel2.setLayout(new GridLayout(14, 1)); jPanel2.add(fullScreen); jPanel2.add(openoverv); jPanel2.add(seqLimit); @@ -1151,6 +1205,7 @@ public class GPreferences extends JPanel jPanel2.add(showUnconserved); jPanel2.add(idItalics); jPanel2.add(smoothFont); + jPanel2.add(scaleProteinToCdna); jPanel2.add(gapLabel); jPanel2.add(wrap); jPanel2.add(sortLabel);