X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=2a3151880c0754be12250d0051c3c19918f98d05;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=88f438e6a72b366b49f134741326d13f275314b1;hpb=486e70a70e56b8ac23fd191c2ac9f8c7366f4fd7;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 88f438e..ad3bfb5 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,35 +1,78 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import jalview.bin.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.EnfinEnvision2OneWay; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.bin.Cache; +import jalview.gui.Help.HelpId; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.BackupFiles; +import jalview.io.FileFormatI; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GPreferences; +import jalview.jbgui.GSequenceLink; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueColourScheme; +import jalview.urls.UrlLinkTableModel; +import jalview.urls.api.UrlProviderFactoryI; +import jalview.urls.api.UrlProviderI; +import jalview.urls.desktop.DesktopUrlProviderFactory; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.UrlConstants; +import jalview.ws.sifts.SiftsSettings; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; +import java.io.File; +import java.util.ArrayList; +import java.util.List; + +import javax.help.HelpSetException; +import javax.swing.JColorChooser; +import javax.swing.JFileChooser; +import javax.swing.JInternalFrame; +import javax.swing.JPanel; +import javax.swing.ListSelectionModel; +import javax.swing.RowFilter; +import javax.swing.RowSorter; +import javax.swing.SortOrder; +import javax.swing.event.DocumentEvent; +import javax.swing.event.DocumentListener; +import javax.swing.event.ListSelectionEvent; +import javax.swing.event.ListSelectionListener; +import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; +import javax.swing.table.TableModel; +import javax.swing.table.TableRowSorter; + +import ext.edu.ucsf.rbvi.strucviz2.StructureManager; /** * DOCUMENT ME! @@ -39,84 +82,130 @@ import jalview.ws.EnfinEnvision2OneWay; */ public class Preferences extends GPreferences { + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; + + public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; + + public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR"; + + public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT"; + + public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; + + 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 CHIMERA_PATH = "CHIMERA_PATH"; + + public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; + + public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; + + public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY"; + + public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START"; + + public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP"; + + public static final String GAP_COLOUR = "GAP_COLOUR"; + + public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; + + 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 static Vector sequenceURLLinks; + public static UrlProviderI sequenceUrlLinks; + + public static UrlLinkTableModel dataModel; + /** - * Holds name and link separated with | character. Sequence IDS and Sequences must be - * $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ - * and separation character for first and second token specified after a pipe character at end |,|. + * Holds name and link separated with | character. Sequence IDS and Sequences + * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and + * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character + * for first and second token specified after a pipe character at end |,|. * (TODO: proper escape for using | to separate ids or sequences */ - public static Vector groupURLLinks; + public static List groupURLLinks; static { - String string = Cache - .getDefault( - "SEQUENCE_LINKS", - "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); - sequenceURLLinks = new Vector(); - - try - { - StringTokenizer st = new StringTokenizer(string, "|"); - while (st.hasMoreElements()) - { - String name = st.nextToken(); - String url = st.nextToken(); - // check for '|' within a regex - int rxstart = url.indexOf("$SEQUENCE_ID$"); - while (rxstart == -1 && url.indexOf("/=$") == -1) - { - url = url + "|" + st.nextToken(); - } - sequenceURLLinks.addElement(name + "|" + url); - } - } catch (Exception ex) + // get links selected to be in the menu (SEQUENCE_LINKS) + // and links entered by the user but not selected (STORED_LINKS) + String inMenuString = Cache.getDefault("SEQUENCE_LINKS", ""); + String notInMenuString = Cache.getDefault("STORED_LINKS", ""); + String defaultUrl = Cache.getDefault("DEFAULT_URL", + UrlConstants.DEFAULT_LABEL); + + // if both links lists are empty, add the DEFAULT_URL link + // otherwise we assume the default link is in one of the lists + if (inMenuString.isEmpty() && notInMenuString.isEmpty()) { - System.out.println(ex + "\nError parsing sequence links"); + inMenuString = UrlConstants.DEFAULT_STRING; } + UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl, + inMenuString, notInMenuString); + sequenceUrlLinks = factory.createUrlProvider(); + dataModel = new UrlLinkTableModel(sequenceUrlLinks); + /** - * TODO: reformulate groupURL encoding so two or more can be stored in the .properties file as '|' separated strings + * TODO: reformulate groupURL encoding so two or more can be stored in the + * .properties file as '|' separated strings */ - - groupURLLinks = new Vector(); - //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); - //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); - - } - Vector nameLinks, urlLinks; + groupURLLinks = new ArrayList<>(); + } JInternalFrame frame; - DasSourceBrowser dasSource; + private WsPreferences wsPrefs; + + private OptionsParam promptEachTimeOpt = new OptionsParam( + MessageManager.getString("label.prompt_each_time"), + "Prompt each time"); + + private OptionsParam lineArtOpt = new OptionsParam( + MessageManager.getString("label.lineart"), "Lineart"); + + private OptionsParam textOpt = new OptionsParam( + MessageManager.getString("action.text"), "Text"); /** * Creates a new Preferences object. */ public Preferences() { - + super(); frame = new JInternalFrame(); frame.setContentPane(this); - dasSource = new DasSourceBrowser(); - dasPanel.add(dasSource, BorderLayout.CENTER); - - int width = 500, height = 420; - if (new jalview.util.Platform().isAMac()) + wsPrefs = new WsPreferences(); + wsTab.add(wsPrefs, BorderLayout.CENTER); + int width = 500, height = 450; + new jalview.util.Platform(); + if (Platform.isAMac()) { width = 570; - height = 460; + height = 480; } - Desktop.addInternalFrame(frame, "Preferences", width, height); + Desktop.addInternalFrame(frame, + 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)); @@ -126,26 +215,30 @@ public class Preferences extends GPreferences quality.setSelected(Cache.getDefault("SHOW_QUALITY", true)); identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true)); openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false)); - showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false)); - - for (int i = 0; i < 13; i++) - { - colour.addItem(ColourSchemeProperty.getColourName(i)); - } - - String string = Cache.getDefault("DEFAULT_COLOUR", "None"); - - colour.setSelectedItem(string); + showUnconserved + .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false)); + showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, 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)); 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 + ""); } @@ -156,10 +249,12 @@ public class Preferences extends GPreferences fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif")); fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10")); - fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN - + "")); + fontStyleCB.setSelectedItem( + Cache.getDefault("FONT_STYLE", Font.PLAIN + "")); smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false)); + scaleProteinToCdna + .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false)); idItalics.setSelected(Cache.getDefault("ID_ITALICS", true)); @@ -170,202 +265,473 @@ public class Preferences extends GPreferences gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-")); - startupCheckbox - .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true)); - startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE", - "http://www.jalview.org/examples/exampleFile_2_3.jar")); - sortby.addItem("No sort"); sortby.addItem("Id"); sortby.addItem("Pairwise Identity"); sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort")); - epsRendering.addItem("Prompt each time"); - epsRendering.addItem("Lineart"); - epsRendering.addItem("Text"); - epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING", - "Prompt each time")); + sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString()); + sortAnnBy + .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString()); + sortAnnBy + .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString()); + SequenceAnnotationOrder savedSort = SequenceAnnotationOrder + .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(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")); - 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)); + /* + * Set Colours tab defaults + */ + protColour.addItem(ResidueColourScheme.NONE); + nucColour.addItem(ResidueColourScheme.NONE); + for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes()) + { + String name = cs.getSchemeName(); + protColour.addItem(name); + nucColour.addItem(name); + } + String oldProp = Cache.getDefault(DEFAULT_COLOUR, + ResidueColourScheme.NONE); + String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null); + protColour.setSelectedItem(newProp != null ? newProp : oldProp); + newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null); + nucColour.setSelectedItem(newProp != null ? newProp : oldProp); + minColour.setBackground( + Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); + maxColour.setBackground( + Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); + + /* + * Set overview panel defaults + */ + gapColour.setBackground( + Cache.getDefaultColour(GAP_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP)); + hiddenColour.setBackground( + Cache.getDefaultColour(HIDDEN_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN)); + useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false)); + gapLabel.setEnabled(!useLegacyGap.isSelected()); + gapColour.setEnabled(!useLegacyGap.isSelected()); + showHiddenAtStart + .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true)); + + /* + * 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, ViewerType.JMOL.name())); + chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, "")); + chimeraPath.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + validateChimeraPath(); + } + }); - modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false)); + if (Cache.getDefault("MAP_WITH_SIFTS", false)) + { + siftsMapping.setSelected(true); + } + else + { + nwMapping.setSelected(true); + } - 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)); - showConsensProfile.setSelected(Cache.getDefault("SHOW_CONSENSUS_PROFILE",false)); - - padGaps.setSelected(Cache.getDefault("PAD_GAPS", false)); + SiftsSettings + .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); - /*************************************************************************** - * Set up Connections + /* + * Set Connections tab defaults */ - nameLinks = new Vector(); - urlLinks = new Vector(); - for (int i = 0; i < sequenceURLLinks.size(); i++) + + // set up sorting + linkUrlTable.setModel(dataModel); + final TableRowSorter sorter = new TableRowSorter<>( + linkUrlTable.getModel()); + linkUrlTable.setRowSorter(sorter); + List sortKeys = new ArrayList<>(); + + UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel(); + sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(), + SortOrder.DESCENDING)); + sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(), + SortOrder.DESCENDING)); + sortKeys.add( + new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING)); + + sorter.setSortKeys(sortKeys); + sorter.sort(); + + // set up filtering + ActionListener onReset; + onReset = new ActionListener() { - String link = sequenceURLLinks.elementAt(i).toString(); - nameLinks.addElement(link.substring(0, link.indexOf("|"))); - urlLinks.addElement(link.substring(link.indexOf("|") + 1)); - } + @Override + public void actionPerformed(ActionEvent e) + { + filterTB.setText(""); + sorter.setRowFilter(RowFilter.regexFilter("")); + } - updateLinkData(); + }; + doReset.addActionListener(onReset); + + // filter to display only custom urls + final RowFilter customUrlFilter = new RowFilter() + { + @Override + public boolean include( + Entry entry) + { + return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry); + } + }; + + final TableRowSorter customSorter = new TableRowSorter<>( + linkUrlTable.getModel()); + customSorter.setRowFilter(customUrlFilter); + + ActionListener onCustomOnly; + onCustomOnly = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filterTB.setText(""); + sorter.setRowFilter(customUrlFilter); + } + }; + userOnly.addActionListener(onCustomOnly); + + filterTB.getDocument().addDocumentListener(new DocumentListener() + { + String caseInsensitiveFlag = "(?i)"; + + @Override + public void changedUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); + } + + @Override + public void removeUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); + } + + @Override + public void insertUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); + } + }); + + // set up list selection functionality + linkUrlTable.getSelectionModel() + .addListSelectionListener(new UrlListSelectionHandler()); + + // set up radio buttons + int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getPrimaryColumn(); + String onClickName = linkUrlTable.getColumnName(onClickCol); + linkUrlTable.getColumn(onClickName) + .setCellRenderer(new RadioButtonRenderer()); + linkUrlTable.getColumn(onClickName) + .setCellEditor(new RadioButtonEditor()); + + // get boolean columns and resize those to min possible + for (int column = 0; column < linkUrlTable.getColumnCount(); column++) + { + if (linkUrlTable.getModel().getColumnClass(column) + .equals(Boolean.class)) + { + TableColumn tableColumn = linkUrlTable.getColumnModel() + .getColumn(column); + int preferredWidth = tableColumn.getMinWidth(); + + TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0, + column); + Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column); + int cwidth = c.getPreferredSize().width + + linkUrlTable.getIntercellSpacing().width; + preferredWidth = Math.max(preferredWidth, cwidth); + + tableColumn.setPreferredWidth(preferredWidth); + } + } useProxy.setSelected(Cache.getDefault("USE_PROXY", false)); - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); + useProxy_actionPerformed(); // make sure useProxy is correctly initialised proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); proxyPortTB.setText(Cache.getDefault("PROXY_PORT", "")); defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", "")); - + usagestats.setSelected(Cache.getDefault("USAGESTATS", false)); - questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here - versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true - annotations_actionPerformed(null); // update the display of the annotation settings - try + // note antisense here: default is true + questionnaire + .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); + versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); + + /* + * Set Output tab defaults + */ + epsRendering.addItem(promptEachTimeOpt); + epsRendering.addItem(lineArtOpt); + epsRendering.addItem(textOpt); + String defaultEPS = Cache.getDefault("EPS_RENDERING", + "Prompt each time"); + if (defaultEPS.equalsIgnoreCase("Text")) { - jbInit(); - } catch (Exception ex) + epsRendering.setSelectedItem(textOpt); + } + else if (defaultEPS.equalsIgnoreCase("Lineart")) + { + epsRendering.setSelectedItem(lineArtOpt); + } + else { - ex.printStackTrace(); + epsRendering.setSelectedItem(promptEachTimeOpt); } + autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); + userIdWidth.setEnabled(!autoIdWidth.isSelected()); + userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); + Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); + userIdWidth.setText(wi == null ? "" : wi.toString()); + // TODO: refactor to use common enum via FormatAdapter and allow extension + // for new flat file formats + 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)); + embbedBioJSON + .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true)); + /* + * 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 + + + /* + * Set Backups tab defaults + */ + loadLastSavedBackupsOptions(); } /** - * DOCUMENT ME! + * Save user selections on the Preferences tabs to the Cache and write out to + * file. * * @param e - * DOCUMENT ME! */ + @Override public void ok_actionPerformed(ActionEvent e) { + if (!validateSettings()) + { + return; + } - Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean - .toString(seqLimit.isSelected())); - Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean - .toString(rightAlign.isSelected())); - Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean - .toString(fullScreen.isSelected())); - Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean - .toString(openoverv.isSelected())); - Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean - .toString(annotations.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean - .toString(conservation.isSelected())); - Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean - .toString(quality.isSelected())); - 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()); - - Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB - .getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB - .getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB - .getSelectedItem().toString()); - - Cache.applicationProperties.setProperty("ID_ITALICS", Boolean - .toString(idItalics.isSelected())); - Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected())); - Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",Boolean.toString(showGroupConsensus.isSelected())); - Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",Boolean.toString(showGroupConservation.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",Boolean.toString(showConsensHistogram.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSENSUS_PROFILE",Boolean.toString(showConsensProfile.isSelected())); - Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean - .toString(smoothFont.isSelected())); - - Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean - .toString(wrap.isSelected())); + /* + * Save Visual settings + */ + Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", + Boolean.toString(seqLimit.isSelected())); + Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", + Boolean.toString(rightAlign.isSelected())); + Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", + Boolean.toString(fullScreen.isSelected())); + Cache.applicationProperties.setProperty("SHOW_OVERVIEW", + Boolean.toString(openoverv.isSelected())); + Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Boolean.toString(annotations.isSelected())); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.toString(conservation.isSelected())); + Cache.applicationProperties.setProperty("SHOW_QUALITY", + Boolean.toString(quality.isSelected())); + Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Boolean.toString(identity.isSelected())); + + Cache.applicationProperties.setProperty("GAP_SYMBOL", + gapSymbolCB.getSelectedItem().toString()); + + Cache.applicationProperties.setProperty("FONT_NAME", + fontNameCB.getSelectedItem().toString()); + Cache.applicationProperties.setProperty("FONT_STYLE", + fontStyleCB.getSelectedItem().toString()); + Cache.applicationProperties.setProperty("FONT_SIZE", + fontSizeCB.getSelectedItem().toString()); + + Cache.applicationProperties.setProperty("ID_ITALICS", + Boolean.toString(idItalics.isSelected())); + Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", + Boolean.toString(showUnconserved.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OCCUPANCY, + Boolean.toString(showOccupancy.isSelected())); + Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", + Boolean.toString(showGroupConsensus.isSelected())); + Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION", + Boolean.toString(showGroupConservation.isSelected())); + Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM", + Boolean.toString(showConsensHistogram.isSelected())); + Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", + Boolean.toString(showConsensLogo.isSelected())); + Cache.applicationProperties.setProperty("ANTI_ALIAS", + Boolean.toString(smoothFont.isSelected())); + Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA, + Boolean.toString(scaleProteinToCdna.isSelected())); + Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", + Boolean.toString(showNpTooltip.isSelected())); + Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", + Boolean.toString(showDbRefTooltip.isSelected())); + + Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", + Boolean.toString(wrap.isSelected())); Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText()); - Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean - .toString(startupCheckbox.isSelected())); + Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", + Boolean.toString(startupCheckbox.isSelected())); - Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty("SORT_ALIGNMENT", + sortby.getSelectedItem().toString()); - if (epsRendering.getSelectedItem().equals("Prompt each time")) - { - Cache.applicationProperties.remove("EPS_RENDERING"); - } - else + // convert description of sort order to enum name for save + SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder + .forDescription(sortAnnBy.getSelectedItem().toString()); + if (annSortOrder != null) { - Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty(SORT_ANNOTATIONS, + annSortOrder.name()); } - if (defaultBrowser.getText().trim().length() < 1) - { - Cache.applicationProperties.remove("DEFAULT_BROWSER"); - } - else - { - Cache.applicationProperties.setProperty("DEFAULT_BROWSER", - defaultBrowser.getText()); - } + final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; + Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, + Boolean.valueOf(showAutocalcFirst).toString()); - jalview.util.BrowserLauncher.resetBrowser(); + /* + * Save Colours settings + */ + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, + protColour.getSelectedItem().toString()); + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, + nucColour.getSelectedItem().toString()); + Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", + minColour.getBackground()); + Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", + maxColour.getBackground()); + + /* + * Save Overview settings + */ + Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground()); + Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground()); + Cache.applicationProperties.setProperty(USE_LEGACY_GAP, + Boolean.toString(useLegacyGap.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START, + Boolean.toString(showHiddenAtStart.isSelected())); + + /* + * 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()); + Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText()); + Cache.applicationProperties.setProperty("MAP_WITH_SIFTS", + Boolean.toString(siftsMapping.isSelected())); + SiftsSettings.setMapWithSifts(siftsMapping.isSelected()); + + /* + * Save Output settings + */ + Cache.applicationProperties.setProperty("EPS_RENDERING", + ((OptionsParam) epsRendering.getSelectedItem()).getCode()); - if (nameLinks.size() > 0) - { - StringBuffer links = new StringBuffer(); - sequenceURLLinks = new Vector(); - for (int i = 0; i < nameLinks.size(); i++) - { - sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" - + urlLinks.elementAt(i)); - links.append(sequenceURLLinks.elementAt(i).toString()); - links.append("|"); - } - // remove last "|" - links.setLength(links.length() - 1); - Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links - .toString()); - } - else - { - Cache.applicationProperties.remove("SEQUENCE_LINKS"); - } + /* + * Save Connections settings + */ + Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); - Cache.applicationProperties.setProperty("USE_PROXY", Boolean - .toString(useProxy.isSelected())); + jalview.util.BrowserLauncher.resetBrowser(); - if (proxyServerTB.getText().trim().length() < 1) + // save user-defined and selected links + String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); + if (menuLinks.isEmpty()) { - Cache.applicationProperties.remove("PROXY_SERVER"); + Cache.applicationProperties.remove("SEQUENCE_LINKS"); } else { - Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB - .getText()); + Cache.applicationProperties.setProperty("SEQUENCE_LINKS", + menuLinks.toString()); } - if (proxyPortTB.getText().trim().length() < 1) + String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false); + if (nonMenuLinks.isEmpty()) { - Cache.applicationProperties.remove("PROXY_PORT"); + Cache.applicationProperties.remove("STORED_LINKS"); } else { - Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB - .getText()); + Cache.applicationProperties.setProperty("STORED_LINKS", + nonMenuLinks.toString()); } + Cache.applicationProperties.setProperty("DEFAULT_URL", + sequenceUrlLinks.getPrimaryUrlId()); + + Cache.applicationProperties.setProperty("USE_PROXY", + Boolean.toString(useProxy.isSelected())); + + Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText()); + + Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText()); + if (useProxy.isSelected()) { System.setProperty("http.proxyHost", proxyServerTB.getText()); @@ -376,46 +742,88 @@ public class Preferences extends GPreferences System.setProperty("http.proxyHost", ""); System.setProperty("http.proxyPort", ""); } - Cache.setProperty("VERSION_CHECK", Boolean - .toString(versioncheck.isSelected())); - if (Cache.getProperty("USAGESTATS")!=null || usagestats.isSelected()) { + Cache.setProperty("VERSION_CHECK", + Boolean.toString(versioncheck.isSelected())); + if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected()) + { // default is false - we only set this if the user has actively agreed - Cache.setProperty("USAGESTATS",Boolean - .toString(usagestats.isSelected())); + Cache.setProperty("USAGESTATS", + Boolean.toString(usagestats.isSelected())); } if (!questionnaire.isSelected()) { Cache.setProperty("NOQUESTIONNAIRES", "true"); - } else { - // special - made easy to edit a property file to disable questionnaires by just adding the given line + } + else + { + // special - made easy to edit a property file to disable questionnaires + // by just adding the given line Cache.removeProperty("NOQUESTIONNAIRES"); } - Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean - .toString(blcjv.isSelected())); - Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean - .toString(clustaljv.isSelected())); - Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean - .toString(fastajv.isSelected())); - Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean - .toString(msfjv.isSelected())); - Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean - .toString(pfamjv.isSelected())); - Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean - .toString(pileupjv.isSelected())); - Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean - .toString(pirjv.isSelected())); - Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean - .toString(modellerOutput.isSelected())); + + /* + * Save Output settings + */ + Cache.applicationProperties.setProperty("BLC_JVSUFFIX", + Boolean.toString(blcjv.isSelected())); + Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", + Boolean.toString(clustaljv.isSelected())); + Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", + Boolean.toString(fastajv.isSelected())); + Cache.applicationProperties.setProperty("MSF_JVSUFFIX", + Boolean.toString(msfjv.isSelected())); + Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", + Boolean.toString(pfamjv.isSelected())); + Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", + Boolean.toString(pileupjv.isSelected())); + Cache.applicationProperties.setProperty("PIR_JVSUFFIX", + Boolean.toString(pirjv.isSelected())); + Cache.applicationProperties.setProperty("PIR_MODELLER", + Boolean.toString(modellerOutput.isSelected())); + Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON", + Boolean.toString(embbedBioJSON.isSelected())); jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected(); - Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean - .toString(autoCalculateConsCheck.isSelected())); - Cache.applicationProperties.setProperty("PAD_GAPS", Boolean - .toString(padGaps.isSelected())); + Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", + Boolean.toString(autoIdWidth.isSelected())); + userIdWidth_actionPerformed(); + Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH", + userIdWidth.getText()); - dasSource.saveProperties(Cache.applicationProperties); + /* + * Save Editing settings + */ + Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", + Boolean.toString(autoCalculateConsCheck.isSelected())); + Cache.applicationProperties.setProperty("SORT_BY_TREE", + Boolean.toString(sortByTree.isSelected())); + Cache.applicationProperties.setProperty("PAD_GAPS", + Boolean.toString(padGaps.isSelected())); + + wsPrefs.updateAndRefreshWsMenuConfig(false); + + /* + * Save Backups settings + */ + Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD, + Boolean.toString(backupfilesConfirmDelete.isSelected())); + Cache.applicationProperties.setProperty(BackupFiles.ENABLED, + Boolean.toString(enableBackupFiles.isSelected())); + Cache.applicationProperties.setProperty(BackupFiles.NO_MAX, + Boolean.toString(backupfilesKeepAll.isSelected())); + Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER, + Boolean.toString(suffixReverse.isSelected())); + Cache.applicationProperties.setProperty(BackupFiles.SUFFIX, + suffixTemplate.getText()); + Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX, + Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4))); + Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS, + Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3))); + Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET", + Integer.toString(getComboIntStringKey(backupfilesPresetsCombo))); Cache.saveProperties(); + Desktop.instance.doConfigureStructurePrefs(); try { frame.setClosed(true); @@ -425,27 +833,53 @@ public class Preferences extends GPreferences } /** + * Do any necessary validation before saving settings. Return focus to the + * first tab which fails validation. + * + * @return + */ + private boolean validateSettings() + { + if (!validateStructure()) + { + structureTab.requestFocusInWindow(); + return false; + } + return true; + } + + @Override + protected boolean validateStructure() + { + return validateChimeraPath(); + + } + + /** * DOCUMENT ME! */ + @Override public void startupFileTextfield_mouseClicked() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" }, - new String[] - { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" }, - jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser chooser = JalviewFileChooser + .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Select startup file"); + chooser.setDialogTitle( + MessageManager.getString("label.select_startup_file")); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { - jalview.bin.Cache.applicationProperties.setProperty( - "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat()); - startupFileTextfield.setText(chooser.getSelectedFile() - .getAbsolutePath()); + FileFormatI format = chooser.getSelectedFormat(); + if (format != null) + { + Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", + format.getName()); + } + startupFileTextfield + .setText(chooser.getSelectedFile().getAbsolutePath()); } } @@ -453,12 +887,15 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try { + wsPrefs.updateWsMenuConfig(true); + wsPrefs.refreshWs_actionPerformed(e); frame.setClosed(true); } catch (Exception ex) { @@ -469,36 +906,49 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void annotations_actionPerformed(ActionEvent e) { conservation.setEnabled(annotations.isSelected()); quality.setEnabled(annotations.isSelected()); identity.setEnabled(annotations.isSelected()); - showConsensHistogram.setEnabled(annotations.isSelected()); - showConsensProfile.setEnabled(annotations.isSelected()); + showOccupancy.setEnabled(annotations.isSelected()); showGroupConsensus.setEnabled(annotations.isSelected()); showGroupConservation.setEnabled(annotations.isSelected()); + showConsensHistogram.setEnabled(annotations.isSelected() + && (identity.isSelected() || showGroupConsensus.isSelected())); + showConsensLogo.setEnabled(annotations.isSelected() + && (identity.isSelected() || showGroupConsensus.isSelected())); } + @Override public void newLink_actionPerformed(ActionEvent e) { - GSequenceLink link = new GSequenceLink(); boolean valid = false; while (!valid) { - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, - "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1, - null) == JOptionPane.OK_OPTION) + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + MessageManager.getString("label.new_sequence_url_link"), + JvOptionPane.OK_CANCEL_OPTION, -1, + null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - nameLinks.addElement(link.getName()); - urlLinks.addElement(link.getURL()); - updateLinkData(); - valid = true; + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName())) + { + ((UrlLinkTableModel) linkUrlTable.getModel()) + .insertRow(link.getName(), link.getURL()); + valid = true; + } + else + { + link.notifyDuplicate(); + continue; + } } } else @@ -508,39 +958,52 @@ public class Preferences extends GPreferences } } + @Override public void editLink_actionPerformed(ActionEvent e) { GSequenceLink link = new GSequenceLink(); - int index = linkNameList.getSelectedIndex(); + int index = linkUrlTable.getSelectedRow(); if (index == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "No link selected!", "No link selected", - JOptionPane.WARNING_MESSAGE); + // button no longer enabled if row is not selected + Cache.log.debug("Edit with no row selected in linkUrlTable"); return; } - link.setName(nameLinks.elementAt(index).toString()); - link.setURL(urlLinks.elementAt(index).toString()); + int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getNameColumn(); + int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getUrlColumn(); + String oldName = linkUrlTable.getValueAt(index, nameCol).toString(); + link.setName(oldName); + link.setURL(linkUrlTable.getValueAt(index, urlCol).toString()); boolean valid = false; while (!valid) { - - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, - "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1, - null) == JOptionPane.OK_OPTION) + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + MessageManager.getString("label.edit_sequence_url_link"), + JvOptionPane.OK_CANCEL_OPTION, -1, + null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - nameLinks.setElementAt(link.getName(), index); - urlLinks.setElementAt(link.getURL(), index); - updateLinkData(); - valid = true; + if ((oldName.equals(link.getName())) + || (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName()))) + { + linkUrlTable.setValueAt(link.getName(), index, nameCol); + linkUrlTable.setValueAt(link.getURL(), index, urlCol); + valid = true; + } + else + { + link.notifyDuplicate(); + continue; + } } } - else { break; @@ -548,31 +1011,32 @@ public class Preferences extends GPreferences } } + @Override public void deleteLink_actionPerformed(ActionEvent e) { - int index = linkNameList.getSelectedIndex(); + int index = linkUrlTable.getSelectedRow(); + int modelIndex = -1; if (index == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "No link selected!", "No link selected", - JOptionPane.WARNING_MESSAGE); + // button no longer enabled if row is not selected + Cache.log.debug("Delete with no row selected in linkUrlTable"); return; } - nameLinks.removeElementAt(index); - urlLinks.removeElementAt(index); - updateLinkData(); - } + else + { + modelIndex = linkUrlTable.convertRowIndexToModel(index); + } - void updateLinkData() - { - linkNameList.setListData(nameLinks); - linkURLList.setListData(urlLinks); + // make sure we use the model index to delete, and not the table index + ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex); } + @Override public void defaultBrowser_mouseClicked(MouseEvent e) { JFileChooser chooser = new JFileChooser("."); - chooser.setDialogTitle("Select default web browser"); + chooser.setDialogTitle( + MessageManager.getString("label.select_default_browser")); int value = chooser.showOpenDialog(this); @@ -582,21 +1046,303 @@ public class Preferences extends GPreferences } } - /* (non-Javadoc) - * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent) + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event + * .ActionEvent) */ + @Override protected void showunconserved_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub super.showunconserved_actionPerformed(e); } - private void jbInit() throws Exception + public static List getGroupURLLinks() { + return groupURLLinks; } - public static Collection getGroupURLLinks() + @Override + public void minColour_actionPerformed(JPanel panel) { - return groupURLLinks; + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_colour_minimum_value"), + minColour.getBackground()); + if (col != null) + { + panel.setBackground(col); + } + panel.repaint(); + } + + @Override + public void maxColour_actionPerformed(JPanel panel) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_colour_maximum_value"), + maxColour.getBackground()); + if (col != null) + { + panel.setBackground(col); + } + panel.repaint(); + } + + @Override + public void gapColour_actionPerformed(JPanel gap) + { + if (!useLegacyGap.isSelected()) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_gap_colour"), + gapColour.getBackground()); + if (col != null) + { + gap.setBackground(col); + } + gap.repaint(); + } + } + + @Override + public void hiddenColour_actionPerformed(JPanel hidden) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_hidden_colour"), + hiddenColour.getBackground()); + if (col != null) + { + hidden.setBackground(col); + } + hidden.repaint(); + } + + @Override + protected void useLegacyGaps_actionPerformed(ActionEvent e) + { + boolean enabled = useLegacyGap.isSelected(); + if (enabled) + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP); + } + else + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + } + gapColour.setEnabled(!enabled); + gapLabel.setEnabled(!enabled); + } + + @Override + protected void resetOvDefaults_actionPerformed(ActionEvent e) + { + useLegacyGap.setSelected(false); + useLegacyGaps_actionPerformed(null); + showHiddenAtStart.setSelected(true); + hiddenColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); + } + + @Override + protected void userIdWidth_actionPerformed() + { + try + { + String val = userIdWidth.getText().trim(); + if (val.length() > 0) + { + Integer iw = Integer.parseInt(val); + if (iw.intValue() < 12) + { + throw new NumberFormatException(); + } + userIdWidth.setText(iw.toString()); + } + } catch (NumberFormatException x) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager + .getString("warn.user_defined_width_requirements"), + MessageManager.getString("label.invalid_id_column_width"), + JvOptionPane.WARNING_MESSAGE); + userIdWidth.setText(""); + } + } + + @Override + protected void autoIdWidth_actionPerformed() + { + userIdWidth.setEnabled(!autoIdWidth.isSelected()); + userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); + } + + /** + * Returns true if chimera path is to a valid executable, else show an error + * dialog. + */ + private boolean validateChimeraPath() + { + if (chimeraPath.getText().trim().length() > 0) + { + File f = new File(chimeraPath.getText()); + if (!f.canExecute()) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.invalid_chimera_path"), + MessageManager.getString("label.invalid_name"), + JvOptionPane.ERROR_MESSAGE); + return false; + } + } + return true; + } + + /** + * If Chimera is selected, check it can be found on default or user-specified + * path, if not show a warning/help dialog. + */ + @Override + protected void structureViewer_actionPerformed(String selectedItem) + { + if (!selectedItem.equals(ViewerType.CHIMERA.name())) + { + return; + } + boolean found = false; + + /* + * Try user-specified and standard paths for Chimera executable. + */ + List paths = StructureManager.getChimeraPaths(); + paths.add(0, chimeraPath.getText()); + for (String path : paths) + { + if (new File(path.trim()).canExecute()) + { + found = true; + break; + } + } + if (!found) + { + String[] options = { "OK", "Help" }; + int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop, + JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.chimera_missing")), + "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, + null, options, options[0]); + if (showHelp == JvOptionPane.NO_OPTION) + { + try + { + Help.showHelpWindow(HelpId.StructureViewer); + } catch (HelpSetException e) + { + e.printStackTrace(); + } + } + } + } + + public class OptionsParam + { + private String name; + + private String code; + + public OptionsParam(String name, String code) + { + this.name = name; + this.code = code; + } + + public String getName() + { + return name; + } + + public void setName(String name) + { + this.name = name; + } + + public String getCode() + { + return code; + } + + public void setCode(String code) + { + this.code = code; + } + + @Override + public String toString() + { + return name; + } + + @Override + public boolean equals(Object that) + { + if (!(that instanceof OptionsParam)) + { + return false; + } + return this.code.equalsIgnoreCase(((OptionsParam) that).code); + } + + @Override + public int hashCode() + { + return name.hashCode() + code.hashCode(); + } + } + + private class UrlListSelectionHandler implements ListSelectionListener + { + + @Override + public void valueChanged(ListSelectionEvent e) + { + ListSelectionModel lsm = (ListSelectionModel) e.getSource(); + + int index = lsm.getMinSelectionIndex(); + if (index == -1) + { + // no selection, so disable delete/edit buttons + editLink.setEnabled(false); + deleteLink.setEnabled(false); + return; + } + int modelIndex = linkUrlTable.convertRowIndexToModel(index); + + // enable/disable edit and delete link buttons + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isRowDeletable(modelIndex)) + { + deleteLink.setEnabled(true); + } + else + { + deleteLink.setEnabled(false); + } + + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isRowEditable(modelIndex)) + { + editLink.setEnabled(true); + } + else + { + editLink.setEnabled(false); + } + } } }