X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=67b45e3a249eddaf4174192abd16b130498395ab;hb=ff20e75c28408c09803b8f9f15c02e7420e709e9;hp=abe175bde917b1d7cc0ad6ac1fe7e3d245288a79;hpb=9d0cd769882991cd8972808394c8ec2290c8158d;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index abe175b..67b45e3 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,29 +20,6 @@ */ package jalview.gui; -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.BackupFilesPresetEntry; -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; @@ -50,16 +27,21 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; import java.awt.event.MouseEvent; import java.io.File; import java.util.ArrayList; import java.util.List; +import java.util.concurrent.CompletableFuture; import javax.help.HelpSetException; -import javax.swing.JColorChooser; +import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JPanel; +import javax.swing.JTabbedPane; +import javax.swing.JTextField; import javax.swing.ListSelectionModel; import javax.swing.RowFilter; import javax.swing.RowSorter; @@ -73,7 +55,39 @@ import javax.swing.table.TableColumn; import javax.swing.table.TableModel; import javax.swing.table.TableRowSorter; +import jalview.hmmer.HmmerCommand; +import jalview.util.FileUtils; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.bin.MemorySetting; +import jalview.ext.pymol.PymolManager; +import jalview.gui.Help.HelpId; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.BackupFiles; +import jalview.io.BackupFilesPresetEntry; +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 jalview.ws2.client.api.WebServiceDiscovererI; +import jalview.ws2.client.ebi.JobDispatcherWSDiscoverer; +import jalview.ws2.client.jpred4.JPred4WSDiscoverer; +import jalview.ws2.client.slivka.SlivkaWSDiscoverer; /** * DOCUMENT ME! @@ -81,50 +95,163 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; * @author $author$ * @version $Revision$ */ -public class Preferences extends GPreferences +public class Preferences extends GPreferences implements ApplicationSingletonI { - public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; - - public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; + // suggested list delimiter character + public static final String COMMA = ","; - public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR"; + public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT"; - public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT"; + public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND"; - public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; + public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI"; + + public static final String ADD_SS_ANN = "ADD_SS_ANN"; public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN"; - public static final String ADD_SS_ANN = "ADD_SS_ANN"; + public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING"; - public static final String USE_RNAVIEW = "USE_RNAVIEW"; + public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX"; - public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB"; + public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN"; - public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY"; + public static final String ANTI_ALIAS = "ANTI_ALIAS"; + + public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS"; + + public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS"; + + public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE"; + + public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS"; public static final String CHIMERA_PATH = "CHIMERA_PATH"; public static final String CHIMERAX_PATH = "CHIMERAX_PATH"; - public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; + public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR"; + + public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR"; + + public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; + public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT"; + + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; + + public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH"; + + public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH"; + + public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS"; + + public static final String FONT_NAME = "FONT_NAME"; + + public static final String FONT_SIZE = "FONT_SIZE"; + + public static final String FONT_STYLE = "FONT_STYLE"; + + public static final String HMMER_PATH = "HMMER_PATH"; + + public static final String CYGWIN_PATH = "CYGWIN_PATH"; + + public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS"; + + public static final String GAP_COLOUR = "GAP_COLOUR"; + + public static final String GAP_SYMBOL = "GAP_SYMBOL"; + + public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; + + public static final String HIDE_INTRONS = "HIDE_INTRONS"; + + public static final String ID_ITALICS = "ID_ITALICS"; + + public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL"; + + public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS"; + + public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES"; + + public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO"; + + public static final String NORMALISE_LOGO = "NORMALISE_LOGO"; + + public static final String PAD_GAPS = "PAD_GAPS"; + + public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT"; + public static final String PYMOL_PATH = "PYMOL_PATH"; + + public static final String QUESTIONNAIRE = "QUESTIONNAIRE"; + + public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING"; + + public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS"; + + public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; + + public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS"; public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; + public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS"; + + public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM"; + + public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO"; + + public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION"; + + public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP"; + + public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS"; + + public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION"; + + public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX"; + + public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP"; 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 SHOW_OVERVIEW = "SHOW_OVERVIEW"; + + public static final String SHOW_QUALITY = "SHOW_QUALITY"; + + public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED"; + + public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT"; + + public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; + + public static final String SORT_BY_TREE = "SORT_BY_TREE"; + + public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB"; + + public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY"; + + public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS"; + + public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN"; + + public static final String USE_FULL_SO = "USE_FULL_SO"; public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP"; - public static final String GAP_COLOUR = "GAP_COLOUR"; + public static final String USE_RNAVIEW = "USE_RNAVIEW"; - public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; + public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS"; + + public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT"; private static final int MIN_FONT_SIZE = 1; private static final int MAX_FONT_SIZE = 30; + private String previousProxyType; + + private static Preferences INSTANCE = null; // add "final" + /** * Holds name and link separated with | character. Sequence ID must be * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$ @@ -135,10 +262,10 @@ public class Preferences extends GPreferences /** * 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 + * 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 List groupURLLinks; @@ -184,19 +311,80 @@ public class Preferences extends GPreferences private OptionsParam textOpt = new OptionsParam( MessageManager.getString("action.text"), "Text"); + // get singleton Preferences instance + public static Preferences getInstance() + { + if (INSTANCE == null || INSTANCE.frame == null + || INSTANCE.frame.isClosed()) + { + INSTANCE = new Preferences(); + } + return INSTANCE; + + /* + * Replace code with the following for Jalvew-JS + Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class); + if (INSTANCE == null || INSTANCE.frame == null + || INSTANCE.frame.isClosed()) + { + ApplicationSingletonProvider.remove(Preferences.class); + INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class); + } + return INSTANCE; + */ + } + + public static void openPreferences() + { + openPreferences(null, null); + } + + public static void openPreferences(TabRef selectTab, String message) + { + Preferences p = getInstance(); + if (selectTab != null) + p.selectTab(selectTab, message); + p.frame.show(); + p.frame.moveToFront(); + p.frame.grabFocus(); + } + + public void selectTab(TabRef selectTab, String message) + { + this.selectTab(selectTab); + if (message != null) + this.setMessage(message); + this.frame.show(); + } + /** * Creates a new Preferences object. */ - public Preferences() + private Preferences() { super(); frame = new JInternalFrame(); frame.setContentPane(this); - wsPrefs = new WsPreferences(); - wsTab.add(wsPrefs, BorderLayout.CENTER); + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + wsPrefs = new WsPreferences(); + wsTab.add(wsPrefs, BorderLayout.CENTER); + } + + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) + addWebServiceTab(tabbedPane, SlivkaWSDiscoverer.getInstance()); + if (Cache.getDefault("SHOW_EBI_SERVICES", true)) + addWebServiceTab(tabbedPane, JobDispatcherWSDiscoverer.getInstance()); + if (Cache.getDefault("SHOW_JPRED4_SERVICES", true)) + addWebServiceTab(tabbedPane, JPred4WSDiscoverer.getInstance()); + int width = 500, height = 450; - new jalview.util.Platform(); - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { width = 570; height = 480; @@ -207,6 +395,63 @@ public class Preferences extends GPreferences frame.setMinimumSize(new Dimension(width, height)); /* + * Set HMMER tab defaults + */ + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) + { + hmmerBackgroundUniprot.setSelected(true); + } + else + { + hmmerBackgroundAlignment.setSelected(true); + } + hmmerSequenceCount + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); + hmmerPath.setText(Cache.getProperty(HMMER_PATH)); + hmmerPath.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + validateHmmerPath(); + } + }); + hmmerPath.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + validateHmmerPath(); + } + }); + if (cygwinPath != null) + { + String path = Cache.getProperty(CYGWIN_PATH); + if (path == null) + { + path = FileUtils.getPathTo("bash"); + } + cygwinPath.setText(path); + cygwinPath.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + validateCygwinPath(); + } + }); + cygwinPath.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + validateCygwinPath(); + } + }); + } + + /* * Set Visual tab defaults */ seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true)); @@ -229,6 +474,9 @@ public class Preferences extends GPreferences Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true)); showConsensLogo .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false)); + showInformationHistogram.setSelected( + Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true)); + showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false)); showNpTooltip .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); showDbRefTooltip @@ -255,7 +503,7 @@ public class Preferences extends GPreferences fontStyleCB.setSelectedItem( Cache.getDefault("FONT_STYLE", Font.PLAIN + "")); - smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false)); + smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true)); scaleProteinToCdna .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false)); @@ -291,8 +539,8 @@ public class Preferences extends GPreferences 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")); + Cache.getDefault("www.jalview.org", "https://www.jalview.org") + + "/examples/exampleFile_2_7.jvp")); /* * Set Colours tab defaults @@ -319,12 +567,10 @@ public class Preferences extends GPreferences /* * 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)); + 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()); @@ -332,39 +578,83 @@ public class Preferences extends GPreferences .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false)); /* - * Set Structure tab defaults. + * Set Structure tab defaults */ - final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false); + final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true); structFromPdb.setSelected(structSelected); - useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false)); - useRnaView.setEnabled(structSelected); - addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false)); + addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true)); addSecondaryStructure.setEnabled(structSelected); - addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false)); + addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true)); addTempFactor.setEnabled(structSelected); - String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()); - structViewer.setSelectedItem(viewerType); - boolean isChimeraX = viewerType.equals(ViewerType.CHIMERAX.name()); - if (viewerType.equals(ViewerType.JMOL.name())) + + /* + * set choice of structure viewer, and path if saved as a preference; + * default to Jmol (first choice) if an unexpected value is found + */ + String viewerType = ViewerType.JMOL.name(); + if (!Platform.isJS()) { - chimeraPath.setText(""); + Cache.getDefault(STRUCTURE_DISPLAY, + ViewerType.JMOL.name()); } - else + // TODO - disable external viewers for JS + structViewer.setSelectedItem(viewerType); + String viewerPath = ""; + ViewerType type = null; + try { - chimeraPath.setText(Cache - .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + type = ViewerType.valueOf(viewerType); + switch (type) + { + case JMOL: + break; + case CHIMERA: + viewerPath = Cache.getDefault(CHIMERA_PATH, ""); + break; + case CHIMERAX: + viewerPath = Cache.getDefault(CHIMERAX_PATH, ""); + break; + case PYMOL: + viewerPath = Cache.getDefault(PYMOL_PATH, ""); + break; + } + } catch (IllegalArgumentException e) + { + Console.error("Unknown structure viewer type: " + viewerType + + ", defaulting to Jmol"); + type = ViewerType.JMOL; } - chimeraPath.addActionListener(new ActionListener() + structureViewerPath.setText(viewerPath); + + structureViewerPath.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - if (validateChimeraPath()) + if (validateViewerPath()) { - Cache.setProperty(structViewer.getSelectedItem() - .equals(ViewerType.CHIMERAX.name()) - ? CHIMERAX_PATH - : CHIMERA_PATH, chimeraPath.getText()); + String path = structureViewerPath.getText(); + try + { + ViewerType type = ViewerType.valueOf(viewerType); + switch (type) + { + case JMOL: + break; + case CHIMERA: + Cache.setProperty(CHIMERA_PATH, path); + break; + case CHIMERAX: + Cache.setProperty(CHIMERAX_PATH, path); + break; + case PYMOL: + Cache.setProperty(PYMOL_PATH, path); + break; + } + } catch (IllegalArgumentException x) + { + Console.error("Failed to set path - unknown viewer type", x); + } } } }); @@ -401,7 +691,8 @@ public class Preferences extends GPreferences new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING)); sorter.setSortKeys(sortKeys); - sorter.sort(); + // BH 2018 setSortKeys will do the sort + // sorter.sort(); // set up filtering ActionListener onReset; @@ -418,7 +709,7 @@ public class Preferences extends GPreferences doReset.addActionListener(onReset); // filter to display only custom urls - final RowFilter customUrlFilter = new RowFilter<>() + final RowFilter customUrlFilter = new RowFilter() { @Override public boolean include( @@ -504,10 +795,36 @@ public class Preferences extends GPreferences } } - useProxy.setSelected(Cache.getDefault("USE_PROXY", false)); - useProxy_actionPerformed(); // make sure useProxy is correctly initialised - proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); - proxyPortTB.setText(Cache.getDefault("PROXY_PORT", "")); + String proxyTypeString = Cache.getDefault("USE_PROXY", "false"); + previousProxyType = proxyTypeString; + switch (proxyTypeString) + { + case Cache.PROXYTYPE_NONE: + proxyType.setSelected(noProxy.getModel(), true); + break; + case Cache.PROXYTYPE_SYSTEM: + proxyType.setSelected(systemProxy.getModel(), true); + break; + case Cache.PROXYTYPE_CUSTOM: + proxyType.setSelected(customProxy.getModel(), true); + break; + default: + Console.warn( + "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): " + + proxyTypeString); + } + proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", "")); + proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", "")); + proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", "")); + proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", "")); + proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false)); + proxyAuthUsernameTB + .setText(Cache.getDefault("PROXY_AUTH_USERNAME", "")); + // we are not storing or retrieving proxy password from .jalview_properties + proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? "" + : new String(Cache.proxyAuthPassword)); + setCustomProxyEnabled(); + applyProxyButtonEnabled(false); defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", "")); @@ -520,23 +837,9 @@ public class Preferences extends GPreferences /* * 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")) - { - epsRendering.setSelectedItem(textOpt); - } - else if (defaultEPS.equalsIgnoreCase("Lineart")) - { - epsRendering.setSelectedItem(lineArtOpt); - } - else - { - epsRendering.setSelectedItem(promptEachTimeOpt); - } + setupOutputCombo(epsRendering, "EPS_RENDERING"); + setupOutputCombo(htmlRendering, "HTML_RENDERING"); + setupOutputCombo(svgRendering, "SVG_RENDERING"); autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); userIdWidth.setEnabled(!autoIdWidth.isSelected()); userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); @@ -565,6 +868,7 @@ public class Preferences extends GPreferences annotations_actionPerformed(null); // update the display of the annotation // settings + /* @@ -573,6 +877,50 @@ public class Preferences extends GPreferences loadLastSavedBackupsOptions(); } + + private void addWebServiceTab(JTabbedPane tabs, WebServiceDiscovererI discoverer) + { + String name = discoverer.getName(); + JPanel tab = new JPanel(); + tab.setLayout(new BorderLayout()); + tab.add(new WS2PreferencesPanel(discoverer), BorderLayout.CENTER); + tabs.add(tab, name + " services"); + } + + /** + * A helper method that sets the items and initial selection in a character + * rendering option list (Prompt each time/Lineart/Text) + * + * @param comboBox + * @param propertyKey + */ + protected void setupOutputCombo(JComboBox comboBox, + String propertyKey) + { + comboBox.addItem(promptEachTimeOpt); + comboBox.addItem(lineArtOpt); + comboBox.addItem(textOpt); + + + /* + * JalviewJS doesn't support Lineart so force it to Text + */ + String defaultOption = Platform.isJS() ? "Text" + : Cache.getDefault(propertyKey, "Prompt each time"); + if (defaultOption.equalsIgnoreCase("Text")) + { + comboBox.setSelectedItem(textOpt); + } + else if (defaultOption.equalsIgnoreCase("Lineart")) + { + comboBox.setSelectedItem(lineArtOpt); + } + else + { + comboBox.setSelectedItem(promptEachTimeOpt); + } + } + /** * Save user selections on the Preferences tabs to the Cache and write out to * file. @@ -587,68 +935,77 @@ public class Preferences extends GPreferences return; } + /* + * Set proxy settings first (to be before web services refresh) + */ + saveProxySettings(); + /* * Save Visual settings */ - Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", + Cache.setPropertyNoSave("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected())); - Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", + Cache.setPropertyNoSave("RIGHT_ALIGN_IDS", Boolean.toString(rightAlign.isSelected())); - Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", + Cache.setPropertyNoSave("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected())); - Cache.applicationProperties.setProperty("SHOW_OVERVIEW", + Cache.setPropertyNoSave("SHOW_OVERVIEW", Boolean.toString(openoverv.isSelected())); - Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Cache.setPropertyNoSave("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Cache.setPropertyNoSave("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected())); - Cache.applicationProperties.setProperty("SHOW_QUALITY", + Cache.setPropertyNoSave("SHOW_QUALITY", Boolean.toString(quality.isSelected())); - Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Cache.setPropertyNoSave("SHOW_IDENTITY", Boolean.toString(identity.isSelected())); - Cache.applicationProperties.setProperty("GAP_SYMBOL", + Cache.setPropertyNoSave("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_NAME", + Cache.setPropertyNoSave("FONT_NAME", fontNameCB.getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_STYLE", + Cache.setPropertyNoSave("FONT_STYLE", fontStyleCB.getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_SIZE", + Cache.setPropertyNoSave("FONT_SIZE", fontSizeCB.getSelectedItem().toString()); - Cache.applicationProperties.setProperty("ID_ITALICS", + Cache.setPropertyNoSave("ID_ITALICS", Boolean.toString(idItalics.isSelected())); - Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", + Cache.setPropertyNoSave("SHOW_UNCONSERVED", Boolean.toString(showUnconserved.isSelected())); - Cache.applicationProperties.setProperty(SHOW_OCCUPANCY, + Cache.setPropertyNoSave(SHOW_OCCUPANCY, Boolean.toString(showOccupancy.isSelected())); - Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", + Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS", Boolean.toString(showGroupConsensus.isSelected())); - Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION", + Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION", Boolean.toString(showGroupConservation.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM", + Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM", Boolean.toString(showConsensHistogram.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", + Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO", Boolean.toString(showConsensLogo.isSelected())); - Cache.applicationProperties.setProperty("ANTI_ALIAS", + Cache.setPropertyNoSave("SHOW_INFORMATION_HISTOGRAM", + Boolean.toString(showConsensHistogram.isSelected())); + Cache.setPropertyNoSave("SHOW_HMM_LOGO", + Boolean.toString(showHMMLogo.isSelected())); + Cache.setPropertyNoSave("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected())); - Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA, + Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA, Boolean.toString(scaleProteinToCdna.isSelected())); - Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", + Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP", Boolean.toString(showNpTooltip.isSelected())); - Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", + Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP", Boolean.toString(showDbRefTooltip.isSelected())); - Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", + Cache.setPropertyNoSave("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected())); - Cache.applicationProperties.setProperty("STARTUP_FILE", + Cache.setPropertyNoSave("STARTUP_FILE", startupFileTextfield.getText()); - Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", + Cache.setPropertyNoSave("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected())); - Cache.applicationProperties.setProperty("SORT_ALIGNMENT", + Cache.setPropertyNoSave("SORT_ALIGNMENT", sortby.getSelectedItem().toString()); // convert description of sort order to enum name for save @@ -656,66 +1013,116 @@ public class Preferences extends GPreferences .forDescription(sortAnnBy.getSelectedItem().toString()); if (annSortOrder != null) { - Cache.applicationProperties.setProperty(SORT_ANNOTATIONS, + Cache.setPropertyNoSave(SORT_ANNOTATIONS, annSortOrder.name()); } final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; - Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, + Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE, Boolean.valueOf(showAutocalcFirst).toString()); /* * Save Colours settings */ - Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, + Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT, protColour.getSelectedItem().toString()); - Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, + Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC, nucColour.getSelectedItem().toString()); - Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", + Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MIN", minColour.getBackground()); - Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", + Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MAX", maxColour.getBackground()); /* + * Save HMMER settings + */ + Cache.setPropertyNoSave(HMMALIGN_TRIM_TERMINI, + Boolean.toString(hmmrTrimTermini.isSelected())); + Cache.setPropertyNoSave(HMMINFO_GLOBAL_BACKGROUND, + Boolean.toString(hmmerBackgroundUniprot.isSelected())); + Cache.setPropertyNoSave(HMMSEARCH_SEQCOUNT, + hmmerSequenceCount.getText()); + Cache.setOrRemove(HMMER_PATH, hmmerPath.getText()); + if (cygwinPath != null) + { + Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText()); + } + AlignFrame[] frames = Desktop.getAlignFrames(); + if (frames != null && frames.length > 0) + { + for (AlignFrame f : frames) + { + f.updateHMMERStatus(); + } + } + + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) + { + hmmerBackgroundUniprot.setSelected(true); + } + else + { + hmmerBackgroundAlignment.setSelected(true); + } + hmmerSequenceCount + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); + hmmerPath.setText(Cache.getProperty(HMMER_PATH)); + + /* * Save Overview settings */ - Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground()); - Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground()); - Cache.applicationProperties.setProperty(USE_LEGACY_GAP, + Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground()); + Cache.setColourPropertyNoSave(HIDDEN_COLOUR, hiddenColour.getBackground()); + Cache.setPropertyNoSave(USE_LEGACY_GAP, Boolean.toString(useLegacyGap.isSelected())); - Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START, + Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START, Boolean.toString(showHiddenAtStart.isSelected())); /* * Save Structure settings */ - Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN, + Cache.setPropertyNoSave(ADD_TEMPFACT_ANN, Boolean.toString(addTempFactor.isSelected())); - Cache.applicationProperties.setProperty(ADD_SS_ANN, + Cache.setPropertyNoSave(ADD_SS_ANN, Boolean.toString(addSecondaryStructure.isSelected())); - Cache.applicationProperties.setProperty(USE_RNAVIEW, - Boolean.toString(useRnaView.isSelected())); - Cache.applicationProperties.setProperty(STRUCT_FROM_PDB, + Cache.setPropertyNoSave(STRUCT_FROM_PDB, Boolean.toString(structFromPdb.isSelected())); - Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, - structViewer.getSelectedItem().toString()); - boolean isChimeraX = structViewer.getSelectedItem().toString() - .equals(ViewerType.CHIMERAX.name()); - Cache.setOrRemove(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, - chimeraPath.getText()); - Cache.applicationProperties.setProperty("MAP_WITH_SIFTS", + if (!Platform.isJS()) { + String viewer = structViewer.getSelectedItem().toString(); + String viewerPath = structureViewerPath.getText(); + Cache.setPropertyNoSave(STRUCTURE_DISPLAY, viewer); + if (viewer.equals(ViewerType.CHIMERA.name())) + { + Cache.setOrRemove(CHIMERA_PATH, viewerPath); + } + else if (viewer.equals(ViewerType.CHIMERAX.name())) + { + Cache.setOrRemove(CHIMERAX_PATH, viewerPath); + } + else if (viewer.equals(ViewerType.PYMOL.name())) + { + Cache.setOrRemove(PYMOL_PATH, viewerPath); + } + } // nojs + Cache.setPropertyNoSave("MAP_WITH_SIFTS", Boolean.toString(siftsMapping.isSelected())); SiftsSettings.setMapWithSifts(siftsMapping.isSelected()); /* * Save Output settings */ - Cache.applicationProperties.setProperty("EPS_RENDERING", + Cache.setPropertyNoSave("EPS_RENDERING", ((OptionsParam) epsRendering.getSelectedItem()).getCode()); + Cache.setPropertyNoSave("HTML_RENDERING", + ((OptionsParam) htmlRendering.getSelectedItem()).getCode()); + Cache.setPropertyNoSave("SVG_RENDERING", + ((OptionsParam) svgRendering.getSelectedItem()).getCode()); /* * Save Connections settings */ + // Proxy settings were already set first (to catch web services) Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); jalview.util.BrowserLauncher.resetBrowser(); @@ -724,45 +1131,28 @@ public class Preferences extends GPreferences String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); if (menuLinks.isEmpty()) { - Cache.applicationProperties.remove("SEQUENCE_LINKS"); + Cache.removePropertyNoSave("SEQUENCE_LINKS"); } else { - Cache.applicationProperties.setProperty("SEQUENCE_LINKS", + Cache.setPropertyNoSave("SEQUENCE_LINKS", menuLinks.toString()); } String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false); if (nonMenuLinks.isEmpty()) { - Cache.applicationProperties.remove("STORED_LINKS"); + Cache.removePropertyNoSave("STORED_LINKS"); } else { - Cache.applicationProperties.setProperty("STORED_LINKS", + Cache.setPropertyNoSave("STORED_LINKS", nonMenuLinks.toString()); } - Cache.applicationProperties.setProperty("DEFAULT_URL", + Cache.setPropertyNoSave("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()); - System.setProperty("http.proxyPort", proxyPortTB.getText()); - } - else - { - System.setProperty("http.proxyHost", ""); - System.setProperty("http.proxyPort", ""); - } Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck.isSelected())); if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected()) @@ -785,69 +1175,85 @@ public class Preferences extends GPreferences /* * Save Output settings */ - Cache.applicationProperties.setProperty("BLC_JVSUFFIX", + Cache.setPropertyNoSave("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected())); - Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", + Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected())); - Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", + Cache.setPropertyNoSave("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected())); - Cache.applicationProperties.setProperty("MSF_JVSUFFIX", + Cache.setPropertyNoSave("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected())); - Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", + Cache.setPropertyNoSave("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected())); - Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", + Cache.setPropertyNoSave("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected())); - Cache.applicationProperties.setProperty("PIR_JVSUFFIX", + Cache.setPropertyNoSave("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected())); - Cache.applicationProperties.setProperty("PIR_MODELLER", + Cache.setPropertyNoSave("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected())); - Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON", + Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON", Boolean.toString(embbedBioJSON.isSelected())); jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected(); - Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", + Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH", Boolean.toString(autoIdWidth.isSelected())); userIdWidth_actionPerformed(); - Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH", + Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH", userIdWidth.getText()); /* * Save Editing settings */ - Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", + Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS", Boolean.toString(autoCalculateConsCheck.isSelected())); - Cache.applicationProperties.setProperty("SORT_BY_TREE", + Cache.setPropertyNoSave("SORT_BY_TREE", Boolean.toString(sortByTree.isSelected())); - Cache.applicationProperties.setProperty("PAD_GAPS", + Cache.setPropertyNoSave("PAD_GAPS", Boolean.toString(padGaps.isSelected())); - wsPrefs.updateAndRefreshWsMenuConfig(false); + if (!Platform.isJS()) + { + wsPrefs.updateAndRefreshWsMenuConfig(false); + } /* * Save Backups settings */ - Cache.applicationProperties.setProperty(BackupFiles.ENABLED, + Cache.setPropertyNoSave(BackupFiles.ENABLED, Boolean.toString(enableBackupFiles.isSelected())); int preset = getComboIntStringKey(backupfilesPresetsCombo); - Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset)); + Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", Integer.toString(preset)); if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) { BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry(); BackupFilesPresetEntry.backupfilesPresetEntriesValues.put( BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE); - Cache.applicationProperties - .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG, + Cache.setPropertyNoSave(BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString()); } BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues .get(preset); - Cache.applicationProperties.setProperty( + Cache.setPropertyNoSave( BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString()); + /* + * Save Memory Settings + */ + Cache.setPropertyNoSave( + MemorySetting.CUSTOMISED_SETTINGS, + Boolean.toString(customiseMemorySetting.isSelected())); + Cache.setPropertyNoSave(MemorySetting.MEMORY_JVMMEMPC, + Integer.toString(jvmMemoryPercentSlider.getValue())); + Cache.setPropertyNoSave(MemorySetting.MEMORY_JVMMEMMAX, + jvmMemoryMaxTextField.getText()); + + /* + * save and close Preferences + */ Cache.saveProperties(); - Desktop.instance.doConfigureStructurePrefs(); + Desktop.getInstance().doConfigureStructurePrefs(); try { frame.setClosed(true); @@ -856,7 +1262,67 @@ public class Preferences extends GPreferences } } - /** + public void saveProxySettings() + { + String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM + : noProxy.isSelected() ? Cache.PROXYTYPE_NONE + : Cache.PROXYTYPE_SYSTEM; + Cache.setPropertyNoSave("USE_PROXY", newProxyType); + Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText()); + Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText()); + Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText()); + Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText()); + Cache.setOrRemove("PROXY_AUTH", + Boolean.toString(proxyAuth.isSelected())); + Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText()); + Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword(); + Cache.setProxyPropertiesFromPreferences(previousProxyType); + if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM) + || !newProxyType.equals(previousProxyType)) + { + // force a re-lookup of ws if proxytype is custom or has changed + wsPrefs.refreshWs_actionPerformed(null); + } + previousProxyType = newProxyType; + } + + public static void setAppletDefaults() + { + + // http://www.jalview.org/old/v2_8/examples/appletParameters.html + + // showConservation true or false Default is true. + // showQuality true or false Default is true. + // showConsensus true or false Default is true. + // showFeatureSettings true or false Shows the feature settings window when + // startin + // showTreeBootstraps true or false (default is true) show or hide branch + // bootstraps + // showTreeDistances true or false (default is true) show or hide branch + // lengths + // showUnlinkedTreeNodes true or false (default is false) indicate if + // unassociated nodes should be highlighted in the tree view + // showUnconserved true of false (default is false) When true, only gaps and + // symbols different to the consensus sequence ions of the alignment + // showGroupConsensus true of false (default is false) When true, shows + // consensus annotation row for any groups on the alignment. (since 2.7) + // showGroupConservation true of false (default is false) When true, shows + // amino-acid property conservation annotation row for any groups on the + // showConsensusHistogram true of false (default is true) When true, shows + // the percentage occurence of the consensus symbol for each column as a + // showSequenceLogo true of false (default is false) When true, shows a + // sequence logo above the consensus sequence (overlaid above the Consensus + + Cache.setPropertyNoSave(SHOW_CONSERVATION, "true"); + Cache.setPropertyNoSave(SHOW_QUALITY, "false"); + Cache.setPropertyNoSave(SHOW_CONSENSUS, "true"); + Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false"); + Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false"); + Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false"); + + // TODO -- just a start here + } + /** * Do any necessary validation before saving settings. Return focus to the * first tab which fails validation. * @@ -875,7 +1341,7 @@ public class Preferences extends GPreferences @Override protected boolean validateStructure() { - return validateChimeraPath(); + return validateViewerPath(); } @@ -885,6 +1351,7 @@ public class Preferences extends GPreferences @Override public void startupFileTextfield_mouseClicked() { + // TODO: JAL-3048 not needed for Jalview-JS String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser chooser = JalviewFileChooser .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); @@ -899,7 +1366,7 @@ public class Preferences extends GPreferences FileFormatI format = chooser.getSelectedFormat(); if (format != null) { - Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", + Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT", format.getName()); } startupFileTextfield @@ -918,8 +1385,11 @@ public class Preferences extends GPreferences { try { - wsPrefs.updateWsMenuConfig(true); - wsPrefs.refreshWs_actionPerformed(e); + if (!Platform.isJS()) + { + wsPrefs.updateWsMenuConfig(true); + wsPrefs.refreshWs_actionPerformed(e); + } frame.setClosed(true); } catch (Exception ex) { @@ -945,6 +1415,8 @@ public class Preferences extends GPreferences && (identity.isSelected() || showGroupConsensus.isSelected())); showConsensLogo.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected())); + showInformationHistogram.setEnabled(annotations.isSelected()); + showHMMLogo.setEnabled(annotations.isSelected()); } @Override @@ -954,7 +1426,7 @@ public class Preferences extends GPreferences boolean valid = false; while (!valid) { - if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link, MessageManager.getString("label.new_sequence_url_link"), JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) @@ -991,7 +1463,7 @@ public class Preferences extends GPreferences if (index == -1) { // button no longer enabled if row is not selected - Cache.log.debug("Edit with no row selected in linkUrlTable"); + Console.debug("Edit with no row selected in linkUrlTable"); return; } @@ -1006,7 +1478,7 @@ public class Preferences extends GPreferences boolean valid = false; while (!valid) { - if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link, MessageManager.getString("label.edit_sequence_url_link"), JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) @@ -1043,7 +1515,7 @@ public class Preferences extends GPreferences if (index == -1) { // button no longer enabled if row is not selected - Cache.log.debug("Delete with no row selected in linkUrlTable"); + Console.debug("Delete with no row selected in linkUrlTable"); return; } else @@ -1058,17 +1530,25 @@ public class Preferences extends GPreferences @Override public void defaultBrowser_mouseClicked(MouseEvent e) { - JFileChooser chooser = new JFileChooser("."); - chooser.setDialogTitle( - MessageManager.getString("label.select_default_browser")); + // TODO: JAL-3048 not needed for j2s + if (!Platform.isJS()) // BH 2019 + /** + * Java only + * + * @j2sIgnore + */ + { + JFileChooser chooser = new JFileChooser("."); + chooser.setDialogTitle( + MessageManager.getString("label.select_default_browser")); - int value = chooser.showOpenDialog(this); + int value = chooser.showOpenDialog(this); - if (value == JFileChooser.APPROVE_OPTION) - { - defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath()); + if (value == JFileChooser.APPROVE_OPTION) + { + defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath()); + } } - } /* @@ -1093,27 +1573,17 @@ public class Preferences extends GPreferences @Override public void minColour_actionPerformed(JPanel panel) { - Color col = JColorChooser.showDialog(this, + JalviewColourChooser.showColourChooser(this, MessageManager.getString("label.select_colour_minimum_value"), - minColour.getBackground()); - if (col != null) - { - panel.setBackground(col); - } - panel.repaint(); + panel); } @Override public void maxColour_actionPerformed(JPanel panel) { - Color col = JColorChooser.showDialog(this, + JalviewColourChooser.showColourChooser(this, MessageManager.getString("label.select_colour_maximum_value"), - maxColour.getBackground()); - if (col != null) - { - panel.setBackground(col); - } - panel.repaint(); + panel); } @Override @@ -1121,28 +1591,18 @@ public class Preferences extends GPreferences { if (!useLegacyGap.isSelected()) { - Color col = JColorChooser.showDialog(this, + JalviewColourChooser.showColourChooser(this, MessageManager.getString("label.select_gap_colour"), - gapColour.getBackground()); - if (col != null) - { - gap.setBackground(col); - } - gap.repaint(); + gap); } } @Override public void hiddenColour_actionPerformed(JPanel hidden) { - Color col = JColorChooser.showDialog(this, + JalviewColourChooser.showColourChooser(this, MessageManager.getString("label.select_hidden_colour"), - hiddenColour.getBackground()); - if (col != null) - { - hidden.setBackground(col); - } - hidden.repaint(); + hidden); } @Override @@ -1190,12 +1650,12 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + userIdWidth.setText(""); + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("warn.user_defined_width_requirements"), MessageManager.getString("label.invalid_id_column_width"), JvOptionPane.WARNING_MESSAGE); - userIdWidth.setText(""); } } @@ -1207,50 +1667,130 @@ public class Preferences extends GPreferences } /** - * Returns true if chimera path is to a valid executable, else show an error - * dialog. + * Returns true if structure viewer path is to a valid executable, else shows an + * error dialog. Does nothing if the path is empty, as is the case for Jmol + * (built in to Jalview) or when Jalview is left to try default paths. */ - private boolean validateChimeraPath() + private boolean validateViewerPath() { - if (chimeraPath.getText().trim().length() > 0) + if (structureViewerPath.getText().trim().length() > 0) { - File f = new File(chimeraPath.getText()); + File f = new File(structureViewerPath.getText()); if (!f.canExecute()) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.invalid_chimera_path"), - MessageManager.getString("label.invalid_name"), + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + MessageManager.getString("label.invalid_viewer_path"), + MessageManager.getString("label.invalid_viewer_path"), JvOptionPane.ERROR_MESSAGE); return false; } } return true; } + + /** + * Returns true if the given text field contains a path to a folder that + * contains an executable with the given name, else false (after showing a + * warning dialog). The executable name will be tried with .exe appended if not + * found. + * + * @param textField + * @param executable + */ + protected boolean validateExecutablePath(JTextField textField, String executable) + { + String folder = textField.getText().trim(); + + if (FileUtils.getExecutable(executable, folder) != null) + { + return true; + } + if (folder.length() > 0) + { + JvOptionPane.showInternalMessageDialog(Desktop.getInstance(), + MessageManager.formatMessage("label.executable_not_found", + executable), + MessageManager.getString("label.invalid_folder"), + JvOptionPane.ERROR_MESSAGE); + } + return false; + } + + /** + * Checks if a file can be executed + * + * @param path + * the path to the file + * @return + */ + public boolean canExecute(String path) + { + File file = new File(path); + if (!file.canExecute()) + { + file = new File(path + ".exe"); + { + if (!file.canExecute()) + { + return false; + } + } + } + return true; + } /** - * If Chimera or ChimeraX is selected, check it can be found on default or - * user-specified path, if not show a warning/help dialog. + * If Chimera or ChimeraX or Pymol 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.JMOL.name())) { - chimeraPath.setEnabled(false); + structureViewerPath.setEnabled(false); + structureViewerPathLabel.setEnabled(false); return; } boolean found = false; - chimeraPath.setEnabled(true); + structureViewerPath.setEnabled(true); + structureViewerPathLabel.setEnabled(true); + structureViewerPathLabel.setText(MessageManager + .formatMessage("label.viewer_path", selectedItem)); /* - * Try user-specified and standard paths for Chimera executable. + * Try user-specified and standard paths for structure viewer executable */ - boolean isChimeraX = selectedItem.equals(ViewerType.CHIMERAX.name()); - chimeraPath.setText(Cache - .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + String viewerPath = ""; + List paths = null; + try + { + ViewerType viewerType = ViewerType.valueOf(selectedItem); + switch (viewerType) + { + case JMOL: + // dealt with above + break; + case CHIMERA: + viewerPath = Cache.getDefault(CHIMERA_PATH, ""); + paths = StructureManager.getChimeraPaths(false); + break; + case CHIMERAX: + viewerPath = Cache.getDefault(CHIMERAX_PATH, ""); + paths = StructureManager.getChimeraPaths(true); + break; + case PYMOL: + viewerPath = Cache.getDefault(PYMOL_PATH, ""); + paths = PymolManager.getPymolPaths(); + break; + } + } catch (IllegalArgumentException e) + { + // only valid entries should be in the drop-down + } + structureViewerPath.setText(viewerPath); - List paths = StructureManager.getChimeraPaths(isChimeraX); - paths.add(0, chimeraPath.getText()); + paths.add(0, structureViewerPath.getText()); for (String path : paths) { if (new File(path.trim()).canExecute()) @@ -1259,16 +1799,19 @@ public class Preferences extends GPreferences break; } } + if (!found) { String[] options = { "OK", "Help" }; - int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop, + int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(), JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.chimera_missing")), + MessageManager.getString("label.viewer_missing")), "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, null, options, options[0]); + if (showHelp == JvOptionPane.NO_OPTION) { + this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null); try { Help.showHelpWindow(HelpId.StructureViewer); @@ -1277,7 +1820,37 @@ public class Preferences extends GPreferences e.printStackTrace(); } } - } + else if (showHelp == JvOptionPane.OK_OPTION) + { + this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null); + CompletableFuture cf = CompletableFuture.runAsync(() -> { + try + { + for (int i = 0; i < 3; i++) + { + structureViewerPath.setBackground(Color.PINK); + Thread.sleep(500); + structureViewerPath.setBackground(Color.WHITE); + Thread.sleep(500); + } + } catch (InterruptedException e) + { + } + }); + } + } + } + + @Override + protected void validateHmmerPath() + { + validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD); + } + + @Override + protected void validateCygwinPath() + { + validateExecutablePath(cygwinPath, "run"); } public class OptionsParam