X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=54b8f5ac42b5628ea778881d109d6a5b97369ab3;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=d8eee6dcee751bf89616295ba4f5f897a1126e34;hpb=61ff8fb4efa315c35149c9d11850d99e3d00c441;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index d8eee6d..54b8f5a 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,6 +20,7 @@ */ package jalview.gui; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -27,6 +28,8 @@ 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; @@ -38,6 +41,7 @@ import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JPanel; +import javax.swing.JTextField; import javax.swing.ListSelectionModel; import javax.swing.RowFilter; import javax.swing.RowSorter; @@ -51,6 +55,8 @@ 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.Cache; @@ -82,51 +88,156 @@ import jalview.ws.sifts.SiftsSettings; * @author $author$ * @version $Revision$ */ -/* - * for merge with Jalview-JS - public class Preferences extends GPreferences implements ApplicationSingletonI - */ -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 class Preferences extends GPreferences implements ApplicationSingletonI +{ + // 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 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 SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; + 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; @@ -135,7 +246,6 @@ public class Preferences extends GPreferences private String previousProxyType; private static Preferences INSTANCE = null; // add "final" - /** * Holds name and link separated with | character. Sequence ID must be * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$ @@ -185,6 +295,7 @@ public class Preferences extends GPreferences private WsPreferences wsPrefs; + private SlivkaPreferences slivkaPrefs; private OptionsParam promptEachTimeOpt = new OptionsParam( MessageManager.getString("label.prompt_each_time"), "Prompt each time"); @@ -240,7 +351,6 @@ public class Preferences extends GPreferences this.setMessage(message); this.frame.show(); } - /** * Creates a new Preferences object. */ @@ -258,6 +368,8 @@ public class Preferences extends GPreferences { wsPrefs = new WsPreferences(); wsTab.add(wsPrefs, BorderLayout.CENTER); + slivkaPrefs = new SlivkaPreferences(); + slivkaTab.add(slivkaPrefs, BorderLayout.CENTER); } int width = 500, height = 450; if (Platform.isAMacAndNotJS()) @@ -271,6 +383,63 @@ 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)); @@ -293,6 +462,9 @@ 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 @@ -402,13 +574,17 @@ public class Preferences extends GPreferences addSecondaryStructure.setEnabled(structSelected); addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true)); addTempFactor.setEnabled(structSelected); - /* * 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 = Cache.getDefault(STRUCTURE_DISPLAY, + String viewerType = ViewerType.JMOL.name(); + if (!Platform.isJS()) + { + Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()); + } + // TODO - disable external viewers for JS structViewer.setSelectedItem(viewerType); String viewerPath = ""; ViewerType type = null; @@ -678,7 +854,8 @@ public class Preferences extends GPreferences annotations_actionPerformed(null); // update the display of the annotation // settings - + + /* * Set Backups tab defaults */ @@ -698,7 +875,7 @@ public class Preferences extends GPreferences comboBox.addItem(promptEachTimeOpt); comboBox.addItem(lineArtOpt); comboBox.addItem(textOpt); - + /* * JalviewJS doesn't support Lineart so force it to Text */ @@ -736,69 +913,72 @@ public class Preferences extends GPreferences * 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 @@ -806,48 +986,85 @@ 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(STRUCT_FROM_PDB, + Cache.setPropertyNoSave(STRUCT_FROM_PDB, Boolean.toString(structFromPdb.isSelected())); + if (!Platform.isJS()) { String viewer = structViewer.getSelectedItem().toString(); String viewerPath = structureViewerPath.getText(); - Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer); + Cache.setPropertyNoSave(STRUCTURE_DISPLAY, viewer); if (viewer.equals(ViewerType.CHIMERA.name())) { Cache.setOrRemove(CHIMERA_PATH, viewerPath); @@ -860,25 +1077,25 @@ public class Preferences extends GPreferences { Cache.setOrRemove(PYMOL_PATH, viewerPath); } - Cache.applicationProperties.setProperty("MAP_WITH_SIFTS", + } // 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.applicationProperties.setProperty("HTML_RENDERING", + Cache.setPropertyNoSave("HTML_RENDERING", ((OptionsParam) htmlRendering.getSelectedItem()).getCode()); - Cache.applicationProperties.setProperty("SVG_RENDERING", + Cache.setPropertyNoSave("SVG_RENDERING", ((OptionsParam) svgRendering.getSelectedItem()).getCode()); /* * Save Connections settings */ - // Proxy settings set first (to catch web services) - + // Proxy settings were already set first (to catch web services) Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); jalview.util.BrowserLauncher.resetBrowser(); @@ -887,26 +1104,26 @@ 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.setProperty("VERSION_CHECK", @@ -931,40 +1148,40 @@ 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())); if (!Platform.isJS()) @@ -975,28 +1192,28 @@ public class Preferences extends GPreferences /* * 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.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset)); if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) { BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry(); BackupFilesPresetEntry.backupfilesPresetEntriesValues.put( BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE); - Cache.applicationProperties.setProperty( - BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString()); + Cache.applicationProperties + .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG, + customBFPE.toString()); } BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues .get(preset); - Cache.applicationProperties.setProperty( + Cache.setPropertyNoSave( BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString()); Cache.saveProperties(); - Desktop.instance.doConfigureStructurePrefs(); + Desktop.getInstance().doConfigureStructurePrefs(); try { frame.setClosed(true); @@ -1004,13 +1221,12 @@ public class Preferences extends GPreferences { } } - public void saveProxySettings() { String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM : noProxy.isSelected() ? Cache.PROXYTYPE_NONE : Cache.PROXYTYPE_SYSTEM; - Cache.applicationProperties.setProperty("USE_PROXY", newProxyType); + Cache.setPropertyNoSave("USE_PROXY", newProxyType); Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText()); Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText()); Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText()); @@ -1029,9 +1245,45 @@ public class Preferences extends GPreferences previousProxyType = newProxyType; } - /** - * Do any necessary validation before saving settings. Return focus to the first - * tab which fails validation. + 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. * * @return */ @@ -1073,7 +1325,7 @@ 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 @@ -1085,7 +1337,7 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ @Override public void cancel_actionPerformed(ActionEvent e) @@ -1107,7 +1359,7 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ @Override public void annotations_actionPerformed(ActionEvent e) @@ -1122,6 +1374,8 @@ 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 @@ -1131,7 +1385,7 @@ 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) @@ -1183,7 +1437,7 @@ 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) @@ -1297,7 +1551,8 @@ public class Preferences extends GPreferences if (!useLegacyGap.isSelected()) { JalviewColourChooser.showColourChooser(this, - MessageManager.getString("label.select_gap_colour"), gap); + MessageManager.getString("label.select_gap_colour"), + gap); } } @@ -1305,7 +1560,8 @@ public class Preferences extends GPreferences public void hiddenColour_actionPerformed(JPanel hidden) { JalviewColourChooser.showColourChooser(this, - MessageManager.getString("label.select_hidden_colour"), hidden); + MessageManager.getString("label.select_hidden_colour"), + hidden); } @Override @@ -1354,7 +1610,7 @@ public class Preferences extends GPreferences } catch (NumberFormatException x) { userIdWidth.setText(""); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("warn.user_defined_width_requirements"), MessageManager.getString("label.invalid_id_column_width"), @@ -1381,7 +1637,7 @@ public class Preferences extends GPreferences File f = new File(structureViewerPath.getText()); if (!f.canExecute()) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.invalid_viewer_path"), MessageManager.getString("label.invalid_viewer_path"), JvOptionPane.ERROR_MESSAGE); @@ -1390,6 +1646,57 @@ public class Preferences extends GPreferences } 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 or Pymol is selected, check it can be found on default @@ -1451,16 +1758,14 @@ 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.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); @@ -1490,7 +1795,19 @@ public class Preferences extends GPreferences } }); } - } + } + } + + @Override + protected void validateHmmerPath() + { + validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD); + } + + @Override + protected void validateCygwinPath() + { + validateExecutablePath(cygwinPath, "run"); } public class OptionsParam