X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=50ee476bd9f8c5c0e036cc08d5948e63d6e3f02b;hb=4cebc1b8abfb0cf42798c8dc601ec5c1cd79c0e4;hp=d9fa3c6851eb531b8d2a631775afe5aa6f53a942;hpb=f7124dc8d666e958ad9925e846e5f46932838bf8;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index d9fa3c6..50ee476 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -24,6 +24,9 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.bin.Cache; import jalview.gui.Help.HelpId; import jalview.gui.StructureViewer.ViewerType; +import jalview.hmmer.HmmerCommand; +import jalview.io.BackupFiles; +import jalview.io.BackupFilesPresetEntry; import jalview.io.FileFormatI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -36,6 +39,7 @@ import jalview.urls.UrlLinkTableModel; import jalview.urls.api.UrlProviderFactoryI; import jalview.urls.api.UrlProviderI; import jalview.urls.desktop.DesktopUrlProviderFactory; +import jalview.util.FileUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.UrlConstants; @@ -48,16 +52,19 @@ 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 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.JTextField; import javax.swing.ListSelectionModel; import javax.swing.RowFilter; import javax.swing.RowSorter; @@ -81,6 +88,15 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; */ public class Preferences extends GPreferences { + // suggested list delimiter character + public static final String COMMA = ","; + + public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT"; + + public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND"; + + public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI"; + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; @@ -102,6 +118,12 @@ public class Preferences extends GPreferences public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY"; public static final String CHIMERA_PATH = "CHIMERA_PATH"; + + 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 SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; @@ -170,6 +192,8 @@ 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"); @@ -188,11 +212,20 @@ public class Preferences extends GPreferences 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); + slivkaPrefs = new SlivkaPreferences(); + slivkaTab.add(slivkaPrefs, BorderLayout.CENTER); + } int width = 500, height = 450; - new jalview.util.Platform(); - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { width = 570; height = 480; @@ -203,6 +236,63 @@ 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)); @@ -225,6 +315,9 @@ 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 @@ -251,7 +344,7 @@ 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)); @@ -325,7 +418,7 @@ public class Preferences extends GPreferences gapLabel.setEnabled(!useLegacyGap.isSelected()); gapColour.setEnabled(!useLegacyGap.isSelected()); showHiddenAtStart - .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true)); + .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false)); /* * Set Structure tab defaults. @@ -400,7 +493,7 @@ 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( @@ -502,23 +595,9 @@ 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()); @@ -547,6 +626,45 @@ public class Preferences extends GPreferences annotations_actionPerformed(null); // update the display of the annotation // settings + + + /* + * Set Backups tab defaults + */ + loadLastSavedBackupsOptions(); + } + + /** + * 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); + } } /** @@ -607,6 +725,10 @@ public class Preferences extends GPreferences Boolean.toString(showConsensHistogram.isSelected())); Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", Boolean.toString(showConsensLogo.isSelected())); + Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM", + Boolean.toString(showConsensHistogram.isSelected())); + Cache.applicationProperties.setProperty("SHOW_HMM_LOGO", + Boolean.toString(showHMMLogo.isSelected())); Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected())); Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA, @@ -653,6 +775,42 @@ public class Preferences extends GPreferences maxColour.getBackground()); /* + * Save HMMER settings + */ + Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI, + Boolean.toString(hmmrTrimTermini.isSelected())); + Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND, + Boolean.toString(hmmerBackgroundUniprot.isSelected())); + Cache.applicationProperties.setProperty(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()); @@ -685,6 +843,10 @@ public class Preferences extends GPreferences */ Cache.applicationProperties.setProperty("EPS_RENDERING", ((OptionsParam) epsRendering.getSelectedItem()).getCode()); + Cache.applicationProperties.setProperty("HTML_RENDERING", + ((OptionsParam) htmlRendering.getSelectedItem()).getCode()); + Cache.applicationProperties.setProperty("SVG_RENDERING", + ((OptionsParam) svgRendering.getSelectedItem()).getCode()); /* * Save Connections settings @@ -794,7 +956,34 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("PAD_GAPS", Boolean.toString(padGaps.isSelected())); - wsPrefs.updateAndRefreshWsMenuConfig(false); + if (!Platform.isJS()) + { + wsPrefs.updateAndRefreshWsMenuConfig(false); + } + + /* + * Save Backups settings + */ + Cache.applicationProperties.setProperty(BackupFiles.ENABLED, + Boolean.toString(enableBackupFiles.isSelected())); + int preset = getComboIntStringKey(backupfilesPresetsCombo); + 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()); + } + + BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues + .get(preset); + Cache.applicationProperties.setProperty( + BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString()); + Cache.saveProperties(); Desktop.instance.doConfigureStructurePrefs(); try @@ -868,8 +1057,11 @@ 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) { @@ -895,6 +1087,8 @@ 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 @@ -1009,8 +1203,11 @@ public class Preferences extends GPreferences public void defaultBrowser_mouseClicked(MouseEvent e) { // TODO: JAL-3048 not needed for j2s - /* - * @j2sNative + if (!Platform.isJS()) // BH 2019 + /** + * Java only + * + * @j2sIgnore */ { JFileChooser chooser = new JFileChooser("."); @@ -1048,27 +1245,17 @@ 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 @@ -1076,28 +1263,18 @@ 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 @@ -1123,7 +1300,7 @@ public class Preferences extends GPreferences { useLegacyGap.setSelected(false); useLegacyGaps_actionPerformed(null); - showHiddenAtStart.setSelected(true); + showHiddenAtStart.setSelected(false); hiddenColour.setBackground( jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); } @@ -1145,12 +1322,12 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { + userIdWidth.setText(""); JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("warn.user_defined_width_requirements"), MessageManager.getString("label.invalid_id_column_width"), JvOptionPane.WARNING_MESSAGE); - userIdWidth.setText(""); } } @@ -1181,6 +1358,57 @@ 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.desktop, + 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 is selected, check it can be found on default or user-specified @@ -1229,6 +1457,18 @@ public class Preferences extends GPreferences } } + @Override + protected void validateHmmerPath() + { + validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD); + } + + @Override + protected void validateCygwinPath() + { + validateExecutablePath(cygwinPath, "run"); + } + public class OptionsParam { private String name;