X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=3667f557298da0a860cce733f2d45f86f3857403;hb=e739c2824d4d6a93c3e0f255780259c7daf2dc21;hp=255c8fc91d371ceccce9c141bf6c8a0494d9c87d;hpb=25a6090732b9f6547fac3d12ddc15ca21b09a840;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 255c8fc..3667f55 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -25,6 +25,7 @@ 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; @@ -104,6 +105,8 @@ public class Preferences extends GPreferences 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 SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; @@ -326,7 +329,7 @@ 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. @@ -339,15 +342,30 @@ public class Preferences extends GPreferences addSecondaryStructure.setEnabled(structSelected); addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false)); addTempFactor.setEnabled(structSelected); - structViewer.setSelectedItem( - Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name())); - chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, "")); + 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())) + { + chimeraPath.setText(""); + } + else + { + chimeraPath.setText(Cache + .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + } chimeraPath.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - validateChimeraPath(); + if (validateChimeraPath()) + { + Cache.setProperty(structViewer.getSelectedItem() + .equals(ViewerType.CHIMERAX.name()) + ? CHIMERAX_PATH + : CHIMERA_PATH, chimeraPath.getText()); + } } }); @@ -400,7 +418,7 @@ 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( @@ -552,31 +570,7 @@ public class Preferences extends GPreferences /* * Set Backups tab defaults */ - enableBackupFiles - .setSelected(Cache.getDefault(BackupFiles.ENABLED, true)); - suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX, - "-v" + BackupFiles.getNumPlaceHolder())); - suffixDigitsSpinner - .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3)); - suffixReverse.setSelected( - Cache.getDefault(BackupFiles.REVERSE_ORDER, false)); - backupfilesKeepAll - .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false)); - backupfilesRollMaxSpinner - .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 4)); - backupfilesConfirmDelete.setSelected( - Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true)); - backupsOptionsSetEnabled(enableBackupFiles.isSelected()); - updateBackupFilesExampleLabel(); - /* - suffixPanel.setPreferredSize( - new Dimension(width, suffixPanel.getHeight())); - keepfilesPanel.setPreferredSize( - new Dimension(width, keepfilesPanel.getHeight())); - exampleFilesPanel.setPreferredSize( - new Dimension(width, exampleFilesPanel.getHeight())); - */ - + loadLastSavedBackupsOptions(); } /** @@ -705,7 +699,10 @@ public class Preferences extends GPreferences Boolean.toString(structFromPdb.isSelected())); Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer.getSelectedItem().toString()); - Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText()); + boolean isChimeraX = structViewer.getSelectedItem().toString() + .equals(ViewerType.CHIMERAX.name()); + Cache.setOrRemove(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, + chimeraPath.getText()); Cache.applicationProperties.setProperty("MAP_WITH_SIFTS", Boolean.toString(siftsMapping.isSelected())); SiftsSettings.setMapWithSifts(siftsMapping.isSelected()); @@ -829,20 +826,25 @@ public class Preferences extends GPreferences /* * Save Backups settings */ - Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD, - Boolean.toString(backupfilesConfirmDelete.isSelected())); Cache.applicationProperties.setProperty(BackupFiles.ENABLED, Boolean.toString(enableBackupFiles.isSelected())); - Cache.applicationProperties.setProperty(BackupFiles.NO_MAX, - Boolean.toString(backupfilesKeepAll.isSelected())); - Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER, - Boolean.toString(suffixReverse.isSelected())); - Cache.applicationProperties.setProperty(BackupFiles.SUFFIX, - suffixTemplate.getText()); - Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX, - Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4))); - Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS, - Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3))); + 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(); @@ -1166,7 +1168,7 @@ 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); } @@ -1226,22 +1228,32 @@ public class Preferences extends GPreferences } /** - * If Chimera is selected, check it can be found on default or user-specified - * path, if not show a warning/help dialog. + * If Chimera or ChimeraX is selected, check it can be found on default or + * user-specified path, if not show a warning/help dialog. */ @Override protected void structureViewer_actionPerformed(String selectedItem) { - if (!selectedItem.equals(ViewerType.CHIMERA.name())) + if (selectedItem.equals(ViewerType.JMOL.name())) { + chimeraPath.setEnabled(false); + chimeraPathLabel.setEnabled(false); return; } boolean found = false; + chimeraPath.setEnabled(true); + chimeraPathLabel.setEnabled(true); + chimeraPathLabel.setText(MessageManager + .formatMessage("label.chimera_path", selectedItem)); /* - * Try user-specified and standard paths for Chimera executable. + * Try user-specified and standard paths for Chimera executable */ - List paths = StructureManager.getChimeraPaths(); + boolean isChimeraX = selectedItem.equals(ViewerType.CHIMERAX.name()); + chimeraPath.setText(Cache + .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + + List paths = StructureManager.getChimeraPaths(isChimeraX); paths.add(0, chimeraPath.getText()); for (String path : paths) {