X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=06d3a602ee7a61439e590501d81fc16d01bccc55;hb=fa9da54fb97cb2eacb1af7859024d90166bddb8f;hp=baed0df5b6ef8ccfbba00b596495e8d29534ef45;hpb=fc46c75d41d5bc962216a96062699ecb2e6e1220;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index baed0df..06d3a60 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -27,7 +27,6 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.awt.event.MouseEvent; import java.io.File; import java.util.ArrayList; import java.util.List; @@ -35,7 +34,6 @@ import java.util.concurrent.CompletableFuture; import javax.help.HelpSetException; import javax.swing.JComboBox; -import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JPanel; import javax.swing.ListSelectionModel; @@ -51,9 +49,12 @@ import javax.swing.table.TableColumn; import javax.swing.table.TableModel; import javax.swing.table.TableRowSorter; +//import edu.stanford.ejalbert.launching.IBrowserLaunching; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; 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; @@ -146,10 +147,10 @@ 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; @@ -396,13 +397,11 @@ public class Preferences extends GPreferences /* * 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); /* @@ -433,7 +432,7 @@ public class Preferences extends GPreferences } } catch (IllegalArgumentException e) { - Cache.log.error("Unknown structure viewer type: " + viewerType + Console.error("Unknown structure viewer type: " + viewerType + ", defaulting to Jmol"); type = ViewerType.JMOL; } @@ -447,26 +446,27 @@ public class Preferences extends GPreferences if (validateViewerPath()) { String path = structureViewerPath.getText(); - try { - ViewerType type = ViewerType.valueOf(viewerType); - switch (type) + try { - 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; + 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); } - } catch (IllegalArgumentException x) - { - Cache.log.error("Failed to set path - unknown viewer type",x); - } } } }); @@ -621,7 +621,7 @@ public class Preferences extends GPreferences proxyType.setSelected(customProxy.getModel(), true); break; default: - Cache.log.warn( + Console.warn( "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): " + proxyTypeString); } @@ -638,8 +638,6 @@ public class Preferences extends GPreferences setCustomProxyEnabled(); applyProxyButtonEnabled(false); - defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", "")); - usagestats.setSelected(Cache.getDefault("USAGESTATS", false)); // note antisense here: default is true questionnaire @@ -685,6 +683,11 @@ public class Preferences extends GPreferences * Set Backups tab defaults */ loadLastSavedBackupsOptions(); + + /* + * Set Startup tab defaults + */ + } /** @@ -845,8 +848,6 @@ public class Preferences extends GPreferences Boolean.toString(addTempFactor.isSelected())); Cache.applicationProperties.setProperty(ADD_SS_ANN, Boolean.toString(addSecondaryStructure.isSelected())); - Cache.applicationProperties.setProperty(USE_RNAVIEW, - Boolean.toString(useRnaView.isSelected())); Cache.applicationProperties.setProperty(STRUCT_FROM_PDB, Boolean.toString(structFromPdb.isSelected())); String viewer = structViewer.getSelectedItem().toString(); @@ -883,10 +884,6 @@ public class Preferences extends GPreferences */ // Proxy settings set first (to catch web services) - Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); - - jalview.util.BrowserLauncher.resetBrowser(); - // save user-defined and selected links String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); if (menuLinks.isEmpty()) @@ -999,6 +996,21 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty( BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString()); + /* + * Save Memory Settings + */ + Cache.applicationProperties.setProperty( + MemorySetting.CUSTOMISED_SETTINGS, + Boolean.toString(customiseMemorySetting.isSelected())); + Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC, + Integer.toString(jvmMemoryPercentSlider.getValue())); + Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX, + jvmMemoryMaxTextField.getText()); + + /* + * save and close Preferences + */ + Cache.saveProperties(); Desktop.instance.doConfigureStructurePrefs(); try @@ -1034,8 +1046,8 @@ public class Preferences extends GPreferences } /** - * Do any necessary validation before saving settings. Return focus to the first - * tab which fails validation. + * Do any necessary validation before saving settings. Return focus to the + * first tab which fails validation. * * @return */ @@ -1089,7 +1101,7 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ @Override public void cancel_actionPerformed(ActionEvent e) @@ -1111,7 +1123,7 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ @Override public void annotations_actionPerformed(ActionEvent e) @@ -1172,7 +1184,7 @@ 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; } @@ -1224,7 +1236,7 @@ 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 @@ -1236,30 +1248,6 @@ public class Preferences extends GPreferences ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex); } - @Override - public void defaultBrowser_mouseClicked(MouseEvent e) - { - // 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); - - if (value == JFileChooser.APPROVE_OPTION) - { - defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath()); - } - } - } - /* * (non-Javadoc) * @@ -1374,8 +1362,8 @@ public class Preferences extends GPreferences } /** - * 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 + * 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 validateViewerPath() @@ -1396,8 +1384,8 @@ public class Preferences extends GPreferences } /** - * 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 + * 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)