From: Jalview Development Admin Date: Tue, 28 May 2019 12:43:21 +0000 (+0100) Subject: Merge branch 'develop' into releases/Release_2_11_Branch X-Git-Tag: Release_2_11_0~9^2^2 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=08013bb0d3f603fa376d0b013f4ccb3ff1642bd7;hp=ce3df766c55f0fad993a6aa5f710ae2a7dd40321 Merge branch 'develop' into releases/Release_2_11_Branch --- diff --git a/build.gradle b/build.gradle index 07a4095..fb311a4 100644 --- a/build.gradle +++ b/build.gradle @@ -846,15 +846,26 @@ task copyInstall4jTemplate(type: Copy) { outputs.files(install4jConf) doLast { + // include file associations in installer def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text ant.replaceregexp( byline: false, flags: "s", match: '', - //match: '', replace: installerFileAssociationsXml, file: install4jConf ) + /* + // include uninstaller applescript app files in dmg + def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text + ant.replaceregexp( + byline: false, + flags: "s", + match: '', + replace: installerDMGUninstallerXml, + file: install4jConf + ) + */ } } diff --git a/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar b/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar index 7230883..c09d3e4 100644 Binary files a/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar and b/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar differ diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar index cb5f670..321b5ce 100644 Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java index 25cd109..0de5c8a 100644 --- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java +++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java @@ -26,6 +26,7 @@ import java.util.zip.GZIPInputStream; import com.sun.management.OperatingSystemMXBean; import java.lang.management.ManagementFactory; +import jalview.bin.MemorySetting; import com.threerings.getdown.util.*; // avoid ambiguity with java.util.Base64 which we can't use as it's 1.8+ @@ -753,28 +754,34 @@ public class Application jvmmempc = config.getInt(appPrefix + "jvmmempc", jvmmempc); } if (0 <= jvmmempc && jvmmempc <= 100) { - final Object o = ManagementFactory.getOperatingSystemMXBean(); - - try { - if (o instanceof OperatingSystemMXBean) { - final OperatingSystemMXBean osb = (OperatingSystemMXBean) o; - long physicalMem = osb.getTotalPhysicalMemorySize(); - long requestedMem = physicalMem*jvmmempc/100; - String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(requestedMem)}; - // remove other max heap size arg - ARG: for (int i = 0; i < _jvmargs.size(); i++) { - if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) { - _jvmargs.remove(i); - } - } - addAll(maxMemHeapArg, _jvmargs); + + long maxMemLong = -1; + + try + { + maxMemLong = MemorySetting.memPercent(jvmmempc); + } catch (Exception e) + { + e.printStackTrace(); + } catch (Throwable t) + { + t.printStackTrace(); + } - } - } - catch (NoClassDefFoundError e) { - // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM - System.out.println("No com.sun.management.OperatingSystemMXBean. Cannot use 'jvmmempc'."); + if (maxMemLong > 0) + { + + String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(maxMemLong)}; + // remove other max heap size arg + ARG: for (int i = 0; i < _jvmargs.size(); i++) { + if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) { + _jvmargs.remove(i); + } } + addAll(maxMemHeapArg, _jvmargs); + + } + } else if (jvmmempc != -1) { System.out.println("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')"); } diff --git a/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java b/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java new file mode 100644 index 0000000..b3bae2d --- /dev/null +++ b/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java @@ -0,0 +1,51 @@ +package jalview.bin; + +import java.lang.management.ManagementFactory; +import java.lang.management.OperatingSystemMXBean; + +public class MemorySetting +{ + public static final long leaveFreeMinMemory = 536870912; // 0.5 GB + + public static final long applicationMinMemory = 536870912; // 0.5 GB + + protected static long getPhysicalMemory() + { + final OperatingSystemMXBean o = ManagementFactory + .getOperatingSystemMXBean(); + + try + { + if (o instanceof com.sun.management.OperatingSystemMXBean) + { + final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o; + return osb.getTotalPhysicalMemorySize(); + } + } catch (NoClassDefFoundError e) + { + // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM + System.out.println("No com.sun.management.OperatingSystemMXBean"); + } + + // We didn't get a com.sun.management.OperatingSystemMXBean. + return -1; + } + + public static long memPercent(int percent) + { + long memPercent = -1; + + long physicalMem = getPhysicalMemory(); + if (physicalMem > applicationMinMemory) + { + // try and set at least applicationMinMemory and thereafter ensure + // leaveFreeMinMemory is left for the OS + memPercent = Math.max(applicationMinMemory, + physicalMem - Math.max(physicalMem * (100 - percent) / 100, + leaveFreeMinMemory)); + } + + return memPercent; + } + +} diff --git a/gradle.properties b/gradle.properties index e49c3ab..57119cb 100644 --- a/gradle.properties +++ b/gradle.properties @@ -59,7 +59,7 @@ getdown_txt_title = Jalview getdown_channel_base = http://www.jalview.org/getdown/jalview getdown_channel_name = TEST getdown_txt_allow_offline = true -getdown_txt_jvmmempc = 95 +getdown_txt_jalview.jvmmempc = 90 getdown_txt_multi_jvmarg = -Dgetdownappdir="%APPDIR%" getdown_txt_strict_comments = true getdown_txt_title = Jalview @@ -100,8 +100,8 @@ install4jResourceDir = utils/install4j install4jTemplate = install4j_template.install4j install4jInfoPlistFileAssociations = file_associations_auto-Info_plist.xml install4jInstallerFileAssociations = file_associations_auto-install4j.xml +install4jDMGUninstallerAppFiles = uninstall_old_jalview_files.xml install4jBuildDir = build/install4j -install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive,unixInstaller install4jFaster = false diff --git a/help/help/html/releases.html b/help/help/html/releases.html index a98b060..287b218 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -134,7 +134,7 @@ li:before {
  • Can use shift + arrow keys to rotate PCA image incrementally
  • - PCA depth queuing with graduated colours
    • + PCA depth cueing with graduated colours Deprecations
      diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar index 7230883..c09d3e4 100644 Binary files a/j11lib/getdown-core.jar and b/j11lib/getdown-core.jar differ diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar index 7230883..c09d3e4 100644 Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 04e8982..f095290 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1354,12 +1354,13 @@ label.append_to_filename = Append to filename (%n is replaced by the backup numb label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above. label.index_digits = Number of digits to use for the backup number (%n) label.summary_of_backups_scheme = Summary of backup scheme +label.scheme_examples = Scheme examples label.increment_index = Increase appended text numbers - newest file has largest number. label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1. label.keep_files = Deleting old backup files label.keep_all_backup_files = Do not delete old backup files label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files -label.autodelete_old_backup_files = Autodelete old backup files: +label.autodelete_old_backup_files = Auto-delete old backup files: label.always_ask = Always ask label.auto_delete = Automatically delete label.filename = filename @@ -1369,10 +1370,18 @@ label.configuration = Configuration label.configure_feature_tooltip = Click to configure variable colour or filters label.schemes = Schemes label.customise = Customise +label.custom = Custom label.default = Default label.single_file = Single backup label.keep_all_versions = Keep all versions label.rolled_backups = Rolled backup files +label.customise_description = Select Customise, make changes, and click on OK to save your own custom scheme +label.custom_description = Your own saved scheme +label.default_description = Keep the last three versions of the file +label.single_file_description = Keep the last version of the file +label.keep_all_versions_description = Keep all previous versions of the file +label.rolled_backups_description = Keep the last nine versions of the file from _bak.1 (newest) to _bak.9 (oldest) +label.cancel_changes_description = Cancel changes made to your last saved Custom scheme label.previously_saved_scheme = Previously saved scheme label.no_backup_files = NO BACKUP FILES label.include_backup_files = Include backup files diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 9efeca1..ec7eb5d 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -32,7 +32,7 @@ action.load_project = Cargar proyecto action.save_project = Guardar proyecto action.save_project_as = Guardar proyecto como... action.quit = Salir -label.quit_jalview = Salir Javliew? +label.quit_jalview = Salir de Jalview? action.expand_views = Expandir vistas action.gather_views = Capturar vistas action.page_setup = Configuración de la página @@ -1355,6 +1355,7 @@ label.append_to_filename = Adjuntar texto (%n es reemplazado por el n label.append_to_filename_tooltip = %n en el texto será reemplazado por el número de respaldo. El texto será después del nombre del archivo. Vea el cuadro de resumen arriba. label.index_digits = Número de dígitos a utilizar para el número de respaldo. label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad +label.scheme_examples = Ejemplos de esquema label.increment_index = Aumente los números de texto adjuntos: el archivo más nuevo tiene el número más grande label.reverse_roll = Ciclos de texto adjuntos: el respaldo más reciente es siempre el número 1 label.keep_files = Borrando los respaldos antiguos @@ -1369,11 +1370,19 @@ label.braced_newest = (mas nuevo) label.configuration = Configuración label.configure_feature_tooltip = Haga clic para configurar el color o los filtros label.schemes = Esquemas -label.customise = Personalizado +label.customise = Personalizar +label.custom = Personal label.default = Defecto label.single_file = Solo uno respaldo label.keep_all_versions = Mantener todas las versiones label.rolled_backups = Ciclos respaldos +label.customise_description = Seleccione Personalizar, haga cambios y haga clic en OK para guardar su propio esquema personalizado +label.custom_description = Tu propio esquema guardado +label.default_description = Conserve las últimas tres versiones del archivo +label.single_file_description = Conserve la última versión del archivo +label.keep_all_versions_description = Mantener todas las versiones anteriores del archivo +label.rolled_backups_description = Mantenga las últimas nueve versiones del archivo desde _bak.1 (más reciente) a _bak.9 (más antigua) +label.cancel_changes_description = Cancelar los cambios realizados en su último esquema personalizado guardado label.previously_saved_scheme = Esquema previamente guardado label.no_backup_files = NO ARCHIVOS DE RESPALDOS label.include_backup_files = Incluir archivos de respaldos diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index c66e63e..449c1fb 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -360,10 +360,12 @@ public class Jalview JalviewTaskbar.setTaskbar(this); } catch (Exception e) { - e.printStackTrace(); + System.out.println("Cannot set Taskbar"); + // e.printStackTrace(); } catch (Throwable t) { - t.printStackTrace(); + System.out.println("Cannot set Taskbar"); + // t.printStackTrace(); } desktop.setVisible(true); diff --git a/src/jalview/bin/JalviewTaskbar.java b/src/jalview/bin/JalviewTaskbar.java index 5747263..7dd0382 100644 --- a/src/jalview/bin/JalviewTaskbar.java +++ b/src/jalview/bin/JalviewTaskbar.java @@ -29,7 +29,7 @@ public class JalviewTaskbar } } catch (Exception e) { - e.printStackTrace(); + System.out.println("Unable to setIconImage()"); } } } diff --git a/src/jalview/bin/Launcher.java b/src/jalview/bin/Launcher.java index aec3acd..412f119 100644 --- a/src/jalview/bin/Launcher.java +++ b/src/jalview/bin/Launcher.java @@ -1,8 +1,8 @@ package jalview.bin; import java.io.File; +import java.io.IOException; import java.lang.management.ManagementFactory; -import java.lang.management.OperatingSystemMXBean; import java.util.ArrayList; public class Launcher @@ -10,7 +10,9 @@ public class Launcher private final static String startClass = "jalview.bin.Jalview"; - private final static int maxHeapSizePerCent = 95; + private final static int maxHeapSizePerCent = 90; + + private final static String maxHeapSizePerCentProperty = "jvmmempc"; private final static String dockIconPath = "JalviewLogo_Huge.png"; @@ -22,6 +24,8 @@ public class Launcher ArrayList command = new ArrayList<>(); command.add(javaBin); + String memSetting = null; + boolean isAMac = System.getProperty("os.name").indexOf("Mac") > -1; for (String jvmArg : ManagementFactory.getRuntimeMXBean() @@ -40,39 +44,81 @@ public class Launcher // add memory setting if not specified boolean memSet = false; boolean dockIcon = false; + boolean dockName = false; ARG: for (int i = 0; i < command.size(); i++) { String arg = command.get(i); if (arg.startsWith("-Xmx")) { + memSetting = arg; memSet = true; } else if (arg.startsWith("-Xdock:icon")) { dockIcon = true; } + else if (arg.startsWith("-Xdock:name")) + { + dockName = true; + } } if (!memSet) { long maxMemLong = -1; - long physicalMem = getPhysicalMemory(); - if (physicalMem > 0) + int percent = maxHeapSizePerCent; + String jvmmempc = System.getProperty(maxHeapSizePerCentProperty); + try + { + if (jvmmempc != null) + { + int trypercent = Integer.parseInt(jvmmempc); + if (0 < trypercent && trypercent <= 100) + { + percent = trypercent; + } + else + { + System.out.println("Property '" + maxHeapSizePerCentProperty + + "' should be in range 1..100"); + } + } + } catch (Exception e) + { + System.out.println("Error parsing " + maxHeapSizePerCentProperty + + " '" + jvmmempc + "'"); + } + + try { - maxMemLong = physicalMem * maxHeapSizePerCent / 100; + maxMemLong = MemorySetting.memPercent(percent); + } catch (Exception e) + { + e.printStackTrace(); + } catch (Throwable t) + { + t.printStackTrace(); } + if (maxMemLong > 0) { - command.add("-Xmx" + Long.toString(maxMemLong)); + memSetting = "-Xmx" + Long.toString(maxMemLong); + command.add(memSetting); } } - if (!dockIcon && isAMac) + if (isAMac) { - command.add("-Xdock:icon=" + dockIconPath); - // -Xdock:name=... doesn't actually work :( - // Leaving it in in case it gets fixed - command.add("-Xdock:name=" + "Jalview"); + if (!dockIcon) + { + command.add("-Xdock:icon=" + dockIconPath); + } + if (!dockName) + { + // -Xdock:name=... doesn't actually work :( + // Leaving it in in case it gets fixed + command.add("-Xdock:name=" + "Jalview"); + } } command.add(startClass); @@ -80,41 +126,53 @@ public class Launcher final ProcessBuilder builder = new ProcessBuilder(command); - System.out.println("COMMAND: " + String.join(" ", builder.command())); + // System.out.println("COMMAND: " + String.join(" ", builder.command())); + System.out.println("Running " + startClass + " with " + + (memSetting == null ? "no memSetting" : memSetting)); try { builder.inheritIO(); Process process = builder.start(); process.waitFor(); - } catch (Exception e) + } catch (IOException e) { - e.printStackTrace(); - } - // System.exit(0); - - } - - public static long getPhysicalMemory() - { - final OperatingSystemMXBean o = ManagementFactory - .getOperatingSystemMXBean(); - - try - { - if (o instanceof com.sun.management.OperatingSystemMXBean) + if (e.getMessage().toLowerCase().contains("memory")) + { + System.out.println("Caught a memory exception: " + e.getMessage()); + // Probably the "Cannot allocate memory" error, try without the memory setting + ArrayList commandNoMem = new ArrayList<>(); + for (int i = 0; i < command.size(); i++) + { + if (!command.get(i).startsWith("-Xmx")) + { + commandNoMem.add(command.get(i)); + } + } + final ProcessBuilder builderNoMem = new ProcessBuilder( + commandNoMem); + System.out.println("NO MEM COMMAND: " + + String.join(" ", builderNoMem.command())); + try + { + builderNoMem.inheritIO(); + Process processNoMem = builderNoMem.start(); + processNoMem.waitFor(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + else { - final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o; - return osb.getTotalPhysicalMemorySize(); + e.printStackTrace(); } - } catch (NoClassDefFoundError e) + } catch (Exception e) { - // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM - System.out.println("No com.sun.management.OperatingSystemMXBean"); + e.printStackTrace(); } + // System.exit(0); - // We didn't get a com.sun.management.OperatingSystemMXBean. - return -1; } } diff --git a/src/jalview/bin/MemorySetting.java b/src/jalview/bin/MemorySetting.java new file mode 100644 index 0000000..b3bae2d --- /dev/null +++ b/src/jalview/bin/MemorySetting.java @@ -0,0 +1,51 @@ +package jalview.bin; + +import java.lang.management.ManagementFactory; +import java.lang.management.OperatingSystemMXBean; + +public class MemorySetting +{ + public static final long leaveFreeMinMemory = 536870912; // 0.5 GB + + public static final long applicationMinMemory = 536870912; // 0.5 GB + + protected static long getPhysicalMemory() + { + final OperatingSystemMXBean o = ManagementFactory + .getOperatingSystemMXBean(); + + try + { + if (o instanceof com.sun.management.OperatingSystemMXBean) + { + final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o; + return osb.getTotalPhysicalMemorySize(); + } + } catch (NoClassDefFoundError e) + { + // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM + System.out.println("No com.sun.management.OperatingSystemMXBean"); + } + + // We didn't get a com.sun.management.OperatingSystemMXBean. + return -1; + } + + public static long memPercent(int percent) + { + long memPercent = -1; + + long physicalMem = getPhysicalMemory(); + if (physicalMem > applicationMinMemory) + { + // try and set at least applicationMinMemory and thereafter ensure + // leaveFreeMinMemory is left for the OS + memPercent = Math.max(applicationMinMemory, + physicalMem - Math.max(physicalMem * (100 - percent) / 100, + leaveFreeMinMemory)); + } + + return memPercent; + } + +} diff --git a/src/jalview/gui/APQHandlers.java b/src/jalview/gui/APQHandlers.java index 31f7a6d..05f5e08 100644 --- a/src/jalview/gui/APQHandlers.java +++ b/src/jalview/gui/APQHandlers.java @@ -86,7 +86,8 @@ public class APQHandlers QuitEvent e, QuitResponse r) { boolean confirmQuit = jalview.bin.Cache - .getDefault(jalviewDesktop.CONFIRM_KEYBOARD_QUIT, + .getDefault( + jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT, true); int n; if (confirmQuit) @@ -134,12 +135,12 @@ public class APQHandlers { System.out.println( "Exception when looking for About, Preferences, Quit Handlers"); - e.printStackTrace(); + // e.printStackTrace(); } catch (Throwable t) { System.out.println( "Throwable when looking for About, Preferences, Quit Handlers"); - t.printStackTrace(); + // t.printStackTrace(); } } diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 41cbad8..0523d41 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -366,12 +366,12 @@ public class Desktop extends jalview.jbgui.GDesktop APQHandlers.setAPQHandlers(this); } catch (Exception e) { - System.out.println("Exception when trying to set APQHandlers"); - e.printStackTrace(); + System.out.println("Cannot set APQHandlers"); + // e.printStackTrace(); } catch (Throwable t) { - System.out.println("Throwable when trying to set APQHandlers"); - t.printStackTrace(); + System.out.println("Cannot set APQHandlers"); + // t.printStackTrace(); } @@ -1134,7 +1134,7 @@ public class Desktop extends jalview.jbgui.GDesktop { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser chooser = JalviewFileChooser - .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true); + .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled()); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( @@ -1299,8 +1299,6 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void quit() { - //System.out.println("********** Desktop.quit()"); - //System.out.println(savingFiles.toString()); Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); @@ -1763,7 +1761,7 @@ public class Desktop extends jalview.jbgui.GDesktop "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY"), suffix, desc, - "Jalview Project", true, true); // last two booleans: allFiles, + "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles, // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java index a2194f4..7456e18 100644 --- a/src/jalview/gui/FeatureTypeSettings.java +++ b/src/jalview/gui/FeatureTypeSettings.java @@ -22,6 +22,7 @@ package jalview.gui; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; +import jalview.bin.Cache; import jalview.datamodel.GraphLine; import jalview.datamodel.features.FeatureAttributes; import jalview.datamodel.features.FeatureAttributes.Datatype; @@ -165,7 +166,7 @@ public class FeatureTypeSettings extends JalviewDialog private JPanel maxColour = new JPanel(); - private JComboBox threshold = new JComboBox<>(); + private JComboBox threshold = new JComboBox<>(); private JSlider slider = new JSlider(); @@ -182,17 +183,17 @@ public class FeatureTypeSettings extends JalviewDialog /* * choice of option for 'colour for no value' */ - private JComboBox noValueCombo; + private JComboBox noValueCombo; /* * choice of what to colour by text (Label or attribute) */ - private JComboBox colourByTextCombo; + private JComboBox colourByTextCombo; /* * choice of what to colour by range (Score or attribute) */ - private JComboBox colourByRangeCombo; + private JComboBox colourByRangeCombo; private JRadioButton andFilters; @@ -1104,7 +1105,7 @@ public class FeatureTypeSettings extends JalviewDialog * @param withRange * @param withText */ - protected JComboBox populateAttributesDropdown( + protected JComboBox populateAttributesDropdown( List attNames, boolean withRange, boolean withText) { List displayAtts = new ArrayList<>(); @@ -1143,9 +1144,11 @@ public class FeatureTypeSettings extends JalviewDialog tooltips.add(desc == null ? "" : desc); } - JComboBox attCombo = JvSwingUtils - .buildComboWithTooltips(displayAtts, tooltips); - + // now convert String List to Object List for buildComboWithTooltips + List displayAttsObjects = new ArrayList<>(displayAtts); + JComboBox attCombo = JvSwingUtils + .buildComboWithTooltips(displayAttsObjects, tooltips); + return attCombo; } @@ -1316,7 +1319,7 @@ public class FeatureTypeSettings extends JalviewDialog * drop-down choice of attribute, with description as a tooltip * if we can obtain it */ - final JComboBox attCombo = populateAttributesDropdown(attNames, + final JComboBox attCombo = populateAttributesDropdown(attNames, true, true); String filterBy = setSelectedAttribute(attCombo, filter); @@ -1444,7 +1447,7 @@ public class FeatureTypeSettings extends JalviewDialog * @param attCombo * @param filter */ - private String setSelectedAttribute(JComboBox attCombo, + private String setSelectedAttribute(JComboBox attCombo, FeatureMatcherI filter) { String item = null; @@ -1661,11 +1664,19 @@ public class FeatureTypeSettings extends JalviewDialog * @param valueField * @param filterIndex */ - protected boolean updateFilter(JComboBox attCombo, + protected boolean updateFilter(JComboBox attCombo, JComboBox condCombo, JTextField valueField, int filterIndex) { - String attName = (String) attCombo.getSelectedItem(); + String attName; + try + { + attName = (String) attCombo.getSelectedItem(); + } catch (Exception e) + { + Cache.log.error("Problem casting Combo box entry to String"); + attName = attCombo.getSelectedItem().toString(); + } Condition cond = (Condition) condCombo.getSelectedItem(); String pattern = valueField.getText().trim(); diff --git a/src/jalview/gui/JvSwingUtils.java b/src/jalview/gui/JvSwingUtils.java index 4658668..d6090e2 100644 --- a/src/jalview/gui/JvSwingUtils.java +++ b/src/jalview/gui/JvSwingUtils.java @@ -319,13 +319,13 @@ public final class JvSwingUtils * @param entries * @param tooltips */ - public static JComboBox buildComboWithTooltips( - List entries, List tooltips) + public static JComboBox buildComboWithTooltips( + List entries, List tooltips) { - JComboBox combo = new JComboBox<>(); + JComboBox combo = new JComboBox<>(); final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer(); combo.setRenderer(renderer); - for (String attName : entries) + for (Object attName : entries) { combo.addItem(attName); } diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index ab09f74..9754e0d 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; @@ -805,22 +806,25 @@ 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))); - Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET", - Integer.toString(getComboIntStringKey(backupfilesPresetsCombo))); + 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(); diff --git a/src/jalview/io/BackupFilenameParts.java b/src/jalview/io/BackupFilenameParts.java index 4f93ece..1504404 100644 --- a/src/jalview/io/BackupFilenameParts.java +++ b/src/jalview/io/BackupFilenameParts.java @@ -1,7 +1,5 @@ package jalview.io; -import jalview.bin.Cache; - import java.io.File; public class BackupFilenameParts @@ -113,7 +111,9 @@ public class BackupFilenameParts String filename, String base, boolean extensionMatch) { BackupFilenameParts bfp = new BackupFilenameParts(); - String template = Cache.getDefault(BackupFiles.SUFFIX, null); + BackupFilesPresetEntry bfpe = BackupFilesPresetEntry + .getSavedBackupEntry(); + String template = bfpe.suffix; if (template == null) { return bfp; @@ -121,8 +121,7 @@ public class BackupFilenameParts int digits; try { - digits = Integer - .parseInt(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, null)); + digits = bfpe.digits; } catch (Exception e) { return bfp; diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java index dbda022..7bb5d31 100644 --- a/src/jalview/io/BackupFiles.java +++ b/src/jalview/io/BackupFiles.java @@ -17,12 +17,8 @@ import java.util.TreeMap; * BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved. * User configurable options are: * BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved. - * BACKUPFILES_SUFFIX - a template to insert after the file extension. Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer. - * BACKUPFILES_NO_MAX - flag to turn off setting a maximum number of backup files to keep. - * BACKUPFILES_ROLL_MAX - the maximum number of backupfiles to keep for any one alignment or project file. - * BACKUPFILES_SUFFIX_DIGITS - the number of digits to insert replace %n with (e.g. BACKUPFILES_SUFFIX_DIGITS = 3 would make "001", "002", etc) - * BACKUPFILES_REVERSE_ORDER - if true then "logfile" style numbering and file rolling will occur. If false then ever-increasing version numbering will occur, but old files will still be deleted if there are more than ROLL_MAX backup files. - * BACKUPFILES_CONFIRM_DELETE_OLD - if true then prompt/confirm with the user when deleting older backup/version files. + * The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM + * (see BackupFilesPresetEntry) */ public class BackupFiles @@ -33,21 +29,8 @@ public class BackupFiles public static final String ENABLED = NS + "_ENABLED"; - public static final String SUFFIX = NS + "_SUFFIX"; - - public static final String NO_MAX = NS + "_NO_MAX"; - - public static final String ROLL_MAX = NS + "_ROLL_MAX"; - - public static final String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS"; - public static final String NUM_PLACEHOLDER = "%n"; - public static final String REVERSE_ORDER = NS + "_REVERSE_ORDER"; - - public static final String CONFIRM_DELETE_OLD = NS - + "_CONFIRM_DELETE_OLD"; - private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS; private static final String TEMP_FILE_EXT = ".tmp"; @@ -101,20 +84,14 @@ public class BackupFiles // REVERSE_ORDER public BackupFiles(File file) { - this(file, ".bak" + NUM_PLACEHOLDER, false, 3, 3, false); - } - - public BackupFiles(File file, String defaultSuffix, boolean defaultNoMax, - int defaultMax, int defaultDigits, boolean defaultReverseOrder) - { classInit(); this.file = file; - this.suffix = Cache.getDefault(SUFFIX, defaultSuffix); - this.noMax = Cache.getDefault(NO_MAX, defaultNoMax); - this.max = Cache.getDefault(ROLL_MAX, defaultMax); - this.digits = Cache.getDefault(SUFFIX_DIGITS, defaultDigits); - this.reverseOrder = Cache.getDefault(REVERSE_ORDER, - defaultReverseOrder); + BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry(); + this.suffix = bfpe.suffix; + this.noMax = bfpe.keepAll; + this.max = bfpe.rollMax; + this.digits = bfpe.digits; + this.reverseOrder = bfpe.reverse; // create a temp file to save new data in File temp = null; @@ -145,7 +122,9 @@ public class BackupFiles public static void classInit() { setEnabled(Cache.getDefault(ENABLED, true)); - setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true)); + BackupFilesPresetEntry bfpe = BackupFilesPresetEntry + .getSavedBackupEntry(); + setConfirmDelete(bfpe.confirmDelete); } public static void setEnabled(boolean flag) diff --git a/src/jalview/io/BackupFilesPresetEntry.java b/src/jalview/io/BackupFilesPresetEntry.java new file mode 100644 index 0000000..4face29 --- /dev/null +++ b/src/jalview/io/BackupFilesPresetEntry.java @@ -0,0 +1,173 @@ +package jalview.io; + +import jalview.bin.Cache; +import jalview.util.MessageManager; + +import java.util.HashMap; +import java.util.Map; +import java.util.StringTokenizer; + +public class BackupFilesPresetEntry +{ + + public String suffix; + + public static final int DIGITSMIN = 1; + + public static final int DIGITSMAX = 6; + + public int digits; + + public boolean reverse; + + public boolean keepAll; + + public static final int ROLLMAXMIN = 1; + + public static final int ROLLMAXMAX = 999; + + public int rollMax; + + public boolean confirmDelete; + + public static final String SAVEDCONFIG = BackupFiles.NS + "_SAVED"; + + public static final String CUSTOMCONFIG = BackupFiles.NS + "_CUSTOM"; + + private static final String stringDelim = "\t"; + + public static final int BACKUPFILESSCHEMECUSTOM = 0; + + public static final int BACKUPFILESSCHEMEDEFAULT = 1; + + public BackupFilesPresetEntry(String suffix, int digits, boolean reverse, + boolean keepAll, int rollMax, boolean confirmDelete) + { + this.suffix = suffix == null ? "" : suffix; + this.digits = digits < DIGITSMIN ? DIGITSMIN + : (digits > DIGITSMAX ? DIGITSMAX : digits); + this.reverse = reverse; + this.keepAll = keepAll; + this.rollMax = rollMax < ROLLMAXMIN ? ROLLMAXMIN + : (rollMax > ROLLMAXMAX ? ROLLMAXMAX : rollMax); + this.confirmDelete = confirmDelete; + } + + public boolean equals(BackupFilesPresetEntry compare) + { + return suffix.equals(compare.suffix) && digits == compare.digits + && reverse == compare.reverse && keepAll == compare.keepAll + && rollMax == compare.rollMax + && confirmDelete == compare.confirmDelete; + } + + @Override + public String toString() + { + StringBuilder sb = new StringBuilder(); + sb.append(suffix); + sb.append(stringDelim); + sb.append(digits); + sb.append(stringDelim); + sb.append(reverse); + sb.append(stringDelim); + sb.append(keepAll); + sb.append(stringDelim); + sb.append(rollMax); + sb.append(stringDelim); + sb.append(confirmDelete); + return sb.toString(); + } + + public static BackupFilesPresetEntry createBackupFilesPresetEntry( + String line) + { + if (line == null) + { + return null; + } + StringTokenizer st = new StringTokenizer(line, stringDelim); + String suffix = null; + int digits = 0; + boolean reverse = false; + boolean keepAll = false; + int rollMax = 0; + boolean confirmDelete = false; + + try + { + suffix = st.nextToken(); + digits = Integer.valueOf(st.nextToken()); + reverse = Boolean.valueOf(st.nextToken()); + keepAll = Boolean.valueOf(st.nextToken()); + rollMax = Integer.valueOf(st.nextToken()); + confirmDelete = Boolean.valueOf(st.nextToken()); + } catch (Exception e) + { + Cache.log.error("Error parsing backupfiles scheme '" + line + "'"); + } + + return new BackupFilesPresetEntry(suffix, digits, reverse, keepAll, + rollMax, confirmDelete); + } + + public static BackupFilesPresetEntry getSavedBackupEntry() + { + String savedPresetString = Cache + .getDefault(BackupFilesPresetEntry.SAVEDCONFIG, null); + BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry + .createBackupFilesPresetEntry(savedPresetString); + if (savedPreset == null) + { + savedPreset = backupfilesPresetEntriesValues + .get(BACKUPFILESSCHEMEDEFAULT); + } + return savedPreset; + } + + public static final IntKeyStringValueEntry[] backupfilesPresetEntries = { + new IntKeyStringValueEntry(BACKUPFILESSCHEMEDEFAULT, + MessageManager.getString("label.default")), + new IntKeyStringValueEntry(2, + MessageManager.getString("label.single_file")), + new IntKeyStringValueEntry(3, + MessageManager.getString("label.keep_all_versions")), + new IntKeyStringValueEntry(4, + MessageManager.getString("label.rolled_backups")), + // ... + // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last) + new IntKeyStringValueEntry(BACKUPFILESSCHEMECUSTOM, + MessageManager.getString("label.custom")) }; + + public static final String[] backupfilesPresetEntryDescriptions = { + MessageManager.getString("label.default_description"), + MessageManager.getString("label.single_file_description"), + MessageManager.getString("label.keep_all_versions_description"), + MessageManager.getString("label.rolled_backups_description"), + MessageManager.getString("label.custom_description") }; + + public static final Map backupfilesPresetEntriesValues = new HashMap() + { + /** + * + */ + private static final long serialVersionUID = 125L; + + { + put(1, new BackupFilesPresetEntry( + ".bak" + BackupFiles.NUM_PLACEHOLDER, 3, false, false, 3, + false)); + put(2, new BackupFilesPresetEntry("~", 1, false, false, 1, false)); + put(3, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER, + 3, false, true, 10, true)); + put(4, new BackupFilesPresetEntry( + "_bak." + BackupFiles.NUM_PLACEHOLDER, 1, true, false, 9, + false)); + + // This gets replaced by GPreferences + put(BACKUPFILESSCHEMECUSTOM, + new BackupFilesPresetEntry("", 0, false, false, 0, false)); + } + }; + +} diff --git a/src/jalview/io/IntKeyStringValueEntry.java b/src/jalview/io/IntKeyStringValueEntry.java new file mode 100644 index 0000000..084dbc5 --- /dev/null +++ b/src/jalview/io/IntKeyStringValueEntry.java @@ -0,0 +1,21 @@ +package jalview.io; + +public class IntKeyStringValueEntry +{ + public final int k; + + public final String v; + + public IntKeyStringValueEntry(int k, String v) + { + this.k = k; + this.v = v; + } + + @Override + public String toString() + { + return v; + } + +} diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index fe85043..f30fa9b 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -435,7 +435,7 @@ public class GDesktop extends JFrame FileMenu.add(inputMenu); FileMenu.add(inputSequence); FileMenu.addSeparator(); - FileMenu.add(saveState); + //FileMenu.add(saveState); FileMenu.add(saveAsState); FileMenu.add(loadState); FileMenu.addSeparator(); diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 87cc87b..60bf1b7 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -31,6 +31,8 @@ import jalview.gui.JvSwingUtils; import jalview.gui.StructureViewer.ViewerType; import jalview.io.BackupFilenameParts; import jalview.io.BackupFiles; +import jalview.io.BackupFilesPresetEntry; +import jalview.io.IntKeyStringValueEntry; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -51,8 +53,8 @@ import java.awt.event.KeyEvent; import java.awt.event.KeyListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; -import java.util.HashMap; -import java.util.Map; +import java.util.Arrays; +import java.util.List; import javax.swing.AbstractCellEditor; import javax.swing.BorderFactory; @@ -63,7 +65,6 @@ import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JLabel; -import javax.swing.JList; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JScrollPane; @@ -296,9 +297,15 @@ public class GPreferences extends JPanel protected JPanel presetsPanel = new JPanel(); + protected JLabel presetsComboLabel = new JLabel(); + + protected JCheckBox customiseCheckbox = new JCheckBox(); + protected JButton revertButton = new JButton(); - protected JComboBox backupfilesPresetsCombo = new JComboBox<>(); + protected JComboBox backupfilesPresetsCombo = new JComboBox<>(); + + private int backupfilesPresetsComboLastSelected = 0; protected JPanel suffixPanel = new JPanel(); @@ -1695,22 +1702,28 @@ public class GPreferences extends JPanel protected void loadLastSavedBackupsOptions() { + BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry + .getSavedBackupEntry(); enableBackupFiles .setSelected(Cache.getDefault(BackupFiles.ENABLED, true)); + + BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry + .createBackupFilesPresetEntry(Cache + .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null)); + if (backupfilesCustomEntry == null) + { + backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues + .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT); + } + BackupFilesPresetEntry.backupfilesPresetEntriesValues.put( + BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, + backupfilesCustomEntry); + setComboIntStringKey(backupfilesPresetsCombo, - Cache.getDefault(BackupFiles.NS + "_PRESET", 1)); - suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX, - ".bak" + BackupFiles.NUM_PLACEHOLDER)); - 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, 3)); - backupfilesConfirmDelete.setSelected( - Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true)); + Cache.getDefault(BackupFiles.NS + "_PRESET", + BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT)); + + backupsSetOptions(savedPreset); backupsOptionsSetEnabled(); updateBackupFilesExampleLabel(); @@ -1718,11 +1731,11 @@ public class GPreferences extends JPanel private boolean warnAboutSuffixReverseChange() { - boolean savedSuffixReverse = Cache.getDefault(BackupFiles.REVERSE_ORDER, - false); - int savedSuffixDigits = Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3); - String savedSuffixTemplate = Cache.getDefault(BackupFiles.SUFFIX, - ".bak" + BackupFiles.NUM_PLACEHOLDER); + BackupFilesPresetEntry bfpe = BackupFilesPresetEntry + .getSavedBackupEntry(); + boolean savedSuffixReverse = bfpe.reverse; + int savedSuffixDigits = bfpe.digits; + String savedSuffixTemplate = bfpe.suffix; boolean nowSuffixReverse = suffixReverse.isSelected(); int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3); @@ -1799,7 +1812,6 @@ public class GPreferences extends JPanel gbc.gridy++; // row 1 backupsTab.add(presetsPanel, gbc); - // gbc.anchor = GridBagConstraints.NORTHWEST; // now using whole row gbc.gridwidth = 2; gbc.gridheight = 1; @@ -1821,50 +1833,10 @@ public class GPreferences extends JPanel return backupsTab; } - protected static final int BACKUPFILESSCHEMECUSTOMISE = 0; - - private static final IntKeyStringValueEntry[] backupfilesPresetEntries = { - new IntKeyStringValueEntry(1, - MessageManager.getString("label.default")), - new IntKeyStringValueEntry(2, - MessageManager.getString("label.single_file")), - new IntKeyStringValueEntry(3, - MessageManager.getString("label.keep_all_versions")), - new IntKeyStringValueEntry(4, - MessageManager.getString("label.rolled_backups")), - // ... - // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last) - new IntKeyStringValueEntry(BACKUPFILESSCHEMECUSTOMISE, - MessageManager.getString("label.customise")) }; - - private static final Map backupfilesPresetEntriesValues = new HashMap() - { - /** - * - */ - private static final long serialVersionUID = 125L; - - { - put(1, new BackupFilesPresetEntry( - ".bak" + BackupFiles.NUM_PLACEHOLDER, 3, false, false, 3, - false)); - put(2, new BackupFilesPresetEntry("~", 1, false, false, 1, false)); - put(3, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER, - 3, false, true, 10, true)); - put(4, new BackupFilesPresetEntry( - "_bak." + BackupFiles.NUM_PLACEHOLDER, 1, true, false, 9, - false)); - } - }; - private JPanel initBackupsTabPresetsPanel() { String title = MessageManager.getString("label.schemes"); - // TitledBorder tb = new TitledBorder(new EmptyBorder(0, 0, 0, 0), title); - // TitledBorder tb = new TitledBorder(title); - // tb.setTitleFont(LABEL_FONT); - // presetsPanel.setBorder(tb); presetsPanel.setLayout(new GridBagLayout()); @@ -1879,24 +1851,53 @@ public class GPreferences extends JPanel // "Scheme: " gbc.gridx = 0; gbc.gridy = 0; - presetsPanel.add(new JLabel(title + ":"), gbc); - for (int i = 0; i < backupfilesPresetEntries.length; i++) + presetsComboLabel = new JLabel(title + ":"); + presetsPanel.add(presetsComboLabel, gbc); + + List entries = Arrays + .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries); + List tooltips = Arrays.asList( + BackupFilesPresetEntry.backupfilesPresetEntryDescriptions); + backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries, + tooltips); + /* + for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++) { - backupfilesPresetsCombo.addItem(backupfilesPresetEntries[i]); + backupfilesPresetsCombo + .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]); } + */ - // put "Previously saved scheme" item in italics (it's not really - // selectable, as such -- it deselects itself when selected) and - // "Customise" in bold - backupfilesPresetsCombo - .setRenderer(new BackupFilesPresetsComboBoxRenderer()); backupfilesPresetsCombo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - backupsTabUpdatePresets(); + int key = getComboIntStringKey(backupfilesPresetsCombo); + if (!customiseCheckbox.isSelected()) + { + backupfilesPresetsComboLastSelected = key; + } + if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) + { + if (customiseCheckbox.isSelected()) + { + // got here by clicking on customiseCheckbox so don't change the values + backupfilesCustomOptionsSetEnabled(); + } + else + { + backupsTabUpdatePresets(); + backupfilesCustomOptionsSetEnabled(); + } + } + else + { + customiseCheckbox.setSelected(false); + backupsTabUpdatePresets(); + backupfilesCustomOptionsSetEnabled(); + } } }); @@ -1905,20 +1906,55 @@ public class GPreferences extends JPanel presetsPanel.add(backupfilesPresetsCombo, gbc); revertButton.setText(MessageManager.getString("label.cancel_changes")); + revertButton.setToolTipText( + MessageManager.getString("label.cancel_changes_description")); revertButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - loadLastSavedBackupsOptions(); + backupsSetOptions( + BackupFilesPresetEntry.backupfilesPresetEntriesValues.get( + BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)); + backupfilesCustomOptionsSetEnabled(); } }); revertButton.setFont(LABEL_FONT); + customiseCheckbox.setFont(LABEL_FONT); + customiseCheckbox.setText(MessageManager.getString("label.customise")); + customiseCheckbox.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + int currently = getComboIntStringKey(backupfilesPresetsCombo); + if (customiseCheckbox.isSelected()) + { + backupfilesPresetsComboLastSelected = currently; + setComboIntStringKey(backupfilesPresetsCombo, + BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM); + } + else + { + setComboIntStringKey(backupfilesPresetsCombo, + backupfilesPresetsComboLastSelected); + + } + backupfilesCustomOptionsSetEnabled(); + } + }); + customiseCheckbox.setToolTipText( + MessageManager.getString("label.customise_description")); + + // customise checkbox + gbc.gridx = 0; + gbc.gridy++; + presetsPanel.add(customiseCheckbox, gbc); + // "Cancel changes" button (aligned with combo box above) gbc.gridx = 1; - gbc.gridy++; presetsPanel.add(revertButton, gbc); return presetsPanel; @@ -1927,7 +1963,7 @@ public class GPreferences extends JPanel private JPanel initBackupsTabFilenameExamplesPanel() { String title = MessageManager - .getString("label.summary_of_backups_scheme"); + .getString("label.scheme_examples"); TitledBorder tb = new TitledBorder(title); exampleFilesPanel.setBorder(tb); exampleFilesPanel.setLayout(new GridBagLayout()); @@ -1953,45 +1989,68 @@ public class GPreferences extends JPanel { IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo .getSelectedItem(); - int key = entry.getKey(); - String value = entry.getValue(); + int key = entry.k; + String value = entry.v; - // BACKUPFILESSCHEMECUSTOMISE (==0) reserved for "Custom" - if (key != BACKUPFILESSCHEMECUSTOMISE) + if (BackupFilesPresetEntry.backupfilesPresetEntriesValues + .containsKey(key)) { - if (backupfilesPresetEntriesValues.containsKey(key)) - { - backupsSetOptions(backupfilesPresetEntriesValues.get(key)); - } - else - { - System.out.println("Preset '" + value + "' not implemented"); - } + backupsSetOptions( + BackupFilesPresetEntry.backupfilesPresetEntriesValues + .get(key)); + } + else + { + Cache.log.error( + "Preset '" + value + "' [key:" + key + "] not implemented"); } - backupfilesCustomOptionsSetEnabled(); + // Custom options will now be enabled when the customiseCheckbox is checked + // (performed above) + // backupfilesCustomOptionsSetEnabled(); updateBackupFilesExampleLabel(); } - protected int getComboIntStringKey(JComboBox c) + protected int getComboIntStringKey( + JComboBox backupfilesPresetsCombo2) { - IntKeyStringValueEntry e = (IntKeyStringValueEntry) c.getSelectedItem(); - return e != null ? e.getKey() : 0; + IntKeyStringValueEntry e; + try + { + e = (IntKeyStringValueEntry) backupfilesPresetsCombo2 + .getSelectedItem(); + } catch (Exception ex) + { + Cache.log.error( + "Problem casting Combo entry to IntKeyStringValueEntry."); + e = null; + } + return e != null ? e.k : 0; } - protected void setComboIntStringKey(JComboBox c, + protected void setComboIntStringKey( + JComboBox backupfilesPresetsCombo2, int key) { - for (int i = 0; i < c.getItemCount(); i++) + for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++) { - IntKeyStringValueEntry e = c.getItemAt(i); - if (e.getKey() == key) + IntKeyStringValueEntry e; + try { - c.setSelectedIndex(i); + e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i); + } catch (Exception ex) + { + Cache.log.error( + "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. "); + continue; + } + if (e.k == key) + { + backupfilesPresetsCombo2.setSelectedIndex(i); break; } } - backupsTabUpdatePresets(); + // backupsTabUpdatePresets(); } private JPanel initBackupsTabSuffixPanel() @@ -2015,16 +2074,18 @@ public class GPreferences extends JPanel { updateBackupFilesExampleLabel(); backupfilesCustomOptionsSetEnabled(); + backupfilesRevertButtonSetEnabled(true); } }); - KeyListener kl = new KeyListener() + suffixTemplate.addKeyListener(new KeyListener() { @Override public void keyReleased(KeyEvent e) { updateBackupFilesExampleLabel(); backupfilesCustomOptionsSetEnabled(); + backupfilesRevertButtonSetEnabled(true); } @Override @@ -2044,26 +2105,25 @@ public class GPreferences extends JPanel } } - }; - suffixTemplate.addKeyListener(kl); + }); // digits spinner suffixDigitsLabel .setText(MessageManager.getString("label.index_digits")); suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT); suffixDigitsLabel.setFont(LABEL_FONT); - int defaultmin = 1; - int defaultmax = 6; ChangeListener c = new ChangeListener() { @Override public void stateChanged(ChangeEvent e) { + backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } }; - setIntegerSpinner(suffixDigitsSpinner, defaultmin, defaultmax, 3, c); + setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN, + BackupFilesPresetEntry.DIGITSMAX, 3, c); suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"), MessageManager.getString("label.increment_index")); @@ -2080,12 +2140,13 @@ public class GPreferences extends JPanel } if (okay) { + backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } else { - boolean savedSuffixReverse = Cache - .getDefault(BackupFiles.REVERSE_ORDER, false); + boolean savedSuffixReverse = BackupFilesPresetEntry + .getSavedBackupEntry().reverse; suffixReverse.setSelected(savedSuffixReverse); } } @@ -2161,6 +2222,7 @@ public class GPreferences extends JPanel @Override public void actionPerformed(ActionEvent e) { + backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } }); @@ -2169,6 +2231,7 @@ public class GPreferences extends JPanel @Override public void actionPerformed(ActionEvent e) { + backupfilesRevertButtonSetEnabled(true); keepRollMaxOptionsEnabled(); updateBackupFilesExampleLabel(); } @@ -2179,15 +2242,26 @@ public class GPreferences extends JPanel @Override public void stateChanged(ChangeEvent e) { + backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } }; - setIntegerSpinner(backupfilesRollMaxSpinner, 1, 999, 4, true, c); + setIntegerSpinner(backupfilesRollMaxSpinner, + BackupFilesPresetEntry.ROLLMAXMIN, + BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c); backupfilesConfirmDelete.setLabels( MessageManager.getString("label.always_ask"), MessageManager.getString("label.auto_delete")); + backupfilesConfirmDelete.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + backupfilesRevertButtonSetEnabled(true); + } + }); // update the enabled section keepRollMaxOptionsEnabled(); @@ -2223,13 +2297,6 @@ public class GPreferences extends JPanel kgbc.gridwidth = GridBagConstraints.REMAINDER; kgbc.fill = GridBagConstraints.HORIZONTAL; kgbc.weightx = 1.0; - /* - keepfilesPanel.add(backupfilesConfirmDelete.getTrueButton(), kgbc); - - // fourth row (indented) - kgbc.gridy = 3; - keepfilesPanel.add(backupfilesConfirmDelete.getFalseButton(), kgbc); - */ JPanel jp = new JPanel(); jp.setLayout(new FlowLayout()); @@ -2285,6 +2352,7 @@ public class GPreferences extends JPanel int uppersurround = 0; StringBuilder exampleSB = new StringBuilder(); boolean firstLine = true; + int lineNumber = 0; if (reverse) { @@ -2295,6 +2363,7 @@ public class GPreferences extends JPanel if (index == min + lowersurround && index < max - uppersurround - 1) { exampleSB.append("\n..."); + lineNumber++; } else if (index > min + lowersurround && index < max - uppersurround) { @@ -2309,6 +2378,7 @@ public class GPreferences extends JPanel else { exampleSB.append("\n"); + lineNumber++; } exampleSB.append(BackupFilenameParts.getBackupFilename(index, base, suffix, digits)); @@ -2348,6 +2418,7 @@ public class GPreferences extends JPanel if (index == min + lowersurround && index < max - uppersurround - 1) { exampleSB.append("\n..."); + lineNumber++; } else if (index > min + lowersurround && index < max - uppersurround) { @@ -2362,6 +2433,7 @@ public class GPreferences extends JPanel else { exampleSB.append("\n"); + lineNumber++; } exampleSB.append(BackupFilenameParts.getBackupFilename(index, base, suffix, digits)); @@ -2390,6 +2462,18 @@ public class GPreferences extends JPanel } + // add some extra empty lines to pad out the example files box. ugh, please tell + // me how to do this better + int remainingLines = lowersurround + uppersurround + 1 - lineNumber; + if (remainingLines > 0) + { + for (int i = 0; i < remainingLines; i++) + { + exampleSB.append("\n "); + lineNumber++; + } + } + backupfilesExampleLabel.setText(exampleSB.toString()); } @@ -2404,7 +2488,7 @@ public class GPreferences extends JPanel i = Integer.parseInt((String) s.getValue()); } catch (Exception e) { - System.out.println( + Cache.log.error( "Exception casting the initial value of s.getValue()"); } } @@ -2436,7 +2520,7 @@ public class GPreferences extends JPanel i = (Integer) s.getValue(); } catch (Exception e) { - System.out.println("Failed casting (Integer) JSpinner s.getValue()"); + Cache.log.error("Failed casting (Integer) JSpinner s.getValue()"); } return i; } @@ -2453,7 +2537,7 @@ public class GPreferences extends JPanel private void backupfilesKeepAllSetEnabled(boolean tryEnabled) { boolean enabled = tryEnabled && enableBackupFiles.isSelected() - && getComboIntStringKey(backupfilesPresetsCombo) == 0 + && customiseCheckbox.isSelected() && suffixTemplate.getText() .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1; keepfilesPanel.setEnabled(enabled); @@ -2474,18 +2558,48 @@ public class GPreferences extends JPanel private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled) { boolean enabled = tryEnabled && enableBackupFiles.isSelected() - && getComboIntStringKey(backupfilesPresetsCombo) == 0; + && customiseCheckbox.isSelected(); suffixPanel.setEnabled(enabled); suffixTemplateLabel.setEnabled(enabled); suffixTemplate.setEnabled(enabled); backupfilesSuffixTemplateDigitsSetEnabled(); } + private void backupfilesRevertButtonSetEnabled(boolean tryEnabled) + { + boolean enabled = tryEnabled && enableBackupFiles.isSelected() + && customiseCheckbox.isSelected() && backupfilesCustomChanged(); + revertButton.setEnabled(enabled); + } + + private boolean backupfilesCustomChanged() + { + BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues + .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM); + BackupFilesPresetEntry current = getBackupfilesCurrentEntry(); + return !custom.equals(current); + } + + protected BackupFilesPresetEntry getBackupfilesCurrentEntry() + { + String suffix = suffixTemplate.getText(); + int digits = getSpinnerInt(suffixDigitsSpinner, 3); + boolean reverse = suffixReverse.isSelected(); + boolean keepAll = backupfilesKeepAll.isSelected(); + int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3); + boolean confirmDelete = backupfilesConfirmDelete.isSelected(); + + BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits, + reverse, keepAll, rollMax, confirmDelete); + + return bfpe; + } + protected void backupfilesCustomOptionsSetEnabled() { - int scheme = getComboIntStringKey(backupfilesPresetsCombo); - boolean enabled = scheme == 0 && enableBackupFiles.isSelected(); + boolean enabled = customiseCheckbox.isSelected(); + backupfilesRevertButtonSetEnabled(enabled); backupfilesSuffixTemplateSetEnabled(enabled); backupfilesKeepAllSetEnabled(enabled); } @@ -2501,7 +2615,10 @@ public class GPreferences extends JPanel { boolean enabled = enableBackupFiles.isSelected(); presetsPanel.setEnabled(enabled); + presetsComboLabel.setEnabled(enabled); backupfilesPresetsCombo.setEnabled(enabled); + customiseCheckbox.setEnabled(enabled); + revertButton.setEnabled(enabled); } protected void backupsOptionsSetEnabled() @@ -2715,85 +2832,3 @@ public class GPreferences extends JPanel } } -class IntKeyStringValueEntry -{ - int k; - - String v; - - public IntKeyStringValueEntry(int k, String v) - { - this.k = k; - this.v = v; - } - - @Override - public String toString() - { - return this.getValue(); - } - - public int getKey() - { - return k; - } - - public String getValue() - { - return v; - } -} - -class BackupFilesPresetEntry -{ - String suffix; - - int digits; - - boolean reverse; - - boolean keepAll; - - int rollMax; - - boolean confirmDelete; - - public BackupFilesPresetEntry(String suffix, int digits, boolean reverse, - boolean keepAll, int rollMax, boolean confirmDelete) - { - this.suffix = suffix; - this.digits = digits; - this.reverse = reverse; - this.keepAll = keepAll; - this.rollMax = rollMax; - this.confirmDelete = confirmDelete; - } -} - -class BackupFilesPresetsComboBoxRenderer extends DefaultListCellRenderer -{ - /** - * - */ - private static final long serialVersionUID = 88L; - - @Override - public Component getListCellRendererComponent(JList list, Object value, - int index, boolean isSelected, boolean cellHasFocus) - { - super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus); - - try { - IntKeyStringValueEntry e = (IntKeyStringValueEntry) value; - if (e.getKey() == GPreferences.BACKUPFILESSCHEMECUSTOMISE) - { - // "Customise" item - this.setFont(this.getFont().deriveFont(Font.BOLD)); - } - } catch (Exception e) { - return this; - } - - return this; - } -} diff --git a/test/jalview/gui/SeqPanelTest.java b/test/jalview/gui/SeqPanelTest.java index 571c75b..cd0b594 100644 --- a/test/jalview/gui/SeqPanelTest.java +++ b/test/jalview/gui/SeqPanelTest.java @@ -39,8 +39,9 @@ import jalview.gui.SeqPanel.MousePos; import jalview.io.DataSourceType; import jalview.io.FileLoader; import jalview.util.MessageManager; +import jalview.viewmodel.ViewportRanges; -import java.awt.event.InputEvent;import java.awt.EventQueue; +import java.awt.EventQueue; import java.awt.event.MouseEvent; import java.lang.reflect.InvocationTargetException; @@ -722,7 +723,8 @@ public class SeqPanelTest int x = 0; final int charWidth = alignFrame.getViewport().getCharWidth(); assertTrue(charWidth > 0); // sanity check - assertEquals(alignFrame.getViewport().getRanges().getStartRes(), 0); + ViewportRanges ranges = alignFrame.getViewport().getRanges(); + assertEquals(ranges.getStartRes(), 0); /* * mouse at top left of unwrapped panel @@ -763,8 +765,10 @@ public class SeqPanelTest false, 0); SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas; int w = seqCanvas.getWidth(); - // limited to number of whole columns, base 0 - int expected = w / charWidth - 1; + // limited to number of whole columns, base 0, + // and to end of visible range + int expected = w / charWidth; + expected = Math.min(expected, ranges.getEndRes()); assertEquals(testee.findColumn(evt), expected); /* diff --git a/test/jalview/io/BackupFilesTest.java b/test/jalview/io/BackupFilesTest.java index 723279d..64cf902 100644 --- a/test/jalview/io/BackupFilesTest.java +++ b/test/jalview/io/BackupFilesTest.java @@ -34,7 +34,8 @@ public class BackupFilesTest } private static boolean actuallyDeleteTmpFiles = true; - private static String testDir = "examples"; + + private static String testDir = "test/jalview/io"; private static String testBasename = "backupfilestest"; @@ -61,7 +62,7 @@ public class BackupFilesTest private static String suffix = "_BACKUPTEST-%n"; - private static int digits = 8; + private static int digits = 6; private static int rollMax = 2; @@ -107,28 +108,28 @@ public class BackupFilesTest } // check 10 backup files - HashMap correctindexmap = new HashMap(); - correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001"); - correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002"); - correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003"); - correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004"); - correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005"); - correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006"); - correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007"); - correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008"); - correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009"); - correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010"); - HashMap wrongindexmap = new HashMap(); + HashMap correctindexmap = new HashMap<>(); + correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-000001"); + correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002"); + correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-000003"); + correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-000004"); + correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-000005"); + correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-000006"); + correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-000007"); + correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-000008"); + correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009"); + correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010"); + HashMap wrongindexmap = new HashMap<>(); wrongindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-1"); - wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002"); - wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003"); - wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004"); - wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005"); - wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006"); - wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007"); - wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008"); - wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009"); - wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010"); + wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002"); + wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-000003"); + wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-000004"); + wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-000005"); + wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-000006"); + wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-000007"); + wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-000008"); + wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009"); + wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010"); int[] indexes2 = { 3, 4, 5, 6, 7, 8, 9, 10 }; int[] indexes3 = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 }; Assert.assertTrue(checkBackupFiles(correctindexmap)); @@ -158,9 +159,9 @@ public class BackupFilesTest // check there are "rollMax" backup files and they are all saved correctly // check 10 backup files - HashMap correctindexmap = new HashMap(); - correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009"); - correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010"); + HashMap correctindexmap = new HashMap<>(); + correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009"); + correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010"); int[] indexes2 = { 10 }; int[] indexes3 = { 8, 9, 10 }; Assert.assertTrue(checkBackupFiles(correctindexmap)); @@ -189,9 +190,9 @@ public class BackupFilesTest // check there are "rollMax" backup files and they are all saved correctly // check 10 backup files - HashMap correctindexmap = new HashMap(); - correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001"); - correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002"); + HashMap correctindexmap = new HashMap<>(); + correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-000001"); + correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002"); int[] indexes2 = { 1 }; int[] indexes3 = { 1, 2, 3 }; Assert.assertTrue(checkBackupFiles(correctindexmap)); @@ -209,6 +210,14 @@ public class BackupFilesTest { Cache.loadProperties("test/jalview/io/testProps.jvprops"); + BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits, + reverse, noMax, rollMax, false); + + Cache.applicationProperties.setProperty(BackupFiles.ENABLED, + Boolean.toString(enabled)); + Cache.applicationProperties.setProperty( + BackupFilesPresetEntry.SAVEDCONFIG, bfpe.toString()); + /* Cache.applicationProperties.setProperty(BackupFiles.ENABLED, Boolean.toString(enabled)); Cache.applicationProperties.setProperty(BackupFiles.SUFFIX, suffix); @@ -222,6 +231,7 @@ public class BackupFilesTest Integer.toString(rollMax)); Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD, "false"); + */ } private void save() diff --git a/examples/backupfilestest.fa b/test/jalview/io/backupfilestest.fa similarity index 100% rename from examples/backupfilestest.fa rename to test/jalview/io/backupfilestest.fa diff --git a/test/jalview/io/testProps.jvprops b/test/jalview/io/testProps.jvprops index f180395..94bc5d9 100644 --- a/test/jalview/io/testProps.jvprops +++ b/test/jalview/io/testProps.jvprops @@ -1,13 +1,10 @@ #---JalviewX Properties File--- #Fri Apr 25 09:54:25 BST 2014 # -BACKUPFILES_ROLL_MAX=2 -BACKUPFILES_REVERSE_ORDER=false -BACKUPFILES_SUFFIX=_BACKUPFILESTESTTMP%n -BACKUPFILES_CONFIRM_DELETE_OLD=false -BACKUPFILES_NO_MAX=false BACKUPFILES_ENABLED=true -BACKUPFILES_SUFFIX_DIGITS=8 +BACKUPFILES_PRESET=0 +BACKUPFILES_SAVED=_BACKUPFILESTESTTMP%n\t6\tfalse\tfalse\t2\tfalse +BACKUPFILES_CUSTOM=_BACKUPFILESTESTTMP%n\t6\tfalse\tfalse\t2\tfalse SCREEN_Y=768 SCREEN_X=936 SHOW_WSDISCOVERY_ERRORS=true diff --git a/utils/install4j/DS_Store b/utils/install4j/DS_Store index 374da46..2eafdbc 100644 Binary files a/utils/install4j/DS_Store and b/utils/install4j/DS_Store differ diff --git a/utils/install4j/DS_Store_1 b/utils/install4j/DS_Store_1 new file mode 100644 index 0000000..374da46 Binary files /dev/null and b/utils/install4j/DS_Store_1 differ diff --git a/utils/install4j/DS_Store_2 b/utils/install4j/DS_Store_2 new file mode 100644 index 0000000..2eafdbc Binary files /dev/null and b/utils/install4j/DS_Store_2 differ diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist b/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist new file mode 100644 index 0000000..c10a834 --- /dev/null +++ b/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist @@ -0,0 +1,52 @@ + + + + + CFBundleAllowMixedLocalizations + + CFBundleDevelopmentRegion + English + CFBundleExecutable + applet + CFBundleIconFile + applet + CFBundleIdentifier + com.apple.ScriptEditor.id.Uninstall-Old-Jalview + CFBundleInfoDictionaryVersion + 6.0 + CFBundleName + Uninstall Old Jalview + CFBundlePackageType + APPL + CFBundleShortVersionString + 1.0 + CFBundleSignature + aplt + LSMinimumSystemVersionByArchitecture + + x86_64 + 10.6 + + LSRequiresCarbon + + WindowState + + bundleDividerCollapsed + + bundlePositionOfDivider + 0.0 + dividerCollapsed + + eventLogLevel + 2 + name + ScriptWindowState + positionOfDivider + 223 + savedFrame + 329 957 700 672 0 0 3360 1867 + selectedTab + description + + + diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet b/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet new file mode 100755 index 0000000..f11986e Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet differ diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/PkgInfo b/utils/install4j/Uninstall Old Jalview.app/Contents/PkgInfo new file mode 100644 index 0000000..3253614 --- /dev/null +++ b/utils/install4j/Uninstall Old Jalview.app/Contents/PkgInfo @@ -0,0 +1 @@ +APPLaplt \ No newline at end of file diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt new file mode 100644 index 0000000..1dce96c Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt differ diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.icns b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.icns new file mode 100644 index 0000000..67a2cbd Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.icns differ diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc new file mode 100644 index 0000000..c41bb4e Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc differ diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf new file mode 100644 index 0000000..76ac711 --- /dev/null +++ b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf @@ -0,0 +1,5 @@ +{\rtf1\ansi\ansicpg1252\cocoartf1561\cocoasubrtf600 +{\fonttbl} +{\colortbl;\red255\green255\blue255;} +{\*\expandedcolortbl;;} +} \ No newline at end of file diff --git a/utils/install4j/Uninstall Old Jalview.scpt b/utils/install4j/Uninstall Old Jalview.scpt new file mode 100644 index 0000000..1692009 Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.scpt differ diff --git a/utils/install4j/install4j_template.install4j b/utils/install4j/install4j_template.install4j index 7a924e2..2f65f51 100644 --- a/utils/install4j/install4j_template.install4j +++ b/utils/install4j/install4j_template.install4j @@ -1,6 +1,6 @@ - + @@ -8,6 +8,8 @@ + + @@ -25,17 +27,23 @@ + + + + + + @@ -50,6 +58,12 @@ + + + + + + + + @@ -149,6 +177,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -700,6 +761,36 @@ return console.askOkCancel(message, true); + + + + + + false + + + ${compiler:sys.shortName} + + + + ${compiler:sys.shortName} + + + + + ../../resources/images/jalview_logos.ico + + + + + ../../resources/images/JalviewLogo_Huge.png + + + + + + !context.getBooleanVariable("sys.programGroupDisabled") + @@ -1666,20 +1757,24 @@ return console.askYesNo(message, true); - + + + + + @@ -1701,20 +1796,24 @@ return console.askYesNo(message, true); - + + + + + @@ -1736,11 +1835,13 @@ return console.askYesNo(message, true); - + + + @@ -1751,6 +1852,31 @@ return console.askYesNo(message, true); + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1758,10 +1884,11 @@ return console.askYesNo(message, true); - + + @@ -1769,6 +1896,7 @@ return console.askYesNo(message, true); + @@ -1782,12 +1910,14 @@ return console.askYesNo(message, true); + - + + @@ -1795,6 +1925,7 @@ return console.askYesNo(message, true); + @@ -1808,10 +1939,17 @@ return console.askYesNo(message, true); + - - + + + + + + + + @@ -1819,9 +1957,10 @@ return console.askYesNo(message, true); - + + @@ -1832,11 +1971,40 @@ return console.askYesNo(message, true); - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1844,18 +2012,25 @@ return console.askYesNo(message, true); - + + + + + + - + + + @@ -1864,13 +2039,15 @@ return console.askYesNo(message, true); + + - + @@ -1881,6 +2058,8 @@ return console.askYesNo(message, true); + + diff --git a/utils/install4j/uninstall_app_dmg_file_inclusions.sh b/utils/install4j/uninstall_app_dmg_file_inclusions.sh new file mode 100644 index 0000000..f5bed50 --- /dev/null +++ b/utils/install4j/uninstall_app_dmg_file_inclusions.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash + +find Uninstall\ Old\ Jalview.app | perl -p -e 'chomp;$_=qq( \n);' > uninstall_old_jalview_files.xml + +# makes the file used to replace the line +# +# (replacement happens in gradle) diff --git a/utils/install4j/uninstall_old_jalview.icns b/utils/install4j/uninstall_old_jalview.icns new file mode 100644 index 0000000..67a2cbd Binary files /dev/null and b/utils/install4j/uninstall_old_jalview.icns differ diff --git a/utils/install4j/uninstall_old_jalview_files.xml b/utils/install4j/uninstall_old_jalview_files.xml new file mode 100644 index 0000000..342fd90 --- /dev/null +++ b/utils/install4j/uninstall_old_jalview_files.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + +