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drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
24 stars 11 forks source link

New experiment GUI do not work on mac #26

Closed barkait closed 6 years ago

barkait commented 6 years ago

Hi,

"File >> New experiment" works great on my PC but when I am trying to do so on my mac(java 9.0.1 Java(TM) SE Runtime Environment (build 9.0.1+11) Java HotSpot(TM) 64-Bit Server VM (build 9.0.1+11, mixed mode)) I get the following error on my terminal. Thanks!

SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/Users/username/OneDrive/my_projects/Aptamers/aptasuite-0.6.3/lib/ch.qos.logback.logback-classic-1.1.3.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/Users/username/OneDrive/my_projects/Aptamers/aptasuite-0.6.3/lib/org.slf4j.slf4j-simple-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder] 12:43:37.718 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false 12:43:37.722 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean' 12:43:37.722 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - No conversion required, value is already a Boolean 12:43:37.724 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0 12:43:37.724 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte' 12:43:37.724 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Converted to Byte value '0' 12:43:37.725 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:
12:43:37.725 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character' 12:43:37.725 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - No conversion required, value is already a Character 12:43:37.726 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0 12:43:37.726 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double' 12:43:37.726 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Converted to Double value '0.0' 12:43:37.727 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0 12:43:37.727 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float' 12:43:37.727 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Converted to Float value '0.0' 12:43:37.727 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0 12:43:37.727 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer' 12:43:37.728 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - No conversion required, value is already a Integer 12:43:37.728 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0 12:43:37.729 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long' 12:43:37.729 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Converted to Long value '0' 12:43:37.729 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0 12:43:37.730 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short' 12:43:37.730 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Converted to Short value '0' 12:43:37.735 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigDecimalConverter - Setting default value: 0.0 12:43:37.735 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigDecimalConverter - Converting 'BigDecimal' value '0.0' to type 'BigDecimal' 12:43:37.735 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigDecimalConverter - No conversion required, value is already a BigDecimal 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigIntegerConverter - Setting default value: 0 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigIntegerConverter - Converting 'BigInteger' value '0' to type 'BigInteger' 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigIntegerConverter - No conversion required, value is already a BigInteger 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean' 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - No conversion required, value is already a Boolean 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte' 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Converted to Byte value '0' 12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:
12:43:37.736 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character' 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - No conversion required, value is already a Character 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double' 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Converted to Double value '0.0' 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float' 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Converted to Float value '0.0' 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer' 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - No conversion required, value is already a Integer 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long' 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Converted to Long value '0' 12:43:37.737 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0 12:43:37.738 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short' 12:43:37.738 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Converted to Short value '0' 12:43:37.738 [JavaFX Application Thread] DEBUG o.a.c.b.converters.StringConverter - Setting default value: 12:43:37.739 [JavaFX Application Thread] DEBUG o.a.c.b.converters.StringConverter - Converting 'String' value '' to type 'String' 12:43:37.747 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Z@bd01a69 12:43:37.747 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'boolean[]' value '[Z@bd01a69' to type 'boolean[]' 12:43:37.747 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a boolean[] 12:43:37.747 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [B@5240c856 12:43:37.747 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'byte[]' value '[B@5240c856' to type 'byte[]' 12:43:37.747 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a byte[] 12:43:37.747 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [C@6cc41524 12:43:37.748 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'char[]' value '[C@6cc41524' to type 'char[]' 12:43:37.749 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a char[] 12:43:37.749 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [D@6d5c2922 12:43:37.749 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'double[]' value '[D@6d5c2922' to type 'double[]' 12:43:37.749 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a double[] 12:43:37.749 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [F@752b0197 12:43:37.749 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'float[]' value '[F@752b0197' to type 'float[]' 12:43:37.750 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a float[] 12:43:37.750 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [I@3c852b95 12:43:37.750 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'int[]' value '[I@3c852b95' to type 'int[]' 12:43:37.750 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a int[] 12:43:37.750 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [J@571125d4 12:43:37.750 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'long[]' value '[J@571125d4' to type 'long[]' 12:43:37.750 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a long[] 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [S@2adbd73f 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'short[]' value '[S@2adbd73f' to type 'short[]' 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a short[] 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigDecimal;@617635c1 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigDecimal[]' value '[Ljava.math.BigDecimal;@617635c1' to type 'BigDecimal[]' 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a BigDecimal[] 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigInteger;@32549e4e 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigInteger[]' value '[Ljava.math.BigInteger;@32549e4e' to type 'BigInteger[]' 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a BigInteger[] 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Boolean;@610ba7b2 12:43:37.751 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Boolean[]' value '[Ljava.lang.Boolean;@610ba7b2' to type 'Boolean[]' 12:43:37.752 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Boolean[] 12:43:37.752 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Byte;@27f510f6 12:43:37.752 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Byte[]' value '[Ljava.lang.Byte;@27f510f6' to type 'Byte[]' 12:43:37.752 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Byte[] 12:43:37.752 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Character;@307400c8 12:43:37.752 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Character[]' value '[Ljava.lang.Character;@307400c8' to type 'Character[]' 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Character[] 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Double;@2424c9bb 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Double[]' value '[Ljava.lang.Double;@2424c9bb' to type 'Double[]' 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Double[] 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Float;@48c20c61 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Float[]' value '[Ljava.lang.Float;@48c20c61' to type 'Float[]' 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Float[] 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Integer;@29676b1a 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Integer[]' value '[Ljava.lang.Integer;@29676b1a' to type 'Integer[]' 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Integer[] 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Long;@28489765 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Long[]' value '[Ljava.lang.Long;@28489765' to type 'Long[]' 12:43:37.753 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Long[] 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Short;@7114be65 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Short[]' value '[Ljava.lang.Short;@7114be65' to type 'Short[]' 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Short[] 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.String;@64a3b080 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'String[]' value '[Ljava.lang.String;@64a3b080' to type 'String[]' 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a String[] 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Class;@4e859e89 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Class[]' value '[Ljava.lang.Class;@4e859e89' to type 'Class[]' 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Class[] 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Date;@1a36f6aa 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Date[]' value '[Ljava.util.Date;@1a36f6aa' to type 'Date[]' 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Date[] 12:43:37.754 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Calendar;@cd13f25 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Calendar[]' value '[Ljava.util.Calendar;@cd13f25' to type 'Calendar[]' 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Calendar[] 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.io.File;@43eca124 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.io.File[]' value '[Ljava.io.File;@43eca124' to type 'java.io.File[]' 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.io.File[] 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Date;@4e7323b2 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Date[]' value '[Ljava.sql.Date;@4e7323b2' to type 'java.sql.Date[]' 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.sql.Date[] 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Time;@12474c20 12:43:37.755 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Time[]' value '[Ljava.sql.Time;@12474c20' to type 'java.sql.Time[]' 12:43:37.756 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.sql.Time[] 12:43:37.756 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Timestamp;@7eb43a6e 12:43:37.756 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Timestamp[]' value '[Ljava.sql.Timestamp;@7eb43a6e' to type 'java.sql.Timestamp[]' 12:43:37.756 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.sql.Timestamp[] 12:43:37.756 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.net.URL;@435b20ad 12:43:37.756 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.net.URL[]' value '[Ljava.net.URL;@435b20ad' to type 'java.net.URL[]' 12:43:37.756 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.net.URL[] WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by javassist.util.proxy.SecurityActions (file:/Users/username/OneDrive/my_projects/Aptamers/aptasuite-0.6.3/lib/org.javassist.javassist-3.18.1-GA.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) WARNING: Please consider reporting this to the maintainers of javassist.util.proxy.SecurityActions WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Exception in thread "JavaFX Application Thread" java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at javafx.fxml/javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1787) at javafx.fxml/javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1670) at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.base/javafx.event.Event.fireEvent(Event.java:198) at javafx.controls/javafx.scene.control.MenuItem.fire(MenuItem.java:465) at javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1380) at javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1333) at javafx.base/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218) at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.base/javafx.event.Event.fireEvent(Event.java:198) at javafx.graphics/javafx.scene.Scene$MouseHandler.process(Scene.java:3876) at javafx.graphics/javafx.scene.Scene$MouseHandler.access$1300(Scene.java:3604) at javafx.graphics/javafx.scene.Scene.processMouseEvent(Scene.java:1874) at javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2613) at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:397) at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295) at java.base/java.security.AccessController.doPrivileged(Native Method) at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:434) at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389) at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:433) at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(View.java:556) at javafx.graphics/com.sun.glass.ui.View.notifyMouse(View.java:942) at javafx.graphics/com.sun.glass.ui.mac.MacView.notifyMouse(MacView.java:127) Caused by: java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at com.sun.javafx.reflect.Trampoline.invoke(MethodUtil.java:76) at jdk.internal.reflect.GeneratedMethodAccessor2.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at javafx.base/com.sun.javafx.reflect.MethodUtil.invoke(MethodUtil.java:275) at javafx.fxml/com.sun.javafx.fxml.MethodHelper.invoke(MethodHelper.java:83) at javafx.fxml/javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1782) ... 41 more Caused by: java.lang.NoClassDefFoundError: javax/annotation/PostConstruct at io.datafx.controller.ViewFactory.createByController(ViewFactory.java:195) at io.datafx.controller.flow.FlowHandler.start(FlowHandler.java:146) at io.datafx.controller.flow.Flow.startInStage(Flow.java:389) at gui.core.RootLayoutController.fileNewExperimentButtonAction(RootLayoutController.java:477) ... 52 more Caused by: java.lang.ClassNotFoundException: javax.annotation.PostConstruct at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582) at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:496) ... 56

drivenbyentropy commented 6 years ago

Hi, Thanks for reporting this. This issue is due to the Javax annotations being removed from the standard Java classpath in versions 9 or higher. The wizard uses a number of annotations through the datafx package (which seems deprecated now). I will replace the wizard with a version not dependent on annotations in the next mayor version.

As a temporary workaround, you could parse the sequences using the CLI by manually creating a config file, running

java -jar /path/to/aptasuite.jar -parse -config path/to/configuration.config

and then open the experiment with the GUI to visualize the result as no other components of AptaSuite use Javax annotations.

Sorry for the inconvenience and thanks again for reporting this.

barkait commented 6 years ago

Thanks for the quick response. When i am trying the CLI i get this message - with an error at the end:

Reading configuration from file. SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/Users/username/OneDrive/my_projects/Aptamers/aptasuite-0.6.3/lib/ch.qos.logback.logback-classic-1.1.3.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/Users/username/OneDrive/my_projects/Aptamers/aptasuite-0.6.3/lib/org.slf4j.slf4j-simple-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder] 09:37:06.162 [main] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false 09:37:06.166 [main] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean' 09:37:06.166 [main] DEBUG o.a.c.b.converters.BooleanConverter - No conversion required, value is already a Boolean 09:37:06.170 [main] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0 09:37:06.171 [main] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte' 09:37:06.171 [main] DEBUG o.a.c.b.converters.ByteConverter - Converted to Byte value '0' 09:37:06.172 [main] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:
09:37:06.173 [main] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character' 09:37:06.174 [main] DEBUG o.a.c.b.c.CharacterConverter - No conversion required, value is already a Character 09:37:06.175 [main] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0 09:37:06.176 [main] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double' 09:37:06.177 [main] DEBUG o.a.c.b.converters.DoubleConverter - Converted to Double value '0.0' 09:37:06.178 [main] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0 09:37:06.178 [main] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float' 09:37:06.178 [main] DEBUG o.a.c.b.converters.FloatConverter - Converted to Float value '0.0' 09:37:06.179 [main] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0 09:37:06.179 [main] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer' 09:37:06.179 [main] DEBUG o.a.c.b.converters.IntegerConverter - No conversion required, value is already a Integer 09:37:06.180 [main] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0 09:37:06.180 [main] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long' 09:37:06.181 [main] DEBUG o.a.c.b.converters.LongConverter - Converted to Long value '0' 09:37:06.181 [main] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0 09:37:06.182 [main] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short' 09:37:06.182 [main] DEBUG o.a.c.b.converters.ShortConverter - Converted to Short value '0' 09:37:06.185 [main] DEBUG o.a.c.b.c.BigDecimalConverter - Setting default value: 0.0 09:37:06.185 [main] DEBUG o.a.c.b.c.BigDecimalConverter - Converting 'BigDecimal' value '0.0' to type 'BigDecimal' 09:37:06.186 [main] DEBUG o.a.c.b.c.BigDecimalConverter - No conversion required, value is already a BigDecimal 09:37:06.186 [main] DEBUG o.a.c.b.c.BigIntegerConverter - Setting default value: 0 09:37:06.187 [main] DEBUG o.a.c.b.c.BigIntegerConverter - Converting 'BigInteger' value '0' to type 'BigInteger' 09:37:06.187 [main] DEBUG o.a.c.b.c.BigIntegerConverter - No conversion required, value is already a BigInteger 09:37:06.187 [main] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false 09:37:06.188 [main] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean' 09:37:06.188 [main] DEBUG o.a.c.b.converters.BooleanConverter - No conversion required, value is already a Boolean 09:37:06.188 [main] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0 09:37:06.188 [main] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte' 09:37:06.188 [main] DEBUG o.a.c.b.converters.ByteConverter - Converted to Byte value '0' 09:37:06.189 [main] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:
09:37:06.189 [main] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character' 09:37:06.190 [main] DEBUG o.a.c.b.c.CharacterConverter - No conversion required, value is already a Character 09:37:06.190 [main] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0 09:37:06.190 [main] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double' 09:37:06.190 [main] DEBUG o.a.c.b.converters.DoubleConverter - Converted to Double value '0.0' 09:37:06.191 [main] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0 09:37:06.191 [main] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float' 09:37:06.191 [main] DEBUG o.a.c.b.converters.FloatConverter - Converted to Float value '0.0' 09:37:06.192 [main] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0 09:37:06.193 [main] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer' 09:37:06.193 [main] DEBUG o.a.c.b.converters.IntegerConverter - No conversion required, value is already a Integer 09:37:06.193 [main] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0 09:37:06.193 [main] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long' 09:37:06.194 [main] DEBUG o.a.c.b.converters.LongConverter - Converted to Long value '0' 09:37:06.194 [main] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0 09:37:06.194 [main] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short' 09:37:06.194 [main] DEBUG o.a.c.b.converters.ShortConverter - Converted to Short value '0' 09:37:06.195 [main] DEBUG o.a.c.b.converters.StringConverter - Setting default value: 09:37:06.195 [main] DEBUG o.a.c.b.converters.StringConverter - Converting 'String' value '' to type 'String' 09:37:06.200 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Z@445b295b 09:37:06.201 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'boolean[]' value '[Z@445b295b' to type 'boolean[]' 09:37:06.207 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a boolean[] 09:37:06.207 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [B@49e5f737 09:37:06.207 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'byte[]' value '[B@49e5f737' to type 'byte[]' 09:37:06.207 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a byte[] 09:37:06.208 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [C@757277dc 09:37:06.208 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'char[]' value '[C@757277dc' to type 'char[]' 09:37:06.208 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a char[] 09:37:06.208 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [D@e4487af 09:37:06.209 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'double[]' value '[D@e4487af' to type 'double[]' 09:37:06.209 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a double[] 09:37:06.209 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [F@c86b9e3 09:37:06.209 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'float[]' value '[F@c86b9e3' to type 'float[]' 09:37:06.209 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a float[] 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [I@3af9c5b7 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'int[]' value '[I@3af9c5b7' to type 'int[]' 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a int[] 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [J@ed7f8b4 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'long[]' value '[J@ed7f8b4' to type 'long[]' 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a long[] 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [S@38102d01 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'short[]' value '[S@38102d01' to type 'short[]' 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a short[] 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigDecimal;@6ab778a 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigDecimal[]' value '[Ljava.math.BigDecimal;@6ab778a' to type 'BigDecimal[]' 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a BigDecimal[] 09:37:06.210 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigInteger;@77f80c04 09:37:06.211 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigInteger[]' value '[Ljava.math.BigInteger;@77f80c04' to type 'BigInteger[]' 09:37:06.211 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a BigInteger[] 09:37:06.211 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Boolean;@5c90e579 09:37:06.211 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Boolean[]' value '[Ljava.lang.Boolean;@5c90e579' to type 'Boolean[]' 09:37:06.212 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Boolean[] 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Byte;@6f45df59 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Byte[]' value '[Ljava.lang.Byte;@6f45df59' to type 'Byte[]' 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Byte[] 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Character;@63070bab 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Character[]' value '[Ljava.lang.Character;@63070bab' to type 'Character[]' 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Character[] 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Double;@291b4bf5 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Double[]' value '[Ljava.lang.Double;@291b4bf5' to type 'Double[]' 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Double[] 09:37:06.213 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Float;@762ef0ea 09:37:06.214 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Float[]' value '[Ljava.lang.Float;@762ef0ea' to type 'Float[]' 09:37:06.214 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Float[] 09:37:06.214 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Integer;@424e1977 09:37:06.214 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Integer[]' value '[Ljava.lang.Integer;@424e1977' to type 'Integer[]' 09:37:06.214 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Integer[] 09:37:06.214 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Long;@117e949d 09:37:06.214 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Long[]' value '[Ljava.lang.Long;@117e949d' to type 'Long[]' 09:37:06.214 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Long[] 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Short;@5f8edcc5 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Short[]' value '[Ljava.lang.Short;@5f8edcc5' to type 'Short[]' 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Short[] 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.String;@1ebd319f 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'String[]' value '[Ljava.lang.String;@1ebd319f' to type 'String[]' 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a String[] 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Class;@15ca7889 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Class[]' value '[Ljava.lang.Class;@15ca7889' to type 'Class[]' 09:37:06.217 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Class[] 09:37:06.218 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Date;@7a675056 09:37:06.218 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Date[]' value '[Ljava.util.Date;@7a675056' to type 'Date[]' 09:37:06.218 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Date[] 09:37:06.218 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Calendar;@6e509ffa 09:37:06.218 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Calendar[]' value '[Ljava.util.Calendar;@6e509ffa' to type 'Calendar[]' 09:37:06.218 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a Calendar[] 09:37:06.219 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.io.File;@683dbc2c 09:37:06.219 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.io.File[]' value '[Ljava.io.File;@683dbc2c' to type 'java.io.File[]' 09:37:06.219 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.io.File[] 09:37:06.219 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Date;@2638011 09:37:06.219 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Date[]' value '[Ljava.sql.Date;@2638011' to type 'java.sql.Date[]' 09:37:06.219 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.sql.Date[] 09:37:06.220 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Time;@6a2b953e 09:37:06.220 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Time[]' value '[Ljava.sql.Time;@6a2b953e' to type 'java.sql.Time[]' 09:37:06.220 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.sql.Time[] 09:37:06.221 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Timestamp;@2f465398 09:37:06.221 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Timestamp[]' value '[Ljava.sql.Timestamp;@2f465398' to type 'java.sql.Timestamp[]' 09:37:06.221 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.sql.Timestamp[] 09:37:06.222 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.net.URL;@623a8092 09:37:06.222 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.net.URL[]' value '[Ljava.net.URL;@623a8092' to type 'java.net.URL[]' 09:37:06.222 [main] DEBUG o.a.c.b.converters.ArrayConverter - No conversion required, value is already a java.net.URL[] 09:37:06.374 [main] INFO o.a.c.b.FluentPropertyBeanIntrospector - Error when creating PropertyDescriptor for public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)! Ignoring this property. 09:37:06.385 [main] DEBUG o.a.c.b.FluentPropertyBeanIntrospector - Exception is: java.beans.IntrospectionException: bad write method arg count: public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object) at java.desktop/java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:696) ~[na:na] at java.desktop/java.beans.PropertyDescriptor.setWriteMethod(PropertyDescriptor.java:356) ~[na:na] at java.desktop/java.beans.PropertyDescriptor.(PropertyDescriptor.java:142) ~[na:na] at org.apache.commons.beanutils.FluentPropertyBeanIntrospector.createFluentPropertyDescritor(FluentPropertyBeanIntrospector.java:178) ~[commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3] at org.apache.commons.beanutils.FluentPropertyBeanIntrospector.introspect(FluentPropertyBeanIntrospector.java:141) ~[commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3] at org.apache.commons.beanutils.PropertyUtilsBean.fetchIntrospectionData(PropertyUtilsBean.java:2245) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3] at org.apache.commons.beanutils.PropertyUtilsBean.getIntrospectionData(PropertyUtilsBean.java:2226) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3] at org.apache.commons.beanutils.PropertyUtilsBean.getPropertyDescriptor(PropertyUtilsBean.java:954) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3] at org.apache.commons.beanutils.PropertyUtilsBean.isWriteable(PropertyUtilsBean.java:1478) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3] at org.apache.commons.configuration2.beanutils.BeanHelper.isPropertyWriteable(BeanHelper.java:521) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.BeanHelper.initProperty(BeanHelper.java:357) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.BeanHelper.initBeanProperties(BeanHelper.java:273) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.BeanHelper.initBean(BeanHelper.java:192) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.BeanHelper$BeanCreationContextImpl.initBean(BeanHelper.java:669) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.DefaultBeanFactory.initBeanInstance(DefaultBeanFactory.java:162) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.DefaultBeanFactory.createBean(DefaultBeanFactory.java:116) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:459) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:479) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:492) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.createResultInstance(BasicConfigurationBuilder.java:447) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.createResult(BasicConfigurationBuilder.java:417) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.getConfiguration(BasicConfigurationBuilder.java:285) [org.apache.commons.commons-configuration2-2.2.jar:2.2] at utilities.Configuration.setConfiguration(Configuration.java:209) [aptasuite-0.6.3.jar:na] at aptasuite.CLI.(CLI.java:104) [aptasuite-0.6.3.jar:na] at aptasuite.Aptasuite.main(Aptasuite.java:63) [aptasuite-0.6.3.jar:na] Using the following parameters: Experiment.name : test Experiment.description : test Experiment.primer5 : GGGAGGACGATGCGG Experiment.primer3 : CAGACGACTCGCCCGA Experiment.randomizedRegionSize : 40 AptaplexParser.isPerFile : true AptaplexParser.reader : FastqReader SelectionCycle.name : [Round0, Round1] SelectionCycle.round : [0, 1] SelectionCycle.isControlSelection : [false, false] SelectionCycle.isCounterSelection : [false, false] AptaplexParser.forwardFiles : [/Users/username/OneDrive/my_projects/Aptamers/Data/short_data/SRR3510044_SHORT.fastq, /Users/username/OneDrive/my_projects/Aptamers/Data/short_data/SRR3510053_SHORT.fastq] Performance.maxNumberOfCores : 8 Experiment.projectPath : /Users/username/OneDrive/my_projects/Aptamers/Data/short_data/2018-02-24_09-18-31_test AptamerPool.backend : MapDBAptamerPool Aptasim.AmplificationEfficiency : 0.995 Export.IncludePrimerRegions : true Aptatrace.Alpha : 10 AptaplexParser.BlockingQueueSize : 500 MapDBAptamerPool.bloomFilterCollisionProbability : 0.001 Aptacluster.KmerSize : 3 MapDBStructurePool.bloomFilterCollisionProbability : 0.001 StructurePool.backend : MapDBStructurePool Aptasim.NucleotideDistribution : [0.25, 0.25, 0.25, 0.25] Aptasim.MinSeedAffinity : 80 Export.compress : true Aptasim.BaseMutationRates : [0.25, 0.25, 0.25, 0.25] Aptasim.HmmDegree : 2 Export.MinimalClusterSize : 1 MapDBAptamerPool.maxTreeMapCapacity : 1000000 Aptasim.MaxSequenceAffinity : 25 Aptasim.SelectionPercentage : 0.2 Aptasim.MutationProbability : 0.05 Export.SequenceFormat : fastq AptaplexParser.PairedEndMaxScoreValue : 55 AptaplexParser.PairedEndMinOverlap : 15 Aptatrace.OutputClusters : true MapDBSelectionCycle.bloomFilterCollisionProbability : 0.001 Aptatrace.FilterClusters : true Export.PoolCardinalityFormat : frequencies AptaplexParser.StoreReverseComplement : false ClusterContainer.backend : MapDBClusterContainer Export.ClusterFilterCriteria : ClusterSize SelectionCycle.backend : MapDBSelectionCycle Aptasim.NumberOfSeeds : 100 MapDBStructurePool.maxTreeMapCapacityBppm : 150000 Aptacluster.EditDistance : 5 Aptasim.NumberOfSequences : 1000000 Parser.backend : AptaplexParser AptaplexParser.BarcodeTolerance : 1 MapDBAptamerPool.bloomFilterCapacity : 250000000 Aptasim.MaxSequenceCount : 10 AptaplexParser.PrimerTolerance : 3 AptaplexParser.PairedEndMaxMutations : 5 MapDBAllocateStartSize : 1073741824 Aptacluster.KmerCutoffIterations : 10000 MapDBAllocateIncrement : 104857600 Aptatrace.KmerLength : 6 Aptacluster.LSHIterations : 5 MapDBStructurePool.maxTreeMapCapacity : 500000 Aptasim.RandomizedRegionSize : 40

If you use this software in your research, please cite AptaPLEX as Hoinka, J., & Przytycka, T. (2016). AptaPLEX - A dedicated, multithreaded demultiplexer for HT-SELEX data. Methods. http://doi.org/10.1016/j.ymeth.2016.04.011 Creating Database Instantiating MapDBAptamerPool Processing selection cycle Round0 Processing selection cycle Round1 Loading took 56842 milliseconds Initializing Experiment Experiment Setup │ ├── Round 0: Round0 │ │ │ ├─ Counter Selections: N/A │ │ │ ├─ Control Selections: N/A │ │ └── Round 1: Round1 │ ├─ Counter Selections: N/A │ ├─ Control Selections: N/A

Initializing parser AptaplexParser Starting AptaPlex: Parsing... Total Reads: Accepted Reads: Contig Assembly Fails: Invalid Alphabet: 5' Primer Error: 3' Primer Error: Invalid Cycle: Total Primer Overlaps: Exception in thread "AptaPlex Main" java.lang.NoSuchMethodError: sun.nio.ch.DirectBuffer.cleaner()Lsun/misc/Cleaner; 0 0 0
at org.mapdb.volume.ByteBufferVol.unmap(ByteBufferVol.java:340) at org.mapdb.volume.MappedFileVol.close(MappedFileVol.java:183) at org.mapdb.StoreDirect.close(StoreDirect.kt:877) at org.mapdb.DB.close(DB.kt:472) at org.mapdb.HTreeMap.close(HTreeMap.kt:1343) at lib.aptamer.datastructures.MapDBAptamerPool.close(MapDBAptamerPool.java:596) at lib.aptamer.datastructures.MapDBAptamerPool.setReadOnly(MapDBAptamerPool.java:730) at lib.parser.aptaplex.AptaPlexParser.parsingCompleted(AptaPlexParser.java:68) at lib.parser.aptaplex.AptaPlexParser.run(AptaPlexParser.java:103) at java.base/java.lang.Thread.run(Thread.java:844) 32000 32000 0 0 0 0 0 0
Parsing Completed in 4.009 seconds.

Selection Cycle Statistics Round0 Round1 Exiting.

drivenbyentropy commented 6 years ago

The second error seems unrelated to the graphical user interface. Could you please open a new ticket for this one and include

I believe this is related to how access to the database files is provided on different OSes.

Thanks again for reporting this!

drivenbyentropy commented 6 years ago

I have removed all dependencies for the library causing the incompatibility with Java9. On my test system (Mac with Java 9), it now runs as expected.

Please let me know if this works for you and reopen the ticket as appropriate.

The version implementing these changes is v0.7.2 or higher.

drivenbyentropy commented 6 years ago

Hmmm, I am reopening this. There seems to be an issue with Java 9 and MapDB (on mac only?). I will look into this further but it seems that a method related to memory mapped files has changed visibility in Java 9 and now causes

java.lang.NoSuchMethodError: sun.nio.ch.DirectBuffer.cleaner()Lsun/misc/Cleaner;
    at org.mapdb.volume.ByteBufferVol.unmap(ByteBufferVol.java:340)
    at org.mapdb.volume.MappedFileVol.close(MappedFileVol.java:183)
    at org.mapdb.StoreDirect.close(StoreDirect.kt:877)
    at org.mapdb.DB.close(DB.kt:472)
    at org.mapdb.HTreeMap.close(HTreeMap.kt:1343)
    at lib.aptamer.datastructures.MapDBAptamerPool.close(MapDBAptamerPool.java:596)
drivenbyentropy commented 6 years ago

Fixed as of v0.7.3. AptaSuite should now work on all platforms. Please test if possible.