use getFieldValues() to also include unchecked checkboxes

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AlignmentAnalysisPanel.js

@@ -140,7 +140,7 @@ Ext4.define('SequenceAnalysis.panel.AlignmentAnalysisPanel', {
         };
 
         //first add the general params
-        Ext4.apply(json, this.down('#runInformation').getForm().getValues());
+        Ext4.apply(json, this.down('#runInformation').getForm().getFieldValues());
 
         //and sample information
         json.analysisIds = this.analyses;

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceAnalysisPanel.js

@@ -256,7 +256,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceAnalysisPanel', {
         };
 
         //first add the general params
-        Ext4.apply(json, this.down('#runInformation').getForm().getValues());
+        Ext4.apply(json, this.down('#runInformation').getForm().getFieldValues());
 
         json['alignment.doAlignment'] = this.down('#doAlignment').getValue();
 

SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantProcessingPanel.js

@@ -453,7 +453,7 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 		};
 
 		//first add the general params
-		Ext4.apply(json, this.down('#runInformation').getForm().getValues());
+		Ext4.apply(json, this.down('#runInformation').getForm().getFieldValues());
 
 		//then append each section
 		var sections = this.query('sequenceanalysis-analysissectionpanel');

SequenceAnalysis/resources/web/SequenceAnalysis/window/OutputHandlerWindow.js

@@ -250,7 +250,8 @@ Ext4.define('SequenceAnalysis.window.OutputHandlerWindow', {
             return;
         }
 
-        var params = this.down('form').getForm().getValues();
+        //Note: use getFieldValues() to also include unchecked checkboxes
+        var params = this.down('form').getForm().getFieldValues();
         var json = {
             handlerType: this.handlerType,
             handlerClass: this.handlerClass,