[SalesForce] How to disable Lightning button after click

You could also consider having the checkboxes in a second component that subscribes to an application event that you fire when you push the master button.

<aura:application >
    <ui:button label="CheckAllBoxes" press="{!c.fireCheckAllCheckboxes}" />
    <!-- iteration -->
        <analysis:ComponentWithCheckbox />
    <!-- /iteration -->
</aura:application>

controller

({
    fireCheckAllCheckboxes : function(component, event, helper) {
        var appevent = $A.get("e.analysis:CheckAllCheckboxes");
        appevent.fire();
    }
})

CheckAllCheckboxes event

<aura:event type="APPLICATION" description="CheckAllCheckboxes" />

ComponentWithCheckbox

<aura:component >
    <aura:handler event="analysis:CheckAllCheckboxes" action="{!c.checkTheBox}" />
    <ui:inputCheckbox aura:id="TheCheckBox" label="Checkbox" />
</aura:component>

ComponentWithCheckboxController

({
    checkTheBox : function(component, event, helper) {
        var TheCheckBox = component.find("TheCheckBox");
        TheCheckBox.set("v.value",true);
    }
})

Also, if the checkboxes all have the same aura:id, calling find() on the component will return an array with all of those components. If that works for you, you could do something like this:

<aura:application >
    <aura:attribute name="numbers" type="Integer[]" default="[0,1,2,3,4,5,6,7]" />

    <ui:button label="CheckAllBoxes" press="{!c.checkAllCheckboxes}" />

    <aura:iteration items="{!v.numbers}" var="number">
        <ui:inputCheckbox label="{!number}" aura:id="DependentCheckbox" />
    </aura:iteration>

</aura:application>

Controller

({
    checkAllCheckboxes : function(component, event, helper) {
        var checkboxes = component.find("DependentCheckbox");
        for (var i = 0; i < checkboxes.length; i++){
            checkboxes[i].set("v.value",true);
        }
    }
})

Make sure your wrapper class is public and has the @AuraEnabled notation in its variables, as well as they are public with get;set; example:

public class wrapperClass{
    @AuraEnabled public List<contact> lstContact{get;set;}
    @AuraEnabled public Integer contactCount{get;set;}
    @AuraEnabled public String headerMsg {get;set;}
}