Apply Theme for Publishing site

public override void FeatureActivated(SPFeatureReceiverProperties properties)

{

   ApplyTheme(properties);

}

/// <summary>

/// Sets master page and css properties for the site collection

/// </summary>

/// <param name="properties"></param>

private void ApplyTheme(SPFeatureReceiverProperties properties)

{

SPSite site = (SPSite)properties.Feature.Parent;

if (site != null)

{

// System Master Page

Uri masterUri = new Uri(site.RootWeb.Url + "/_catalogs/masterpage/v4.master");

site.RootWeb.MasterUrl = masterUri.AbsolutePath;

// Publishing Master Page

Uri customMasterUri = new Uri(site.RootWeb.Url + "/_catalogs/masterpage/mycustom.master");

site.RootWeb.CustomMasterUrl = customMasterUri.AbsolutePath;

//logo and css

site.RootWeb.SiteLogoUrl = "/_layouts/MyProjectName/Images/mycustomlogo.jpg";

site.RootWeb.AlternateCssUrl = "/Style Library/MyProjectName/css/mycustomcss.css";

site.RootWeb.Update();

}

}