I am not sure that the code you were reading was high quality (I've reviewed some bioinformatics code in the past and it is unfortunately often not written by professional developers). For example, that third constructor is not a copy constructor and generally there are problems in this code, so I wouldn't "read too much into it".
The first constructor is a default constructor. It only initializes the bare minimum and lets users set the rest with getters and setters. Other constructors are often "convenience constructors" that help create objects with less calls. However, this can often lead to inconsistencies between constructors. In fact, there is recent research that shows that a default constructor with subsequent calls to setters is preferable.
There are also certain cases where a default constructor is critical. For example, certain frameworks like digester (used to create objects directly from XML) use default constructors. JavaBeans in general use default constructors, etc.
Also, some classes inherit from other classes. you may see a default constructor when the initialization of the parent object is "good enough".
In this specific case, if that constructor was not defined, one would have to know all the details in advance. That is not always preferable.
And finally, some IDEs automatically generate a default constructor, it is possible that whoever wrote the class was afraid to eliminate it.
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