Working with the HMM Module

Once the model is loaded, a new HMM Module interface, similar to the one illustrated in Figure , will appear. It shows the user all the methods and algorithms that can be used with the specific type of HMM model he chose to work with. These methods and algorithms are the same ones implemented for the corresponding MTK plugins, and, for this reason, we will not describe them here. The user who wishes to learn more about each one, should refer to section of this manual.

Figure: HMM Module (a) method's and algorithm's interface; (b) chain structure visualization.

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Let's continue with our example. As stated above, the interface shown in Figure shows us the available methods and algorithms for the hierarchical Gilbert HMM model. To execute any of them, just click on it's corresponding tab, specify the necessary parameters, and click on the Run button. Each method's output will be stored in a file (which is described in appendix ), and it's result can be viewed by clicking the Results button. The HMM Module also allows the user to view every chain's structure of his HMM (both upper-level chain and lower-level chains) using Tangram-II's Matrix Visualization Module. All he has to do is click on the View Matrix button and select which chain he wishes to see. Figure shows the hidden chain of the model we have created.