source: branches/stable/GDE/MUSCLE/src/maketree.cpp

#include "muscle.h"
#include "msa.h"
#include "textfile.h"
#include "tree.h"

void DoMakeTree()
        {
        if (g_pstrInFileName == 0 || g_pstrOutFileName == 0)
                Quit("-maketree requires -in <msa> and -out <treefile>");

        SetStartTime();

        SetSeqWeightMethod(g_SeqWeight1);

        TextFile MSAFile(g_pstrInFileName);

        MSA msa;
        msa.FromFile(MSAFile);

        unsigned uSeqCount = msa.GetSeqCount();
        MSA::SetIdCount(uSeqCount);

// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                msa.SetSeqId(uSeqIndex, uSeqIndex);
        SetMuscleInputMSA(msa);

        Progress("%u sequences", uSeqCount);

        Tree tree;
        TreeFromMSA(msa, tree, g_Cluster2, g_Distance2, g_Root2);

        TextFile TreeFile(g_pstrOutFileName, true);
        tree.ToFile(TreeFile);

        Progress("Tree created");
        }