#define LABELSIZE	300

class Sequence
{
public:
	char Label[300];
	bool IsActive;
	char* Data;
	int Length;

	void LoadFromFile(char* filename);
};

BArray<Sequence> GSequences;




class PhyloTreeNode
{
public:
	Sequence* BaseSequence;
	PhyloTreeNode *Child1, *Child2;	
	char Label[300];

	char* GetName() {if (BaseSequence) return BaseSquence->Label; return Label;};

	PhyloTreeNode() {BaseSequence=0; Child1=0; Child2=0; Label[0]=0;};
	~PhyloTreeNode() { if (Child1) delete Child1; if (Child2) delete child2; }
};

class PhyloTree
{
public:
	PhyloTreeNode* Root;
	char Label[LABELSIZE];

	PhyloTree() {Root=0; Label[0]=0;};
	~PhyloTree() {if (Root) delete Root;};	
};

BArray<PhyloTree> GPhyloTrees;
PhyloTree* GPriPhyloTree = NULL;





class MSAString
{
public:
	Sequence* BaseSequence;
	char* Data;
	int Length;

	void Init(int len, Sequence* seq) {Data=new char[len]; Length=len; BaseSequence=seq;};
	void UnInit() {if (Data) delete [] Data; Length=0; Data=0; BaseSequence=0;};
	
	MSAString() {Data=0; Length=0; BaseSequence=0;};
	~MSAString() {UnInit();};
};

class MSA
{
public:
	char Label[LABELSIZE];
	BArray<MSAString> Strings;
	int NumStrings;
	int StringLength;
};

BArray<MSA> GMSAs;
MSA* GPriMSA = NULL;



#define HE_Sequence_Set_Change		1
#define HE_Sequence_Single_Change	2 /* WPARAM = &sequence */
#define HE_PhyloTree_Set_Change		3
#define HE_PhyloTree_Pri_Change		4
#define HE_PhyloTree_Single_Change	3 /* WPARAM = &PhyloTree */
#define HE_MSA_Set_Change		5
#define HE_MSA_Pri_Change		6
#define HE_MSA_Single_Change		6 /* WPARAM = &MSA */

void SendHyperEvent(LPARAM type, WPARAM extra)
{
	// ...
}

void LoadSequences(char* filesnames)
{
	// ...

	SendHyperEvent( HE_Sequence_Set_Change, 0);
}

void CreatePhyloTreeFromMSA()
{
	int count = 0;
	int i;
	BAMem<PhyloTreeNode*> nodes;

	if (!GPriMSA)
	{
		MessageBox(MainWnd, "No primary MSA.", "Tree Create Error", MB_OK);
		return;
	}


	for (i=0; i<GPriMSA->Strings.Length(); i++)
	{
		//Sequence* seq = &GSequences[i];
		Sequence* seq = GPriMSA->Strings[i].BaseSequence;
		if (seq->IsActive)
		{
			PhyloTreeNode* node = new PhyloTreeNode();
			*nodes.Add() = node;
			node->BaseSequence = seq;
			strcpy(node->Label, seq->Label);
		}
	}

	if (nodes.Length() < 1)
	{
		MessageBox(MainWnd, "Not active sequences in the MSA.", "Tree Create Error", MB_OK);
		return;
	}

	while (nodes.Length() > 1)
	{
		PhyloTreeNode *a, *b, *n;

		int i = (rand() % nodes.Length());
		a = *node[i];
		nodes.Remove(i);

		i = (rand() % nodes.Length());
		b = *node[i];
		nodes.Remove(i);

		n = new PhyloTreeNode();
		n->BaseSequence = 0;
		n->Child1 = a;
		n->Child2 = b;
		strcpy(n->Label, "internal");

		*nodes.Add() = n;
	}

	PhyloTree* tree = GPhyloTrees.Add();
	tree->Root = *nodes[0];
	strcpy(tree->Label, "Tree_01");

	SendHyperEvent( HE_PhyloTree_Set_Change, 0 );
	GPriMSA = msa;
	SendHyperEvent( HE_PhyloTree_Pri_Change, 0 );
}

void CreateMSAFromSequences()
{
	int longest = 0;
	int i;
	for (i=0; i<GSequences.Length(); i++)
	{
		Sequence* seq = &GSequences[i];
		if ((seq->IsActive) && (seq->Length > longest))
			longest = seq->Length;
	}
	if (longest == 0)
	{
		MessageBox(MainWnd, "No Active Sequences", "MSA Create Error", MB_OK);
	}

	MSA* msa = GMSAs.Add();
	strcpy(msa->Label, "MSA_01" );
	for (i=0; i<GSequences.Length(); i++)
	{
		Sequence* seq = &GSequences[i];
		if (seq->IsActive)
		{
			MSAString* ms = msa->String.Add();
			ms->Init(longest, seq);
			int r;
			for (r=0; r<seq->Length; r++)
				ms->Data[r] = seq->Data[r];
			ms->Length = seq->Length;
			while (ms->Length < longest)
			{
				int at = (rand() % ms->Length);
				for (r=ms->Length; r>at; r--)
					ms->Data[r] = ms->Data[r-1];
				ms->Data[at] = '-';
				ms->Length++;
			}
		}
	}


	SendHyperEvent( HE_MSA_Set_Change, 0 );
	GPriMSA = msa;
	SendHyperEvent( HE_MSA_Pri_Change, 0 );
}