#include "muscle.h" #include #include #include "msa.h" #include "textfile.h" const unsigned uCharsPerLine = 60; const int MIN_NAME = 10; const int MAX_NAME = 32; extern void AssignColors(const MSA &a, int **Colors); static int **MakeColors(const MSA &a) { const unsigned uSeqCount = a.GetSeqCount(); const unsigned uColCount = a.GetColCount(); int **Colors = new int *[uSeqCount]; for (unsigned i = 0; i < uSeqCount; ++i) { Colors[i] = new int[uColCount]; memset(Colors[i], 0, uColCount*sizeof(int)); } AssignColors(a, Colors); return Colors; } static void ChangeColor(TextFile &File, int From, int To) { if (From == To) return; #define COLOR_WHITE "FFFFFF" #define COLOR_GRAY "C0C0C0" #define COLOR_BLACK "000000" #define COLOR_RED "FF0000" #define COLOR_GREEN "00FF00" #define COLOR_BLUE "5590FF" #define COLOR_LIGHTBLUE "77FFFF" #define X(c) File.PutString(""); switch (To) { case 0: X(COLOR_WHITE) break; case 1: X(COLOR_GRAY) break; case 2: X(COLOR_BLUE) break; case 3: X(COLOR_LIGHTBLUE) break; } } #define COLOR_WINDOW "FFEEE0" void MSA::ToHTMLFile(TextFile &File) const { File.PutString("\n"); File.PutString("\n"); File.PutString("

");

	int **Colors = MakeColors(*this);

	int iLongestNameLength = 0;
	for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)
		{
		const char *ptrName = GetSeqName(uSeqIndex);
		const char *ptrBlank = strchr(ptrName, ' ');
		int iLength;
		if (0 != ptrBlank)
			iLength = (int) (ptrBlank - ptrName);
		else
			iLength = (int) strlen(ptrName);
		if (iLength > iLongestNameLength)
			iLongestNameLength = iLength;
		}
	if (iLongestNameLength > MAX_NAME)
		iLongestNameLength = MAX_NAME;
	if (iLongestNameLength < MIN_NAME)
		iLongestNameLength = MIN_NAME;

	unsigned uLineCount = (GetColCount() - 1)/uCharsPerLine + 1;
	int CurrentColor = -1;
	for (unsigned uLineIndex = 0; uLineIndex < uLineCount; ++uLineIndex)
		{
		File.PutString("\n");
		unsigned uStartColIndex = uLineIndex*uCharsPerLine;
		unsigned uEndColIndex = uStartColIndex + uCharsPerLine - 1;
		if (uEndColIndex >= GetColCount())
			uEndColIndex = GetColCount() - 1;
		char Name[MAX_NAME+1];
		for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)
			{
			const char *ptrName = GetSeqName(uSeqIndex);
			const char *ptrBlank = strchr(ptrName, ' ');
			int iLength;
			if (0 != ptrBlank)
				iLength = (int) (ptrBlank - ptrName);
			else
				iLength = (int) strlen(ptrName);
			if (iLength > MAX_NAME)
				iLength = MAX_NAME;
			memset(Name, ' ', MAX_NAME);
			memcpy(Name, ptrName, iLength);
			Name[iLongestNameLength] = 0;

//			File.PutString("");
			CurrentColor = -1;
			File.PutString("");
			File.PutFormat("%s      ", Name);
			File.PutString("");
			for (unsigned uColIndex = uStartColIndex; uColIndex <= uEndColIndex;
			  ++uColIndex)
				{
				const int Color = Colors[uSeqIndex][uColIndex];
				ChangeColor(File, CurrentColor, Color);
				CurrentColor = Color;
				const char c = GetChar(uSeqIndex, uColIndex);
				if (Color == 0)
					File.PutFormat("%c", tolower(c));
				else
					File.PutFormat("%c", toupper(c));
				}
			File.PutString("\n");
			}
		}
	File.PutString("\n");
	File.PutString("

\n"); File.PutString("\n"); File.PutString("\n"); }