seqan-dev 1.3.1-1 / usr / include / seqan / misc / misc_svg.h

// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
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//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
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//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
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// ==========================================================================

#ifndef SEQAN_HEADER_MISC_SVG_H
#define SEQAN_HEADER_MISC_SVG_H

namespace SEQAN_NAMESPACE_MAIN
{

//////////////////////////////////////////////////////////////////////////////
// SVG File Context
//////////////////////////////////////////////////////////////////////////////

struct SVGFile
{
	std::fstream file;

	Pair<int> cursor;
	String<CharString> style;
	
	int dpSequence;
	int dpMatrix;
	int dpTrace;
	
	int text;
	
	int readForward;
	int readReverse;
	int readText;
	int rulerTextTicks;
	int rulerTextLabel;

	friend inline void svgWriteHeader(SVGFile &svg);
	friend inline void svgWriteFooter(SVGFile &svg);
	
	template <typename TFileName>
	friend inline bool open(SVGFile &svg, TFileName const &fileName);
	friend inline bool close(SVGFile &svg);
	
	SVGFile():
		cursor(0,0) 
	{
		resetStyles();
	}

	SVGFile(char const *fileName):
		cursor(0,0) 
	{
		resetStyles();
		open(*this, fileName);
	}

	~SVGFile()
	{
		close(*this);
	}

private:

	inline void resetStyles()
	{
		clear(style);
		readText = dpSequence = length(style);
		appendValue(style, "style=\"text-anchor:middle; font-family:Bitstream Vera Sans,Verdana,sans-serif;\" font-size=\"18px\"");
		text = length(style);
		appendValue(style, "style=\"text-anchor:middle; font-family:Courier New,Verdana,sans-serif; font-weight:bold;\" font-size=\"20px\"");
		rulerTextTicks = length(style);
		appendValue(style, "style=\"text-anchor:middle; font-family:Verdana,sans-serif;\" font-size=\"6px\"");
		rulerTextLabel = length(style);
		appendValue(style, "style=\"text-anchor:left; font-family:Verdana,sans-serif; font-weight:bold;\" font-size=\"8px\"");

		dpMatrix = length(style);
		appendValue(style, "style=\"stroke:lightgray;stroke-width:1;\" marker-end=\"url(#startMarkerNormal)\"");
		dpTrace = length(style);
		appendValue(style, "style=\"stroke:black;stroke-width:2;\" marker-end=\"url(#startMarkerBold)\"");

		readForward = length(style);
		appendValue(style, "style=\"stroke:darkblue;stroke-width:3;\"");
		appendValue(style, "style=\"stroke:lightblue;stroke-width:1;\"");
		appendValue(style, "style=\"stroke:darkblue;stroke-width:3;\" marker-end=\"url(#startMarkerForward)\"");
		appendValue(style, "style=\"stroke:lightblue;stroke-width:1;\" marker-end=\"url(#startMarkerForward)\"");
		readReverse = length(style);
		appendValue(style, "style=\"stroke:darkred;stroke-width:3;\"");
		appendValue(style, "style=\"stroke:salmon;stroke-width:1;\"");
		appendValue(style, "style=\"stroke:darkred;stroke-width:3;\" marker-end=\"url(#startMarkerReverse)\"");
		appendValue(style, "style=\"stroke:salmon;stroke-width:1;\" marker-end=\"url(#startMarkerReverse)\"");
	}
};

inline void svgWriteHeader(SVGFile &svg)
{
	svg.file << "<?xml version=\"1.0\"?>" << std::endl;
	svg.file << "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"" << std::endl;
	svg.file << "  \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">" << std::endl;
	svg.file << std::endl;
	svg.file << "<svg version=\"1.1\"" << std::endl;
	svg.file << "    xmlns=\"http://www.w3.org/2000/svg\"" << std::endl;
	svg.file << "    xmlns:xlink=\"http://www.w3.org/1999/xlink\">" << std::endl;
    svg.file << "<defs>" << std::endl;

	// trace back arrow markers
    svg.file << "	<g id=\"arrowMarker\" stroke-linecap=\"round\">" << std::endl;
    svg.file << "		<line x1=\"-6\" y1=\"1.5\" x2=\"0\" y2=\"0\" />" << std::endl;
    svg.file << "		<line x1=\"-6\" y1=\"-1.5\" x2=\"0\" y2=\"0\" />" << std::endl;
    svg.file << "	</g>" << std::endl;
    svg.file << "	<marker id=\"startMarkerNormal\" markerWidth=\"6\" markerHeight=\"3\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
    svg.file << "		<use xlink:href=\"#arrowMarker\" stroke=\"lightgray\" />" << std::endl;
    svg.file << "	</marker>" << std::endl;
    svg.file << "	<marker id=\"startMarkerBold\" markerWidth=\"6\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
    svg.file << "		<use xlink:href=\"#arrowMarker\" stroke-width=\"2\" stroke=\"black\" />" << std::endl;
    svg.file << "	</marker>" << std::endl;

	// read mapping arrow markers
    svg.file << "	<marker id=\"startMarkerForward\" markerWidth=\"10\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
    svg.file << "		<polyline points=\"-8,0 -9,-6 3,0 -9,6 -8,0\" fill=\"darkblue\" />" << std::endl;
    svg.file << "	</marker>" << std::endl;
    svg.file << "	<marker id=\"startMarkerReverse\" markerWidth=\"10\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
    svg.file << "		<polyline points=\"-8,0 -9,-6 3,0 -9,6 -8,0\" fill=\"darkred\" />" << std::endl;
    svg.file << "	</marker>" << std::endl;
	
    svg.file << " </defs>" << std::endl;
	svg.file << std::endl;
}

inline void svgWriteFooter(SVGFile &svg)
{
	svg.file << std::endl;
	svg.file << "</svg>" << std::endl;
}


template <typename TFileName>
inline bool open(SVGFile &svg, TFileName const &fileName)
{
	svg.file.open(fileName, std::ios_base::out);
	if (!svg.file.is_open()) return false;
	svgWriteHeader(svg);
	return true;
}

inline bool close(SVGFile &svg)
{
	if (svg.file.is_open())
	{
		svgWriteFooter(svg);
		svg.file.close();
	}
	return true;
}

template <typename TChar>
inline void
_streamPut(SVGFile & svg, TChar character)
{
	if (convert<char>(character) == '\n')
	{
		++svg.cursor.i2;
		svg.cursor.i1 = 0;
	} else if (convert<char>(character) == '\t')
	{
		svg.cursor.i1 = (svg.cursor.i1 & ~7) + 8;
	} else
	{
		if (convert<char>(character) != ' ')
		{
			svg.file << "<g transform=\"translate(" << svg.cursor.i1*20+10 << ',' << svg.cursor.i2*20+10 << ")\"><text y=\"0.3em\" " << svg.style[svg.text] << '>';
			_streamPut(svg.file, convert<char>(character));
			svg.file << "</text></g>" << std::endl;
		}
		++svg.cursor.i1;
	}
}

template <typename TFormatTag, typename TContigGaps, typename TContigName>
inline void _printContig(
	SVGFile &svg, 
	Tag<TFormatTag> const &format,
	AlignedReadLayout &, 
	TContigGaps &contigGaps,
	TContigName const &contigName)
{
	typedef typename Iterator<TContigGaps, Standard>::Type TContigIterator;

	TContigIterator cit = begin(contigGaps, Standard());
	TContigIterator citEnd = end(contigGaps, Standard());	
	for (__int64 ofs = 0; cit != citEnd; ++cit, ++ofs)
	{
		if (!isGap(cit))
		{
			if (ofs == 0)
			{
				svg.file << "<g transform=\"translate(" << ofs*20+2 << ',' << svg.cursor.i2*20+10 << ")\"><text y=\"0.3em\" " << svg.style[svg.rulerTextLabel] << '>';
				svg.file << contigName << "</text></g>" << std::endl;
			}
			
			__int64 seqPos = cit.current.seqPos + 1;
			if (seqPos % 5 == 0)
			{
				if (seqPos % 10 == 0)
				{
					if (ofs >= 5)
					{
						svg.file << "<g transform=\"translate(" << ofs*20+10 << ',' << svg.cursor.i2*20+10 << ")\"><text y=\"0.3em\" " << svg.style[svg.rulerTextTicks] << '>';
						svg.file << seqPos << "</text></g>" << std::endl;
					}
					
					svg.file << "<line x1=\"" << ofs*20+10 << "\" x2=\"" << ofs*20+10 << "\" ";
					svg.file << "y1=\"" << svg.cursor.i2*20+12 << "\" y2=\"" << svg.cursor.i2*20+15 << "\" ";
				} else {
					svg.file << "<line x1=\"" << ofs*20+10 << "\" x2=\"" << ofs*20+10 << "\" ";
					svg.file << "y1=\"" << svg.cursor.i2*20+12 << "\" y2=\"" << svg.cursor.i2*20+15 << "\" ";
				}
				svg.file << "stroke-width=\"1\" stroke=\"gray\" />" << std::endl;
			}
		}
	}
	_streamPut(svg, '\n');
	
	int savedStyle = svg.text;
	svg.text = svg.readText;
	write(svg, contigGaps, "", format);
	svg.text = savedStyle;
}

template <typename TFormatTag, typename TContigGaps, typename TReadGaps, typename TAlignedRead, typename TLine>
inline void _printRead(
	SVGFile &svg, 
	Tag<TFormatTag> const &,
	AlignedReadLayout &layout, 
	TContigGaps &contigGaps,
	TReadGaps &readGaps,
	TAlignedRead &alignedRead,
	TLine line)
{
	typedef typename Iterator<TContigGaps, Standard>::Type TContigIterator;
	typedef typename Iterator<TReadGaps, Standard>::Type TIterator;

	__int64 x;
	__int64 xEnd;
	int style, arrow;
	const char *first;
	const char *second;
	if (alignedRead.beginPos < alignedRead.endPos)
	{
		xEnd = alignedRead.beginPos * 20;
		x = xEnd + 5;
		first = "<line x1=\"";
		second = "\" x2=\"";
		style = svg.readForward;
		arrow = 0;
	} else {
		xEnd = alignedRead.endPos * 20;
		x = xEnd + 10;
		first = "<line x2=\"";
		second = "\" x1=\"";
		style = svg.readReverse;
		arrow = 2;
	}
	line = svg.cursor.i2 * 20 + 10;
	
	if (length(layout.mateCoords) <= alignedRead.pairMatchId)
		resize(layout.mateCoords, alignedRead.pairMatchId + 1, Pair<int>(-1,-1));
	else
	{
		if (layout.mateCoords[alignedRead.pairMatchId].i2 != -1)
		{
			Pair<__int64> a(alignedRead.beginPos * 20, line);
			Pair<__int64> b(layout.mateCoords[alignedRead.pairMatchId]);
			if (a.i1 < b.i1)
			{
				Pair<__int64> tmp = a;
				a = b;
				b = tmp;
			}
			__int64 dx = (b.i1 - a.i1);
			__int64 dy = (b.i2 - a.i2);
			
			svg.file << "<path d=\"M " << a.i1 << ',' << a.i2;
			svg.file << " C " << a.i1+dy/10 << ',' << a.i2-dx/10;
			svg.file << ' ' << b.i1+dy/10 << ',' << b.i2-dx/10;
			svg.file << ' ' << b.i1 << ',' << b.i2;
			svg.file << "\" stroke-width=\"2\" stroke=\"black\" stroke-opacity=\"0.2\" fill=\"none\"/>";
		}
		else
			layout.mateCoords[alignedRead.pairMatchId] = Pair<int>(alignedRead.beginPos * 20, line);
	}
	

	TContigIterator cit = begin(contigGaps, Standard()) + _min(alignedRead.beginPos, alignedRead.endPos);
	TIterator it = begin(readGaps, Standard());
	TIterator itEnd = end(readGaps, Standard());
	int lastWasGap = -1;
	int inGap;
	
	for (; it != itEnd; ++it, ++cit, xEnd += 20)
	{
		inGap = isGap(it);
		if (lastWasGap != inGap || inGap != static_cast<int>(isGap(cit)) || (!inGap && convert<Dna5>(*cit) != convert<Dna5>(*it)))
		{
			if (x < xEnd && lastWasGap != -1)
			{
				svg.file << first << x << "\" y1=\"" << line << second << xEnd; 
				svg.file << "\" y2=\"" << line << "\" " << svg.style[style + arrow + lastWasGap] << " />" << std::endl;
				arrow = 0;
			}
			lastWasGap = inGap;
			x = xEnd;
			if (!inGap && convert<Dna5>(*cit) != convert<Dna5>(*it))
			{
				svg.file << "<g transform=\"translate(" << xEnd + 10 << ',' << line << ")\"><text y=\"0.3em\" " << svg.style[svg.readText] << '>';
				_streamPut(svg.file, convert<char>(*it));
				svg.file << "</text></g>" << std::endl;
				x += 20;
				arrow = 0;
			}
		}
	}
	if (x < xEnd && lastWasGap != -1)
	{
		if (alignedRead.beginPos < alignedRead.endPos)
		{
			arrow = 2;
			xEnd -= 10;
		} else
			xEnd -= 5;
		svg.file << first << x << "\" y1=\"" << line << second << xEnd;
		svg.file << "\" y2=\"" << line << "\" " << svg.style[style + arrow + lastWasGap] << " />" << std::endl;
	}
}


//////////////////////////////////////////////////////////////////////////////
// stream operators
//////////////////////////////////////////////////////////////////////////////
/*
template <typename TSource>
inline SVGFile &
operator << (SVGFile & target, 
			 TSource  source)
{
SEQAN_CHECKPOINT
	write(target, source);
	return target;
}
*/

inline SVGFile &
operator << (SVGFile & target, char source)
{
SEQAN_CHECKPOINT
	write(target, source);
	return target;
}

inline SVGFile &
operator << (SVGFile & target, char const *source)
{
SEQAN_CHECKPOINT
	write(target, source);
	return target;
}


template <typename TStringSet, typename TTrace, typename TIndexPair>
void
_alignNeedlemanWunschMatrix(SVGFile& svg,
							  TStringSet const& str,
							  TTrace const& trace,
							  TIndexPair const&)
{
SEQAN_CHECKPOINT
	typedef typename Size<TStringSet>::Type TSize;
	typedef typename Value<TTrace>::Type TTraceValue;

	// TraceBack values
	const int Diagonal = 0; 
	const int Horizontal = 1; 
	const int Vertical = 2;
	
	// Initialization
	TSize numCols = length(str[0]);
	TSize numRows = length(str[1]);

	// Print trace matrix	
	for (TSize pos0 = 0; pos0 < numCols; ++pos0)
	{
		for (TSize pos1 = 0; pos1 < numRows; ++pos1)
		{
			int tv =(int)trace[pos0*numRows + pos1];
				if (tv & (1 << Diagonal))
					svg.file << "<line x2=\"" << pos0*20+10 << "\" y2=\"" << pos1*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;
				
				if (tv & (1 << Horizontal))
					svg.file << "<line x2=\"" << pos0*20+10 << "\" y2=\"" << (pos1+1)*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;

				if (tv & (1 << Vertical))
					svg.file << "<line x2=\"" << (pos0+1)*20+10 << "\" y2=\"" << pos1*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;
		}
	}

	// Print sequences
	for (TSize pos0 = 0; pos0 < numCols; ++pos0)
		svg.file << "<g transform=\"translate(" << pos0*20+20 << ",5)\"><text y=\"0.3em\" " << svg.style[svg.dpSequence] << '>' << str[0][pos0] << "</text></g>" << std::endl;

	for (TSize pos1 = 0; pos1 < numRows; ++pos1)
		svg.file << "<g transform=\"translate(0," << pos1*20+25 << ")\"><text y=\"0.3em\" " << svg.style[svg.dpSequence] << '>' << str[1][pos1] << "</text></g>" << std::endl;
}

template <typename TStringSet, typename TId, typename TPos, typename TTraceValue>
inline void
_alignTracePrint(SVGFile& svg,
				   TStringSet const&,
				   TId const,
				   TPos pos1,
				   TId const,
				   TPos pos2,
				   TPos const segLen,
				   TTraceValue const tv)
{
	// TraceBack values
	TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2;

	svg.file << "<line x2=\"" << pos1*20+10 << "\" y2=\"" << pos2*20+10 << "\"";
	if (tv == Diagonal) {
		pos1 += segLen; pos2 += segLen;
	} else if (tv == Horizontal) {
		pos1 += segLen;
	} else if (tv == Vertical) {
		pos2 += segLen;
	}
	svg.file << " x1=\"" << pos1*20+10 << "\" y1=\"" << pos2*20+10;
	svg.file << "\" " << svg.style[svg.dpTrace] << " />" << std::endl;
}

//////////////////////////////////////////////////////////////////////////////



} //namespace SEQAN_NAMESPACE_MAIN

#endif //#ifndef SEQAN_HEADER_...