peakrank_advanced.cpp

来自「MS-Clustering is designed to rapidly clu」· C++ 代码 · 共 1,022 行 · 第 1/3 页

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	// add features for flanking pairs of amino acids
	if (cut_idx>1)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2]*num_aas+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas*num_aas;

	if (cut_idx<length-2)
		sample.add_real_feature(r_idx+amino_acids[cut_idx]*num_aas+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas*num_aas;

	
	// X != R
	// features of the form  |LXK   |LXXK   |LXXXK   |LXXXXK
	if (cut_idx < length-2 &&
		amino_acids[cut_idx+2]==LysIdx &&
		amino_acids[cut_idx] != LysIdx && amino_acids[cut_idx] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-3 &&
		amino_acids[cut_idx+3]==LysIdx &&
		amino_acids[cut_idx] != LysIdx && amino_acids[cut_idx] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-4 &&
		amino_acids[cut_idx+4]==LysIdx &&
		amino_acids[cut_idx] != LysIdx && amino_acids[cut_idx] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-5 &&
		amino_acids[cut_idx+5]==LysIdx &&
		amino_acids[cut_idx] != LysIdx && amino_acids[cut_idx] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx+4] != ArgIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	// features of the form  |XLXK  |XLXXK  |XLXXXK  |XLXXXXK
	if (cut_idx < length-3 &&
		amino_acids[cut_idx+3]==LysIdx &&
		amino_acids[cut_idx+1] != LysIdx && amino_acids[cut_idx+1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx 
		&& amino_acids[cut_idx] != LysIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-4 &&
		amino_acids[cut_idx+4]==LysIdx &&
		amino_acids[cut_idx+1] != LysIdx && amino_acids[cut_idx+1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx] != LysIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-5 &&
		amino_acids[cut_idx+5]==LysIdx &&
		amino_acids[cut_idx+1] != LysIdx && amino_acids[cut_idx+1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx+4] != ArgIdx 
		&& amino_acids[cut_idx] != LysIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-6 &&
		amino_acids[cut_idx+6]==LysIdx &&
		amino_acids[cut_idx+1] != LysIdx && amino_acids[cut_idx+1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx+4] != ArgIdx &&
		amino_acids[cut_idx+5] != ArgIdx && amino_acids[cut_idx] != LysIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas;


	// features of the form L|XK   L|XXK   L|XXXK   L|XXXXK
	if (cut_idx>0 &&cut_idx < length-1 &&
		amino_acids[cut_idx+1]==LysIdx &&
		amino_acids[cut_idx-1] != LysIdx && amino_acids[cut_idx-1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>0 &&cut_idx < length-2 &&
		amino_acids[cut_idx+2]==LysIdx &&
		amino_acids[cut_idx-1] != LysIdx && amino_acids[cut_idx-1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+1] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>0 &&cut_idx < length-3 &&
		amino_acids[cut_idx+3]==LysIdx &&
		amino_acids[cut_idx-1] != LysIdx && amino_acids[cut_idx-1] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>0 && cut_idx < length-4 &&
		amino_acids[cut_idx+4]==LysIdx &&
		amino_acids[cut_idx-1] != LysIdx && amino_acids[cut_idx-1] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx] != ArgIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	
	// features of the form  |LXR   |LXXR   |LXXXR   |LXXXXR
		if (cut_idx < length-2 &&
		amino_acids[cut_idx+2]==ArgIdx &&
		amino_acids[cut_idx] != LysIdx && amino_acids[cut_idx] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-3 &&
		amino_acids[cut_idx+3]==ArgIdx &&
		amino_acids[cut_idx] != LysIdx && amino_acids[cut_idx] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-4 &&
		amino_acids[cut_idx+4]==ArgIdx &&
		amino_acids[cut_idx] != LysIdx && amino_acids[cut_idx] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-5 &&
		amino_acids[cut_idx+5]==ArgIdx &&
		amino_acids[cut_idx] != LysIdx && amino_acids[cut_idx] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx+4] != ArgIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	// features of the form  |XLXR  |XLXXR  |XLXXXR  |XLXXXXR
		if (cut_idx < length-3 &&
		amino_acids[cut_idx+3]==ArgIdx &&
		amino_acids[cut_idx+1] != LysIdx && amino_acids[cut_idx+1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx] != LysIdx &&
		amino_acids[cut_idx+2] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-4 &&
		amino_acids[cut_idx+4]==ArgIdx &&
		amino_acids[cut_idx+1] != LysIdx && amino_acids[cut_idx+1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx] != LysIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-5 &&
		amino_acids[cut_idx+5]==ArgIdx &&
		amino_acids[cut_idx+1] != LysIdx && amino_acids[cut_idx+1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx+4] != ArgIdx &&
		amino_acids[cut_idx] != LysIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx < length-6 &&
		amino_acids[cut_idx+6]==ArgIdx &&
		amino_acids[cut_idx+1] != LysIdx && amino_acids[cut_idx+1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx+4] != ArgIdx &&
		amino_acids[cut_idx+5] != ArgIdx && amino_acids[cut_idx] != LysIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx+1],cut_prop);
	r_idx+=num_aas;

	// features of the form L|XR   L|XXR   L|XXXR   L|XXXXR

	if (cut_idx>0 &&cut_idx < length-1 &&
		amino_acids[cut_idx+1]==ArgIdx &&
		amino_acids[cut_idx-1] != LysIdx && amino_acids[cut_idx-1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>0 &&cut_idx < length-2 &&
		amino_acids[cut_idx+2]==ArgIdx &&
		amino_acids[cut_idx-1] != LysIdx && amino_acids[cut_idx-1] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx && amino_acids[cut_idx+1] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>0 &&cut_idx < length-3 &&
		amino_acids[cut_idx+3]==ArgIdx &&
		amino_acids[cut_idx-1] != LysIdx && amino_acids[cut_idx-1] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx] != ArgIdx)
			sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>0 && cut_idx < length-4 &&
		amino_acids[cut_idx+4]==ArgIdx &&
		amino_acids[cut_idx-1] != LysIdx && amino_acids[cut_idx-1] != ArgIdx &&
		amino_acids[cut_idx+1] != ArgIdx && amino_acids[cut_idx+2] != ArgIdx &&
		amino_acids[cut_idx+3] != ArgIdx && amino_acids[cut_idx] != ArgIdx )
			sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;
	

	// features of the form KXF KXXF KXXXF KXXXXF
	if (cut_idx>2 && amino_acids[cut_idx-3] == LysIdx &&amino_acids[cut_idx-2] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>3 && amino_acids[cut_idx-4] == LysIdx && amino_acids[cut_idx-3] != ArgIdx &&
		amino_acids[cut_idx-2] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>4 && amino_acids[cut_idx-5] == LysIdx && amino_acids[cut_idx-4] != ArgIdx &&
		amino_acids[cut_idx-3] != ArgIdx && amino_acids[cut_idx-2] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>5 && amino_acids[cut_idx-6] == LysIdx && amino_acids[cut_idx-5] != ArgIdx &&
		amino_acids[cut_idx-4] != ArgIdx && amino_acids[cut_idx-3] != ArgIdx &&
		amino_acids[cut_idx-2] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	// features of the form KXFX KXXFX KXXXFX KXXXXFX
	if (cut_idx>3 && amino_acids[cut_idx-4] == LysIdx && amino_acids[cut_idx-3] != ArgIdx &&
		amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>4 && amino_acids[cut_idx-5] == LysIdx && amino_acids[cut_idx-4] != ArgIdx &&
		amino_acids[cut_idx-3] != ArgIdx && amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>5 && amino_acids[cut_idx-6] == LysIdx && amino_acids[cut_idx-5] != ArgIdx &&
		amino_acids[cut_idx-4] != ArgIdx && amino_acids[cut_idx-3] != ArgIdx && 
		amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>6 && amino_acids[cut_idx-7] == LysIdx && amino_acids[cut_idx-6] != ArgIdx &&
		amino_acids[cut_idx-5] != ArgIdx && amino_acids[cut_idx-4] != ArgIdx && 
		amino_acids[cut_idx-3] != ArgIdx && amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2],cut_prop);
	r_idx+=num_aas;

	// features of the form KX|F KXX|F KXXX|F KXXXX|F
	if (cut_idx>1 && cut_idx<length && amino_acids[cut_idx-2] == LysIdx && 
		amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>2 && cut_idx<length && amino_acids[cut_idx-3] == LysIdx && 
		amino_acids[cut_idx-2] != ArgIdx && amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>3 && cut_idx<length && amino_acids[cut_idx-4] == LysIdx && 
		amino_acids[cut_idx-3] != ArgIdx && amino_acids[cut_idx-2] != ArgIdx && 
		amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>4 && cut_idx<length && amino_acids[cut_idx-5] == LysIdx && 
		amino_acids[cut_idx-4] != ArgIdx && amino_acids[cut_idx-3] != ArgIdx && 
		amino_acids[cut_idx-2] != ArgIdx && amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

		// features of the form RXF RXXF RXXXF RXXXXF
	if (cut_idx>2 && amino_acids[cut_idx-3] == ArgIdx &&amino_acids[cut_idx-2] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>3 && amino_acids[cut_idx-4] == ArgIdx && amino_acids[cut_idx-3] != ArgIdx &&
		amino_acids[cut_idx-2] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>4 && amino_acids[cut_idx-5] == ArgIdx && amino_acids[cut_idx-4] != ArgIdx &&
		amino_acids[cut_idx-3] != ArgIdx && amino_acids[cut_idx-2] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>5 && amino_acids[cut_idx-6] == ArgIdx && amino_acids[cut_idx-5] != ArgIdx &&
		amino_acids[cut_idx-4] != ArgIdx && amino_acids[cut_idx-3] != ArgIdx &&
		amino_acids[cut_idx-2] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-1],cut_prop);
	r_idx+=num_aas;

	// features of the form RXFX RXXFX RXXXFX RXXXXFX
	if (cut_idx>3 && amino_acids[cut_idx-4] == ArgIdx && amino_acids[cut_idx-3] != ArgIdx &&
		amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>4 && amino_acids[cut_idx-5] == ArgIdx && amino_acids[cut_idx-4] != ArgIdx &&
		amino_acids[cut_idx-3] != ArgIdx && amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>5 && amino_acids[cut_idx-6] == ArgIdx && amino_acids[cut_idx-5] != ArgIdx &&
		amino_acids[cut_idx-4] != ArgIdx && amino_acids[cut_idx-3] != ArgIdx && 
		amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>6 && amino_acids[cut_idx-7] == ArgIdx && amino_acids[cut_idx-6] != ArgIdx &&
		amino_acids[cut_idx-5] != ArgIdx && amino_acids[cut_idx-4] != ArgIdx && 
		amino_acids[cut_idx-3] != ArgIdx && amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx-2],cut_prop);
	r_idx+=num_aas;

	// features of the form RX|F RXX|F RXXX|F RXXXX|F
	if (cut_idx>1 && cut_idx<length && amino_acids[cut_idx-2] == ArgIdx && 
		amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>2 && cut_idx<length && amino_acids[cut_idx-3] == ArgIdx && 
		amino_acids[cut_idx-2] != ArgIdx && amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>3 && cut_idx<length && amino_acids[cut_idx-4] == ArgIdx && 
		amino_acids[cut_idx-3] != ArgIdx && amino_acids[cut_idx-2] != ArgIdx && 
		amino_acids[cut_idx-1] != ArgIdx)
		sample.add_real_feature(r_idx+amino_acids[cut_idx],cut_prop);
	r_idx+=num_aas;

	if (cut_idx>4 && cut_idx<length && amino_acids[cut_idx-5] == ArgIdx && 
		amino_acids[cut_idx-4] != ArgIdx && amino_acids[cut_idx-3] != ArgIdx && 
		amino_acids[cut_idx-2] != ArgIdx && amino_acids[cut_idx-1] != ArgIdx)
123

peakrank_advanced.cpp - 源码说明

本页面展示了「MS-Clustering is designed to rapidly cluster large MS/MS datasets. The program merges similar spectr」中的 peakrank_advanced.cpp 源码文件，采用 C++ 编程语言编写，共 1,022 行代码。您可以在线阅读完整代码内容，也可以返回资源详情页下载完整源码包进行本地学习和开发。

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