X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.h;h=102b44d57030561244c8ba6205f7c02c831b9b36;hp=337e5b33a6b1d8100effe484c230d42c7fd93f58;hb=d1faab5efe1c28700890bdec5b4d8e817fa1dab2;hpb=173a1a82a4e4aa6bef8e4ba77bce342fb9c6563e

diff --git a/mothur.h b/mothur.h
index 337e5b3..102b44d 100644
--- a/mothur.h
+++ b/mothur.h
@@ -36,11 +36,13 @@
 #include <map>
 #include <string>
 #include <list>
+#include <string.h>
 
 //math
 #include <cmath>
 #include <math.h>
 #include <algorithm>
+#include <numeric>
 
 //misc
 #include <cerrno>
@@ -52,10 +54,12 @@
 #endif
 /***********************************************************************/
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 	#include <sys/wait.h>
 	#include <sys/time.h>
 	#include <sys/resource.h>
+	#include <sys/types.h>
+	#include <sys/stat.h>
 	#include <unistd.h>
 	
 	#ifdef USE_READLINE
@@ -68,6 +72,8 @@
 	#include <direct.h> //get cwd
 	#include <windows.h>
 	#include <psapi.h>
+	#include <direct.h>
+	#include <tchar.h>
 
 #endif
 
@@ -80,7 +86,9 @@ using namespace std;
 #define isnan(x) ((x) != (x))
 #define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
 
+
 typedef unsigned long ull;
+typedef unsigned short intDist;
 
 struct IntNode {
 	int lvalue;
@@ -100,6 +108,86 @@ struct ThreadNode {
 	IntNode* right;
 };
 
+struct diffPair {
+	float	prob;
+	float	reverseProb;
+	
+	diffPair() {
+		prob = 0; reverseProb = 0;
+	}
+	diffPair(float p, float rp) {
+		prob = p;
+		reverseProb = rp;
+	}
+};
+
+/**********************************************************/
+struct CommonHeader {
+	unsigned int magicNumber;
+	string version;
+	unsigned long long indexOffset;
+	unsigned int indexLength;
+	unsigned int numReads;
+	unsigned short headerLength;
+	unsigned short keyLength;
+	unsigned short numFlowsPerRead;
+	int flogramFormatCode;
+	string flowChars; //length depends on number flow reads
+	string keySequence; //length depends on key length
+	
+	CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
+	~CommonHeader() { }
+};
+/**********************************************************/
+struct Header {
+	unsigned short headerLength;
+	unsigned short nameLength;
+	unsigned int numBases;
+	unsigned short clipQualLeft;
+	unsigned short clipQualRight;
+	unsigned short clipAdapterLeft;
+	unsigned short clipAdapterRight;
+	string name; //length depends on nameLength
+	string timestamp;
+	string region;
+	string xy;
+	
+	Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
+	~Header() { }
+};
+/**********************************************************/
+struct seqRead {
+	vector<unsigned short> flowgram;
+	vector<unsigned int> flowIndex;
+	string bases;
+	vector<unsigned int> qualScores;
+	
+	seqRead() { }
+	~seqRead() { }
+};
+
+/***********************************************************************/
+struct PDistCell{
+	ull index;
+	float dist;
+	PDistCell() :  index(0), dist(0) {};
+	PDistCell(ull c, float d) :  index(c), dist(d) {}
+};
+/***********************************************************************/
+struct consTax{
+	string name;
+    string taxonomy;
+    int abundance;
+	consTax() :  name(""), taxonomy("unknown"), abundance(0) {};
+	consTax(string n, string t, int a) :  name(n), taxonomy(t), abundance(a) {}
+};
+/***********************************************************************/
+struct consTax2{
+    string taxonomy;
+    int abundance;
+	consTax2() :  taxonomy("unknown"), abundance(0) {};
+	consTax2(string t, int a) :  taxonomy(t), abundance(a) {}
+};
 /************************************************************/
 struct clusterNode {
 	int numSeq;
@@ -111,9 +199,9 @@ struct clusterNode {
 struct seqDist {
 	int seq1;
 	int seq2;
-	float dist;
+	double dist;
 	seqDist() {}
-	seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
+	seqDist(int s1, int s2, double d) : seq1(s1), seq2(s2), dist(d) {}
 	~seqDist() {}
 };
 /************************************************************/
@@ -122,6 +210,68 @@ struct distlinePair {
 	int end;
 	
 };
+/************************************************************/
+struct seqPriorityNode {
+	int numIdentical;
+	string seq;
+	string name;
+	seqPriorityNode() {}
+	seqPriorityNode(int n, string s, string nm) : numIdentical(n), seq(s), name(nm) {}
+	~seqPriorityNode() {}
+};
+/************************************************************/
+struct compGroup {
+	string group1;
+	string group2;
+	compGroup() {}
+	compGroup(string s, string nm) : group1(s), group2(nm) {}
+    string getCombo() { return group1+"-"+group2; }
+	~compGroup() {}
+};
+/***************************************************************/
+struct spearmanRank {
+	string name;
+	float score;
+	
+	spearmanRank(string n, float s) : name(n), score(s) {}
+};
+//***********************************************************************
+inline bool compareIndexes(PDistCell left, PDistCell right){
+	return (left.index > right.index);	
+}
+//********************************************************************************************************************
+inline bool compareSpearman(spearmanRank left, spearmanRank right){
+	return (left.score < right.score);	
+}
+//********************************************************************************************************************
+inline double max(double left, double right){
+    if (left > right) { return left; }
+    else { return right; }
+}
+//********************************************************************************************************************
+inline double max(int left, double right){
+    double value = left;
+    if (left > right) { return value; }
+    else { return right; }
+}
+//********************************************************************************************************************
+inline double max(double left, int right){
+    double value = right;
+    if (left > value) { return left; }
+    else { return value; }
+}
+//********************************************************************************************************************
+//sorts highest to lowest
+inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right){
+	if (left.numIdentical > right.numIdentical) {
+        return true;
+    }else if (left.numIdentical == right.numIdentical) {
+        if (left.seq > right.seq) { return true; }
+        else { return false; }
+    }
+    return false;	
+} 
+ 
 /************************************************************/
 //sorts lowest to highest
 inline bool compareDistLinePairs(distlinePair left, distlinePair right){
@@ -131,7 +281,15 @@ inline bool compareDistLinePairs(distlinePair left, distlinePair right){
 //sorts lowest to highest
 inline bool compareSequenceDistance(seqDist left, seqDist right){
 	return (left.dist < right.dist);	
-} 
+}
+//********************************************************************************************************************
+//returns sign of double
+inline double sign(double temp){
+	//find sign
+    if (temp > 0)       { return 1.0;   }
+    else if (temp < 0)  { return -1.0;  }
+    return 0;
+}
 /***********************************************************************/
 
 // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
@@ -152,7 +310,8 @@ void convert(const string& s, T& x, bool failIfLeftoverChars = true){
 			throw BadConversion(s);
 	
 }
-
+//**********************************************************************************************************************
+template <typename T> int sgn(T val){ return (val > T(0)) - (val < T(0)); }
 //**********************************************************************************************************************
 
 template<typename T>
@@ -219,5 +378,15 @@ string toString(const T&x, int i){
 }
 //**********************************************************************************************************************
 
+template<class T>
+T fromString(const string& s){
+	istringstream stream (s);
+	T t;
+	stream >> t;
+	return t;
+}
+
+//**********************************************************************************************************************
+
 #endif