X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=mothur.h;h=b4fc3ce1c41171c0cde75a83f6365e12873984bc;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hp=cd14056b21ba82f9d6c07e650fcf210616e7a882;hpb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;p=mothur.git

diff --git a/mothur.h b/mothur.h
index cd14056..b4fc3ce 100644
--- a/mothur.h
+++ b/mothur.h
@@ -120,6 +120,52 @@ struct diffPair {
 		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;
@@ -127,6 +173,21 @@ struct PDistCell{
 	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;
@@ -149,6 +210,16 @@ struct distlinePair {
 	int end;
 	
 };
+/************************************************************/
+struct oligosPair {
+	string forward;
+	string reverse;
+	
+	oligosPair() { forward = ""; reverse = "";  }
+	oligosPair(string f, string r) : forward(f), reverse(r) {}
+	~oligosPair() {}
+};
+
 /************************************************************/
 struct seqPriorityNode {
 	int numIdentical;
@@ -158,6 +229,15 @@ struct 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;
@@ -170,10 +250,26 @@ inline bool compareIndexes(PDistCell left, PDistCell right){
 	return (left.index > right.index);	
 }
 //********************************************************************************************************************
-//sorts highest to lowest
 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){
@@ -185,11 +281,7 @@ inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right)
     }
     return false;	
 } 
-//********************************************************************************************************************
-//sorts lowest to highest
-inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
-	return (left.score < right.score);	
-} 
+ 
 /************************************************************/
 //sorts lowest to highest
 inline bool compareDistLinePairs(distlinePair left, distlinePair right){
@@ -199,7 +291,15 @@ 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