added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index 32f4778a7c1ee19db25eeb4e1eafaf74fabcd617..b4fc3ce1c41171c0cde75a83f6365e12873984bc 100644 (file)
--- 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;
@@ -164,6 +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;
@@ -196,7 +252,24 @@ inline bool compareIndexes(PDistCell left, PDistCell right){
 //********************************************************************************************************************
 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){