@@ -1,6 +1,6 @@

 Package: CNEr 

-Version: 1.1.1

-Date: 2014-03-12

+Version: 1.1.2

+Date: 2014-03-23

 Title: CNE detection and visualization.

 Description: Large-scale identification and advanced visualization of sets of conserved noncoding elements.

 Author: Ge Tan <ge.tan09@imperial.ac.uk> 

@@ -19,4 +19,5 @@ NeedsCompilation: yes

 LazyData: no

 Collate: AllGenerics.R AllClasses.R utils.R ceScan.R plot.R 

          makeGeneDbFromUCSC.R io.R scoringMatrix.R subAxt-methods.R

+         Axt-methods.R

@@ -12,6 +12,7 @@ setGeneric("subAxt", function(x, chr, start, end, #strand=c("+", "-", "*"),

                               qSize=NULL) 

                       standardGeneric("subAxt")

                       )

+setGeneric("matchDistr", function(x) standardGeneric("matchDistr"))

 ### -----------------------------------------------------------------

 ### CNE class related

new file mode 100644

@@ -0,0 +1,22 @@

+### -----------------------------------------------------------------

+### summary function for Axt

+### Not Expotred!

+### This implementation is too slow for large Axt. Should implment in C.

+setMethod("matchDistr", signature(x="Axt"),

+          function(x){

+            matchFreq <- table(unlist(mapply(paste0, 

+                               strsplit(as.character(targetSeqs(x)), ""), 

+                               strsplit(as.character(querySeqs(x)), ""))))

+            matchFreq <- matchFreq / sum(matchFreq)

+            freqMatrix <- matrix(0, ncol=6, nrow=6)

+            colnames(freqMatrix) <- c("A", "C", "G", "T", "-", "N")

+            rownames(freqMatrix) <- c("A", "C", "G", "T", "-", "N")

+            for(i in 1:length(matchFreq)){

+              splittedNames <- strsplit(names(matchFreq)[i], "")[[1]]

+              freqMatrix[splittedNames[1], splittedNames[2]] <-

+                matchFreq[i]

+            }

+            return(freqMatrix)

+          }

+          )

+

new file mode 100644

@@ -0,0 +1,63 @@

+/********************************************************************

+ *                        Alignment related function

+ *                        Author: Ge Tan

+ *******************************************************************/

+#include "Rdefines.h"

+

+SEXP subAlignment(SEXP axttStart, SEXP axttEnd, SEXP axttSym,

+                  SEXP axtqStart, SEXP axtqEnd, SEXP axtqSym,

+                  SEXP subtStart, SEXP subtEnd, SEXP symCount){

+// The input must have same length and subtStart,subtEnd must be inside 

+// the range of axttStart,axttEnd.

+  int nrAxt = GET_LENGTH(symCount);

+  int i, j;

+  SEXP returnList;

+  PROTECT(returnList = NEW_LIST(6));

+  SEXP newtStart, newtEnd, newtSym, newqStart, newqEnd, newqSym;

+  newtStart = NEW_INTEGER(nrAxt);

+  newtEnd = NEW_INTEGER(nrAxt);

+  newtSym = NEW_CHARACTER(nrAxt);

+  newqStart = NEW_INTEGER(nrAxt);

+  newqEnd = NEW_INTEGER(nrAxt);

+  newqSym = NEW_CHARACTER(nrAxt);

+  SET_VECTOR_ELT(returnList, 0, newtStart);

+  SET_VECTOR_ELT(returnList, 1, newtEnd);

+  SET_VECTOR_ELT(returnList, 2, newtSym);

+  SET_VECTOR_ELT(returnList, 3, newqStart);

+  SET_VECTOR_ELT(returnList, 4, newqEnd);

+  SET_VECTOR_ELT(returnList, 5, newqSym);

+  int nrGapsTarget, nrGapsQuery, cpStartTarget, cpEndTarget, cpStartQuery, cpEndQuery;

+  for(i=0; i<nrAxt; i++){

+    // Rprintf("The char %d \n", i);

+    nrGapsTarget = 0;

+    nrGapsQuery = 0;

+    cpStartTarget = 0;

+    cpEndTarget = 0;

+    for(j=0; j<INTEGER(symCount)[i]; j++){

+      if(CHAR(STRING_ELT(axttSym, i))[j] == '_' || 

+          CHAR(STRING_ELT(axttSym, i))[j] == '-'){

+        //Rprintf("%c ", CHAR(STRING_ELT(axttSym, i))[j]);

+        nrGapsTarget++;

+      }

+      if(CHAR(STRING_ELT(axtqSym, i))[j] == '_' ||

+          CHAR(STRING_ELT(axtqSym, i))[j] == '-'){

+        nrGapsQuery++;

+      }

+      if(INTEGER(subtStart) == INTEGER(axttStart) + j - nrGapsTarget){

+        cpStartTarget = j;

+        INTEGER(newqStart) = j + INTEGER(axtqStart) 

+      }

+      if(INTEGER(subtEnd) == INTEGER(axttStart) + j - nrGapsTarget){

+        cpENdTarget = j;

+      }

+      

+    }

+    Rprintf("\n");

+  }

+  UNPROTECT(1);

+  return(R_NilValue);

+}

+

+

+

+