@@ -1,11 +1,10 @@

-

 *.Po

 *.Tpo

 *.lo

 *~

 *.o

 .dirstamp

-

+src/Makevars

 src/imslib/Makefile

 .deps

 src/imslib/config.log

@@ -1,3 +1,12 @@

+2010-11-04  Steffen Neumann  <sneumann@ipb-halle.de>

+	* Corrected bug that leads to wrong monoisotopic masses for molecules 

+	  containing elements where the most abundant isotope is not the first one,

+	  discovered by Ralf Tautenhahn

+

+2010-10-22  Steffen Neumann  <sneumann@ipb-halle.de>

+	* R/elements.R: Added remaining elements to PSE,

+	  contributed by Canteri Roberto (http://m2b2.fbk.eu/en/people)

+

 2010-05-18  Steffen Neumann  <sneumann@ipb-halle.de>

 	* added Runit test infrastructure

@@ -1,7 +1,7 @@

 Package: Rdisop

 Title: Decomposition of Isotopic Patterns

-Version: 1.11.0

-Date: 2010-04-02

+Version: 1.11.2

+Date: 2010-11-04

 Author: Anton Pervukhin <apervukh@minet.uni-jena.de>, Steffen Neumann <sneumann@ipb-halle.de> 

 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>

 Description: Identification of metabolites using high precision mass

@@ -2403,7 +2403,7 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu

 echo "Configuring libims.a in imslib..."

 cd src/imslib

 ./configure --enable-shared --disable-static

-make -j 6 src/libims.la

+make $MAKEFLAGS src/libims.la

 cd ../../

 IMS_CFLAGS=-I./imslib/src/

@@ -11,9 +11,4 @@ test.cid24892761 <- function() {

 }

-## test.cid <- function() {

-##   checkEqualsNumeric(,

-##                      getMolecule("",elem,z=0)$exactmass) 

-## }

-

new file mode 100644

@@ -0,0 +1,9 @@

+

+test.monoisotopicMasses <- function() {

+  elem <- initializePSE()

+  all(sapply(elem, function(x) {x$mass == as.integer(getMolecule(x$name, elem)$exactmass)}))

+  

+}

+

+

+

@@ -5,6 +5,7 @@

 #include <ostream>

 #include <ims/isotopedistribution.h>

 #include <iostream>

+#include <float.h>  // FLT_MAX

 namespace ims {

@@ -50,6 +51,11 @@ class Element {

 		 */

 		typedef isotopes_type::size_type size_type;

+                /**

+                 * Special value to detect most abundant isotope automagically

+                 */

+                static const size_type MONOISOTOPIC=0;

+

 		/**

 		 * Mass of electron.

 		 */

@@ -148,8 +154,34 @@ class Element {

 		 * @param index Index of element's isotope.

 		 * @return mass of element's isotope with a given index.

 		 */

-		mass_type getMass(size_type index = 0) const {

-			return isotopes.getMass(index);

+		mass_type getMass(size_type index = MONOISOTOPIC) const {

+		  if (index != MONOISOTOPIC) {

+		    return isotopes.getMass(index);

+		  } else {

+/* 		    std::cerr << std::endl; */

+		    

+		    IsotopeDistribution::abundance_type maxval=-FLT_MAX;

+		    int maxindex=0;

+		    

+		    for (int i=0; i < IsotopeDistribution::SIZE; i++) {

+/* 		      std::cerr << "Abundance is " << isotopes.getAbundance(i) << std::endl; */

+		      

+		      if (isotopes.getAbundance(i) > 0.5) { 

+			// 50% is the absolute majority here, 

+			// skip remaining isotopes

+/* 			std::cerr << "Early return mass "  */

+/* 				  << isotopes.getMass(i) */

+/* 				  << " of isotope " << i << std::endl ; */

+			return isotopes.getMass(i);

+		      }

+		      if (isotopes.getAbundance(i) > maxval) {

+			maxval = isotopes.getAbundance(i);

+			maxindex = i;

+		      }

+		    }

+		    

+		    return isotopes.getMass(maxindex);

+		  }

 		}

 		/**