individual and combined mode export done

doc/xtandem_pipeline.tex

@@ -495,7 +495,9 @@ This tab displays the number of spectra observed by sample, for each top protein
 \begin{description}
 \item[Group ID] The Group ID to which the spectrum belongs.
 \item[Sub-Group ID] The Sub-Group to which the protein belongs. All the proteins in a sub-group are identified with the same valid peptides.
-\item[Top Protein Description] 
+\item[Top Protein Description] Description of the first protein listed in this subgroup
+\item[Number of proteins] Total number of proteins listed in this subgroup
+\item[sample names columns] one column for each sample containing the number of assigned spectra per subgroup
 \end{description}
 \normalsize
 
@@ -508,6 +510,53 @@ This tab displays the number of spectra observed by sample, for each top protein
 
 
 
+\subsection{Compar specific  tab (Fig~\ref{ods_combined_compar_specific})}
+\label{ods_compar_specific_tab}
+This tab displays the number of specific spectra observed by sample, for each top protein of a subgroup. 
+A spectra is considered as specific if it is only present in one subgroup and no other subgroups of the same group.
+If there is only one subgroup in a group, all the spectra of this protein are considered specific.
+\small
+\begin{description}
+\item[Group ID] The Group ID to which the spectrum belongs.
+\item[Sub-Group ID] The Sub-Group to which the protein belongs. All the proteins in a sub-group are identified with the same valid peptides.
+\item[Top Protein Description] Description of the first protein listed in this subgroup
+\item[Number of proteins] Total number of proteins listed in this subgroup
+\item[sample names columns] one column for each sample containing the number of assigned specific spectra per subgroup
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/ods_combined_compar_specific}
+\caption{compar\_Specific results}
+\label{ods_combined_compar_specific}
+\end{figure}
+
+
+
+
+\subsection{Compar PAI  tab (Fig~\ref{ods_combined_compar_pai})}
+\label{ods_compar_pai_tab}
+This tab displays the protein abundance index (PAI) and the exponentially modified PAI (emPAI) by sample, for each top protein of a subgroup. This is convenient to have an idea of the presence/absence of a subgroup of proteins in a sample, and an indication about relative abundance in each samples.
+\small
+\begin{description}
+\item[Group ID] Group ID of this protein
+\item[Sub-Group ID] Sub-Group of this protein
+\item[Top Protein Description] Description of the first protein listed in this subgroup
+\item[Number of proteins] Total number of proteins listed in this subgroup
+\item[PAI] PAI of the top protein of this subgroup in a particular sample
+\item[emPAI] emPAI of the top protein of this subgroup in a particular sample
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/ods_combined_compar_pai}
+\caption{compar\_PAI results}
+\label{ods_combined_compar_pai}
+\end{figure}
+
+
+
+
 
 
 

src/fr/inra/pappso/xtandempipeline/grouping/Group.java

@@ -166,6 +166,12 @@ public class Group extends HashKey4GroupsSet implements Comparable<Group> {
 		return (sequences.size());
 	}
 
+	/** count the number of specific spectra for a protein in one sample
+	 * 
+	 * @param hashProt
+	 * @param sample
+	 * @return
+	 */
 	public int getNumberOfSpecificPeptideInSubGroupToSample(
 			HashSampleScanSetProt hashProt, GrpMsSample sample) {
 		int count = 0;