Some further minor corrections

[chloroplast13.git] / annotated.tex

diff --git a/annotated.tex b/annotated.tex
index e9e30496d4504bd9018a1ea27125c400919fd288..8cc8016578e3561089b2c6ebc0ab006c4251bde7 100644 (file)
--- a/annotated.tex
+++ b/annotated.tex
@@ -190,9 +190,9 @@ to extract core genes, as explained in Algorithm \ref{Alg3:thirdM}.
 \STATE $geneList=\text{empty list}$
 \STATE $common=set(dir(NCBI\_Genes)) \cap set(dir(Dogma\_Genes))$
 \FOR{$\text{gene in common}$}
 \STATE $geneList=\text{empty list}$
 \STATE $common=set(dir(NCBI\_Genes)) \cap set(dir(Dogma\_Genes))$
 \FOR{$\text{gene in common}$}

-       \STATE $gen1 \leftarrow open(NCBI\_Genes(gene)).read()$         
-       \STATE $gen2 \leftarrow open(Dogma\_Genes(gene)).read()$
-       \STATE $score \leftarrow geneChk(gen1,gen2)$
+       \STATE $g1 \leftarrow open(NCBI\_Genes(gene)).read()$   
+       \STATE $g2 \leftarrow open(Dogma\_Genes(gene)).read()$
+       \STATE $score \leftarrow geneChk(g1,g2)$

        \IF {$score > Threshold$}
                \STATE $geneList \leftarrow gene$
        \ENDIF 
        \IF {$score > Threshold$}
                \STATE $geneList \leftarrow gene$
        \ENDIF 


@@ -210,18 +210,16 @@ geneChk subroutine.
 \caption{Find the Maximum Similarity Score between two sequences}
 \label{Alg3:genechk}
 \begin{algorithmic} 
 \caption{Find the Maximum Similarity Score between two sequences}
 \label{Alg3:genechk}
 \begin{algorithmic} 

-\REQUIRE $gen1,gen2 \leftarrow \text{NCBI gene sequence, Dogma gene sequence}$
+\REQUIRE $g1,g2 \leftarrow \text{NCBI gene sequence, Dogma gene sequence}$

 \ENSURE $\text{Maximum similarity score}$
 \ENSURE $\text{Maximum similarity score}$

-\STATE $Score1 \leftarrow needle(gen1,gen2)$
-\STATE $Score2 \leftarrow needle(gen1,Reverse(gen2))$
-\STATE $Score3 \leftarrow needle(gen1,Complement(gen2))$
-\STATE $Score4 \leftarrow needle(gen1,Reverse(Complement(gen2)))$
-\RETURN $max(Score1, Score2, Score3, Score4)$
+\STATE $score1 \leftarrow needle(g1,g2)$
+\STATE $score2 \leftarrow needle(g1,Reverse(g2))$
+\STATE $score3 \leftarrow needle(g1,Complement(g2))$
+\STATE $score4 \leftarrow needle(g1,Reverse(Complement(g2)))$
+\RETURN $max(score1,score2,score3,score4)$

 \end{algorithmic}
 \end{algorithm}  
 
 \end{algorithmic}
 \end{algorithm}  
 

-% THIS SUBSECTION MUST BE IMPROVED 
-

 \subsubsection{Intersection Core Matrix (\textit{ICM})}
 
 To extract  core genes, we  iteratively collect the maximum  number of
 \subsubsection{Intersection Core Matrix (\textit{ICM})}
 
 To extract  core genes, we  iteratively collect the maximum  number of