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TranSyT
transyt-scraper
Commits
65220629
Commit
65220629
authored
Jul 11, 2018
by
Davide Lagoa
Browse files
blast changes
parent
c2fb1c3c
Changes
4
Hide whitespace changes
Inline
Side-by-side
src/main/java/blast/Blast.java
View file @
65220629
...
...
@@ -92,7 +92,7 @@ public class Blast implements Observer{
logger
.
info
(
"Blast process initialized!"
);
RunSimilaritySearch
run_similaritySearch
=
new
RunSimilaritySearch
(
tcdbGenes
,
0.
1
,
RunSimilaritySearch
run_similaritySearch
=
new
RunSimilaritySearch
(
tcdbGenes
,
0.
3
,
Method
.
SmithWaterman
,
sequences
,
new
AtomicBoolean
(
false
),
new
AtomicInteger
(
0
),
new
AtomicInteger
(
0
),
AlignmentScoreType
.
ALIGNMENT
);
run_similaritySearch
.
setTcdbFastaFilePath
(
tcdbFastaFile
);
...
...
src/main/java/tcdb/reactionsGenerator/GenerateTransportReactions.java
View file @
65220629
...
...
@@ -1677,13 +1677,13 @@ public class GenerateTransportReactions {
for
(
int
i
=
0
;
i
<
reactants
.
size
();
i
++)
{
String
auxReact
=
reactants
.
get
(
i
).
replaceAll
(
"\\(in\\)"
,
""
).
replaceAll
(
"\\(out\\)"
,
""
).
replace
(
"\\+"
,
""
);
String
auxReact
=
reactants
.
get
(
i
).
replaceAll
(
"\\(in\\)"
,
""
).
replaceAll
(
"\\(out\\)"
,
""
).
replace
(
"\\+"
,
""
);
//this replace("\\+", "") might not be correct
String
[]
auxReactMetab
=
auxReact
.
split
(
"\\s+"
);
for
(
int
j
=
0
;
j
<
products
.
size
();
j
++)
{
String
auxProd
=
products
.
get
(
j
).
replaceAll
(
"\\(in\\)"
,
""
).
replaceAll
(
"\\(out\\)"
,
""
).
replace
(
"\\+"
,
""
);
String
auxProd
=
products
.
get
(
j
).
replaceAll
(
"\\(in\\)"
,
""
).
replaceAll
(
"\\(out\\)"
,
""
).
replace
(
"\\+"
,
""
);
//this replace("\\+", "") might not be correct
String
[]
auxProdMetab
=
auxProd
.
split
(
"\\s+"
);
...
...
target/classes/META-INF/maven/tcdb/triage/pom.properties
View file @
65220629
#Generated by Maven Integration for Eclipse
#
Fri
Jul 0
6
1
2
:5
1:1
9 BST 2018
#
Tue
Jul
1
0 1
3
:5
5:4
9 BST 2018
m2e.projectLocation
=
C
\:\\
Users
\\
Davide
\\
Biosynth2
\\
triage
m2e.projectName
=
triage
groupId
=
tcdb
...
...
target/classes/blast/Blast.class
View file @
65220629
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