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SimAquaLife
SturioSaintSeurin
Commits
ad365ec9
Commit
ad365ec9
authored
May 19, 2017
by
Dumoulin Nicolas
Browse files
cleanup
parent
11afd67a
Changes
49
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.classpath
deleted
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11afd67a
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry
kind=
"src"
output=
"target/classes"
path=
"src"
>
<attributes>
<attribute
name=
"optional"
value=
"true"
/>
<attribute
name=
"maven.pomderived"
value=
"true"
/>
</attributes>
</classpathentry>
<classpathentry
kind=
"con"
path=
"org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"
>
<attributes>
<attribute
name=
"maven.pomderived"
value=
"true"
/>
</attributes>
</classpathentry>
<classpathentry
kind=
"con"
path=
"org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"
>
<attributes>
<attribute
name=
"maven.pomderived"
value=
"true"
/>
</attributes>
</classpathentry>
<classpathentry
kind=
"output"
path=
"target/classes"
/>
</classpath>
.gitignore
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.classpath
.project
.settings
target
.project
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<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>
SturioSaintSeurin
</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>
org.eclipse.jdt.core.javabuilder
</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>
org.eclipse.m2e.core.maven2Builder
</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>
org.eclipse.m2e.core.maven2Nature
</nature>
<nature>
org.eclipse.jdt.core.javanature
</nature>
</natures>
</projectDescription>
.settings/org.eclipse.core.resources.prefs
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eclipse.preferences.version=1
encoding/<project>=ISO-8859-15
encoding/src=ISO-8859-15
.settings/org.eclipse.jdt.core.prefs
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eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.6
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.source=1.6
.settings/org.eclipse.m2e.core.prefs
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activeProfiles=
eclipse.preferences.version=1
resolveWorkspaceProjects=true
version=1
.svn/entries
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12
.svn/format
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<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>
SturioSaintSeurin
</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>
org.eclipse.jdt.core.javabuilder
</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>
org.eclipse.m2e.core.maven2Builder
</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>
org.eclipse.m2e.core.maven2Nature
</nature>
<nature>
org.eclipse.jdt.core.javanature
</nature>
</natures>
</projectDescription>
.svn/pristine/03/0364424290f30b92993711930f524170969c88c5.svn-base
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11afd67a
eclipse.preferences.version=1
encoding/<project>=ISO-8859-15
encoding/src=ISO-8859-15
.svn/pristine/09/09a593e73b6dfe70254123aa3ffeca6975f6207e.svn-base
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11afd67a
/**
*
Patrick
.
Lambert
*
@
author
Patrick
Lambert
*
@
copyright
Copyright
(
c
)
2014
,
Irstea
*
*
This
program
is
free
software
:
you
can
redistribute
it
and
/
or
modify
*
it
under
the
terms
of
the
GNU
General
Public
License
as
published
by
*
the
Free
Software
Foundation
,
either
version
3
of
the
License
,
or
*
(
at
your
option
)
any
later
version
.
*
*
This
program
is
distributed
in
the
hope
that
it
will
be
useful
,
*
but
WITHOUT
ANY
WARRANTY
;
without
even
the
implied
warranty
of
*
MERCHANTABILITY
or
FITNESS
FOR
A
PARTICULAR
PURPOSE
.
See
the
*
GNU
General
Public
License
for
more
details
.
*
*
You
should
have
received
a
copy
of
the
GNU
General
Public
License
*
along
with
this
program
.
If
not
,
see
<
http
://
www
.
gnu
.
org
/
licenses
/>.
*/
package
species
;
import
java
.
lang
.
reflect
.
InvocationTargetException
;
import
java
.
util
.
ArrayList
;
import
java
.
util
.
LinkedList
;
import
java
.
util
.
List
;
import
java
.
util
.
Map
;
import
java
.
util
.
Map
.
Entry
;
import
java
.
util
.
TreeMap
;
import
species
.
Sturgeon
.
Gender
;
import
species
.
Sturgeon
.
Status
;
import
environment
.
Station
;
import
fr
.
cemagref
.
observation
.
kernel
.
Observable
;
import
fr
.
cemagref
.
simaqualife
.
kernel
.
AquaNismsGroup
;
import
fr
.
cemagref
.
simaqualife
.
pilot
.
Pilot
;
/**
*
*/
public
class
SturgeonGroup
extends
AquaNismsGroup
<
Sturgeon
,
Station
>
{
private
transient
Map
<
String
,
List
<
Sturgeon
>>
batches
;
private
transient
List
<
Integer
>
femaleSpawnerNbHistory
;
private
transient
List
<
Double
>
larvaeProductionHistory
;
private
transient
double
annualLarvaeProduction
;
@
Override
public
void
initTransientParameters
(
Pilot
pilot
)
throws
IllegalArgumentException
,
IllegalAccessException
,
InvocationTargetException
{
//
TODO
Auto
-
generated
method
stub
super
.
initTransientParameters
(
pilot
);
batches
=
new
TreeMap
<
String
,
List
<
Sturgeon
>>();
femaleSpawnerNbHistory
=
new
LinkedList
<
Integer
>();
larvaeProductionHistory
=
new
LinkedList
<
Double
>();
}
@
Override
public
void
addAquaNism
(
Sturgeon
fish
)
{
super
.
addAquaNism
(
fish
);
if
(
batches
.
containsKey
(
fish
.
getBatchName
())){
batches
.
get
(
fish
.
getBatchName
()).
add
(
fish
);
}
else
{
List
<
Sturgeon
>
batch
=
new
ArrayList
<
Sturgeon
>();
batch
.
add
(
fish
);
batches
.
put
(
fish
.
getBatchName
(),
batch
);
}
}
@
Override
public
void
removeAquaNism
(
Sturgeon
fish
)
{
//
TODO
Auto
-
generated
method
stub
super
.
removeAquaNism
(
fish
);
batches
.
get
(
fish
.
getBatchName
()).
remove
(
fish
);
}
public
void
printNumberInBatches
(){
int
total
=
0
;
for
(
Entry
<
String
,
List
<
Sturgeon
>>
entry
:
batches
.
entrySet
()){
System
.
out
.
println
(
" "
+
entry
.
getKey
()+
":
\t
"
+
entry
.
getValue
().
size
());
total
+=
entry
.
getValue
().
size
();
}
System
.
out
.
println
(
"-->"
+
total
+
"vs"
+
this
.
getAquaNismsList
().
size
());
}
@
Observable
(
description
=
"Fish number"
)
public
int
getFishNumber
()
{
if
(
this
.
getAquaNismsList
()
!= null)
return
this
.
getAquaNismsList
().
size
();
else
return
0
;
}
public
Integer
[]
getFemaleHistory
()
{
return
(
Integer
[])
femaleSpawnerNbHistory
.
toArray
();
}
@
Observable
(
description
=
"nb of female ready to spawn"
)
public
int
getNumberOfFemaleInMaturation
()
{
int
nb
=
0
;
for
(
Sturgeon
fish
:
this
.
getAquaNismsList
()){
if
(
fish
.
getGender
()
==
Gender
.
FEMALE
&
fish
.
isReadyToSpawn
()){
nb
++;
}
}
return
nb
;
}
@
Observable
(
description
=
"nb of male ready to spawn"
)
public
int
getNumberOfMaleInMaturation
()
{
int
nb
=
0
;
for
(
Sturgeon
fish
:
this
.
getAquaNismsList
()){
if
(
fish
.
getGender
()
==
Gender
.
MALE
&
fish
.
isReadyToSpawn
()){
nb
++;
}
}
return
nb
;
}
@
Observable
(
description
=
"nb of normal fish"
)
public
int
getNormalFishNumber
()
{
int
nb
=
0
;
for
(
Sturgeon
fish
:
this
.
getAquaNismsList
()){
if
(
fish
.
getStatus
()
==
Status
.
NORMAL
){
nb
++;
}
}
return
nb
;
}
@
Observable
(
description
=
"nb of deformed fish"
)
public
int
getDeformedFishNumber
()
{
int
nb
=
0
;
for
(
Sturgeon
fish
:
this
.
getAquaNismsList
()){
if
(
fish
.
getStatus
()
==
Status
.
DEFORMED
){
nb
++;
}
}
return
nb
;
}
@
Observable
(
description
=
"annual larvae production"
)
public
double
getAnnualLarvaeProduction
()
{
return
Math
.
round
(
annualLarvaeProduction
*
1000.
)/
1000.
;
}
public
void
setAnnualLarvaeProduction
(
double
annualLarvaeProduction
)
{
this
.
annualLarvaeProduction
=
annualLarvaeProduction
;
}
public
void
setLarvaeProductionHistory
(
List
<
Double
>
larvaeProductionHistory
)
{
this
.
larvaeProductionHistory
=
larvaeProductionHistory
;
}
public
Map
<
String
,
List
<
Sturgeon
>>
getBatches
()
{
return
batches
;
}
public
List
<
Integer
>
getFemaleSpawnerNbHistory
()
{
return
femaleSpawnerNbHistory
;
}
public
List
<
Double
>
getLarvaeProductionHistory
()
{
return
larvaeProductionHistory
;
}
@
Observable
(
description
=
"female spawner history"
)
public
Integer
[]
getFemaleSpawnersArray
()
{
Integer
[]
output
=
new
Integer
[
femaleSpawnerNbHistory
.
size
()];
for
(
int
i
=
0
;
i
<
femaleSpawnerNbHistory
.
size
();
i
++){
output
[
i
]
=
femaleSpawnerNbHistory
.
get
(
i
);
}
return
output
;
}
@
Observable
(
description
=
"female spawner history"
)
public
String
getFemaleSpawnersString
()
{
String
output
=
""
;
String
sep
=
""
;
for
(
int
i
=
0
;
i
<
femaleSpawnerNbHistory
.
size
();
i
++){
output
=
output
.
concat
(
sep
).
concat
(
femaleSpawnerNbHistory
.
get
(
i
).
toString
());
sep
=
", "
;
}
return
output
;
}
@
Observable
(
description
=
"larvae hsitory history"
)
public
String
getLarvaeProductionString
()
{
String
output
=
""
;
String
sep
=
""
;
for
(
int
i
=
0
;
i
<
larvaeProductionHistory
.
size
();
i
++){
output
=
output
.
concat
(
sep
).
concat
(
larvaeProductionHistory
.
get
(
i
).
toString
());
sep
=
", "
;
}
return
output
;
}
}
.svn/pristine/0f/0fb6877ccd1a8bd8ba27aafa0bc880517de4bdac.svn-base
deleted
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<!-- ************************************************************* -->
<!-- *** POM Relationships *************************************** -->
<!-- ************************************************************* -->
<groupId>SturioSaintSeurin</groupId>
<artifactId>SturioSaintSeurin</artifactId>
<version>0.0.1-SNAPSHOT</version>
<dependencies>
<dependency>
<groupId>fr.cemagref</groupId>
<artifactId>simaqualife</artifactId>
<version>2.0</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
<type>jar</type>
</dependency>
</dependencies>
<!-- ************************************************************* -->
<!-- *** Project Information ************************************* -->
<!-- ************************************************************* -->
<name>${project.artifactId} ${project.version}</name>
<description></description>
<url></url>
<licenses>
<license>
<name>GPL</name>
<url>http://www.gnu.org/copyleft/gpl.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<!-- ************************************************************* -->
<!-- *** Build Settings ****************************************** -->
<!-- ************************************************************* -->
<packaging>jar</packaging>
<build>
<sourceDirectory>src</sourceDirectory>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>assembly</goal>
</goals>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<configuration>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>resources</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<extensions>true</extensions>
<configuration>
<manifestLocation>target/META-INF</manifestLocation>
<finalName>${symbolic.name}_${project.version}</finalName>
<instructions>
<Bundle-Name>${project.groupId}.${project.artifactId}</Bundle-Name>
<Bundle-SymbolicName>${project.groupId}.${project.artifactId}</Bundle-SymbolicName>
<Import-Package>*;resolution:=optional</Import-Package>
<Export-Package>fr.cemagref.simaqualife.extensions.pilot.BatchRunner;fr.cemagref.simaqualife.*;miscellaneous.*</Export-Package>
<Embed-Dependency>*;scope=!provided;inline=true</Embed-Dependency>
<Embed-Transitive>true</Embed-Transitive>
<eclipse.buddypolicy>global</eclipse.buddypolicy>
</instructions>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>trac.clermont.cemagref.fr.nexus.public</id>
<url>http://trac.clermont.cemagref.fr/nexus/content/groups/public</url>
</repository>
<repository>
<id>trac.clermont.cemagref.fr.nexus.snapshots</id>
<url>http://trac.clermont.cemagref.fr/nexus/content/repositories/snapshots</url>
</repository>
<repository>
<id>maven2-repository.dev.java.net</id>
<name>Java.net repository</name>
<url>http://download.java.net/maven/2</url>
</repository>
</repositories>
<properties>
<project.build.sourceEncoding>ISO-8859-15</project.build.sourceEncoding>
<build.timestamp>${maven.build.timestamp}</build.timestamp>
<netbeans.hint.license>gpl30</netbeans.hint.license>
</properties>
</project>
\ No newline at end of file
.svn/pristine/16/165a0396af4cd4e5d2a986c7688a6eeefa80191b.svn-base
deleted
100644 → 0
View file @
11afd67a
/**
*
Patrick
.
Lambert
*
@
author
Patrick
Lambert
*
@
copyright
Copyright
(
c
)
2014
,
Irstea
*
*
This
program
is
free
software
:
you
can
redistribute
it
and
/
or
modify
*
it
under
the
terms
of
the
GNU
General
Public
License
as
published
by
*
the
Free
Software
Foundation
,
either
version
3
of
the
License
,
or
*
(
at
your
option
)
any
later
version
.
*
*
This
program
is
distributed
in
the
hope
that
it
will
be
useful
,
*
but
WITHOUT
ANY
WARRANTY
;
without
even
the
implied
warranty
of
*
MERCHANTABILITY
or
FITNESS
FOR
A
PARTICULAR
PURPOSE
.
See
the
*
GNU
General
Public
License
for
more
details
.
*
*
You
should
have
received
a
copy
of
the
GNU
General
Public
License
*
along
with
this
program
.
If
not
,
see
<
http
://
www
.
gnu
.
org
/
licenses
/>.
*/
/**
*
*/
package
environment
;
\ No newline at end of file
.svn/pristine/1b/1b6713d3bad9b10658390d20fdac65c5e656b1c2.svn-base
deleted
100644 → 0
View file @
11afd67a
package
observer
;
import
java
.
lang
.
reflect
.
InvocationTargetException
;
import
fr
.
cemagref
.
observation
.
kernel
.
ObservablesHandler
;
import
fr
.
cemagref
.
observation
.
observers
.
ConsoleObserver
;
import
fr
.
cemagref
.
ohoui
.
annotations
.
Description
;
import
java
.
util
.
ArrayList
;
import
java
.
util
.
Arrays
;
import
java
.
util
.
List
;
import
java
.
util
.
logging
.
Level
;
import
java
.
util
.
logging
.
Logger
;
public
class
MyCSVObserver
extends
ConsoleObserver
{
@
Description
(
name
=
"Field separator"
,
tooltip
=
""
)
protected
char
separator
=
';'
;
private
List
<
String
>
observables
;
protected
transient
List
<
ObservablesHandler
.
ObservableFetcher
>
fetchers
;
/**
*
<
code
>
classObservable
</
code
>
is
used
to
display
name
of
attributes
as
*
header
*/
private
transient
ObservablesHandler
classObservable
;
public
MyCSVObserver
()
{
}
public
MyCSVObserver
(
boolean
sysout
,
String
outputFile
)
{
super
(
sysout
,
outputFile
);
}
public
MyCSVObserver
(
boolean
sysout
,
String
outputFile
,
String
...
obsvervables
)
{
super
(
sysout
,
outputFile
);
this
.
observables
=
Arrays
.
asList
(
obsvervables
);
}
public
List
<
String
>
getObservables
()
{
return
observables
;
}
@
Override
public
void
addObservable
(
ObservablesHandler
classObservable
)
{
ObservablesHandler
bak
=
this
.
classObservable
;
this
.
classObservable
=
classObservable
;
if
(
bak
!= null) // The observable has been changed
{
this
.
init
();
}
}
@
Override
public
void
valueChanged
(
ObservablesHandler
clObservable
,
Object
instance
,
long
t
)
{
if
(
isInDates
(
t
))
{
StringBuffer
buf
=
new
StringBuffer
();
StringBuffer
sbSeparator
=
new
StringBuffer
(
" "
+
this
.
separator
+
" "
);
//
print
current
Time
buf
.
append
(
t
);
//
print
value
of
each
field
for
(
ObservablesHandler
.
ObservableFetcher
fetcher
:
fetchers
)
{
buf
.
append
(
sbSeparator
);
Object
value
=
getValue
(
fetcher
,
instance
);
buf
.
append
(
value
==
null
?
"N/A"
:
value
);
}
outputStream
.
println
(
buf
);
}
}
/**
*
*
@
param
fetcher
*
@
param
instance
*
@
return
the
value
returned
by
the
fetcher
or
null
if
a
problem
has
*
occured
due
to
the
introspection
.
*/
protected
Object
getValue
(
ObservablesHandler
.
ObservableFetcher
fetcher
,
Object
instance
)
{
try
{
return
fetcher
.
fetchValue
(
instance
);
}
catch
(
IllegalArgumentException
ex
)
{
Logger
.
getLogger
(
MyCSVObserver
.
class
.
getName
()).
log
(
Level
.
SEVERE
,
null
,
ex
);
return
null
;
}
catch
(
IllegalAccessException
ex
)
{
Logger
.
getLogger
(
MyCSVObserver
.
class
.
getName
()).
log
(
Level
.
SEVERE
,
null
,
ex
);
return
null
;
}
catch
(
InvocationTargetException
ex
)
{
Logger
.
getLogger
(
MyCSVObserver
.
class
.
getName
()).
log
(
Level
.
SEVERE
,
null
,
ex
);
return
null
;
}
}
@
Override
public
void
init
()
{
super
.
init
();
if
(
classObservable
!= null) {
fetchers
=
new
ArrayList
<
ObservablesHandler
.
ObservableFetcher
>();
if
(
observables
!= null) {
for
(
String
name
:
observables
)
{
fetchers
.
add
(
classObservable
.
getObservableFetcherByName
(
name
));
}
}
else
{
fetchers
.
addAll
(
Arrays
.
asList
(
classObservable
.
getObservableFetchers
()));
}
//
Headers
printing
StringBuffer
buf
=
new
StringBuffer
();
StringBuffer
sbSeparator
=
new
StringBuffer
(
" "
+
this
.
separator
+
" "
);
buf
.
append
(
"Year"
);
buf
.
append
(
sbSeparator
);