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vidjil
vidjil
Commits
61690c60
Commit
61690c60
authored
Dec 12, 2014
by
Marc Duez
Browse files
Merge branch 'master' of
git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil
parents
773992d5
d366ba02
Changes
8
Hide whitespace changes
Inline
Side-by-side
browser/css/dark.css
View file @
61690c60
...
...
@@ -613,7 +613,7 @@ span .substitution {
border-color
:
#333333
;
}
#file_menu
,
#a
nalysis_menu
{
#a
xis_choice
{
z-index
:
2
;
border
:
solid
;
position
:
fixed
;
...
...
@@ -896,7 +896,7 @@ span.logo {
#file_menu
,
#tagSelector
,
.closeButton
,
#a
nalysis_menu
{
#a
xis_choice
{
border-color
:
#333333
;
}
#info_window
td
{
...
...
browser/css/light.css
View file @
61690c60
...
...
@@ -613,7 +613,7 @@ span .substitution {
border-color
:
#cccccc
;
}
#file_menu
,
#a
nalysis_menu
{
#a
xis_choice
{
z-index
:
2
;
border
:
solid
;
position
:
fixed
;
...
...
@@ -896,7 +896,7 @@ span.logo {
#file_menu
,
#tagSelector
,
.closeButton
,
#a
nalysis_menu
{
#a
xis_choice
{
border-color
:
#cccccc
;
}
#info_window
td
{
...
...
browser/css/vidjil.less
View file @
61690c60
...
...
@@ -743,7 +743,7 @@ span .substitution{
border-color:@border;
}
#file_menu, #a
nalysis_menu
{
#file_menu, #a
xis_choice
{
z-index:2;
border:solid;
position: fixed;
...
...
@@ -1035,7 +1035,7 @@ span.logo
color: grey;
}
.selector, #list_menu, #top-container, .list_clones, .bot-bar, #bot-container, #popup-container, #file_menu, #tagSelector, .closeButton, #a
nalysis_menu
.selector, #list_menu, #top-container, .list_clones, .bot-bar, #bot-container, #popup-container, #file_menu, #tagSelector, .closeButton, #a
xis_choice
{
border-color: @border;
}
...
...
browser/index.html
View file @
61690c60
...
...
@@ -103,14 +103,14 @@
m.load('upload_json','upload_pref', 200)"
>
start
</button>
</div>
<div
id=
"a
nalysis_menu
"
>
<div
id=
"a
xis_choice
"
>
<span
class=
"closeButton"
onclick=
"cancel();"
>
X
</span>
<h2>
analysis menu
</h2>
Analysis file:
<br/>
<input
id=
"upload_analysis"
type=
"file"
name=
"analysis"
/></br></br>
<button
onclick=
"document.getElementById('a
nalysis_menu
').style.display='none';
<button
onclick=
"document.getElementById('a
xis_choice
').style.display='none';
m.loadAnalysis('upload_analysis');"
>
start
</button>
</div>
...
...
@@ -142,7 +142,7 @@
<a
class=
"buttonSelector"
onclick=
"javascript:m.saveAnalysis()"
>
export analysis
</a>
<a
class=
"buttonSelector"
onclick=
"javascript:pdf.make()"
>
export pdf (graph + selected clones)
</a>
<a
class=
"buttonSelector"
onclick=
"javascript:pdf.makeGraph()"
>
export pdf (graph)
</a>
<a
class=
"buttonSelector"
onclick=
"javascript:m.exportCSV()"
>
export
CSV
</a>
<a
class=
"buttonSelector"
onclick=
"javascript:m.exportCSV()"
>
export
csv (visible clones)
</a>
</div>
<div
class=
"menu_box"
>
<div
id=
"upload_list"
>
...
...
@@ -218,8 +218,9 @@
<div
class=
"menu_box"
>
normalization method
</br>
<div
class=
"buttonSelector"
onclick=
"m.changeNormMethod('quantitative')"
><input
type=
"radio"
name=
"normalize_method"
value=
"quantitative"
checked
>
quantitative
</input></div>
<div
class=
"buttonSelector"
onclick=
"m.changeNormMethod('rescale')"
><input
type=
"radio"
name=
"normalize_method"
value=
"rescale"
>
rescale
</input></div>
<div
class=
"buttonSelector"
onclick=
"m.changeNormMethod('constant')"
><input
type=
"radio"
name=
"normalize_method"
value=
"constant"
checked
>
constant
</input></div>
<div
class=
"buttonSelector"
onclick=
"m.changeNormMethod('to-100')"
><input
type=
"radio"
name=
"normalize_method"
value=
"to-100"
>
to 100%
</input></div>
</div>
<div
class=
"menu_box"
>
...
...
browser/js/builder.js
View file @
61690c60
...
...
@@ -133,7 +133,7 @@ Builder.prototype = {
input
.
name
=
"
normalize_list
"
if
(
self
.
m
.
normalization
.
id
==
i
)
input
.
checked
=
true
;
var
text
=
document
.
createTextNode
(
self
.
m
.
clone
(
i
).
getName
()
+
"
=>
"
+
self
.
m
.
clone
(
i
).
expected
)
var
text
=
document
.
createTextNode
(
self
.
m
.
clone
(
i
).
getName
()
+
"
→
"
+
self
.
m
.
clone
(
i
).
expected
)
var
div
=
document
.
createElement
(
"
div
"
)
div
.
onclick
=
function
()
{
...
...
@@ -158,7 +158,7 @@ Builder.prototype = {
input
.
name
=
"
normalize_list
"
if
(
self
.
m
.
normalization
.
id
==
key
)
input
.
checked
=
true
;
var
text
=
document
.
createTextNode
(
key
+
"
=>
"
+
self
.
m
.
data
[
key
].
expected
)
var
text
=
document
.
createTextNode
(
key
+
"
→
"
+
self
.
m
.
data
[
key
].
expected
)
var
div
=
document
.
createElement
(
"
div
"
)
div
.
onclick
=
function
()
{
...
...
browser/js/menu.js
View file @
61690c60
...
...
@@ -31,19 +31,19 @@ function loadData() {
document
.
getElementById
(
"
file_menu
"
)
.
style
.
display
=
"
block
"
;
document
.
getElementById
(
"
a
nalysis_menu
"
)
document
.
getElementById
(
"
a
xis_choice
"
)
.
style
.
display
=
"
none
"
;
}
function
loadAnalysis
()
{
document
.
getElementById
(
"
a
nalysis_menu
"
)
document
.
getElementById
(
"
a
xis_choice
"
)
.
style
.
display
=
"
block
"
;
document
.
getElementById
(
"
file_menu
"
)
.
style
.
display
=
"
none
"
;
}
function
cancel
()
{
document
.
getElementById
(
"
a
nalysis_menu
"
)
document
.
getElementById
(
"
a
xis_choice
"
)
.
style
.
display
=
"
none
"
;
document
.
getElementById
(
"
file_menu
"
)
.
style
.
display
=
"
none
"
;
...
...
browser/js/model.js
View file @
61690c60
...
...
@@ -76,7 +76,7 @@ Model.prototype = {
this
.
norm
=
false
;
this
.
normalization
=
{
"
method
"
:
"
quantitative
"
,
"
method
"
:
"
constant
"
,
"
A
"
:
[],
"
B
"
:
0
,
"
id
"
:
-
1
...
...
@@ -741,7 +741,7 @@ Model.prototype = {
var
A
=
this
.
normalization
.
A
[
time
]
/* standard/spike at point time */
var
B
=
this
.
normalization
.
B
/* standard/spike expected value */
if
(
this
.
normalization
.
method
==
"
rescale
"
||
original_size
<=
A
){
if
(
this
.
normalization
.
method
==
"
constant
"
||
original_size
<=
A
){
normalized_size
=
(
original_size
*
B
)
/
A
}
else
{
normalized_size
=
B
+
(
(
original_size
-
A
)
*
(
(
1
-
B
)
/
(
1
-
A
)
)
)
...
...
@@ -1569,7 +1569,7 @@ Model.prototype = {
//header
var
csv
=
"
name,id,system,tag,v,d,j,sequence
"
for
(
var
i
=
0
;
i
<
this
.
samples
.
order
.
length
;
i
++
)
csv
+=
"
,reads_
"
+
i
for
(
var
i
=
0
;
i
<
this
.
samples
.
order
.
length
;
i
++
)
csv
+=
"
,
size
_
"
+
i
for
(
var
i
=
0
;
i
<
this
.
samples
.
order
.
length
;
i
++
)
csv
+=
"
,
ratio
_
"
+
i
csv
+=
"
\n
"
//only non-empty active clones and "other"
...
...
server/web2py/applications/vidjil/views/patient/index.html
View file @
61690c60
{{extend 'db_layout.html'}}
{{import vidjil_utils}}
<h3>
Patient list
</h3>
<h3></h3>
<div
class=
"db_block"
>
<div
class=
"db_block_
righ
t"
>
<div
class=
"db_block_
lef
t"
>
search
<input
id=
"db_filter_input"
type=
"text"
value=
"{{=request.vars["
filter
"]}}"
onchange=
"db.call('patient/index', {'filter' : this.value} )"
>
</div>
...
...
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