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Philipp Spohr
YoshikoWrapper
Commits
a49f59eb
Commit
a49f59eb
authored
Dec 14, 2017
by
Philipp Spohr
Browse files
Fixes to meta-graph bugs introduced recently
parent
f36972a0
Changes
5
Hide whitespace changes
Inline
Side-by-side
src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
View file @
a49f59eb
...
...
@@ -203,22 +203,24 @@ public class SolutionTab extends JPanel {
layout
=
new
GroupLayout
(
this
);
layout
.
setHorizontalGroup
(
layout
.
createParallelGroup
(
Alignment
.
CENTER
,
true
)
.
addComponent
(
createClusterView
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
PREFERRED_SIZE
)
.
addComponent
(
createMetaGraph
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
PREFERRED_SIZE
)
.
addGap
(
8
)
.
addComponent
(
clusterCount
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
Short
.
MAX_VALUE
)
.
addComponent
(
hideSingles
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
Short
.
MAX_VALUE
)
.
addGap
(
8
)
.
addComponent
(
scrollPane
,
PREFERRED_SIZE
,
PREFERRED_SIZE
,
Short
.
MAX_VALUE
)
.
addComponent
(
createClusterView
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
PREFERRED_SIZE
)
.
addComponent
(
createMetaGraph
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
PREFERRED_SIZE
)
.
addGap
(
4
)
);
layout
.
setVerticalGroup
(
layout
.
createSequentialGroup
()
.
addComponent
(
createClusterView
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
DEFAULT_SIZE
)
.
addComponent
(
createMetaGraph
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
DEFAULT_SIZE
)
.
addGap
(
8
)
.
addComponent
(
clusterCount
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
DEFAULT_SIZE
)
.
addComponent
(
hideSingles
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
DEFAULT_SIZE
)
.
addGap
(
8
)
.
addComponent
(
scrollPane
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
DEFAULT_SIZE
)
.
addComponent
(
createClusterView
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
DEFAULT_SIZE
)
.
addComponent
(
createMetaGraph
,
DEFAULT_SIZE
,
DEFAULT_SIZE
,
DEFAULT_SIZE
)
.
addGap
(
4
)
);
this
.
setLayout
(
layout
);
...
...
src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
View file @
a49f59eb
...
...
@@ -22,6 +22,10 @@ public class CreateClusterViewsTask implements Task {
@Tunable
public
ArrayList
<
YoshikoCluster
>
clusters
;
//TODO: Make Tunable, reference by ID?
/**
* Killswitch, used to determine if the algorithm has been terminated.
* We can use this to cancel at a given point (so we don't need to finish the entire task)
*/
private
boolean
isTerminated
;
/**
...
...
@@ -77,11 +81,8 @@ public class CreateClusterViewsTask implements Task {
StyleManager
.
style
(
subnetView
,
CyCore
.
visualMappingManager
.
getCurrentVisualStyle
());
CyCore
.
networkViewManager
.
addNetworkView
(
subnetView
);
}
}
);
}
}
...
...
src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
View file @
a49f59eb
...
...
@@ -94,7 +94,7 @@ public class CreateMetaGraphTask extends AbstractTask{
//Link clusters node in meta graph and subnet graph to use Cytoscape Nested Network feature
clusterNode
.
setNetworkPointer
(
subnet
);
//Set node attributes
metaGraph
.
getRow
(
clusterNode
).
set
(
"name"
,
LocalizationManager
.
get
(
"clusters"
)+
" "
+
c
.
getID
());
metaGraph
.
getRow
(
clusterNode
).
set
(
"name"
,
LocalizationManager
.
get
(
"clusters"
)+
" "
+
(
c
.
getID
()
+
1
)
);
metaGraph
.
getRow
(
clusterNode
).
set
(
StyleManager
.
CLUSTERSIZE_COLUMN_NAME
,
c
.
getSize
());
map
.
put
(
c
,
clusterNode
);
}
...
...
@@ -105,12 +105,13 @@ public class CreateMetaGraphTask extends AbstractTask{
taskMonitor
.
setStatusMessage
(
LocalizationManager
.
get
(
"metaGraph_edges"
));
Iterator
<
YoshikoCluster
>
it1
=
solution
.
getClusters
().
iterator
();
Iterator
<
YoshikoCluster
>
it2
=
solution
.
getClusters
().
iterator
();
while
(
it1
.
hasNext
())
{
YoshikoCluster
c1
=
it1
.
next
();
Iterator
<
YoshikoCluster
>
it2
=
solution
.
getClusters
().
iterator
();
while
(
it2
.
hasNext
())
{
YoshikoCluster
c2
=
it2
.
next
();
System
.
out
.
println
(
"Debug: Processing edges between cluster "
+
c1
.
getID
()+
" and "
+
c2
.
getID
());
if
(
isTerminated
)
{
throw
new
Exception
(
"Terminated by user!"
);
...
...
@@ -126,7 +127,9 @@ public class CreateMetaGraphTask extends AbstractTask{
for
(
CyNode
c1n
:
c1
.
getSubNetwork
().
getNodeList
())
{
for
(
CyNode
c2n
:
c2
.
getSubNetwork
().
getNodeList
())
{
if
(
solution
.
getOriginalGraph
().
containsEdge
(
c1n
,
c2n
)
||
solution
.
getOriginalGraph
().
containsEdge
(
c2n
,
c1n
))
{
System
.
out
.
println
(
"Debug: Found relevant edge from "
+
c1n
.
getSUID
()+
" to "
+
c2n
.
getSUID
());
if
(!
metaGraph
.
containsEdge
(
map
.
get
(
c1
),
map
.
get
(
c2
))){
System
.
out
.
println
(
"We create a new edge for it"
);
CyEdge
edge
=
metaGraph
.
addEdge
(
map
.
get
(
c1
),
map
.
get
(
c2
),
false
);
metaGraph
.
getRow
(
edge
).
set
(
StyleManager
.
EDGESTRENGTH_COLUMN_NAME
,
1
);
}
...
...
src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
View file @
a49f59eb
...
...
@@ -9,16 +9,32 @@ import org.cytoscape.work.Tunable;
import
de.hhu.ba.yoshikoWrapper.core.ResultList
;
import
de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster
;
import
de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult
;
import
de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution
;
/**
* A task that retrieves the clusters associated with a given solution in a given result. This is meant to be used via CyRest / command line functionality exclusively
*
* @author Philipp Spohr, Dec 12, 2017
*
*/
public
class
GetClustersTask
implements
ObservableTask
{
/**
* The ID of the result for which the clusters are to be retrieved
*/
@Tunable
(
description
=
"The result ID for which the solutions should be displayed"
,
context
=
"nogui"
)
public
int
resultID
=
-
1
;
/**
* The ID of the solution for which the clusters are to be retrieved
*/
@Tunable
(
description
=
"The solution ID for which the solutions should be displayed"
,
context
=
"nogui"
)
public
long
solutionID
=
-
1
;
/**
* The clusters as a collection when they are retrieved
*/
private
Collection
<
YoshikoCluster
>
clusters
;
@Override
...
...
src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
View file @
a49f59eb
...
...
@@ -10,11 +10,23 @@ import de.hhu.ba.yoshikoWrapper.core.ResultList;
import
de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult
;
import
de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution
;
/**
* Basic task that retrieves solutions associated with a run (result)
* This is meant to be invoked from cmd / CyRest exclusively to receive solution IDs
* @author Philipp Spohr, Dec 12, 2017
*
*/
public
class
GetSolutionsTask
implements
ObservableTask
{
/**
* The result ID for the result/run for which the solutions are to be retrieved
*/
@Tunable
(
description
=
"The result ID for which the solutions should be displayed"
,
context
=
"nogui"
)
public
int
resultID
=
-
1
;
/**
* The solutions as a collection in case the task was successful
*/
private
Collection
<
YoshikoSolution
>
solutions
;
@Override
...
...
@@ -27,9 +39,7 @@ public class GetSolutionsTask implements ObservableTask {
}
@Override
public
void
cancel
()
{
// TODO Auto-generated method stub
}
public
void
cancel
()
{}
//There is nothing here that remains in an instable state as we are simply reading / retrieving data
@SuppressWarnings
(
"unchecked"
)
@Override
...
...
@@ -44,4 +54,5 @@ public class GetSolutionsTask implements ObservableTask {
return
null
;
}
}
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