diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java
index 1fbcaac81d772d4823c42011b40a246ce02ff402..d564e2090eeb1390ff8ca2e4d79bab943c35bc3e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java
@@ -1,16 +1,16 @@
/*******************************************************************************
* Copyright (C) 2017 Philipp Spohr
- *
+ *
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
- *
+ *
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
- *
+ *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -25,9 +25,9 @@ import org.cytoscape.property.AbstractConfigDirPropsReader;
import org.cytoscape.property.CyProperty;
public class ConfigurationManager extends AbstractConfigDirPropsReader{
-
+
public ConfigurationManager(String appName, String fileName){
super(appName, fileName, CyProperty.SavePolicy.CONFIG_DIR);
- this.getProperties().list(System.out);
- }
+ //this.getProperties().list(System.out);
+ }
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
index a3bb7fa6cf3e324f4dd72c32f0c47081095bca5e..4fed5acd72fa1fa90317556258a1e1fcba0b5fe5 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -4,12 +4,16 @@ package de.hhu.ba.yoshikoWrapper.core;
import java.io.IOException;
import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
public class ParameterSet implements TunableValidator
{
+ @Tunable(description="Network to analyze for clusters", context="nogui")
+ public CyNetwork net = CyCore.cy.getCurrentNetwork();
+
@Tunable(description="Time Limit for the ILP mode", context="nogui")
public int timeLimit = -1;
@@ -50,16 +54,26 @@ public class ParameterSet implements TunableValidator
@Override
public ValidationState getValidationState(Appendable errMsg) {
- if (!checkBitmask(reductionRulesBitMask)) {
- try {
- errMsg.append("The Bitmask provided is invalid! Needs to be six bit binary (example: 011001)");
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ System.out.println("DEBUG: Running VALIDATION of tunables"); //TODO: Move to logger (if it would work)
+ try {
+ if (net!= null) {
+ //Verify column validity
+ CyColumn weightColumn = net.getDefaultEdgeTable().getColumn(weightColumnName);
+ if (weightColumn == null) {
+ errMsg.append("Could not find a column named: "+weightColumnName+"\n");
+ return ValidationState.INVALID;
+ }
+ }
+ if (!checkBitmask(reductionRulesBitMask)) {
+ errMsg.append("The Bitmask provided is invalid! Needs to be six bit binary (example: 011001)\n");
+ return ValidationState.INVALID;
}
- return ValidationState.INVALID;
+ return ValidationState.OK;
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
}
- return ValidationState.OK;
+ return ValidationState.INVALID;
}
/**
@@ -79,4 +93,5 @@ public class ParameterSet implements TunableValidator
return true;
}
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
index 0efd7a5ebe459ca6abf1dea4ce09e1686abab805..2ba55c798ecc670560d3ba5e7e5f1669f3917666 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
@@ -314,7 +314,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
if (YoshikoLoader.isLibraryLoaded()){
AbstractTask yoshiko = new AlgorithmTask(
popupLevel,
- networkToBeProcessed,
fetchParameters(networkToBeProcessed)
);
/**
@@ -345,6 +344,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
*/
private ParameterSet fetchParameters(CyNetwork net) {
ParameterSet ret = new ParameterSet();
+ ret.net = net;
ret.timeLimit = opModePanel.getTimeLimit();
ret.weightColumnName = ecPanel.getWeightColumn().getName();
ret.permanentColumn = ecPanel.getPermanentColumn();
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
index eab819be1f5b29b128c855e53f36b9b328fc19e9..dfb0eebb8bd3b79d670aff1c0e263905e3923105 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
@@ -185,7 +185,7 @@ NetworkAboutToBeDestroyedListener
verticalGroup
.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(invalidLabel,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
- .addComponent(tabbedPane,PREFERRED_SIZE, DEFAULT_SIZE,Short.MAX_VALUE)
+ .addComponent(tabbedPane,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(destroyButton,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
index 86650f2e9bc0cff915607b316e3039bd7d516415..83a7ef3ae76973f81b6a4bf2d751de1de2a89d9a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
@@ -218,8 +218,8 @@ public class SolutionTab extends JPanel {
.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)
+ .addGap(4)
+ .addComponent(scrollPane,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addGap(4)
);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
index dc9e5cc66d1be0ab208b55a210d73e4f931d7335..ebd95002c5446435990241db14abeee6ce3b0b02 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
@@ -45,7 +45,6 @@ public class CommandTaskFactory implements TaskFactory{
else if (command == YoshikoCommand.PERFORM_ALGORITHM) {
return new TaskIterator(
new AlgorithmTask(
- null,
null,
new ParameterSet()
)
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
index cbc64bb4d4c4a3a8afcfa969ec50940d393701ae..31ea1ea1c33c23d839589d2a3aa2496c32d4817b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -77,8 +77,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
@ContainsTunables
public ParameterSet parameterSet = null;
- @Tunable(description="Network to analyze for clusters", context="nogui")
- public CyNetwork net = CyCore.cy.getCurrentNetwork();
+
//Temps, pointing to and need to be freed in C++
private LibraryInput c_input;
@@ -98,12 +97,10 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
*/
public AlgorithmTask(
Window statusWindow,
- CyNetwork net,
ParameterSet parameterSet
)
{
this.statusWindow = statusWindow;
- this.net = net;
this.parameterSet = parameterSet;
}
@@ -115,8 +112,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
taskMonitor.setTitle(LocalizationManager.get("yoshTask"));
taskMonitor.setProgress(0.0);
- //Get current network
- if (net == null) {
+ //Check current network
+ if (parameterSet.net == null) {
logger.warn("CoreAlgorithm called on a net that is NULL!");
throw new Exception("CoreAlgorithm called on a net that is NULL!"); //TODO: Localize
}
@@ -131,14 +128,14 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
}
//Create a node map to identify nodes and eges in the solution
- NodeMap nodeMap = new NodeMap(net);
+ NodeMap nodeMap = new NodeMap(parameterSet.net);
taskMonitor.setProgress(0.1);
//Generate an c_input instance from the network
c_input = NetworkParser.parseNetwork(
- net,
+ parameterSet.net,
nodeMap,
- net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName),
+ parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName), //Simplify
parameterSet.permanentColumn,
parameterSet.forbiddenColumn,
parameterSet.defaultDeletionCost
@@ -146,8 +143,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
taskMonitor.setProgress(0.2);
boolean containsRealValues = GraphAnalyzer.containsRealValues(
- net,
- net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName),
+ parameterSet.net,
+ parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName),
parameterSet.permanentColumn,
parameterSet.forbiddenColumn,
parameterSet.defaultInsertionCost,
@@ -184,7 +181,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO: Localize
- result = new YoshikoResult(net,c_result.getFlags());
+ result = new YoshikoResult(parameterSet.net,c_result.getFlags());
//Loop over (multiple) solutions
for (long i=0;i<numberOfSolutions;i++) {
@@ -195,8 +192,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
- net.getDefaultNodeTable().deleteColumn(columnName);
- net.getDefaultNodeTable().createColumn(columnName, String.class, false);
+ parameterSet.net.getDefaultNodeTable().deleteColumn(columnName);
+ parameterSet.net.getDefaultNodeTable().createColumn(columnName, String.class, false);
//Fetch number of clusters in the solution
long numberOfClusters = c_result.getNumberOfClusters(i);
@@ -218,7 +215,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
CyNode node = nodeMap.indexOf(nodeID); //<<< Another int/long conversion
cluster.addNode(node);
- net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
+ parameterSet.net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
}
//Register clusters with solution for further reference
solution.addCluster(cluster);