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 87da79a3c3a696e288a56a4ae30390e1f11bf963..753d5bb3f4ce91fe61c17142c67b0d847896a861 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -22,5 +22,7 @@ public class ParameterSet {
public boolean useHeuristic;
public int solCount;
public boolean disableMultiThreading;
+ /**Describes whether auto configuration of the reduction rules is to be used. Overrides the bit mask.**/
+ public boolean suggestReduction;
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
index dfc6d39ea6efbcff99994b46f3b760d66d3610ca..51c1dafca4c2ad4ca4b6d1358563520ce860b464 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
@@ -2,10 +2,19 @@ package de.hhu.ba.yoshikoWrapper.cytoUtil;
import java.util.List;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyRow;
+import org.slf4j.Logger;
+
+import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
+
public class GraphAnalyzer {
+
+ private static Logger logger = YoshikoLogger.getInstance().getLogger();
+
public static boolean isMultiGraph(CyNetwork net) {
//TODO: Better algorithm?
@@ -47,4 +56,87 @@ public class GraphAnalyzer {
}
return false;
}
+
+ /**
+ * Generates a fitting bitmask by choosing the reduction rules that appear to be the best choice based on current research
+ * @param containsRealValues
+ * @param heuristic
+ * @return
+ */
+ public static String suggestReductionRules(boolean containsRealValues, boolean heuristic) {
+
+ //TODO: Maybe also choose SNR Factor?
+ //TODO: More research, identify good rules
+
+ boolean useCRule = false,useCCRule= false,useACRule= false,useHERule= false,usePDRRule= false,useSNRule = false;
+ String ret = "";
+
+ //First of all: We don't choose any rules when in heuristic mode
+ if (!heuristic) {
+ //We check if the graph contains real weights
+ if (!containsRealValues) {
+ useCRule = true;
+ useCCRule = true;
+ useACRule = true;
+ useHERule = true;
+ }
+ usePDRRule = true;
+ useSNRule = true;
+ }
+
+ ret += (useCRule ? "1" : "0");
+ ret += (useCCRule ? "1" : "0");
+ ret += (useACRule ? "1" : "0");
+ ret += (useHERule ? "1" : "0");
+ ret += (usePDRRule ? "1" : "0");
+ ret += (useSNRule ? "1" : "0");
+
+ //logger.info("Suggesting the following reduction-rules bitmask: "+ret);
+ System.out.println("Suggesting the following reduction-rules bitmask: "+ret);
+
+ return ret;
+ }
+
+ public static boolean containsRealValues(
+ CyNetwork net,
+ CyColumn weightColumn,
+ CyColumn permanentColumn,
+ CyColumn forbiddenColumn,
+ double defaultInsertionCost,
+ double defaultDeletionCost)
+ {
+ //Simple checks: Deletion and Insertion Costs
+ if (defaultInsertionCost % 1 != 0 || defaultDeletionCost % 1 != 0) {
+ return true;
+ }
+
+ if (net != null){
+ //Fetch edges
+ List<CyEdge> edges = net.getEdgeList();
+
+ //Loop over edges
+ for (CyEdge e : edges) {
+
+ //Fetch entry and check if it exists
+ CyRow edgeEntry = net.getRow(e);
+
+ //Check if there is a weight column defined, else skip
+ if (weightColumn != null){
+ //Check if the column contains an entry for the respective edge
+ //It is possible, that there are missing entries
+ if (edgeEntry.get(weightColumn.getName(), weightColumn.getType()) != null){
+ if (weightColumn.getType() == Double.class) {
+ double weight = edgeEntry.get(weightColumn.getName(), Double.class);
+ if (weight%1!=0) {
+ return true;
+ }
+ }
+ }
+ }
+ }
+ }
+ return false;
+ }
+
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
index b2441e51e7f980f045986c10438796b23d953dae..7394b3efaf5d4b92ba579d8d3b55722a82fffe70 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
@@ -31,7 +31,7 @@ import de.hhu.ba.yoshikoWrapper.swig.SolutionFlags;
/**Basic data class that represents a CES instance internally. By using this class the C++ resources can be freed upon retrieval.
*
*/
-public class YoshikoResult {
+public class YoshikoResult{
private CyNetwork originalGraph;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
index 2ee951a40ec47fb72e35de0dfb8d5f3263197868..ccbc108a8db5bb79d4000ba07a0280b74c6a239d 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.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
@@ -34,47 +34,47 @@ import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial") //Will never be serialized
public class EditCostPanel extends JPanel {
-
+
//SWING COMPONENTS
private final ColumnMapper columnMapper;
-
+
private final DoubleInputField icField;
private final DoubleInputField dcField;
-
+
private final JLabel icLabel;
private final JLabel dcLabel;
-
- private final HelpButton helpButton;
-
+
+ //private final HelpButton helpButton;
+
public EditCostPanel() {
//Initialize components
- helpButton = new HelpButton();
-
+ //helpButton = new HelpButton();
+
columnMapper = new ColumnMapper();
-
+
icField = new DoubleInputField(Double.NEGATIVE_INFINITY,0);
dcField = new DoubleInputField(0,Double.POSITIVE_INFINITY);
-
+
icField.setText("-1.0");
icField.setToolTipText(LocalizationManager.get("icTooltip"));
dcField.setText("1.0");
-
+
icLabel = new JLabel(LocalizationManager.get("defaultInsertion"));
dcLabel = new JLabel(LocalizationManager.get("defaultDeletion"));
//Add components
SwingUtil.addAll(this,icLabel,icField);
SwingUtil.addAll(this,dcLabel,dcField);
- SwingUtil.addAll(helpButton);
+ //SwingUtil.addAll(helpButton);
SwingUtil.addAll(this,columnMapper);
-
+
//Layout
GroupLayout layout = new GroupLayout(this);
-
+
layout.setHorizontalGroup(layout.createParallelGroup()
- .addComponent(helpButton,Alignment.TRAILING)
+ //.addComponent(helpButton,Alignment.TRAILING)
.addComponent(columnMapper)
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(Alignment.LEADING)
@@ -88,9 +88,9 @@ public class EditCostPanel extends JPanel {
)
)
);
-
+
layout.setVerticalGroup(layout.createSequentialGroup()
- .addComponent(helpButton)
+ //.addComponent(helpButton)
.addComponent(columnMapper)
.addGroup(layout.createParallelGroup(Alignment.BASELINE)
.addComponent(icLabel)
@@ -103,20 +103,20 @@ public class EditCostPanel extends JPanel {
.addComponent(dcField)
)
);
-
+
this.setLayout(layout);
-
+
}
//SETTER / GETTER
public CyColumn getWeightColumn() {
return columnMapper.getEditingCostColumn();
}
-
+
public CyColumn getPermanentColumn() {
return columnMapper.getPermanentColumn();
}
-
+
public CyColumn getForbiddenColumn() {
return columnMapper.getForbiddenColumn();
}
@@ -124,7 +124,7 @@ public class EditCostPanel extends JPanel {
public double getDefaultInsertionCost() {
return icField.getValueAsDouble();
}
-
+
public double getDefaultDeletionCost() {
return dcField.getValueAsDouble();
}
@@ -132,5 +132,5 @@ public class EditCostPanel extends JPanel {
public ColumnMapper getColumnMapper() {
return columnMapper;
}
-
+
}
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 5c521c5319b22c3e908887d83e34784ede30649f..c14921df077395293038e273d2af5b8d6227c611 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
@@ -58,7 +58,9 @@ import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.CommandExecutor;
import de.hhu.ba.yoshikoWrapper.cytoUtil.GraphAnalyzer;
+import de.hhu.ba.yoshikoWrapper.help.HelpLinks;
import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.swing.LibraryPanelFactory;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@@ -117,7 +119,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
@Override
public void actionPerformed(ActionEvent e) {
- //CommandExecutorTaskFactory fac;
+ CommandExecutor.executeCommand("cybrowser", "show",HelpLinks.mainInfo , null);
}
});
@@ -312,7 +314,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
AbstractTask yoshiko = new AlgorithmTask(
popupLevel,
networkToBeProcessed,
- fetchParameter()
+ fetchParameters(networkToBeProcessed)
);
/**
* Don't queue multiple runs at once because that will get messy
@@ -340,7 +342,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
* Fetches all the parameters from the various swing components and packs them into a neat abstract wrapper class
* @return The currently selected parameter wrapped in a ParameterSet
*/
- private ParameterSet fetchParameter() {
+ private ParameterSet fetchParameters(CyNetwork net) {
ParameterSet ret = new ParameterSet();
ret.timeLimit = opModePanel.getTimeLimit();
ret.weightColumn = ecPanel.getWeightColumn();
@@ -348,11 +350,12 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
ret.forbiddenColumn = ecPanel.getForbiddenColumn();
ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
+ ret.useHeuristic = opModePanel.useHeuristic();
ret.reductionRulesBitMask = reductionRulesChooser.getBitMask();
+ ret.suggestReduction = reductionRulesChooser.useAutoConfig();
ret.snrMultFactor = reductionRulesChooser.getMultFactor();
ret.useTriangleCuts = opModePanel.useTriangleCuts();
ret.usePartitionCuts = opModePanel.usePartitionCuts();
- ret.useHeuristic = opModePanel.useHeuristic();
ret.solCount = opModePanel.getSolCount();
ret.disableMultiThreading = opModePanel.isMultiThreadingDisabled();
return ret;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ReductionRulesChooser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ReductionRulesChooser.java
index cd7a02a091363e6f65a7623bde842944442905b3..4697947ac309f1a3eccfd26eba99622f933c1786 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ReductionRulesChooser.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ReductionRulesChooser.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
@@ -25,12 +25,16 @@ import static javax.swing.GroupLayout.DEFAULT_SIZE;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
import javax.swing.BoxLayout;
import javax.swing.GroupLayout;
import javax.swing.JCheckBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
+import javax.swing.JSeparator;
+import javax.swing.SwingConstants;
import javax.swing.GroupLayout.Alignment;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -39,40 +43,54 @@ import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial")
public class ReductionRulesChooser extends JPanel{
+ private final JCheckBox useAutoConfig;
+
+ private final JSeparator separator;
+
private final JCheckBox useCRule;
private final JCheckBox useCCRule;
private final JCheckBox useACRule;
private final JCheckBox useHERule;
private final JCheckBox usePDRRule;
private final JCheckBox useSNRule;
-
+
private final DoubleInputField multFactor;
-
+
private final JPanel SNPanel;
-
+
public ReductionRulesChooser() {
//Initialize subcomponents
+ useAutoConfig = new JCheckBox(LocalizationManager.get("autoConfig"));
+ useAutoConfig.addItemListener(new ItemListener() {
+
+ @Override
+ public void itemStateChanged(ItemEvent e) {
+ enableRuleSelection(e.getStateChange()== ItemEvent.DESELECTED ? true : false);
+ }
+
+ });
+ separator = new JSeparator(SwingConstants.HORIZONTAL);
+ //TODO: Localization
useCRule = new JCheckBox("Use Clique Rule");
useCCRule = new JCheckBox("Use Critical-Clique Rule");
useACRule = new JCheckBox("Use Almost-Clique Rule");
useHERule = new JCheckBox("Use Heavy-Edge 3 in 1 Rule");
usePDRRule = new JCheckBox("Use Parameter Dependent Reduction Rule");
useSNRule = new JCheckBox("Use Similar Neighborhood Rule");
+
multFactor = new DoubleInputField(1, Double.POSITIVE_INFINITY);
multFactor.setText("1.0");
+
SNPanel = new JPanel();
SNPanel.setLayout(new BoxLayout(SNPanel,BoxLayout.X_AXIS));
+
SwingUtil.addAll(SNPanel,new JLabel(LocalizationManager.get("multFactor")),multFactor);
-
- useSNRule.setSelected(true);
- useCRule.setSelected(true);
- useCCRule.setSelected(true);
- useACRule.setSelected(true);
- useHERule.setSelected(true);
- usePDRRule.setSelected(true);
-
+
+ enableRuleSelection(false);
+ useAutoConfig.setSelected(true);
+
useSNRule.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
@@ -84,9 +102,11 @@ public class ReductionRulesChooser extends JPanel{
}
}
});
-
-
+
+
SwingUtil.addAll(this,
+ useAutoConfig,
+ separator,
useCRule,
useCCRule,
useACRule,
@@ -95,23 +115,27 @@ public class ReductionRulesChooser extends JPanel{
useSNRule,
SNPanel
);
-
+
//Layout
GroupLayout layout = new GroupLayout(this);
-
+
layout.setAutoCreateGaps(true);
-
+
layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
+ .addComponent(useAutoConfig, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+ .addComponent(separator, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
- .addComponent(useCCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+ .addComponent(useCCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useACRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useHERule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(usePDRRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useSNRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
- .addComponent(SNPanel, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+ .addComponent(SNPanel, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
);
-
+
layout.setVerticalGroup(layout.createSequentialGroup()
+ .addComponent(useAutoConfig, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+ .addComponent(separator, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useCCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useACRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
@@ -120,12 +144,23 @@ public class ReductionRulesChooser extends JPanel{
.addComponent(useSNRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(SNPanel, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
);
-
+
this.setLayout(layout);
-
+
}
-
-
+
+
+ protected void enableRuleSelection(boolean enable) {
+ useCRule.setEnabled(enable);
+ useCCRule.setEnabled(enable);
+ useACRule.setEnabled(enable);
+ useHERule.setEnabled(enable);
+ usePDRRule.setEnabled(enable);
+ useSNRule.setEnabled(enable);
+ multFactor.setEnabled(enable);
+ }
+
+
/** Creates a 6 Bit bitmask representing the currently selected choice of reduction rules.
* @return
*/
@@ -139,7 +174,11 @@ public class ReductionRulesChooser extends JPanel{
ret += (useSNRule.isSelected() ? "1" : "0");
return ret;
}
-
+
+ public boolean useAutoConfig() {
+ return useAutoConfig.isSelected();
+ }
+
public double getMultFactor() {
if (useSNRule.isSelected()) {
return multFactor.getValueAsDouble();
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 e698fb2f39404732fca7dbb7666d61d02ed7d342..e8e92cf4f5d83908ccd7058653a685c152cc8af6 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
@@ -51,7 +51,7 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
-import de.hhu.ba.yoshikoWrapper.tasks.CreateClusterViews;
+import de.hhu.ba.yoshikoWrapper.tasks.CreateClusterViewsTask;
import de.hhu.ba.yoshikoWrapper.tasks.CreateMetaGraphTask;
/**
* Swing Component, that represents one solution of a Yoshiko result and displays it
@@ -149,7 +149,7 @@ public class SolutionTab extends JPanel {
}
CyCore.dialogTaskManager.execute(
new TaskIterator(1,
- new CreateClusterViews(
+ new CreateClusterViewsTask(
selectedClusters
)
)
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 f340ed6b14ed06c4ab631c7362c01711e94894f2..6dcc7d1f1988b7b7e0ec80ccf57d0cd5faddac34 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
@@ -3,7 +3,9 @@ package de.hhu.ba.yoshikoWrapper.taskFactories;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
+import de.hhu.ba.yoshikoWrapper.tasks.CreateClusterViewsTask;
public class CommandTaskFactory implements TaskFactory{
@@ -21,7 +23,11 @@ public class CommandTaskFactory implements TaskFactory{
public TaskIterator createTaskIterator() {
//We simply switch between the possible commands
if (command == YoshikoCommand.CREATE_CLUSTER_VIEW) {
- return null;
+ return new TaskIterator(
+ new CreateClusterViewsTask(
+ null
+ )
+ );
}
else if (command == YoshikoCommand.CREATE_META_GRAPH) {
return null;
@@ -31,7 +37,7 @@ public class CommandTaskFactory implements TaskFactory{
new AlgorithmTask(
null,
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 c7e2a583e758d986056a7c5d3a28066cf79e15d8..0535700545e8dd0835df9fc31449ddbb00bd38bf 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -32,6 +32,7 @@ import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.ContainsTunables;
+import org.cytoscape.work.ObservableTask;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
import org.slf4j.Logger;
@@ -41,6 +42,7 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.NetworkParser;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import de.hhu.ba.yoshikoWrapper.core.StatusInformer;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.GraphAnalyzer;
import de.hhu.ba.yoshikoWrapper.cytoUtil.NodeMap;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
@@ -54,7 +56,7 @@ import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
-public class AlgorithmTask extends AbstractTask {
+public class AlgorithmTask extends AbstractTask implements ObservableTask {
//Constants
private static final String SOLUTION_COLUMN_PREFIX = "yoshikoSolution_"; //TODO: Make customizable?
@@ -77,12 +79,15 @@ public class AlgorithmTask extends AbstractTask {
public CyNetwork net;
//Temps, pointing to and need to be freed in C++
- private LibraryInput input;
- private ClusterEditingSolutions result;
- private CoreAlgorithm ca;
+ private LibraryInput c_input;
+ private ClusterEditingSolutions c_result;
+ private CoreAlgorithm c_algorithm;
private ResultPanel resultPanel;
+ private YoshikoResult result;
+
+
/**
* Default constructor, creates a new AlgorithmTask
* @param statusWindow The Window in which the status-bar is to be shown, can be null
@@ -111,7 +116,7 @@ public class AlgorithmTask extends AbstractTask {
//Get current network
if (net == null) {
logger.warn("CoreAlgorithm called on a net that is NULL!");
- throw new Exception("CoreAlgorithm called on a net that is NULL!");
+ throw new Exception("CoreAlgorithm called on a net that is NULL!"); //TODO: Localize
}
//Set time limit
@@ -127,8 +132,8 @@ public class AlgorithmTask extends AbstractTask {
NodeMap nodeMap = new NodeMap(net);
taskMonitor.setProgress(0.1);
- //Generate an input instance from the network
- input = NetworkParser.parseNetwork(
+ //Generate an c_input instance from the network
+ c_input = NetworkParser.parseNetwork(
net,
nodeMap,
parameterSet.weightColumn,
@@ -138,11 +143,24 @@ public class AlgorithmTask extends AbstractTask {
);
taskMonitor.setProgress(0.2);
+ boolean containsRealValues = GraphAnalyzer.containsRealValues(
+ net,
+ parameterSet.weightColumn,
+ parameterSet.permanentColumn,
+ parameterSet.forbiddenColumn,
+ parameterSet.defaultInsertionCost,
+ parameterSet.defaultDeletionCost);
+
+ //Suggest reduction rules
+ if (parameterSet.suggestReduction) {
+ parameterSet.reductionRulesBitMask = GraphAnalyzer.suggestReductionRules(containsRealValues, parameterSet.useHeuristic);
+ }
+
//Set the default value for insertion cost
- input.setDefaultInsertionCost(parameterSet.defaultInsertionCost);
+ c_input.setDefaultInsertionCost(parameterSet.defaultInsertionCost);
//Call Yoshiko <<< Algorithm is performed here
- ca = LibraryInterface.getRun(input,
+ c_algorithm = LibraryInterface.getRun(c_input,
parameterSet.solCount,
parameterSet.reductionRulesBitMask,
parameterSet.snrMultFactor,
@@ -152,26 +170,26 @@ public class AlgorithmTask extends AbstractTask {
);
- ca.registerCplexInformer(new StatusInformer(statusWindow,taskMonitor));
+ c_algorithm.registerCplexInformer(new StatusInformer(statusWindow,taskMonitor));
- result = ca.run();
+ c_result = c_algorithm.run();
taskMonitor.setProgress(0.9);
- checkForInvalidSolutions(result);
+ checkForInvalidSolutions(c_result);
- long numberOfSolutions = result.getNumberOfSolutions();
+ long numberOfSolutions = c_result.getNumberOfSolutions();
taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO: Localize
- YoshikoResult yoshikoResult = new YoshikoResult(net,result.getFlags());
+ result = new YoshikoResult(net,c_result.getFlags());
//Loop over (multiple) solutions
for (long i=0;i<numberOfSolutions;i++) {
taskMonitor.setStatusMessage("Processing solution "+(i+1)+" of "+numberOfSolutions);
- YoshikoSolution solution = new YoshikoSolution(yoshikoResult,i);
+ YoshikoSolution solution = new YoshikoSolution(result,i);
String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
@@ -179,7 +197,7 @@ public class AlgorithmTask extends AbstractTask {
net.getDefaultNodeTable().createColumn(columnName, String.class, false);
//Fetch number of clusters in the solution
- long numberOfClusters = result.getNumberOfClusters(i);
+ long numberOfClusters = c_result.getNumberOfClusters(i);
//Loop over clusters
for (long k=0;k<numberOfClusters;k++) {
@@ -189,7 +207,7 @@ public class AlgorithmTask extends AbstractTask {
taskMonitor.setStatusMessage("Processing clusters "+(k+1)+" of "+numberOfClusters);
- IntVector clusterVector = result.getCluster(i, k);
+ IntVector clusterVector = c_result.getCluster(i, k);
long sizeOfCluster = clusterVector.size();
for (int l=0;l<sizeOfCluster;l++) { //Unsafe mismatch int long
@@ -205,18 +223,18 @@ public class AlgorithmTask extends AbstractTask {
}
//Sort clusters by size, descending as the biggest clusters are usually the most relevant
solution.clusters.sort(YoshikoCluster.lessThanComparator);
- //Register solution with result for further reference
- yoshikoResult.addSolution(solution);
+ //Register solution with c_result for further reference
+ result.addSolution(solution);
}
taskMonitor.setProgress(0.99);
//At this point the C++ objects can be freed, in case that the algorithm terminates beforehand they need to be cleaned-up elsewhere
- ca.delete();
- input.delete();
- result.delete();
+ c_algorithm.delete();
+ c_input.delete();
+ c_result.delete();
//Generate solutionsPanel
- resultPanel = new ResultPanel(yoshikoResult);
+ resultPanel = new ResultPanel(result);
//Show solution panel
CyCore.registrar.registerService(resultPanel,CytoPanelComponent.class, new Properties());
@@ -231,16 +249,16 @@ public class AlgorithmTask extends AbstractTask {
private void checkForInvalidSolutions(ClusterEditingSolutions result) throws Exception {
if (result == null) {
- //There was no result object generated at all
+ //There was no c_result object generated at all
throw new Exception(LocalizationManager.get("noFeasible"));
}
if (result.getNumberOfSolutions() == 0) {
- //The result object is empty
+ //The c_result object is empty
throw new Exception(LocalizationManager.get("noFeasible"));
}
if (result.getNumberOfSolutions() == 1) {
- //The result doesn't contain any clusters
+ //The c_result doesn't contain any clusters
if (result.getNumberOfClusters(0) == 0) {
throw new Exception(LocalizationManager.get("noFeasible"));
}
@@ -251,21 +269,30 @@ public class AlgorithmTask extends AbstractTask {
@Override
public void cancel() {
//Free C++ resources
- if (ca != null) {
+ if (c_algorithm != null) {
System.out.println("Deleting CoreAlgorithm instance!");
- ca.cancel();
- ca.delete();
+ c_algorithm.cancel();
+ c_algorithm.delete();
}
- if (input != null) {
- input.delete();
+ if (c_input != null) {
+ c_input.delete();
}
- if (result != null) {
- result.delete();
+ if (c_result != null) {
+ c_result.delete();
}
- //Delete (incomplete) result panel
+ //Delete (incomplete) c_result panel
if (resultPanel != null) {
resultPanel.deleteSolution();
}
super.cancel();
}
+
+ @Override
+ public <R> R getResults(Class<? extends R> type) {
+ //TODO:
+ if (type.equals(YoshikoResult.class)) {
+ return (R) (result!=null ? result : null);
+ }
+ return null;
+ }
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
similarity index 92%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
index a5674a7ab6dff36f5f5e70afee44af3280afb41a..72d6270300e9c7cb0f846599e7681cd24cc4245c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
@@ -17,10 +17,10 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
-public class CreateClusterViews implements Task {
+public class CreateClusterViewsTask implements Task {
@Tunable
- public ArrayList<YoshikoCluster> clusters;
+ public ArrayList<YoshikoCluster> clusters; //TODO: Make Tunable, reference by ID?
private boolean isTerminated;
@@ -35,7 +35,7 @@ public class CreateClusterViews implements Task {
*/
private ArrayList<CySubNetwork> initializedSubNetworks;
- public CreateClusterViews(ArrayList<YoshikoCluster> clusters) {
+ public CreateClusterViewsTask(ArrayList<YoshikoCluster> clusters) {
this.clusters = clusters;
this.previousView = CyCore.cy.getCurrentNetworkView();
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index 69c2d91bf4b04128faea4709f51fafbe40b7c513..b20a177a70f2a91e877d6071906459d786118ec7 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -26,6 +26,8 @@
about = Yoshiko Cytoscape App
aboutButton = About Yoshiko
aboutTitle = Yoshiko Plugin Info
+autoConfig = Choose reduction rules automatically
+
clusters = Cluster
clusterFound = Clusters found:
clusterSize = Cluster Size: