diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index cb54e9179257c3e961a92fb7a51d6d50a27b2a7e..dbf57cc9c3fbca33b63de4bdcad3f8b655cbafa3 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -55,8 +55,8 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.NetChangeListener;
import de.hhu.ba.yoshikoWrapper.core.YoshUtil;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
-import de.hhu.ba.yoshikoWrapper.gui.HintManager;
-import de.hhu.ba.yoshikoWrapper.gui.MainPanel;
+import de.hhu.ba.yoshikoWrapper.swing.HintManager;
+import de.hhu.ba.yoshikoWrapper.swing.components.MainPanel;
/**
* Entry point for the application as required by the Cytoscape API
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
index 58ec22117215531a4dc0af61245007d8fe470329..dbdfd41503c6efacdc3be5c018aae111fa73814a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.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
@@ -24,8 +24,6 @@ package de.hhu.ba.yoshikoWrapper.core;
import java.awt.Window;
import java.util.Properties;
-import javax.swing.JOptionPane;
-
import org.cytoscape.application.swing.CytoPanel;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
@@ -39,19 +37,18 @@ import org.slf4j.Logger;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
-import de.hhu.ba.yoshikoWrapper.gui.ResultPanel;
import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
import de.hhu.ba.yoshikoWrapper.swig.ClusterEditingSolutions;
import de.hhu.ba.yoshikoWrapper.swig.CoreAlgorithm;
-import de.hhu.ba.yoshikoWrapper.swig.CplexInformer;
import de.hhu.ba.yoshikoWrapper.swig.IntVector;
import de.hhu.ba.yoshikoWrapper.swig.LibraryInput;
import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
+import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
public class AlgorithmTask extends AbstractTask {
-
-
+
+
//Symbolic links
private static Logger logger = YoshikoLogger.getInstance().getLogger();
private Window statusWindow;
@@ -59,19 +56,19 @@ public class AlgorithmTask extends AbstractTask {
//Parameters
private final ParameterSet parameterSet;
private final CyNetwork net;
-
+
//Temps, need to be freed in C++
private LibraryInput input;
private ClusterEditingSolutions result;
private CoreAlgorithm ca;
-
- private ResultPanel resultPanel;
+
+ private ResultPanel resultPanel;
public AlgorithmTask(// <<< Too many variables here, some should be grouped later TODO:
Window statusWindow,
CyNetwork net,
ParameterSet parameterSet
- )
+ )
{
this.statusWindow = statusWindow;
this.net = net;
@@ -84,13 +81,13 @@ public class AlgorithmTask extends AbstractTask {
taskMonitor.setTitle(LocalizationManager.get("yoshTask"));
taskMonitor.setProgress(0.0);
-
+
//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!");
}
-
+
//Set time limit
LibraryInterface.setTimeLimit(parameterSet.timeLimit);
if (parameterSet.disableMultiThreading) {
@@ -109,7 +106,7 @@ public class AlgorithmTask extends AbstractTask {
net,
nodeMap,
parameterSet.weightColumn,
- parameterSet.permanentColumn,
+ parameterSet.permanentColumn,
parameterSet.forbiddenColumn,
parameterSet.defaultDeletionCost
);
@@ -117,93 +114,66 @@ public class AlgorithmTask extends AbstractTask {
//Set the default value for insertion cost
input.setDefaultInsertionCost(parameterSet.defaultInsertionCost);
-
+
//Call Yoshiko <<< Algorithm is performed here
- ca = LibraryInterface.getRun(input,
+ ca = LibraryInterface.getRun(input,
parameterSet.solCount,
parameterSet.reductionRulesBitMask,
- parameterSet.snrMultFactor,
+ parameterSet.snrMultFactor,
parameterSet.usePartitionCuts,
parameterSet.useTriangleCuts,
parameterSet.useHeuristic
);
- class CallbackHandler extends CplexInformer{
-
- @Override
- public boolean continueOnTimeout() {
- try {
- int result = JOptionPane.showConfirmDialog(
- statusWindow,
- LocalizationManager.get("continueTimeout"),
- LocalizationManager.get("timeoutTitle"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.INFORMATION_MESSAGE
- );
- if (result == JOptionPane.YES_OPTION) {
- return true;
- }
- return false;
- }
- catch(Exception e) {
- e.printStackTrace();
- return false;
- }
- }
-
- @Override
- public void updateGap(double gap) {
- taskMonitor.setStatusMessage(LocalizationManager.get("currentGap")+": "+YoshUtil.twoDecimals.format(gap)+"%");
- }
- }
-
- ca.registerCplexInformer(new CallbackHandler());
-
+
+
+ ca.registerCplexInformer(new StatusInformer(statusWindow,taskMonitor));
+
result = ca.run();
-
+
taskMonitor.setProgress(0.9);
-
+
checkForInvalidSolutions(result);
long numberOfSolutions = result.getNumberOfSolutions();
-
+
taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO localize
-
+
YoshikoResult yoshikoResult = new YoshikoResult();
yoshikoResult.flags = result.getFlags();
-
+
System.out.print("ILP FLAG: "+yoshikoResult.flags.getIlpGenerated());
-
+
//Loop over (multiple) solutions
for (long i=0;i<numberOfSolutions;i++) {
-
+
taskMonitor.setStatusMessage("Processing solution "+(i+1)+" of "+numberOfSolutions);
YoshikoSolution solution = new YoshikoSolution(net);
String columnName = "YOSHIKO_SOLUTION_"+(i+1);
-
+
net.getDefaultNodeTable().deleteColumn(columnName);
net.getDefaultNodeTable().createColumn(columnName, String.class, false);
-
+
//Fetch number of clusters in the solution
long numberOfClusters = result.getNumberOfClusters(i);
-
+
//Loop over cluster
for (long k=0;k<numberOfClusters;k++) {
//Create java instance
YoshikoCluster cluster = new YoshikoCluster(k,net);
-
+
taskMonitor.setStatusMessage("Processing cluster "+(k+1)+" of "+numberOfClusters);
-
+
IntVector clusterVector = result.getCluster(i, k);
-
+
long sizeOfCluster = clusterVector.size();
for (int l=0;l<sizeOfCluster;l++) { //Unsafe mismatch int long
taskMonitor.setStatusMessage("Processing entry "+(l+1)+ " of "+sizeOfCluster);
int nodeID = clusterVector.get(l);
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?)
}
cluster.getSubNetwork();
@@ -217,7 +187,7 @@ public class AlgorithmTask extends AbstractTask {
ca.delete();
input.delete();
result.delete();
-
+
//Generate solutionsPanel
resultPanel = new ResultPanel(yoshikoResult);
@@ -230,13 +200,13 @@ public class AlgorithmTask extends AbstractTask {
eastPanel.setState(CytoPanelState.DOCK);
}
-
+
private void checkForInvalidSolutions(ClusterEditingSolutions result) throws Exception {
if (result == null) {
//There was no result object generated at all
throw new Exception(LocalizationManager.get("noFeasible"));
}
-
+
if (result.getNumberOfSolutions() == 0) {
//The result object is empty
throw new Exception(LocalizationManager.get("noFeasible"));
@@ -247,7 +217,7 @@ public class AlgorithmTask extends AbstractTask {
throw new Exception(LocalizationManager.get("noFeasible"));
}
}
-
+
}
@Override
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetChangeListener.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetChangeListener.java
index 1ada0eafb38400c7b783570d991156c6255d6cee..8ab86ea60035262519110fac6637573507c70f54 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetChangeListener.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetChangeListener.java
@@ -34,7 +34,7 @@ import org.cytoscape.model.events.RemovedEdgesListener;
import org.cytoscape.session.events.SessionLoadedEvent;
import org.cytoscape.session.events.SessionLoadedListener;
-import de.hhu.ba.yoshikoWrapper.gui.ColumnMapper;
+import de.hhu.ba.yoshikoWrapper.swing.components.ColumnMapper;
public class NetChangeListener
implements //everything
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/StatusInformer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/StatusInformer.java
new file mode 100644
index 0000000000000000000000000000000000000000..b4b054e358cc517fe1f6312b96ebffce60fb0992
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/StatusInformer.java
@@ -0,0 +1,78 @@
+package de.hhu.ba.yoshikoWrapper.core;
+
+import java.awt.Window;
+
+import javax.swing.JOptionPane;
+
+import org.cytoscape.work.TaskMonitor;
+
+import de.hhu.ba.yoshikoWrapper.swig.CplexInformer;
+import de.hhu.ba.yoshikoWrapper.swig.YoshikoState;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+
+public class StatusInformer extends CplexInformer {
+
+ private final Window statusWindow;
+ private final TaskMonitor taskMonitor;
+
+ public StatusInformer(Window statusWindow, TaskMonitor taskMonitor) {
+ this.statusWindow = statusWindow;
+ this.taskMonitor = taskMonitor;
+ };
+
+ @Override
+ public boolean continueOnTimeout() {
+ try {
+ int result = JOptionPane.showConfirmDialog(
+ statusWindow,
+ LocalizationManager.get("continueTimeout"),
+ LocalizationManager.get("timeoutTitle"),
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.INFORMATION_MESSAGE
+ );
+ if (result == JOptionPane.YES_OPTION) {
+ return true;
+ }
+ return false;
+ }
+ catch(Exception e) {
+ e.printStackTrace();
+ return false;
+ }
+ }
+
+ @Override
+ public void updateStatus(YoshikoState state, double value) {
+ if (state == YoshikoState.SOLVING_ILP){
+ taskMonitor.setStatusMessage(LocalizationManager.get("currentGap")+": "+SwingUtil.twoDecimals.format(value)+"%");
+ }
+ }
+
+ @Override
+ public void updateStatus(YoshikoState state) {
+ //TODO: Might improve performance via HashMap but probably irrelevant
+ if (state == YoshikoState.REDUCTION_AC) {
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_reductionAC"));
+ }
+ else if (state == YoshikoState.REDUCTION_CC) {
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_reductionCC"));
+ }
+ else if (state == YoshikoState.REDUCTION_CR) {
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_reductionCR"));
+ }
+ else if (state == YoshikoState.REDUCTION_HE) {
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_reductionHE"));
+ }
+ else if (state == YoshikoState.REDUCTION_MR) {
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_reductionMR"));
+ }
+ else if (state == YoshikoState.REDUCTION_PD) {
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_reductionPD"));
+ }
+ else if (state == YoshikoState.REDUCTION_SN) {
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_reductionSN"));
+ }
+ }
+
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java
index 9f195d07159f260d2c62a63f9b88e53264d3434a..1dee005777ccb195f646d7880b0288cc1930c15f 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java
@@ -1,10 +1,7 @@
package de.hhu.ba.yoshikoWrapper.core;
-import java.text.DecimalFormat;
-
import org.osgi.framework.Version;
public class YoshUtil {
- final static DecimalFormat twoDecimals =new DecimalFormat("0.00");
public static Version version;
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java
index 509926c0f20fbd0d0220cb05d6ab8a186d5d235d..b5eccc11a43f51ec3f43564f8703caa8f044c3eb 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java
@@ -22,19 +22,18 @@ public class StyleManager {
public static final double MAX_NODE_SIZE = 30.0;
- private static void apply (CyNetworkView view, VisualStyle style) {
+
+ public static void style(CyNetworkView view, VisualStyle style) {
CyCore.visualMappingManager.setVisualStyle(style,view);
style.apply(view);
view.updateView();
}
- public static void style(CyNetworkView view, VisualStyle style) {
- apply(view,style);
- }
-
public static void styleWithMapping(CyNetworkView view, VisualStyle style) {
style = CyCore.visualStyleFactory.createVisualStyle(style);
+ CyCore.visualMappingManager.setVisualStyle(style,view);
+
//Define style for solution
ContinuousMapping<Integer, Double> contMapNodes = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
@@ -81,7 +80,9 @@ public class StyleManager {
style.addVisualMappingFunction(contMapNodes);
style.addVisualMappingFunction(contMapEdges);
- apply(view,style);
+
+ style.apply(view);
+ view.updateView();
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
index 69e330a354e85c43267d23ef07d955f1a9e440d0..63e208af500eddd9c62d90a8dd1d64f18821276c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
@@ -138,12 +138,12 @@ public class YoshikoCluster {
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setStatusMessage("Generating cluster view for C:"+id);
- StyleManager.style(view, CyCore.visualMappingManager.getCurrentVisualStyle());
view.setVisualProperty(NETWORK_WIDTH, new Double(width));
view.setVisualProperty(NETWORK_HEIGHT, new Double(height));
view.fitContent();
- view.updateView();
+
+ StyleManager.style(view, CyCore.visualMappingManager.getCurrentVisualStyle());
RenderingEngine<CyNetwork> renderingEngine = CyCore.renderingEngineFactory.createRenderingEngine(label, view);
SwingUtilities.invokeLater(new Runnable() {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
index 62081dbf1a57029e9c4d4e30ccef5f0872bb0a77..bd705af8c5f56118a560ff77295127622dcaea19 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -32,6 +32,9 @@ import org.cytoscape.model.CyEdge.Type;
import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskMonitor;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -83,7 +86,6 @@ public class YoshikoSolution {
CyCore.networkManager.addNetwork(subnet);
//Create network view and register it
CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
- CyCore.networkViewManager.addNetworkView(subnetView);
//layout cluster
CyCore.dialogTaskManager.execute(
layout.createTaskIterator(
@@ -96,6 +98,8 @@ public class YoshikoSolution {
StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
+ CyCore.networkViewManager.addNetworkView(subnetView);
+
clusterNode.setNetworkPointer(subnet);
//Set node attributes
metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
@@ -132,24 +136,38 @@ public class YoshikoSolution {
}
CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
- //layout solution
- CyCore.dialogTaskManager.execute(
- layout.createTaskIterator(
- view,
- layout.getDefaultLayoutContext(),
- CyLayoutAlgorithm.ALL_NODE_VIEWS,
- null
- )
+
+ //Layout and style solution
+
+ TaskIterator it = layout.createTaskIterator(
+ view,
+ layout.getDefaultLayoutContext(),
+ CyLayoutAlgorithm.ALL_NODE_VIEWS,
+ null
);
+ it.append(new Task() {
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ StyleManager.styleWithMapping(view, CyCore.visualMappingManager.getCurrentVisualStyle());
+ }
+
+ @Override
+ public void cancel() {}
+
+ });
+
+ CyCore.dialogTaskManager.execute(
+ it
+ );
CyCore.networkManager.addNetwork(metaGraph);
CyCore.networkViewManager.addNetworkView(
view
);
- StyleManager.styleWithMapping(view, CyCore.visualMappingManager.getCurrentVisualStyle());
+ view.updateView();
CyCore.cy.setCurrentNetworkView(view);
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java b/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
index cd73d0adafae758eebe24039851dca1ce490ac80..7ffd96f118b38a343fc4eb8a365160e48793dd8b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
@@ -4,7 +4,7 @@ import java.net.URI;
import java.net.URISyntaxException;
import java.util.HashMap;
-import de.hhu.ba.yoshikoWrapper.gui.EditCostPanel;
+import de.hhu.ba.yoshikoWrapper.swing.components.EditCostPanel;
public final class HelpLinks {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CplexInformer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CplexInformer.java
index 818781d0e92f90f75eefff93b8db6c92e6915dbd..f9feb9b44ea8207324f4271c2e5d22141709b1e0 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CplexInformer.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CplexInformer.java
@@ -50,8 +50,12 @@ public class CplexInformer {
LibraryInterfaceJNI.CplexInformer_change_ownership(this, swigCPtr, true);
}
- public void updateGap(double gap) {
- if (getClass() == CplexInformer.class) LibraryInterfaceJNI.CplexInformer_updateGap(swigCPtr, this, gap); else LibraryInterfaceJNI.CplexInformer_updateGapSwigExplicitCplexInformer(swigCPtr, this, gap);
+ public void updateStatus(YoshikoState state) {
+ if (getClass() == CplexInformer.class) LibraryInterfaceJNI.CplexInformer_updateStatus__SWIG_0(swigCPtr, this, state.swigValue()); else LibraryInterfaceJNI.CplexInformer_updateStatusSwigExplicitCplexInformer__SWIG_0(swigCPtr, this, state.swigValue());
+ }
+
+ public void updateStatus(YoshikoState state, double value) {
+ if (getClass() == CplexInformer.class) LibraryInterfaceJNI.CplexInformer_updateStatus__SWIG_1(swigCPtr, this, state.swigValue(), value); else LibraryInterfaceJNI.CplexInformer_updateStatusSwigExplicitCplexInformer__SWIG_1(swigCPtr, this, state.swigValue(), value);
}
public boolean continueOnTimeout() {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
index 7048875c1a01367e1e6bcb58af2f9aa8599c18ed..d8ca6b3480f17f78f152ba932a33280599946bb2 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
@@ -57,8 +57,10 @@ public class LibraryInterfaceJNI {
public final static native void LibraryInput_addEdge__SWIG_1(long jarg1, LibraryInput jarg1_, long jarg2, long jarg3, double jarg4, boolean jarg5, boolean jarg6);
public final static native void LibraryInput_setSize(long jarg1, LibraryInput jarg1_, long jarg2);
public final static native void LibraryInput_setDefaultInsertionCost(long jarg1, LibraryInput jarg1_, double jarg2);
- public final static native void CplexInformer_updateGap(long jarg1, CplexInformer jarg1_, double jarg2);
- public final static native void CplexInformer_updateGapSwigExplicitCplexInformer(long jarg1, CplexInformer jarg1_, double jarg2);
+ public final static native void CplexInformer_updateStatus__SWIG_0(long jarg1, CplexInformer jarg1_, int jarg2);
+ public final static native void CplexInformer_updateStatusSwigExplicitCplexInformer__SWIG_0(long jarg1, CplexInformer jarg1_, int jarg2);
+ public final static native void CplexInformer_updateStatus__SWIG_1(long jarg1, CplexInformer jarg1_, int jarg2, double jarg3);
+ public final static native void CplexInformer_updateStatusSwigExplicitCplexInformer__SWIG_1(long jarg1, CplexInformer jarg1_, int jarg2, double jarg3);
public final static native boolean CplexInformer_continueOnTimeout(long jarg1, CplexInformer jarg1_);
public final static native boolean CplexInformer_continueOnTimeoutSwigExplicitCplexInformer(long jarg1, CplexInformer jarg1_);
public final static native void delete_CplexInformer(long jarg1);
@@ -75,8 +77,11 @@ public class LibraryInterfaceJNI {
public final static native void setVerbosity(int jarg1);
public final static native long getRun(long jarg1, LibraryInput jarg1_, int jarg2, String jarg3, double jarg4, boolean jarg5, boolean jarg6, boolean jarg7);
- public static void SwigDirector_CplexInformer_updateGap(CplexInformer jself, double gap) {
- jself.updateGap(gap);
+ public static void SwigDirector_CplexInformer_updateStatus__SWIG_0(CplexInformer jself, int state) {
+ jself.updateStatus(YoshikoState.swigToEnum(state));
+ }
+ public static void SwigDirector_CplexInformer_updateStatus__SWIG_1(CplexInformer jself, int state, double value) {
+ jself.updateStatus(YoshikoState.swigToEnum(state), value);
}
public static boolean SwigDirector_CplexInformer_continueOnTimeout(CplexInformer jself) {
return jself.continueOnTimeout();
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/YoshikoState.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/YoshikoState.java
new file mode 100644
index 0000000000000000000000000000000000000000..b588da06abdab6a93a0eab2cd3ac276c51617c0b
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/YoshikoState.java
@@ -0,0 +1,63 @@
+/* ----------------------------------------------------------------------------
+ * This file was automatically generated by SWIG (http://www.swig.org).
+ * Version 3.0.8
+ *
+ * Do not make changes to this file unless you know what you are doing--modify
+ * the SWIG interface file instead.
+ * ----------------------------------------------------------------------------- */
+
+package de.hhu.ba.yoshikoWrapper.swig;
+
+public final class YoshikoState {
+ public final static YoshikoState PARSING_INPUT = new YoshikoState("PARSING_INPUT", 0);
+ public final static YoshikoState REDUCTION_AC = new YoshikoState("REDUCTION_AC", 1);
+ public final static YoshikoState REDUCTION_CR = new YoshikoState("REDUCTION_CR", 2);
+ public final static YoshikoState REDUCTION_CC = new YoshikoState("REDUCTION_CC", 3);
+ public final static YoshikoState REDUCTION_PD = new YoshikoState("REDUCTION_PD", 4);
+ public final static YoshikoState REDUCTION_HE = new YoshikoState("REDUCTION_HE", 5);
+ public final static YoshikoState REDUCTION_MR = new YoshikoState("REDUCTION_MR", 6);
+ public final static YoshikoState REDUCTION_SN = new YoshikoState("REDUCTION_SN", 7);
+ public final static YoshikoState SOLVING_HEURISTIC = new YoshikoState("SOLVING_HEURISTIC", 8);
+ public final static YoshikoState SOLVING_ILP = new YoshikoState("SOLVING_ILP", 9);
+ public final static YoshikoState PROCESS_SOLUTION = new YoshikoState("PROCESS_SOLUTION", 10);
+
+ public final int swigValue() {
+ return swigValue;
+ }
+
+ public String toString() {
+ return swigName;
+ }
+
+ public static YoshikoState swigToEnum(int swigValue) {
+ if (swigValue < swigValues.length && swigValue >= 0 && swigValues[swigValue].swigValue == swigValue)
+ return swigValues[swigValue];
+ for (int i = 0; i < swigValues.length; i++)
+ if (swigValues[i].swigValue == swigValue)
+ return swigValues[i];
+ throw new IllegalArgumentException("No enum " + YoshikoState.class + " with value " + swigValue);
+ }
+
+ private YoshikoState(String swigName) {
+ this.swigName = swigName;
+ this.swigValue = swigNext++;
+ }
+
+ private YoshikoState(String swigName, int swigValue) {
+ this.swigName = swigName;
+ this.swigValue = swigValue;
+ swigNext = swigValue+1;
+ }
+
+ private YoshikoState(String swigName, YoshikoState swigEnum) {
+ this.swigName = swigName;
+ this.swigValue = swigEnum.swigValue;
+ swigNext = this.swigValue+1;
+ }
+
+ private static YoshikoState[] swigValues = { PARSING_INPUT, REDUCTION_AC, REDUCTION_CR, REDUCTION_CC, REDUCTION_PD, REDUCTION_HE, REDUCTION_MR, REDUCTION_SN, SOLVING_HEURISTIC, SOLVING_ILP, PROCESS_SOLUTION };
+ private static int swigNext = 0;
+ private final int swigValue;
+ private final String swigName;
+}
+
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/AboutDialog.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/AboutDialogFactory.java
similarity index 90%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/AboutDialog.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/AboutDialogFactory.java
index 4c3c3be57e29de6df5105ec98b24d4aa7c962f18..915093c4f50779a988c24cf7c5060e97cec784af 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/AboutDialog.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/AboutDialogFactory.java
@@ -1,4 +1,4 @@
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing;
import javax.swing.GroupLayout;
import javax.swing.GroupLayout.Alignment;
@@ -8,11 +8,12 @@ import javax.swing.JPanel;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.YoshUtil;
+import de.hhu.ba.yoshikoWrapper.swing.components.YoshikoHeader;
/**Factory for a simple About-Dialog that provides some basic info about the software
*
*/
-public class AboutDialog{
+public class AboutDialogFactory{
private static JPanel getDialogPanel() {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EnableWhenSelectedListener.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/EnableWhenSelectedListener.java
similarity index 97%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/EnableWhenSelectedListener.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/EnableWhenSelectedListener.java
index e021d4d2fab29ece3ce285f14d81634101b09fb0..1c88a7a3766c47d619b105dacc4cd9ae329c246f 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EnableWhenSelectedListener.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/EnableWhenSelectedListener.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/FormatHelper.java
similarity index 98%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/FormatHelper.java
index 3d3733f6a86ec5f1fe49b3330b5ee04aac88232d..faa161f9e27e14f73989bd24d293a9139e490836 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/FormatHelper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/FormatHelper.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing;
import java.text.DecimalFormat;
import java.text.NumberFormat;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/HintManager.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/HintManager.java
similarity index 97%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/HintManager.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/HintManager.java
index 09296f68d42fcc5afc5fb96eb38d08fd466c73be..d34d98737ece6da220b9ecf28879a0a94cfcd547 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/HintManager.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/HintManager.java
@@ -1,4 +1,4 @@
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing;
import java.util.Collections;
import java.util.HashMap;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageSwitcherPanelFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanelFactory.java
similarity index 94%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageSwitcherPanelFactory.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanelFactory.java
index 3c1c3666897995ae0f8475b62db4cb4d644f09da..0d408884c60bdd98e28eb9a5f0046d3931a530ab 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageSwitcherPanelFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanelFactory.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing;
import javax.swing.BoxLayout;
@@ -27,6 +27,7 @@ import javax.swing.BoxLayout;
import org.cytoscape.util.swing.BasicCollapsiblePanel;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.swing.components.LanguageSwitcher;
public class LanguageSwitcherPanelFactory{
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LibraryPanelFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LibraryPanelFactory.java
similarity index 96%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/LibraryPanelFactory.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/LibraryPanelFactory.java
index 5e631f265e8673ac211ddc911472e66fe3d25f55..6c7714c533db78a0a0f624c04d8ca7af2e934b64 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LibraryPanelFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LibraryPanelFactory.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing;
import java.awt.Desktop;
import java.awt.event.ActionEvent;
@@ -39,6 +39,8 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
+import de.hhu.ba.yoshikoWrapper.swing.components.LibStatusPanel;
+import de.hhu.ba.yoshikoWrapper.swing.components.YLibChooser;
public class LibraryPanelFactory{
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SwingUtil.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.java
similarity index 85%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/SwingUtil.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.java
index e2d3fa88c3c2bc6eaa7ce0ac7bed68125335bb13..b190b5a375f7332e3cd60781d6578608ee844950 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SwingUtil.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.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
@@ -19,16 +19,19 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing;
import java.awt.Container;
+import java.text.DecimalFormat;
import javax.swing.JComponent;
public class SwingUtil {
- static void addAll(Container container, JComponent ... components) {
+ public static void addAll(Container container, JComponent ... components) {
for (JComponent c: components) {
container.add(c);
}
}
+
+ public final static DecimalFormat twoDecimals =new DecimalFormat("0.00");
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
similarity index 97%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
index 91ff58290531f0253b7f47d65a1be1555dc7c6ad..5ae0d703c74b66ad45c9072093ec65cfcb467dbe 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.Color;
import java.awt.event.MouseEvent;
@@ -38,6 +38,7 @@ import org.cytoscape.util.swing.BasicCollapsiblePanel;
import de.hhu.ba.yoshikoWrapper.core.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial")
public class ClusterView extends JPanel {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
similarity index 97%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
index 84b9f9bd0714e9274a0ed21bd6175d2e25685e33..6878cdff42fa3c0c7036e72e7000eec3b701a1d5 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import javax.swing.GroupLayout;
import javax.swing.JCheckBox;
@@ -31,6 +31,8 @@ import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.swing.EnableWhenSelectedListener;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial") //will never be serialized
public class ColumnMapper extends JPanel{
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/DoubleInputField.java
similarity index 94%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/DoubleInputField.java
index 1c3f1b19f9b3ae8b5fdc0b3ba364885702bcf91d..24a031bbc5de788dc78197f29f49ddace1a2de53 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/DoubleInputField.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/DoubleInputField.java
@@ -19,10 +19,12 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import javax.swing.JFormattedTextField;
+import de.hhu.ba.yoshikoWrapper.swing.FormatHelper;
+
/**
* Provides a more strict input field that only accepts double
*/
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
similarity index 97%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
index 1d67f7a5bfef0c14bd6e90ab5a8bb9f86204e1f3..2ee951a40ec47fb72e35de0dfb8d5f3263197868 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/EditCostPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import javax.swing.GroupLayout;
@@ -30,6 +30,7 @@ import javax.swing.GroupLayout.Alignment;
import org.cytoscape.model.CyColumn;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial") //Will never be serialized
public class EditCostPanel extends JPanel {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/HelpButton.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java
similarity index 94%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/HelpButton.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java
index 19b00f789b66d8d714dd00f4da58e94c09daeb6f..af91028102125b43aabee9f046ab51283cf5573f 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/HelpButton.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java
@@ -1,4 +1,4 @@
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.Insets;
import java.awt.event.ActionEvent;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/IntegerInputField.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/IntegerInputField.java
similarity index 94%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/IntegerInputField.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/IntegerInputField.java
index c9edadcfaa3769b13ea428050ea5ae210b8faeff..04ffa2f772d4fb3a85a799cceddcdbff4399b690 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/IntegerInputField.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/IntegerInputField.java
@@ -19,11 +19,13 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import javax.swing.JFormattedTextField;
import javax.swing.text.NumberFormatter;
+import de.hhu.ba.yoshikoWrapper.swing.FormatHelper;
+
/**
* Provides a more strict input field that only accepts integers
*/
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageRenderer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LanguageRenderer.java
similarity index 94%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageRenderer.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LanguageRenderer.java
index 118e2b78dcce06d6e27bab28fe0f0326392378f5..3cabc956e19accbedc56bc36d3fab494cbaf41e1 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageRenderer.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LanguageRenderer.java
@@ -1,4 +1,4 @@
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.Component;
import java.util.Locale;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageSwitcher.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LanguageSwitcher.java
similarity index 97%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageSwitcher.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LanguageSwitcher.java
index 3086a1ace248006d6e11697f21d1e32f7142500f..0fa132bf8893e582d70895c50f7a64899ff9e3bb 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageSwitcher.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LanguageSwitcher.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LibStatusPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LibStatusPanel.java
similarity index 86%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/LibStatusPanel.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LibStatusPanel.java
index f1690c032b4f76587bd79a0584219e33fe736e90..212cde9752b630d8d801e891263c72c44bff3958 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/LibStatusPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LibStatusPanel.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
@@ -19,21 +19,22 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.Color;
import javax.swing.JLabel;
import de.hhu.ba.yoshikoWrapper.core.GraphicsLoader;
-
+/**
+ * Simple JLabel visually representing whether or not the Yoshiko Lib is loaded
+ *
+ */
+@SuppressWarnings("serial")
public class LibStatusPanel extends JLabel {
-
/**
- *
+ * Adjusts the style accordingly by changing its color and updating its text
*/
- private static final long serialVersionUID = 6178348169993497344L;
-
public void setStyle(boolean libraryLoaded) {
if(libraryLoaded) {
this.setText("YOSHIKO LIBRARY READY!");
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
similarity index 96%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
index 3a97ea88cf03566b1ae68809433631c457a77fe0..3c34e3a2b15740ab2243d8c78b0db52f7cbe5c9c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import static javax.swing.GroupLayout.DEFAULT_SIZE;
import static javax.swing.GroupLayout.PREFERRED_SIZE;
@@ -57,6 +57,11 @@ import de.hhu.ba.yoshikoWrapper.core.Hint;
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.swing.AboutDialogFactory;
+import de.hhu.ba.yoshikoWrapper.swing.HintManager;
+import de.hhu.ba.yoshikoWrapper.swing.LanguageSwitcherPanelFactory;
+import de.hhu.ba.yoshikoWrapper.swing.LibraryPanelFactory;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
/**This class describes the Swing Panel that the user interacts with in cytoscape
*
@@ -101,7 +106,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
@Override
public void actionPerformed(ActionEvent e) {
- AboutDialog.showDialog();
+ AboutDialogFactory.showDialog();
}
});
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/OperationModePanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
similarity index 98%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/OperationModePanel.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
index a92ee23345bc2e52fdbec7544a614b23e550e08b..6fa6d0ee625ec693de1430c0483a80a114f18aa3 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/OperationModePanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -33,6 +33,7 @@ import javax.swing.JPanel;
import javax.swing.JRadioButton;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
import javax.swing.GroupLayout.Alignment;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ReductionRulesChooser.java
similarity index 98%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ReductionRulesChooser.java
index c24ead35395a43b8baf0c1b054cdc097fe89b6c3..cd7a02a091363e6f65a7623bde842944442905b3 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ReductionRulesChooser.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import static javax.swing.GroupLayout.DEFAULT_SIZE;
@@ -34,6 +34,7 @@ import javax.swing.JPanel;
import javax.swing.GroupLayout.Alignment;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial")
public class ReductionRulesChooser extends JPanel{
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ResultPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
similarity index 98%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/ResultPanel.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
index 0f551cfce2e807028443d3f512843e08e905689f..226f87a6d3bbbfefc42856bc03d38ba428e7aac5 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ResultPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.Color;
import java.awt.Component;
@@ -44,6 +44,7 @@ import de.hhu.ba.yoshikoWrapper.core.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
/**Swing component that contains ALL solutions that are found during one run.
* Conforms to CY 3.5 by being a CytoPanelComponent which is the norm for "result" panels
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionNumberChooser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionNumberChooser.java
similarity index 95%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionNumberChooser.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionNumberChooser.java
index 6f7e860354b2e5f70495b1b35271b4a8722cee46..32436d7b8cd33a51bbaa087f37320764c73a4d60 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionNumberChooser.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionNumberChooser.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import javax.swing.JLabel;
import javax.swing.JPanel;
@@ -27,6 +27,7 @@ import javax.swing.JSpinner;
import javax.swing.SpinnerNumberModel;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial")
public class SolutionNumberChooser extends JPanel {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
similarity index 96%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
index 4ef005df628b5db3f7fb74ebb19fecc15ac6f6db..ecc1bd984f281a42316d799d186d9557ed9e3e34 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/SolutionTab.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
@@ -35,6 +35,7 @@ import javax.swing.JScrollPane;
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;
@SuppressWarnings("serial")
public class SolutionTab extends JPanel {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/TimeLimitSetter.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/TimeLimitSetter.java
similarity index 96%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/TimeLimitSetter.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/TimeLimitSetter.java
index 41d9f0a827be5623f44bf4308651af1f53a8c7e0..0c8ce0ef037eae15a5c944c47c74252fff8dbced 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/TimeLimitSetter.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/TimeLimitSetter.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -29,6 +29,7 @@ import javax.swing.JCheckBox;
import javax.swing.JPanel;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial")
public class TimeLimitSetter extends JPanel{
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/YLibChooser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/YLibChooser.java
similarity index 93%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/YLibChooser.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/YLibChooser.java
index 3beb2bd295be1dd0276239a4bb84701e1cc88090..c5e8ae72a8a8e960d7482e215ce84434f7b3c717 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/YLibChooser.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/YLibChooser.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
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import java.io.File;
@@ -31,11 +31,8 @@ import javax.swing.filechooser.FileFilter;
* @author Philipp Spohr, Aug 6, 2017
*
*/
+@SuppressWarnings("serial")
public class YLibChooser extends JFileChooser {
- /**
- *
- */
- private static final long serialVersionUID = -2528894543739757962L;
/**
* Default constructor
@@ -54,7 +51,7 @@ public class YLibChooser extends JFileChooser {
public String getDescription() {
return "Compiled Yoshiko-Libraries";
}
-
+
});
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/YoshikoHeader.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/YoshikoHeader.java
similarity index 97%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/YoshikoHeader.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/YoshikoHeader.java
index 46846446a3c1c4f6d663c15c812132a2db3dff28..f484334629eddc377215704e5c5fa0c9fab70e5c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/YoshikoHeader.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/YoshikoHeader.java
@@ -19,7 +19,7 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing.components;
import javax.swing.Box;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/package-info.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..732e8db897c3b06b782bbc06376da49500c6b207
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/package-info.java
@@ -0,0 +1,8 @@
+/**
+ *
+ */
+/**
+ * @author Philipp Spohr, Sep 9, 2017
+ *
+ */
+package de.hhu.ba.yoshikoWrapper.swing.components;
\ No newline at end of file
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/package-info.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/package-info.java
similarity index 97%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/gui/package-info.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/package-info.java
index e0d4d454fb10c0039e2f7c7a05ef3d05fa625854..c8f8b807c1cdb28a7a2568881296bf25fb3c3564 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/package-info.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/package-info.java
@@ -23,4 +23,4 @@
/**This package contains all Swing extensions and components (frontend)
*
*/
-package de.hhu.ba.yoshikoWrapper.gui;
+package de.hhu.ba.yoshikoWrapper.swing;
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index 7f746036358937dd8a529e6a8d648efed5ac39bb..2ad94d1f5426f26dbc1d6b371805a8ade0f022e2 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -62,6 +62,16 @@ resultsPanelTitle = Yoshiko Results
run = Perform Algorithm
showAdvanced = Show advanced options
solution = Solution
+
+status_reductionAC = Applying "Almost-Clique" reduction rule
+status_reductionCR = Applying "Clique" reduction rule
+status_reductionCC = Applying "Critical-Clique" reduction rule
+status_reductionHE = Applying "Heavy-Edge 3 in 1" reduction rule
+status_reductionMR = Applying "Merging" reduction rule
+status_reductionPD = Applying "Parameter-Dependent" reduction rule
+status_reductionSN = Applying "Similar-Neighborhood" reduction rule
+
+
switchLanguage = Plugin language
timeLimitILP = Use time limit for ILP (s):
timedOutMessage = The ILP exceeded the time-limit!
diff --git a/thesis/tex/Chapter/dm_impl.tex b/thesis/tex/Chapter/dm_impl.tex
index 5fd0654cd52f3c916d93f332a881268995497bcf..f190adc56c8192ba2d36578b5a5381dc8677294d 100644
--- a/thesis/tex/Chapter/dm_impl.tex
+++ b/thesis/tex/Chapter/dm_impl.tex
@@ -1 +1,20 @@
The Yoshiko Wrapper provides a clean and simple interface to generate the model.
+\subparagraph{Mapping edge costs}
+The user has the possibility to use a numeric Cytoscape column of the node table as a source for the edge-cost function $C$.
+\subparagraph{Insertion and deletion cost}
+The default values $C_I$ and $C_D$ can be set by the user and default to $C_I=-1$ and $C_D=1$.
+It should be noted, that the insertion cost value is not normalized or in any way adjusted when a mapping is used. This means that the user needs to adjust this value wisely to fit the data.
+As an example the user might have mapped the edge costs to a column containing values in the range of $10^6-10^7$.
+The default insertion cost of $-1$ will be irrelevant in comparison and the algorithm will most likely insert all missing edges and generate one big cluster as a solution.
+Overall the ratio $R = \frac{|C_I|}{C_D}$ should give you a rough idea how the algorithm will operate.\\
+$R > 1$ means, that the algorithm is more likely to delete edges to generate cliques, a value of $R<1$ means insertions are more likely.
+\subparagraph{Mapping permanent or forbidden edges}
+The Yoshiko app has additional convenience functions:
+The user can map edges to a boolean Cytoscape column to mark them as either
+\textbf{forbidden} (meaning that those edges will never be part of the solution) or
+\textbf{permanent} (meaning that those edges will always be part of the solution).
+Marking an edge e as forbidden is equivalent to $C(e)=-\infty$,
+marking an edge e as permanent is equivalent to $C(e)=\infty$.
+This way the user is able to apply expert knowledge about the input instance to increase the quality of the solution.
+
+
diff --git a/thesis/tex/Chapter/dm_theory.tex b/thesis/tex/Chapter/dm_theory.tex
index 3b59bff440bb91783a42f4ee0f7903a8bb883483..7e6d4a1b3a6cade379f6f53559c1833885c4bd35 100644
--- a/thesis/tex/Chapter/dm_theory.tex
+++ b/thesis/tex/Chapter/dm_theory.tex
@@ -1,3 +1,4 @@
+
The Yoshiko algorithm models the data as a complete graph
$G=(V,E)$
with an associated edge-cost function
@@ -6,4 +7,5 @@ $C: E \rightarrow \mathbb{R}
\cup \lbrace \infty \rbrace $.
As many input instances do not describe a full graph, missing edges and costs need to be modeled.
This is achieved by using default values for insertion or deletion.
-A default insertion cost is used whenever the input instance does not contain an edge.
\ No newline at end of file
+A default insertion cost $C_I \in [-\infty,0]$ is used as $C(e)$ whenever the input instance does not contain an edge $e$.
+A default deletion cost $C_D \in [0,\infty ]$ is used as $C(e)$ whenever the input instance does contain an edge $e$ that has no cost associated yet.
\ No newline at end of file
diff --git a/thesis/tex/Thesis.pdf b/thesis/tex/Thesis.pdf
index ec03507e8e31722c79eae799cbd08b26f839bc39..5bedb831aec3862fe4aaaf5bcfe99681ba19e901 100644
Binary files a/thesis/tex/Thesis.pdf and b/thesis/tex/Thesis.pdf differ