diff --git a/pom.xml b/pom.xml
index 6298c173d2b4d859036608d1c5e826d618045912..8c1c573b5d73422d4530376eab8d301cbf9e0da8 100644
--- a/pom.xml
+++ b/pom.xml
@@ -25,17 +25,17 @@
<properties>
<bundle.symbolicName>de.hhu.ba.yoshikoWrapper</bundle.symbolicName>
<bundle.namespace>de.hhu.ba.yoshikoWrapper</bundle.namespace>
- <cytoscape.api.version>3.6.0</cytoscape.api.version>
+ <cytoscape.api.version>3.7.2</cytoscape.api.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version>
<osgi.api.version>4.2.0</osgi.api.version>
</properties>
<groupId>de.hhu.ba</groupId>
- <artifactId>yoshikoWrapper</artifactId>
- <version>0.1.5</version>
+ <artifactId>yoshikoStandalone</artifactId>
+ <version>0.1.1</version>
- <name>YoshikoWrapper</name>
+ <name>YoshikoStandalone</name>
<build>
<plugins>
@@ -43,7 +43,7 @@
<inherited>true</inherited>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
- <version>3.0</version>
+ <version>3.7.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
@@ -121,6 +121,11 @@
<artifactId>org.osgi.core</artifactId>
<version>${osgi.api.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.jgrapht</groupId>
+ <artifactId>jgrapht-core</artifactId>
+ <version>1.3.1</version>
+ </dependency>
<dependency>
<groupId>junit</groupId>
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index f34df8026716566d65a387afae841db54cfa564b..d1862a67d71841823a52278522ac68f08fc02950 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -51,7 +51,6 @@ import static org.cytoscape.work.ServiceProperties.COMMAND_NAMESPACE;
import de.hhu.ba.yoshikoWrapper.core.ConfigurationManager;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
-import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
import de.hhu.ba.yoshikoWrapper.swing.components.MainPanel;
import de.hhu.ba.yoshikoWrapper.taskFactories.CommandTaskFactory;
import de.hhu.ba.yoshikoWrapper.taskFactories.YoshikoCommand;
@@ -101,14 +100,6 @@ public class CyActivator extends AbstractCyActivator {
//Set language according to settings -> Default to enUS
LocalizationManager.switchLanguage(cm.getProperties().getProperty("locale", "enUS"));
- //Attempt to find the Yoshiko lib in a previously stored location and load it
- //TODO: Move into a separate handler to keep CyActivator clean
- if (!YoshikoLoader.isLibraryLoaded()){
- String pathToYosh = cm.getProperties().getProperty("pathToYoshiko");
- if (pathToYosh != null && pathToYosh != "null") {
- YoshikoLoader.loadLibrary(pathToYosh);
- }
- }
//Register commands / CyRest //TODO: Group shared calls for better code readability / less lines of code
TaskFactory commandTaskFactory_PERFORM_ALGORITHM = new CommandTaskFactory(YoshikoCommand.PERFORM_ALGORITHM);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
deleted file mode 100644
index 64d16b7924508984994bac10bcbe746078cb8839..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*******************************************************************************
- * 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
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- ******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.core;
-
-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.cytoUtil.NodeMap;
-import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
-import de.hhu.ba.yoshikoWrapper.swig.LibraryInput;
-
-public class NetworkParser {
-
- //Symbolic Links
- private static Logger logger = YoshikoLogger.getInstance().getLogger();
-
- public static LibraryInput parseNetwork (
- CyNetwork net,
- NodeMap nodeMap,
- CyColumn weightColumn,
- CyColumn permanentColumn,
- CyColumn forbiddenColumn,
- double deletionCostDefault
- ) throws NetworkParsingException
- {
- //Create an empty instance / fetch C++ object pointer
- LibraryInput generatedInput = new LibraryInput();
- if (net != null){
- //Create an empty full graph with a given size
- generatedInput.setSize(net.getNodeCount());
- //Fetch edges
- List<CyEdge> edges = net.getEdgeList();
-
- //Loop over edges
- for (CyEdge e : edges) {
-
- //Parse editing costs
- double weight = deletionCostDefault;
-
- //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() == Integer.class) {
- weight = 1.0*edgeEntry.get(weightColumn.getName(), Integer.class);
- }
- else if (weightColumn.getType() == Double.class) {
- weight = edgeEntry.get(weightColumn.getName(), Double.class);
- }
- }
- }
-
- //Parse Forbidden/Permanent markers
- boolean forbidden = false;
- boolean permanent = false;
-
- if (permanentColumn != null) {
- //Additional check as it is not required to have a value in every row
- if (edgeEntry.get(permanentColumn.getName(), Boolean.class) != null) {
- permanent = (boolean)edgeEntry.get(permanentColumn.getName(), Boolean.class);
- }
- }
- if (forbiddenColumn != null) {
- //Additional check as it is not required to have a value in every row
- if (edgeEntry.get(forbiddenColumn.getName(), Boolean.class) != null) {
- forbidden = (boolean)edgeEntry.get(forbiddenColumn.getName(), Boolean.class);
- }
- }
-
- //Check for edges that are forbidden AND permanent -> Throw exception
- if (forbidden && permanent) {
- throw new NetworkParsingException(LocalizationManager.get("dualInfinityError"));
- }
-
- logger.debug("Found Edge: "+edgeEntry.get("name", String.class)+ " with weight:"+weight);
-
- generatedInput.addEdge(
- nodeMap.get(e.getSource()),
- nodeMap.get(e.getTarget()),
- weight,
- permanent,
- forbidden
- );
-
- }
- }
- return generatedInput;
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java
deleted file mode 100644
index c556b9d2a906d896b01282bbe1aefaf26eab65a7..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package de.hhu.ba.yoshikoWrapper.core;
-
-/**
- * Simple Exception that should be thrown when the CyNetwork combined with the given parameters can not be parsed in a meaningful WCE instance
- * @author Philipp Spohr, Dec 12, 2017
- *
- */
-@SuppressWarnings("serial")
-public class NetworkParsingException extends Exception {
-
- private String msg;
-
- public NetworkParsingException(String msg) {
- this.msg = msg;
- }
-
- @Override
- public String getMessage() {
- return LocalizationManager.get("networkParsingException")+" "+msg;
- }
-
-}
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 b027e2986c3adcf3ebebef10a727ae6d33eaf2fc..166d95fa6fea99dd36a3d259c42b1ab359b45377 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -108,7 +108,7 @@ public class ParameterSet implements TunableValidator
permanentColumn = new ListSingleSelection<CyColumn>(booleanColumns);
//Don't select any columns by default
- weightColumn.setSelectedValue(null);
+ weightColumn.setSelectedValue(numericColumns.get(1));
forbiddenColumn.setSelectedValue(null);
permanentColumn.setSelectedValue(null);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/StatusInformer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/StatusInformer.java
deleted file mode 100644
index cbc49a77cbcdcc91e12c6a13e351ce872eb5bc53..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/StatusInformer.java
+++ /dev/null
@@ -1,84 +0,0 @@
-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){
- if (value <= 1.0) {
- 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"));
- }
-
- else if (state == YoshikoState.SOLVING_ILP) {
- taskMonitor.setStatusMessage(LocalizationManager.get("status_solvingILP"));
- }
- }
-
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
deleted file mode 100644
index 0777d464a22f62cd6bc0df0621913cf1dfce2cdc..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*******************************************************************************
- * 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
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- ******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.core;
-
-import java.io.File;
-
-
-import org.slf4j.Logger;
-
-import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
-import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
-
-public class YoshikoLoader {
-
- public static final String REQUIRED_VERSION = "2.2.0";
-
- private static boolean isLoaded;
-
- //Symbolic Links
- private static Logger logger = YoshikoLogger.getInstance().getLogger();
-
- public static void loadLibrary(String libPath) {
- //Attempt to load from a previously stored path
- File f = new File (libPath);
- if (!f.exists()) {
- logger.info("Could not load the Yoshiko-library from a previously saved path! You might need to set the path manually.");
- return;
- }
-
- try {
- logger.info("Attempting to load library @: "+libPath);
- //Verify version ending
- if (!libPath.substring(0,libPath.lastIndexOf(".")).endsWith(REQUIRED_VERSION)) {
- logger.info(LocalizationManager.get("libFail")+" "+REQUIRED_VERSION);
- return;
- }
- //Perform actual loading
- System.load(libPath);
-
- }
- catch(UnsatisfiedLinkError e) {
- //This might happen as Java doesn't unload native libs
- //One such case might be reloading the Cytoscape app on-the-fly
- logger.error(e.getMessage());
- }
- LibraryInterface.setVerbosity(3);
- //update cfg
- CyCore.cm.getProperties().setProperty("pathToYoshiko", libPath);
- isLoaded = true;
- }
-
- //SETTER / GETTER
-
- public static boolean isLibraryLoaded() {
- return isLoaded;
- }
-
-}
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 16bb1f782a56f19b1f2ec3584415e3e744614d71..ab22f2024ff9b50071db0d9ccf18770064853154 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
@@ -27,7 +27,6 @@ import java.util.HashMap;
import org.cytoscape.model.CyNetwork;
import de.hhu.ba.yoshikoWrapper.core.ResultList;
-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.
@@ -39,14 +38,13 @@ public class YoshikoResult{
private HashMap<Long,YoshikoSolution> solutions;
- private SolutionFlags flags;
private int id;
- public YoshikoResult(CyNetwork net, SolutionFlags flags) {
+ public YoshikoResult(CyNetwork net) {
solutions = new HashMap<Long,YoshikoSolution>();
this.originalGraph = net;
- this.flags = flags;
+
ResultList.add(this);
}
@@ -62,9 +60,6 @@ public class YoshikoResult{
/**
* @return the flags associated with this result
*/
- public SolutionFlags getFlags() {
- return flags;
- }
public void addSolution(YoshikoSolution solution) {
solutions.put(solution.getId(),solution);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/ClusterEditingSolutions.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/ClusterEditingSolutions.java
deleted file mode 100644
index ae586e770de1d3b690605f796256845df2c7054e..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/ClusterEditingSolutions.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class ClusterEditingSolutions {
- private transient long swigCPtr;
- protected transient boolean swigCMemOwn;
-
- protected ClusterEditingSolutions(long cPtr, boolean cMemoryOwn) {
- swigCMemOwn = cMemoryOwn;
- swigCPtr = cPtr;
- }
-
- protected static long getCPtr(ClusterEditingSolutions obj) {
- return (obj == null) ? 0 : obj.swigCPtr;
- }
-
- protected void finalize() {
- delete();
- }
-
- public synchronized void delete() {
- if (swigCPtr != 0) {
- if (swigCMemOwn) {
- swigCMemOwn = false;
- LibraryInterfaceJNI.delete_ClusterEditingSolutions(swigCPtr);
- }
- swigCPtr = 0;
- }
- }
-
- public long getNumberOfClusters(long i) {
- return LibraryInterfaceJNI.ClusterEditingSolutions_getNumberOfClusters(swigCPtr, this, i);
- }
-
- public IntVector getCluster(long i, long k) {
- return new IntVector(LibraryInterfaceJNI.ClusterEditingSolutions_getCluster(swigCPtr, this, i, k), false);
- }
-
- public SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t getSolution(long i) {
- return new SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t(LibraryInterfaceJNI.ClusterEditingSolutions_getSolution(swigCPtr, this, i), false);
- }
-
- public long getNumberOfSolutions() {
- return LibraryInterfaceJNI.ClusterEditingSolutions_getNumberOfSolutions(swigCPtr, this);
- }
-
- public SolutionFlags getFlags() {
- return new SolutionFlags(LibraryInterfaceJNI.ClusterEditingSolutions_getFlags(swigCPtr, this), true);
- }
-
- public void setFlags(SolutionFlags f) {
- LibraryInterfaceJNI.ClusterEditingSolutions_setFlags(swigCPtr, this, SolutionFlags.getCPtr(f), f);
- }
-
- public void printSolution(long index) {
- LibraryInterfaceJNI.ClusterEditingSolutions_printSolution(swigCPtr, this, index);
- }
-
- public ClusterEditingSolutions() {
- this(LibraryInterfaceJNI.new_ClusterEditingSolutions(), true);
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CoreAlgorithm.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CoreAlgorithm.java
deleted file mode 100644
index 53f898899dc96ded618242cbf87b4b061c5ec030..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CoreAlgorithm.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class CoreAlgorithm {
- private transient long swigCPtr;
- protected transient boolean swigCMemOwn;
-
- protected CoreAlgorithm(long cPtr, boolean cMemoryOwn) {
- swigCMemOwn = cMemoryOwn;
- swigCPtr = cPtr;
- }
-
- protected static long getCPtr(CoreAlgorithm obj) {
- return (obj == null) ? 0 : obj.swigCPtr;
- }
-
- protected void finalize() {
- delete();
- }
-
- public synchronized void delete() {
- if (swigCPtr != 0) {
- if (swigCMemOwn) {
- swigCMemOwn = false;
- LibraryInterfaceJNI.delete_CoreAlgorithm(swigCPtr);
- }
- swigCPtr = 0;
- }
- }
-
- public ClusterEditingSolutions run() {
- long cPtr = LibraryInterfaceJNI.CoreAlgorithm_run(swigCPtr, this);
- return (cPtr == 0) ? null : new ClusterEditingSolutions(cPtr, false);
- }
-
- public void registerCplexInformer(CplexInformer informer) {
- LibraryInterfaceJNI.CoreAlgorithm_registerCplexInformer(swigCPtr, this, CplexInformer.getCPtr(informer), informer);
- }
-
- public void cancel() {
- LibraryInterfaceJNI.CoreAlgorithm_cancel(swigCPtr, this);
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CplexInformer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CplexInformer.java
deleted file mode 100644
index f9feb9b44ea8207324f4271c2e5d22141709b1e0..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/CplexInformer.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class CplexInformer {
- private transient long swigCPtr;
- protected transient boolean swigCMemOwn;
-
- protected CplexInformer(long cPtr, boolean cMemoryOwn) {
- swigCMemOwn = cMemoryOwn;
- swigCPtr = cPtr;
- }
-
- protected static long getCPtr(CplexInformer obj) {
- return (obj == null) ? 0 : obj.swigCPtr;
- }
-
- protected void finalize() {
- delete();
- }
-
- public synchronized void delete() {
- if (swigCPtr != 0) {
- if (swigCMemOwn) {
- swigCMemOwn = false;
- LibraryInterfaceJNI.delete_CplexInformer(swigCPtr);
- }
- swigCPtr = 0;
- }
- }
-
- protected void swigDirectorDisconnect() {
- swigCMemOwn = false;
- delete();
- }
-
- public void swigReleaseOwnership() {
- swigCMemOwn = false;
- LibraryInterfaceJNI.CplexInformer_change_ownership(this, swigCPtr, false);
- }
-
- public void swigTakeOwnership() {
- swigCMemOwn = true;
- LibraryInterfaceJNI.CplexInformer_change_ownership(this, swigCPtr, true);
- }
-
- 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() {
- return (getClass() == CplexInformer.class) ? LibraryInterfaceJNI.CplexInformer_continueOnTimeout(swigCPtr, this) : LibraryInterfaceJNI.CplexInformer_continueOnTimeoutSwigExplicitCplexInformer(swigCPtr, this);
- }
-
- public CplexInformer() {
- this(LibraryInterfaceJNI.new_CplexInformer(), true);
- LibraryInterfaceJNI.CplexInformer_director_connect(this, swigCPtr, swigCMemOwn, true);
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/DoubleVector.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/DoubleVector.java
deleted file mode 100644
index 3cc3bde8320fbc88eeef394849f194df8c56b101..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/DoubleVector.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class DoubleVector {
- private transient long swigCPtr;
- protected transient boolean swigCMemOwn;
-
- protected DoubleVector(long cPtr, boolean cMemoryOwn) {
- swigCMemOwn = cMemoryOwn;
- swigCPtr = cPtr;
- }
-
- protected static long getCPtr(DoubleVector obj) {
- return (obj == null) ? 0 : obj.swigCPtr;
- }
-
- protected void finalize() {
- delete();
- }
-
- public synchronized void delete() {
- if (swigCPtr != 0) {
- if (swigCMemOwn) {
- swigCMemOwn = false;
- LibraryInterfaceJNI.delete_DoubleVector(swigCPtr);
- }
- swigCPtr = 0;
- }
- }
-
- public DoubleVector() {
- this(LibraryInterfaceJNI.new_DoubleVector__SWIG_0(), true);
- }
-
- public DoubleVector(long n) {
- this(LibraryInterfaceJNI.new_DoubleVector__SWIG_1(n), true);
- }
-
- public long size() {
- return LibraryInterfaceJNI.DoubleVector_size(swigCPtr, this);
- }
-
- public long capacity() {
- return LibraryInterfaceJNI.DoubleVector_capacity(swigCPtr, this);
- }
-
- public void reserve(long n) {
- LibraryInterfaceJNI.DoubleVector_reserve(swigCPtr, this, n);
- }
-
- public boolean isEmpty() {
- return LibraryInterfaceJNI.DoubleVector_isEmpty(swigCPtr, this);
- }
-
- public void clear() {
- LibraryInterfaceJNI.DoubleVector_clear(swigCPtr, this);
- }
-
- public void add(double x) {
- LibraryInterfaceJNI.DoubleVector_add(swigCPtr, this, x);
- }
-
- public double get(int i) {
- return LibraryInterfaceJNI.DoubleVector_get(swigCPtr, this, i);
- }
-
- public void set(int i, double val) {
- LibraryInterfaceJNI.DoubleVector_set(swigCPtr, this, i, val);
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/IntVector.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/IntVector.java
deleted file mode 100644
index e894d457075f9ade78a542d20b1990b1a445d38f..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/IntVector.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class IntVector {
- private transient long swigCPtr;
- protected transient boolean swigCMemOwn;
-
- protected IntVector(long cPtr, boolean cMemoryOwn) {
- swigCMemOwn = cMemoryOwn;
- swigCPtr = cPtr;
- }
-
- protected static long getCPtr(IntVector obj) {
- return (obj == null) ? 0 : obj.swigCPtr;
- }
-
- protected void finalize() {
- delete();
- }
-
- public synchronized void delete() {
- if (swigCPtr != 0) {
- if (swigCMemOwn) {
- swigCMemOwn = false;
- LibraryInterfaceJNI.delete_IntVector(swigCPtr);
- }
- swigCPtr = 0;
- }
- }
-
- public IntVector() {
- this(LibraryInterfaceJNI.new_IntVector__SWIG_0(), true);
- }
-
- public IntVector(long n) {
- this(LibraryInterfaceJNI.new_IntVector__SWIG_1(n), true);
- }
-
- public long size() {
- return LibraryInterfaceJNI.IntVector_size(swigCPtr, this);
- }
-
- public long capacity() {
- return LibraryInterfaceJNI.IntVector_capacity(swigCPtr, this);
- }
-
- public void reserve(long n) {
- LibraryInterfaceJNI.IntVector_reserve(swigCPtr, this, n);
- }
-
- public boolean isEmpty() {
- return LibraryInterfaceJNI.IntVector_isEmpty(swigCPtr, this);
- }
-
- public void clear() {
- LibraryInterfaceJNI.IntVector_clear(swigCPtr, this);
- }
-
- public void add(int x) {
- LibraryInterfaceJNI.IntVector_add(swigCPtr, this, x);
- }
-
- public int get(int i) {
- return LibraryInterfaceJNI.IntVector_get(swigCPtr, this, i);
- }
-
- public void set(int i, int val) {
- LibraryInterfaceJNI.IntVector_set(swigCPtr, this, i, val);
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInput.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInput.java
deleted file mode 100644
index a2c4e84c6933e82c13f6ca1f27feba03a50120f0..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInput.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class LibraryInput {
- private transient long swigCPtr;
- protected transient boolean swigCMemOwn;
-
- protected LibraryInput(long cPtr, boolean cMemoryOwn) {
- swigCMemOwn = cMemoryOwn;
- swigCPtr = cPtr;
- }
-
- protected static long getCPtr(LibraryInput obj) {
- return (obj == null) ? 0 : obj.swigCPtr;
- }
-
- protected void finalize() {
- delete();
- }
-
- public synchronized void delete() {
- if (swigCPtr != 0) {
- if (swigCMemOwn) {
- swigCMemOwn = false;
- LibraryInterfaceJNI.delete_LibraryInput(swigCPtr);
- }
- swigCPtr = 0;
- }
- }
-
- public LibraryInput() {
- this(LibraryInterfaceJNI.new_LibraryInput(), true);
- }
-
- public void addEdge(long sourceID, long targetID, double cost) {
- LibraryInterfaceJNI.LibraryInput_addEdge__SWIG_0(swigCPtr, this, sourceID, targetID, cost);
- }
-
- public void addEdge(long sourceID, long targetID, double cost, boolean permanent, boolean forbidden) {
- LibraryInterfaceJNI.LibraryInput_addEdge__SWIG_1(swigCPtr, this, sourceID, targetID, cost, permanent, forbidden);
- }
-
- public void setSize(long id) {
- LibraryInterfaceJNI.LibraryInput_setSize(swigCPtr, this, id);
- }
-
- public void setDefaultInsertionCost(double cost) {
- LibraryInterfaceJNI.LibraryInput_setDefaultInsertionCost(swigCPtr, this, cost);
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
deleted file mode 100644
index 227ab8a923211019d5bf0f831f9055addfadd5f1..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class LibraryInterface {
- public static String getVersionString() {
- return LibraryInterfaceJNI.getVersionString();
- }
-
- public static void setTimeLimit(int limit) {
- LibraryInterfaceJNI.setTimeLimit(limit);
- }
-
- public static void setThreadLimit(int limit) {
- LibraryInterfaceJNI.setThreadLimit(limit);
- }
-
- public static void setVerbosity(int level) {
- LibraryInterfaceJNI.setVerbosity(level);
- }
-
- public static CoreAlgorithm getRun(LibraryInput input, int nrOptimalSolutions, String rulesBitMask, double multiplicativeFactor, boolean useHeuristic, boolean separatePartitionCuts, boolean separateTriangles, int targetClusterCount) {
- long cPtr = LibraryInterfaceJNI.getRun(LibraryInput.getCPtr(input), input, nrOptimalSolutions, rulesBitMask, multiplicativeFactor, useHeuristic, separatePartitionCuts, separateTriangles, targetClusterCount);
- return (cPtr == 0) ? null : new CoreAlgorithm(cPtr, false);
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
deleted file mode 100644
index 49549a4b657af8b0dd0a8ef300f2319e92c77f75..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
+++ /dev/null
@@ -1,99 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class LibraryInterfaceJNI {
- public final static native long new_SolutionFlags();
- public final static native void SolutionFlags_totalCost_set(long jarg1, SolutionFlags jarg1_, double jarg2);
- public final static native double SolutionFlags_totalCost_get(long jarg1, SolutionFlags jarg1_);
- public final static native void SolutionFlags_timedOut_set(long jarg1, SolutionFlags jarg1_, boolean jarg2);
- public final static native boolean SolutionFlags_timedOut_get(long jarg1, SolutionFlags jarg1_);
- public final static native void SolutionFlags_ilpGenerated_set(long jarg1, SolutionFlags jarg1_, boolean jarg2);
- public final static native boolean SolutionFlags_ilpGenerated_get(long jarg1, SolutionFlags jarg1_);
- public final static native void SolutionFlags_optimal_set(long jarg1, SolutionFlags jarg1_, boolean jarg2);
- public final static native boolean SolutionFlags_optimal_get(long jarg1, SolutionFlags jarg1_);
- public final static native void SolutionFlags_reducedInstances_set(long jarg1, SolutionFlags jarg1_, int jarg2);
- public final static native int SolutionFlags_reducedInstances_get(long jarg1, SolutionFlags jarg1_);
- public final static native void SolutionFlags_solvedInstances_set(long jarg1, SolutionFlags jarg1_, int jarg2);
- public final static native int SolutionFlags_solvedInstances_get(long jarg1, SolutionFlags jarg1_);
- public final static native void SolutionFlags_lastGap_set(long jarg1, SolutionFlags jarg1_, double jarg2);
- public final static native double SolutionFlags_lastGap_get(long jarg1, SolutionFlags jarg1_);
- public final static native void delete_SolutionFlags(long jarg1);
- public final static native long new_IntVector__SWIG_0();
- public final static native long new_IntVector__SWIG_1(long jarg1);
- public final static native long IntVector_size(long jarg1, IntVector jarg1_);
- public final static native long IntVector_capacity(long jarg1, IntVector jarg1_);
- public final static native void IntVector_reserve(long jarg1, IntVector jarg1_, long jarg2);
- public final static native boolean IntVector_isEmpty(long jarg1, IntVector jarg1_);
- public final static native void IntVector_clear(long jarg1, IntVector jarg1_);
- public final static native void IntVector_add(long jarg1, IntVector jarg1_, int jarg2);
- public final static native int IntVector_get(long jarg1, IntVector jarg1_, int jarg2);
- public final static native void IntVector_set(long jarg1, IntVector jarg1_, int jarg2, int jarg3);
- public final static native void delete_IntVector(long jarg1);
- public final static native long new_DoubleVector__SWIG_0();
- public final static native long new_DoubleVector__SWIG_1(long jarg1);
- public final static native long DoubleVector_size(long jarg1, DoubleVector jarg1_);
- public final static native long DoubleVector_capacity(long jarg1, DoubleVector jarg1_);
- public final static native void DoubleVector_reserve(long jarg1, DoubleVector jarg1_, long jarg2);
- public final static native boolean DoubleVector_isEmpty(long jarg1, DoubleVector jarg1_);
- public final static native void DoubleVector_clear(long jarg1, DoubleVector jarg1_);
- public final static native void DoubleVector_add(long jarg1, DoubleVector jarg1_, double jarg2);
- public final static native double DoubleVector_get(long jarg1, DoubleVector jarg1_, int jarg2);
- public final static native void DoubleVector_set(long jarg1, DoubleVector jarg1_, int jarg2, double jarg3);
- public final static native void delete_DoubleVector(long jarg1);
- public final static native long ClusterEditingSolutions_getNumberOfClusters(long jarg1, ClusterEditingSolutions jarg1_, long jarg2);
- public final static native long ClusterEditingSolutions_getCluster(long jarg1, ClusterEditingSolutions jarg1_, long jarg2, long jarg3);
- public final static native long ClusterEditingSolutions_getSolution(long jarg1, ClusterEditingSolutions jarg1_, long jarg2);
- public final static native long ClusterEditingSolutions_getNumberOfSolutions(long jarg1, ClusterEditingSolutions jarg1_);
- public final static native long ClusterEditingSolutions_getFlags(long jarg1, ClusterEditingSolutions jarg1_);
- public final static native void ClusterEditingSolutions_setFlags(long jarg1, ClusterEditingSolutions jarg1_, long jarg2, SolutionFlags jarg2_);
- public final static native void ClusterEditingSolutions_printSolution(long jarg1, ClusterEditingSolutions jarg1_, long jarg2);
- public final static native long new_ClusterEditingSolutions();
- public final static native void delete_ClusterEditingSolutions(long jarg1);
- public final static native long new_LibraryInput();
- public final static native void delete_LibraryInput(long jarg1);
- public final static native void LibraryInput_addEdge__SWIG_0(long jarg1, LibraryInput jarg1_, long jarg2, long jarg3, double jarg4);
- 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_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);
- public final static native long new_CplexInformer();
- public final static native void CplexInformer_director_connect(CplexInformer obj, long cptr, boolean mem_own, boolean weak_global);
- public final static native void CplexInformer_change_ownership(CplexInformer obj, long cptr, boolean take_or_release);
- public final static native long CoreAlgorithm_run(long jarg1, CoreAlgorithm jarg1_);
- public final static native void CoreAlgorithm_registerCplexInformer(long jarg1, CoreAlgorithm jarg1_, long jarg2, CplexInformer jarg2_);
- public final static native void CoreAlgorithm_cancel(long jarg1, CoreAlgorithm jarg1_);
- public final static native void delete_CoreAlgorithm(long jarg1);
- public final static native String getVersionString();
- public final static native void setTimeLimit(int jarg1);
- public final static native void setThreadLimit(int jarg1);
- 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, int jarg8);
-
- 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();
- }
-
- private final static native void swig_module_init();
- static {
- swig_module_init();
- }
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t.java
deleted file mode 100644
index 5f06b6495c6f94fcc62edbe282f5dec04e779d58..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t {
- private transient long swigCPtr;
-
- protected SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t(long cPtr, @SuppressWarnings("unused") boolean futureUse) {
- swigCPtr = cPtr;
- }
-
- protected SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t() {
- swigCPtr = 0;
- }
-
- protected static long getCPtr(SWIGTYPE_p_std__vectorT_std__vectorT_int_t_t obj) {
- return (obj == null) ? 0 : obj.swigCPtr;
- }
-}
-
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/SolutionFlags.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/SolutionFlags.java
deleted file mode 100644
index cff40e0f4503b1a95f04f3283073d82bb8482a02..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/SolutionFlags.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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 class SolutionFlags {
- private transient long swigCPtr;
- protected transient boolean swigCMemOwn;
-
- protected SolutionFlags(long cPtr, boolean cMemoryOwn) {
- swigCMemOwn = cMemoryOwn;
- swigCPtr = cPtr;
- }
-
- protected static long getCPtr(SolutionFlags obj) {
- return (obj == null) ? 0 : obj.swigCPtr;
- }
-
- protected void finalize() {
- delete();
- }
-
- public synchronized void delete() {
- if (swigCPtr != 0) {
- if (swigCMemOwn) {
- swigCMemOwn = false;
- LibraryInterfaceJNI.delete_SolutionFlags(swigCPtr);
- }
- swigCPtr = 0;
- }
- }
-
- public SolutionFlags() {
- this(LibraryInterfaceJNI.new_SolutionFlags(), true);
- }
-
- public void setTotalCost(double value) {
- LibraryInterfaceJNI.SolutionFlags_totalCost_set(swigCPtr, this, value);
- }
-
- public double getTotalCost() {
- return LibraryInterfaceJNI.SolutionFlags_totalCost_get(swigCPtr, this);
- }
-
- public void setTimedOut(boolean value) {
- LibraryInterfaceJNI.SolutionFlags_timedOut_set(swigCPtr, this, value);
- }
-
- public boolean getTimedOut() {
- return LibraryInterfaceJNI.SolutionFlags_timedOut_get(swigCPtr, this);
- }
-
- public void setIlpGenerated(boolean value) {
- LibraryInterfaceJNI.SolutionFlags_ilpGenerated_set(swigCPtr, this, value);
- }
-
- public boolean getIlpGenerated() {
- return LibraryInterfaceJNI.SolutionFlags_ilpGenerated_get(swigCPtr, this);
- }
-
- public void setOptimal(boolean value) {
- LibraryInterfaceJNI.SolutionFlags_optimal_set(swigCPtr, this, value);
- }
-
- public boolean getOptimal() {
- return LibraryInterfaceJNI.SolutionFlags_optimal_get(swigCPtr, this);
- }
-
- public void setReducedInstances(int value) {
- LibraryInterfaceJNI.SolutionFlags_reducedInstances_set(swigCPtr, this, value);
- }
-
- public int getReducedInstances() {
- return LibraryInterfaceJNI.SolutionFlags_reducedInstances_get(swigCPtr, this);
- }
-
- public void setSolvedInstances(int value) {
- LibraryInterfaceJNI.SolutionFlags_solvedInstances_set(swigCPtr, this, value);
- }
-
- public int getSolvedInstances() {
- return LibraryInterfaceJNI.SolutionFlags_solvedInstances_get(swigCPtr, this);
- }
-
- public void setLastGap(double value) {
- LibraryInterfaceJNI.SolutionFlags_lastGap_set(swigCPtr, this, value);
- }
-
- public double getLastGap() {
- return LibraryInterfaceJNI.SolutionFlags_lastGap_get(swigCPtr, this);
- }
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/YoshikoState.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/YoshikoState.java
deleted file mode 100644
index b588da06abdab6a93a0eab2cd3ac276c51617c0b..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/YoshikoState.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/* ----------------------------------------------------------------------------
- * 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/swing/LibraryPanelFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LibraryPanelFactory.java
deleted file mode 100644
index 72ab8aa22857806d19527a5db76de5192f774d85..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LibraryPanelFactory.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*******************************************************************************
- * 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
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- ******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.swing;
-
-import java.awt.Desktop;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.net.URI;
-
-import javax.swing.GroupLayout;
-import javax.swing.JButton;
-import javax.swing.JFileChooser;
-import javax.swing.GroupLayout.Alignment;
-
-
-import org.cytoscape.util.swing.BasicCollapsiblePanel;
-
-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.swing.components.LibStatusPanel;
-
-public class LibraryPanelFactory{
-
-
- public static BasicCollapsiblePanel createLibraryPanel() {
- final BasicCollapsiblePanel ret = new BasicCollapsiblePanel(LocalizationManager.get("libraryPanel"));
-
- final LibStatusPanel libStatusPanel;
- final JButton searchLibButton;
- final JButton getYoshiko;
-
- //SWING COMPONENT INITIALIZATION
- libStatusPanel = new LibStatusPanel();
- searchLibButton = new JButton(LocalizationManager.get("resolveLibPath"));
-
- libStatusPanel.setStyle(YoshikoLoader.isLibraryLoaded());
-
- searchLibButton.setEnabled(!YoshikoLoader.isLibraryLoaded());
-
- searchLibButton.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- final JFileChooser c = new JFileChooser();
- int returnVal = c.showOpenDialog(ret);
- if (returnVal == JFileChooser.APPROVE_OPTION) {
- YoshikoLoader.loadLibrary(c.getSelectedFile().getAbsolutePath());
- }
- libStatusPanel.setStyle(YoshikoLoader.isLibraryLoaded());
- searchLibButton.setEnabled(!YoshikoLoader.isLibraryLoaded());
- }
- });
-
- getYoshiko = new JButton(LocalizationManager.get("getYoshiko"));
- getYoshiko.addActionListener(new ActionListener() {
-
- @Override
- public void actionPerformed(ActionEvent e) {
- // TODO: Far Future: Fetch Yoshiko and auto-compile
- Desktop desktop = Desktop.getDesktop();
- if (desktop != null){
- if(desktop.isSupported(Desktop.Action.BROWSE)) {
- try {
- desktop.browse(URI.create("https://github.com/spqrPh/yoshiko"));
- } catch (Exception ex) {
- YoshikoLogger.getInstance().getLogger().info("Can't access desktop browser!");
- ex.printStackTrace();
- }
- }
- }
- }
-
- });
-
- SwingUtil.addAll(ret,
- libStatusPanel,
- searchLibButton,
- getYoshiko
- );
-
- //Layout
- GroupLayout layout = new GroupLayout(ret.getContentPane());
-
- layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
- .addComponent(libStatusPanel)
- .addComponent(searchLibButton)
- .addComponent(getYoshiko)
- );
-
- layout.setVerticalGroup(layout.createSequentialGroup()
- .addComponent(libStatusPanel)
- .addComponent(searchLibButton)
- .addComponent(getYoshiko)
- );
-
-
- ret.getContentPane().setLayout(layout);
-
- return ret;
- }
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LibStatusPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LibStatusPanel.java
deleted file mode 100644
index 719915e834f5047260cf69cc982fb8b84f7a8775..0000000000000000000000000000000000000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/LibStatusPanel.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*******************************************************************************
- * 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
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- ******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.swing.components;
-
-import java.awt.Color;
-
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-
-import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
-import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
-import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
-import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
-/**
- * Simple JPanel visually representing whether or not the Yoshiko Lib is loaded and showing some basic info
- *
- */
-@SuppressWarnings("serial")
-public class LibStatusPanel extends JPanel {
-
- final JLabel yoshikoVersionLabel;
-
- public LibStatusPanel() {
- yoshikoVersionLabel = new JLabel();
- this.add(yoshikoVersionLabel);
- }
-
- /**
- * Adjusts the style accordingly by changing its color and updating its text
- */
- public void setStyle(boolean libraryLoaded) {
- if(libraryLoaded) {
- yoshikoVersionLabel.setText(LocalizationManager.get("yoshVersion")+" "+YoshikoLoader.REQUIRED_VERSION+"("+LibraryInterface.getVersionString()+")");
- yoshikoVersionLabel.setForeground(GraphicsLoader.yoshikoGreen);
- }
- else {
- yoshikoVersionLabel.setText(LocalizationManager.get("noLibTitle"));
- yoshikoVersionLabel.setForeground(Color.RED);
- }
- }
-
-}
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 b8277bc372c9f538336b697bbd04340ce1112096..8d2ddfbab332f3a914a46b5fd137c4545005430e 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
@@ -47,24 +47,24 @@ import javax.swing.JScrollPane;
import javax.swing.LayoutStyle;
import javax.swing.ScrollPaneConstants;
+import de.hhu.ba.yoshikoWrapper.taskFactories.CommandTaskFactory;
+import de.hhu.ba.yoshikoWrapper.taskFactories.YoshikoCommand;
+import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.util.swing.BasicCollapsiblePanel;
-import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskIterator;
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;
-import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
+import org.cytoscape.work.TaskManager;
/**This class describes the Swing Panel that the user interacts with in cytoscape
*
@@ -91,7 +91,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
private final LanguageSwitcherPanel langPanel;
private final BasicCollapsiblePanel langWrapper;
- private final BasicCollapsiblePanel libraryPanel;
//Those don't work really as collapsible panels and cause glitches which forces the workaround of wrapping them
//Probably someone used getClass() == instead of instanceof so extending BasicCollapsiblePanel is sadly not possible
@@ -137,12 +136,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
langWrapper = new BasicCollapsiblePanel(LocalizationManager.get("switchLanguage"));
langWrapper.add(langPanel);
- libraryPanel = LibraryPanelFactory.createLibraryPanel();
- //If no library is loaded yet the obvious panel should be showing up
- if (!YoshikoLoader.isLibraryLoaded()) {
- libraryPanel.setCollapsed(false);
- }
-
ecPanel = new EditCostPanel();
ecPanelWrapper = new BasicCollapsiblePanel(LocalizationManager.get("editingCostPanel"));
ecPanelWrapper.add(ecPanel);
@@ -162,7 +155,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
//Add components to the scrollable part of the main panel
SwingUtil.addAll(scrollableContent,
langWrapper,
- libraryPanel,
ecPanelWrapper,
reductionWrapper,
opWrapper
@@ -217,7 +209,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
scrollLayout.setHorizontalGroup(scrollLayout.createParallelGroup(Alignment.LEADING,true)
.addComponent(langWrapper,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
- .addComponent(libraryPanel,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(ecPanelWrapper,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(reductionWrapper,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(opWrapper,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
@@ -236,7 +227,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
scrollLayout.setVerticalGroup(scrollLayout.createSequentialGroup()
.addComponent(langWrapper,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
- .addComponent(libraryPanel,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(ecPanelWrapper,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(reductionWrapper,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(opWrapper,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
@@ -287,18 +277,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
);
}
- //Annotation: Currently Cytoscape is really weird concerning directed/undirected edges
- //There is an API function isDirected() for edges but all edges are directed
- //I'll leave this commented out until CS makes sense
-
-// if (GraphAnalyzer.isDirected(networkToBeProcessed)) {
-// JOptionPane.showMessageDialog(
-// null,
-// LocalizationManager.get("directedGraphWarning"),
-// LocalizationManager.get("optionpane_title"),
-// JOptionPane.WARNING_MESSAGE
-// );
-// }
//SWING BLACK MAGIC
Window noWindow = null;
@@ -311,30 +289,16 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
statusWindow.setAlwaysOnTop(false);
//SWING BLACK MAGIC
- if (YoshikoLoader.isLibraryLoaded()){
- AbstractTask yoshiko = new AlgorithmTask(
- popupLevel,
- fetchParameters(networkToBeProcessed)
- );
- /**
- * Don't queue multiple runs at once because that will get messy
- */
- if (!iterator.hasNext()) {
- iterator.append(yoshiko);
+ CommandTaskFactory commandTaskFactory = new CommandTaskFactory(YoshikoCommand.PERFORM_ALGORITHM);
+ TaskIterator taskIterator = commandTaskFactory.createTaskIterator();
- CyCore.dialogTaskManager.setExecutionContext(statusWindow);
- CyCore.dialogTaskManager.execute(iterator);
-
- }
- }
- else {
- JOptionPane.showMessageDialog(
- null,
- LocalizationManager.get("noLibTitle"),
- LocalizationManager.get("noLibMessage"),
- JOptionPane.ERROR_MESSAGE
- );
+ try {
+ CyCore.runAndWait(taskIterator);
+ } catch (InterruptedException ex) {
+ ex.printStackTrace();
}
+
+ System.out.println();
}
};
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
index d276d08c05343ca9a817a6aeeb697059abd0867f..9d39b11d65d0212a18d43bff3806c3f73413d8f4 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
@@ -125,34 +125,6 @@ NetworkAboutToBeDestroyedListener
marker = new BasicCollapsiblePanel(LocalizationManager.get("solutionMarker"));
marker.setLayout(new BoxLayout(marker,BoxLayout.Y_AXIS));
- JLabel costLabel = new JLabel(LocalizationManager.get("cost")+" "+result.getFlags().getTotalCost());
- marker.add(costLabel);
-
- if (result.getFlags().getIlpGenerated()) {
- //TODO: Move to MarkerPanel for better codestyle
- //Optional Markers
-
- if(result.getFlags().getOptimal()) {
- JLabel optimalLabel;
- optimalLabel = new JLabel(LocalizationManager.get("optimal"));
- optimalLabel.setForeground(GraphicsLoader.yoshikoGreen);
- marker.add(optimalLabel);
- }
- else {
- JLabel optimalLabel;
- optimalLabel = new JLabel(LocalizationManager.get("notOptimal"));
- optimalLabel.setForeground(Color.RED);
- marker.add(optimalLabel);
- marker.add(new JLabel(result.getFlags().getSolvedInstances()+"/"+result.getFlags().getReducedInstances()+" "+LocalizationManager.get("redSolved")));
- marker.add(new JLabel(LocalizationManager.get("lastInstanceGap")+" "+(int)(100*result.getFlags().getLastGap())+"%"));
- }
-
- if (result.getFlags().getTimedOut()) {
- marker.add(new JLabel(LocalizationManager.get("timeoutMarker")));
- }
- marker.setCollapsed(false);
- }
-
this.add(marker);
destroyButton = new JButton(LocalizationManager.get("discardSolution"));
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 3d0d53fb7412c0e7905c422f419a78718ce20882..65c4a5e0a3f019cff91d7e1f2c8a63569fbe0f3a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -22,16 +22,10 @@
package de.hhu.ba.yoshikoWrapper.tasks;
import java.awt.Window;
-import java.util.Properties;
-import javax.swing.SwingUtilities;
-
-import org.cytoscape.application.swing.CytoPanel;
-import org.cytoscape.application.swing.CytoPanelComponent;
-import org.cytoscape.application.swing.CytoPanelName;
-import org.cytoscape.application.swing.CytoPanelState;
-import org.cytoscape.model.CyColumn;
-import org.cytoscape.model.CyNode;
+import de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm.YoshikoAlgoritmController;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyTable;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.ContainsTunables;
import org.cytoscape.work.ObservableTask;
@@ -41,20 +35,9 @@ import org.slf4j.Logger;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
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;
-import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
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.IntVector;
-import de.hhu.ba.yoshikoWrapper.swig.LibraryInput;
-import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
@@ -77,13 +60,6 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
@ContainsTunables
public ParameterSet parameterSet = null;
-
-
- //Temps, pointing to and need to be freed in C++
- private LibraryInput c_input;
- private ClusterEditingSolutions c_result;
- private CoreAlgorithm c_algorithm;
-
private ResultPanel resultPanel;
private YoshikoResult result;
@@ -92,7 +68,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
/**
* Default constructor, creates a new AlgorithmTask
* @param statusWindow The Window in which the status-bar is to be shown, can be null
- * @param net The network that is to be clustered
+ // * @param net The network that is to be clustered
* @param parameterSet The parameter set specifying the clustering mode
*/
public AlgorithmTask(
@@ -106,6 +82,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ CyNetwork networkToBeProcessed = CyCore.cy.getCurrentNetwork();
//TODO: Improve setProgress values
@@ -118,15 +95,13 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
throw new Exception("CoreAlgorithm called on a net that is NULL!"); //TODO: Localize
}
- //Set time limit
- LibraryInterface.setTimeLimit(parameterSet.timeLimit);
- if (parameterSet.disableMultiThreading) {
- LibraryInterface.setThreadLimit(1);
- }
- else {
- LibraryInterface.setThreadLimit(0);
- }
+ YoshikoAlgoritmController yoshikoAlgoritmController = new YoshikoAlgoritmController(parameterSet);
+ yoshikoAlgoritmController.controllAlgorithm();
+
+ CyTable table = networkToBeProcessed.getDefaultEdgeTable();
+
+/*
//Create a node map to identify nodes and eges in the solution
NodeMap nodeMap = new NodeMap(parameterSet.net);
taskMonitor.setProgress(0.1);
@@ -136,15 +111,6 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
CyColumn permanentColumn = parameterSet.getPermanentColumn();
CyColumn forbiddenColumn = parameterSet.getForbiddenColumn();
- //Generate an c_input instance from the network
- c_input = NetworkParser.parseNetwork(
- parameterSet.net,
- nodeMap,
- weightColumn,
- permanentColumn,
- forbiddenColumn,
- parameterSet.defaultDeletionCost
- );
taskMonitor.setProgress(0.2);
boolean containsRealValues = GraphAnalyzer.containsRealValues(
@@ -155,90 +121,19 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
parameterSet.defaultInsertionCost,
parameterSet.defaultDeletionCost);
- //Suggest reduction rules
- if (parameterSet.suggestReduction) {
- parameterSet.reductionRulesBitMask = GraphAnalyzer.suggestReductionRules(containsRealValues, parameterSet.useHeuristic);
- }
- //Set the default value for insertion cost
- c_input.setDefaultInsertionCost(parameterSet.defaultInsertionCost);
-
- System.out.print(parameterSet.toString()); //TODO: Move to debug logger
-
- //Call Yoshiko <<< Algorithm is performed here
- c_algorithm = LibraryInterface.getRun(c_input,
- parameterSet.solCount,
- parameterSet.reductionRulesBitMask,
- parameterSet.snrMultFactor,
- parameterSet.useHeuristic,
- parameterSet.usePartitionCuts,
- parameterSet.useTriangleCuts,
- parameterSet.clusterCount
- );
- c_algorithm.registerCplexInformer(new StatusInformer(statusWindow,taskMonitor));
-
- c_result = c_algorithm.run();
+ System.out.print(parameterSet.toString()); //TODO: Move to debug logger
taskMonitor.setProgress(0.9);
- checkForInvalidSolutions(c_result);
-
- long numberOfSolutions = c_result.getNumberOfSolutions();
-
- taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO: Localize
-
- result = new YoshikoResult(parameterSet.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(result,i);
-
- String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
+ taskMonitor.setStatusMessage("Found: "+"okkkkkkkkkkkkk solutions!"); //TODO: Localize
- parameterSet.net.getDefaultNodeTable().deleteColumn(columnName);
- parameterSet.net.getDefaultNodeTable().createColumn(columnName, String.class, false);
- //Fetch number of clusters in the solution
- long numberOfClusters = c_result.getNumberOfClusters(i);
-
- //Loop over clusters
- for (long k=0;k<numberOfClusters;k++) {
- //Create java instance
- YoshikoCluster cluster = new YoshikoCluster(solution,k);
-
-
- taskMonitor.setStatusMessage("Processing clusters "+(k+1)+" of "+numberOfClusters);
-
- IntVector clusterVector = c_result.getCluster(i, k);
-
- long sizeOfCluster = clusterVector.size();
- for (int l=0;l<sizeOfCluster;l++) { //Unsafe mismatch int long
- //taskMonitor.setStatusMessage("Processing node "+(l+1)+ " of "+sizeOfCluster);
- int nodeID = clusterVector.get(l);
- CyNode node = nodeMap.indexOf(nodeID); //<<< Another int/long conversion
- cluster.addNode(node);
-
- parameterSet.net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
- }
- //Register clusters with solution for further reference
- solution.addCluster(cluster);
- }
- //Sort clusters by size, descending as the biggest clusters are usually the most relevant
- //solution.sortClusters(YoshikoCluster.lessThanComparator);
- //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
- c_algorithm.delete();
- c_input.delete();
- c_result.delete();
+
//Generate solutionsPanel
resultPanel = new ResultPanel(result);
@@ -261,54 +156,10 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
}
);
//eastPanel.getThisComponent().revalidate();
-
+*/
}
- /**
- * Simple helper function that analyzes C++ results and identifies solutions that are not usable or meaningful
- * @param result The ClusterEditingSolutions object generated in C++ by a Yoshiko run
- * @throws Exception Throws an exception if the result is not usable
- */
- private void checkForInvalidSolutions(ClusterEditingSolutions result) throws Exception {
- //TODO: Feasible might be the wrong word here
- if (result == null) {
- //There was no c_result object generated at all
- throw new Exception(LocalizationManager.get("noFeasible"));
- }
-
- if (result.getNumberOfSolutions() == 0) {
- //The c_result object is empty
- throw new Exception(LocalizationManager.get("noFeasible"));
- }
- if (result.getNumberOfSolutions() == 1) {
- //The c_result doesn't contain any clusters
- if (result.getNumberOfClusters(0) == 0) {
- throw new Exception(LocalizationManager.get("noFeasible"));
- }
- }
-
- }
- @Override
- public void cancel() {
- //Free C++ resources
- if (c_algorithm != null) {
- //System.out.println("Deleting CoreAlgorithm instance!");
- c_algorithm.cancel();
- c_algorithm.delete();
- }
- if (c_input != null) {
- c_input.delete();
- }
- if (c_result != null) {
- c_result.delete();
- }
- //Delete (incomplete) c_result panel
- if (resultPanel != null) {
- resultPanel.deleteResult();
- }
- super.cancel();
- }
@SuppressWarnings("unchecked")
@Override
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/BinaryHeap.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/BinaryHeap.java
new file mode 100644
index 0000000000000000000000000000000000000000..a9156e409187bf8fb31c8585aa5dc1f281c5f3e1
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/BinaryHeap.java
@@ -0,0 +1,130 @@
+package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
+
+import java.util.*;
+
+public class BinaryHeap {
+ ArrayList<Double> list = new ArrayList();
+ HashMap<Integer, YoshikoEdge> map = new HashMap<>();
+
+ public BinaryHeap(){
+ list.add(Double.NEGATIVE_INFINITY);
+ map.put(0, null);
+ }
+
+ public void add(YoshikoEdge edge){
+
+ list.add(edge.maxIcfIcp);
+ map.put(list.size()-1, edge);
+
+ checkParent(list.size()-1);
+ }
+
+ public void add(Set<YoshikoEdge> edgeSet){
+ for(YoshikoEdge edge : edgeSet){
+ add(edge);
+ }
+ }
+
+ public void remove(YoshikoEdge edge){
+ int index = getIndexFromValue(edge);
+
+ if (index < 0){
+ //Die Kante wurde bereits auf "forbidden" gesetzt
+ return;
+ }
+
+ map.replace(index, map.get(map.size()-1));
+ map.remove(map.size()-1);
+
+ list.set(index, list.get(list.size()-1));
+ list.remove(list.size()-1);
+ }
+
+ public void remove(Set<YoshikoEdge> edgeSet){
+ for (YoshikoEdge edge : edgeSet){
+ remove(edge);
+ }
+ }
+
+ public YoshikoEdge popMax(){
+ double maxVal = Double.NEGATIVE_INFINITY;
+ for (Double i : list){
+ if (i > maxVal){
+ maxVal = i;
+ }
+ }
+
+ int index = list.indexOf(maxVal);
+
+ YoshikoEdge e = map.get(index);
+
+ map.replace(index, map.get(map.size()-1));
+ map.remove(map.size()-1);
+
+ list.set(index, list.get(list.size()-1));
+ list.remove(list.size()-1);
+
+ return e;
+ }
+
+
+
+ public void checkUptatedNode(YoshikoEdge edge){
+ int index = getIndexFromValue(edge);
+
+ checkParent(index);
+ checkChild(index);
+ }
+
+ public int size(){
+ return list.size()-1;
+ }
+
+ private void checkParent(int index){
+ int parentIndex = index / 2;
+ if (list.get(index) < list.get(parentIndex)){
+ swap(index, parentIndex);
+
+ checkParent(parentIndex);
+ }
+ }
+
+ private void checkChild(int index){
+ int childIndex = index * 2;
+ if (list.size()-1 < childIndex){
+ return;
+ }else if(list.size()-1 == childIndex){
+
+ }else if (list.get(childIndex) < list.get(childIndex+1)){
+ childIndex++;
+ }
+
+ if (list.get(index) > list.get(childIndex)){
+ swap(index, childIndex);
+
+ checkChild(childIndex);
+ }
+ }
+
+ private void swap(int index, int parentIndex){
+ double tmpVal = list.get(index);
+ list.set(index, list.get(parentIndex));
+ list.set(parentIndex, tmpVal);
+
+ YoshikoEdge tmpEdge = map.get(index);
+ map.replace(index, map.get(parentIndex));
+ map.replace(parentIndex, tmpEdge);
+ }
+
+ private int getIndexFromValue(YoshikoEdge edge){
+ for (Map.Entry<Integer, YoshikoEdge> entry : map.entrySet()) {
+ if (entry.getKey() == 0){
+ //Der erste DummyEintrag im Heap soll ignoriert werden
+ }
+ else if (entry.getValue().equals(edge)) {
+ return entry.getKey();
+ }
+ }
+ return -1;
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/ClusteringAlgorithm.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/ClusteringAlgorithm.java
new file mode 100644
index 0000000000000000000000000000000000000000..f4cbd5a2e354103d9b52e76ffb2f0a88f4aac6cc
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/ClusteringAlgorithm.java
@@ -0,0 +1,335 @@
+package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
+
+import java.util.Set;
+
+
+public class ClusteringAlgorithm {
+
+ private YoshikoGraph g;
+ private BinaryHeap bHeap;
+ private double clusteringCost;
+
+ public void runAlgorithm(YoshikoGraph g){
+ this.g = g;
+ clusteringCost = 0;
+
+ bHeap = new BinaryHeap();
+
+ initializeQueue();
+
+ //workHeap();
+ System.out.println(clusteringCost);
+ }
+
+ private void initializeQueue(){
+ bHeap = new BinaryHeap();
+
+ Set<YoshikoEdge> edgeSet = g.edgeSet;
+ Set<Long> nodeSet = g.nodeSet;
+
+ calculateIcf(nodeSet, edgeSet);
+ System.out.println();
+ /*calculateIcp(nodeSet, edgeSet);
+ calculateMaxIcpIcf(edgeSet);
+
+ addAllNotForbidden(edgeSet);*/
+ }
+/*
+ private void addAllNotForbidden(Set<MyDefaultWeightedEdge> edgeSet){
+ for (MyDefaultWeightedEdge e : edgeSet){
+ if(g.getEdgeWeight(e) != Double.NEGATIVE_INFINITY){
+ bHeap.add(e);
+ }
+ }
+ }
+*/
+ private void calculateIcf(Set<Long> nodeSet, Set<YoshikoEdge> edgeSet){
+ int i=0;
+ for (YoshikoEdge edge : edgeSet){
+ System.out.println(i);
+ i++;
+ double icf = 0;
+
+ if (edge.weight>0){
+ icf = edge.weight;
+ }
+
+ for (long v : nodeSet){
+ long v1 = edge.source;
+ long v2 = edge.target;
+ if ((v == v1)||v == v2){
+ continue;
+ }
+ if (g.getEdge(v, v1).weight > 0 && g.getEdge(v, v2).weight > 0) {
+ icf = icf + Math.min(g.getEdge(v, v1).weight, g.getEdge(v, v2).weight);
+ }
+ }
+ edge.icf = icf;
+ }
+ }
+/*
+ private void calculateIcp(Set<Long> vertexSet, Set<YoshikoEdge> edgeSet){
+ for (YoshikoEdge edge : edgeSet){
+ double icp = 0;
+
+ if (g.getEdgeWeight(edge) < 0){
+ icp = -(g.getEdgeWeight(edge));
+ }
+
+ for (Long v : vertexSet){
+ MyVertex v1 = g.getEdgeSource(edge);
+ MyVertex v2 = g.getEdgeTarget(edge);
+ if (v.equals(v1)||v.equals(v2)){
+ continue;
+ }
+
+ if (g.getEdgeWeight(g.getEdge(v, v1)) > 0 && g.getEdgeWeight(g.getEdge(v, v2)) < 0) {
+ icp = icp + Math.min(g.getEdgeWeight(g.getEdge(v, v1)), -g.getEdgeWeight(g.getEdge(v, v2)));
+ }else if (g.getEdgeWeight(g.getEdge(v, v1)) < 0 && g.getEdgeWeight(g.getEdge(v, v2)) > 0) {
+ icp = icp + Math.min(-g.getEdgeWeight(g.getEdge(v, v1)), g.getEdgeWeight(g.getEdge(v, v2)));
+ }
+ edge.icp = icp;
+ }
+ }
+ }
+
+ private void calculateMaxIcpIcf(Set<YoshikoEdge> edgeSet){
+ for (YoshikoEdge edge : edgeSet){
+ edge.calculateMaxIcfIcp();
+ }
+ }
+
+ private void workHeap(){
+ while (bHeap.size() > 0){
+ System.out.println(bHeap.size());
+ MyDefaultWeightedEdge e = bHeap.popMax();
+
+ if (e.icf >= e.icp){
+ if(g.getEdgeWeight(e) < 0){
+ clusteringCost -= g.getEdgeWeight(e);
+ }
+ makeEdgePermanent(e);
+ }
+ else{
+ if(g.getEdgeWeight(e) > 0){
+ clusteringCost += g.getEdgeWeight(e);
+ }
+ makeEdgeForbidden(e);
+ }
+ }
+ }
+
+ private void makeEdgePermanent(MyDefaultWeightedEdge e){
+ substactInfluenceOfVerticesOnIcfIcp(e);
+
+ MyVertex mergedVertex = mergeVertexes(e);
+ calculateNewEdgesIcfIcp(mergedVertex);
+
+ addInfluenceOfVertexOnIcfIcp(mergedVertex);
+
+ System.out.println("perm");
+ }
+
+ private MyVertex mergeVertexes(MyDefaultWeightedEdge e){
+ MyVertex p1 = g.getEdgeSource(e);
+ MyVertex p2 = g.getEdgeTarget(e);
+
+ MyVertex mergedVertex = new MyVertex(p1, p2);
+ g.addVertex(mergedVertex);
+
+ Set<MyVertex> vSet = g.vertexSet();
+
+ for (MyVertex v : vSet) {
+ if ((v.equals(p1))||(v.equals(p2))||(v.equals(mergedVertex))){
+ continue;
+ }
+
+ MyDefaultWeightedEdge p1Edge = g.getEdge(p1, v);
+ double p1EdgeWeight = g.getEdgeWeight(p1Edge);
+
+ MyDefaultWeightedEdge p2Edge = g.getEdge(p2, v);
+ double p2EdgeWeight = g.getEdgeWeight(p2Edge);
+
+ MyDefaultWeightedEdge newEdge = g.addEdge(mergedVertex, v);
+ g.setEdgeWeight(newEdge, p1EdgeWeight+p2EdgeWeight);
+ }
+
+ bHeap.remove(g.outgoingEdgesOf(p1));
+ g.removeVertex(p1);
+
+ bHeap.remove(g.outgoingEdgesOf(p2));
+ g.removeVertex(p2);
+
+ return mergedVertex;
+ }
+
+ private void calculateNewEdgesIcfIcp(MyVertex mergedVertex){
+ Set<Long> vertexSet = g.vertexSet();
+ Set<YoshikoEdge> newEdgesSet = g.outgoingEdgesOf(mergedVertex);
+
+ calculateIcf(vertexSet, newEdgesSet);
+ calculateIcp(vertexSet, newEdgesSet);
+ calculateMaxIcpIcf(newEdgesSet);
+
+ for(YoshikoEdge edge : newEdgesSet){
+ if (g.getEdgeWeight(edge) == Double.NEGATIVE_INFINITY){
+ continue;
+ }
+ bHeap.add(edge);
+ }
+
+ }
+
+ private void substactInfluenceOfVerticesOnIcfIcp(MyDefaultWeightedEdge e){
+ MyVertex p1 = g.getEdgeSource(e);
+ MyVertex p2 = g.getEdgeTarget(e);
+
+ Set<MyDefaultWeightedEdge> edgeSet = g.edgeSet();
+ for (MyDefaultWeightedEdge edge : edgeSet){
+ MyVertex v1 = g.getEdgeSource(edge);
+ MyVertex v2 = g.getEdgeTarget(edge);
+
+ if (v1.equals(p1)||v1.equals(p2)||v2.equals(p1)||v2.equals(p2)){
+ continue;
+ }
+
+ //Subtraiere Einfluss des Dreiecks v1p1v2 auf icf
+ MyDefaultWeightedEdge ux = g.getEdge(v1, p1);
+ MyDefaultWeightedEdge vx = g.getEdge(v2, p1);
+
+ if (g.getEdgeWeight(ux) > 0 && g.getEdgeWeight(vx) > 0){
+ edge.icf -= Math.min(g.getEdgeWeight(ux), g.getEdgeWeight(vx));
+ }
+
+ //Subtraiere Einfluss des Dreiecks v1p2v2 auf icf
+ ux = g.getEdge(v1, p2);
+ vx = g.getEdge(v2, p2);
+
+ if (g.getEdgeWeight(ux) > 0 && g.getEdgeWeight(vx) > 0){
+ edge.icf -= Math.min(g.getEdgeWeight(ux), g.getEdgeWeight(vx));
+ }
+
+ //Subtraiere Einfluss des Dreiecks v1p1v2 auf icp
+ ux = g.getEdge(v1, p1);
+ vx = g.getEdge(v2, p1);
+
+ if (g.getEdgeWeight(ux) > 0 && g.getEdgeWeight(vx) < 0){
+ edge.icp -= Math.min(g.getEdgeWeight(ux), -g.getEdgeWeight(vx));
+ }else if (g.getEdgeWeight(ux) < 0 && g.getEdgeWeight(vx) > 0){
+ edge.icp -= Math.min(-g.getEdgeWeight(ux), g.getEdgeWeight(vx));
+ }
+
+ //Subtraiere Einfluss des Dreiecks v1p2v2 auf icp
+ ux = g.getEdge(v1, p2);
+ vx = g.getEdge(v2, p2);
+
+ if (g.getEdgeWeight(ux) > 0 && g.getEdgeWeight(vx) < 0){
+ edge.icp -= Math.min(g.getEdgeWeight(ux), -g.getEdgeWeight(vx));
+ }else if (g.getEdgeWeight(ux) < 0 && g.getEdgeWeight(vx) > 0){
+ edge.icp -= Math.min(-g.getEdgeWeight(ux), g.getEdgeWeight(vx));
+ }
+
+ edge.maxIcfIcp = Math.max(edge.icf, edge.icf);
+ }
+ }
+
+ private void addInfluenceOfVertexOnIcfIcp(MyVertex mergedVertex) {
+ Set<MyDefaultWeightedEdge> edgeSet = g.edgeSet();
+
+ for (MyDefaultWeightedEdge edge : edgeSet){
+ MyVertex v1 = g.getEdgeSource(edge);
+ MyVertex v2 = g.getEdgeTarget(edge);
+
+ if (v1.equals(mergedVertex)||v1.equals(mergedVertex)){
+ continue;
+ }
+
+ //Addiere Einfluss des Dreiecks v1-MergedVertex-v2 auf icf
+ MyDefaultWeightedEdge ux = g.getEdge(v1, mergedVertex);
+ MyDefaultWeightedEdge vx = g.getEdge(v2, mergedVertex);
+
+ if (g.getEdgeWeight(ux) > 0 && g.getEdgeWeight(vx) > 0){
+ edge.icf += Math.min(g.getEdgeWeight(ux), g.getEdgeWeight(vx));
+ }
+
+
+ //Addiere Einfluss des Dreiecks v1-MergedVertex-v2 auf icp
+ ux = g.getEdge(v1, mergedVertex);
+ vx = g.getEdge(v2, mergedVertex);
+
+ if (g.getEdgeWeight(ux) > 0 && g.getEdgeWeight(vx) < 0){
+ edge.icp += Math.min(g.getEdgeWeight(ux), -g.getEdgeWeight(vx));
+ }else if (g.getEdgeWeight(ux) < 0 && g.getEdgeWeight(vx) > 0){
+ edge.icp += Math.min(-g.getEdgeWeight(ux), g.getEdgeWeight(vx));
+ }
+
+ }
+ }
+
+ private void makeEdgeForbidden(MyDefaultWeightedEdge e){
+ editInfluenzeOfForbiddenEdge(e);
+
+ g.setEdgeWeight(e, Double.NEGATIVE_INFINITY);
+ bHeap.remove(e);
+ System.out.println("rm");
+ }
+
+ private void editInfluenzeOfForbiddenEdge(MyDefaultWeightedEdge forbiddenEdge){
+ MyVertex x1 = g.getEdgeSource(forbiddenEdge);
+ MyVertex x2 = g.getEdgeTarget(forbiddenEdge);
+
+ Set<MyDefaultWeightedEdge> v1EdgeSet = g.outgoingEdgesOf(x1);
+ for (MyDefaultWeightedEdge edge : v1EdgeSet){
+ MyVertex v1 = x1;
+ MyVertex v2 = g.getEdgeTarget(edge);
+ if (v2.equals(v1)){
+ v2 = g.getEdgeSource(edge);
+ }
+ if (v1.equals(x2)||v2.equals(x2)){
+ continue;
+ }
+
+ MyDefaultWeightedEdge edge2 = g.getEdge(v2, x2);
+
+ if (g.getEdgeWeight(forbiddenEdge)>0 && g.getEdgeWeight(edge2) > 0){
+ edge.icf -= Math.min(g.getEdgeWeight(forbiddenEdge), g.getEdgeWeight(edge2));
+ edge.icp += g.getEdgeWeight(edge2);
+ }
+
+ if (g.getEdgeWeight(forbiddenEdge) > 0 && g.getEdgeWeight(edge2) < 0){
+ edge.icp -= Math.min(g.getEdgeWeight(forbiddenEdge), -g.getEdgeWeight(edge2));
+ } else if (g.getEdgeWeight(forbiddenEdge) < 0 && g.getEdgeWeight(edge2) > 0){
+ if (g.getEdgeWeight(forbiddenEdge)*(-1) < g.getEdgeWeight(edge2)){
+ edge.icp += g.getEdgeWeight(edge2)+g.getEdgeWeight(forbiddenEdge);
+ }
+ }
+ }
+
+ Set<MyDefaultWeightedEdge> v2EdgeSet = g.outgoingEdgesOf(x2);
+ for (MyDefaultWeightedEdge edge : v2EdgeSet){
+ MyVertex v1 = x2;
+ MyVertex v2 = g.getEdgeTarget(edge);
+ if (v2.equals(v1)){
+ v2 = g.getEdgeSource(edge);
+ }
+ if (v1.equals(x1)||v2.equals(x1)){
+ continue;
+ }
+
+ MyDefaultWeightedEdge edge2 = g.getEdge(v2, x1);
+
+ if (g.getEdgeWeight(forbiddenEdge)>0 && g.getEdgeWeight(edge2) > 0){
+ edge.icf -= Math.min(g.getEdgeWeight(forbiddenEdge), g.getEdgeWeight(edge2));
+ edge.icp += g.getEdgeWeight(edge2);
+ }
+
+ if (g.getEdgeWeight(forbiddenEdge) > 0 && g.getEdgeWeight(edge2) < 0){
+ edge.icp -= Math.min(g.getEdgeWeight(forbiddenEdge), -g.getEdgeWeight(edge2));
+ } else if (g.getEdgeWeight(forbiddenEdge) < 0 && g.getEdgeWeight(edge2) > 0){
+ if (g.getEdgeWeight(forbiddenEdge)*(-1) < g.getEdgeWeight(edge2)){
+ edge.icp += g.getEdgeWeight(edge2)+g.getEdgeWeight(forbiddenEdge);
+ }
+ }
+ }
+ }*/
+}
\ No newline at end of file
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java
new file mode 100644
index 0000000000000000000000000000000000000000..ad87b23f871b3ea9d1f92b060b9e818046cb86f9
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/GraphTranslator.java
@@ -0,0 +1,101 @@
+package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
+
+import com.sun.scenario.effect.impl.sw.sse.SSEBlend_SRC_OUTPeer;
+import de.hhu.ba.yoshikoWrapper.CyActivator;
+import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
+import org.cytoscape.model.*;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+public class GraphTranslator {
+ private CyNetwork network;
+ private ParameterSet parameterSet;
+
+ private double deletionCostDefault;
+ private double insertionCostDefault;
+
+ CyColumn weightColumn;
+
+ public GraphTranslator(ParameterSet parameterSet){
+ this.parameterSet = parameterSet;
+ this.network = parameterSet.net;
+ this.weightColumn = parameterSet.getWeightColumn();
+ this.deletionCostDefault = parameterSet.defaultDeletionCost;
+ this.insertionCostDefault = parameterSet.defaultInsertionCost;
+ }
+
+ public YoshikoGraph translateGraph(){
+ YoshikoGraph g = this.makeGraph();
+ this.makeGraphComplete(g);
+ return g;
+ }
+
+ private YoshikoGraph makeGraph(){
+ YoshikoGraph g = new YoshikoGraph();
+
+ List<CyNode> nodeList = network.getNodeList();
+ List<CyEdge> edgeList = network.getEdgeList();
+
+ for (CyNode n : nodeList){
+ g.addNode(n.getSUID());
+ }
+
+ for (CyEdge e : edgeList){
+ YoshikoEdge yoshikoEdge = new YoshikoEdge(e.getSource().getSUID(), e.getTarget().getSUID(), this.extractValue(e), e.getSUID().intValue());
+ g.addEdge(yoshikoEdge);
+ }
+
+ return g;
+ }
+
+ private YoshikoGraph makeGraphComplete(YoshikoGraph g){
+ Set<Long> nodeSet = g.getNodeSet();
+ Set<Long> usedINodes = new HashSet<>();
+
+ Set<YoshikoEdge> edgesToAdd = new HashSet<>();
+ int edgeID = 1;
+ for (long i : nodeSet){
+ usedINodes.add(i);
+ for (long j : nodeSet){
+ if (!usedINodes.contains(j)){
+ YoshikoEdge e = new YoshikoEdge(i, j, insertionCostDefault, -edgeID);
+ if (!g.containsEdge(e)){
+ edgesToAdd.add(e);
+ System.out.println(edgeID);
+ edgeID++;
+ }
+ }
+ }
+ }
+
+
+ g.addEdge(edgesToAdd);
+ return g;
+ }
+
+ private double extractValue(CyEdge edge){
+ //Parse editing costs
+ double weight = deletionCostDefault;
+
+ //Fetch entry and check if it exists
+ CyRow edgeEntry = network.getRow(edge);
+
+ //Check if the column contains an entry for the respective edge
+ //It is possible, that there are missing entries
+ if (weightColumn != null){
+ if (edgeEntry.get(weightColumn.getName(), weightColumn.getType()) != null){
+ if (weightColumn.getType() == Integer.class) {
+ weight = 1.0*edgeEntry.get(weightColumn.getName(), Integer.class);
+ }
+ else if (weightColumn.getType() == Double.class) {
+ weight = edgeEntry.get(weightColumn.getName(), Double.class);
+ }
+ }
+
+ }
+ return weight;
+ }
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/MyDefaultWeightedEdge.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/MyDefaultWeightedEdge.java
new file mode 100644
index 0000000000000000000000000000000000000000..aea98ea831af0b8ae01b556e6a71f6592324b0d4
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/MyDefaultWeightedEdge.java
@@ -0,0 +1,8 @@
+package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
+
+import org.jgrapht.Graph;
+import org.jgrapht.graph.DefaultWeightedEdge;
+
+
+public class MyDefaultWeightedEdge extends DefaultWeightedEdge{
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java
new file mode 100644
index 0000000000000000000000000000000000000000..35d6bcc848c741874dc93a2905d5dfead6816690
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoAlgoritmController.java
@@ -0,0 +1,37 @@
+package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
+
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTable;
+import org.jgrapht.Graph;
+import org.jgrapht.graph.SimpleWeightedGraph;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+
+public class YoshikoAlgoritmController {
+
+ private CyNetwork network;
+ private ParameterSet parameterSet;
+
+ public YoshikoAlgoritmController(ParameterSet parameterSet){
+ this.parameterSet = parameterSet;
+ this.network = parameterSet.net;
+ }
+
+ public void controllAlgorithm(){
+ GraphTranslator translator = new GraphTranslator(parameterSet);
+ YoshikoGraph graph = translator.translateGraph();
+
+ ClusteringAlgorithm clusteringAlgorithm = new ClusteringAlgorithm();
+ clusteringAlgorithm.runAlgorithm(graph);
+
+ System.out.println();
+ }
+
+
+}
\ No newline at end of file
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoEdge.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoEdge.java
new file mode 100644
index 0000000000000000000000000000000000000000..9fef387cd73633ca1003ac12f8023dab2d968396
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoEdge.java
@@ -0,0 +1,36 @@
+package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
+
+public class YoshikoEdge implements Comparable{
+ int id;
+ long source;
+ long target;
+ double weight;
+
+ double icf;
+ double icp;
+ double maxIcfIcp;
+
+ public YoshikoEdge(long source, long target, Double weight, int id){
+ this.source = source;
+ this.target = target;
+ this.weight = weight;
+ this.id = id;
+ }
+
+ public void calculateMaxIcfIcp(){
+ if (icp >icf ){
+ maxIcfIcp = icp;
+ } else {
+ maxIcfIcp = icf;
+ }
+ }
+
+ @Override
+ public int compareTo(Object o) {
+ if (o==this){
+ return 0;
+ }
+ YoshikoEdge e = (YoshikoEdge) o;
+ return this.id - e.id;
+ }
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoGraph.java b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoGraph.java
new file mode 100644
index 0000000000000000000000000000000000000000..cc70d3ae0561b5556d2a033922ecbb701ec77443
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/yoshikoAlgorithm/YoshikoGraph.java
@@ -0,0 +1,82 @@
+package de.hhu.ba.yoshikoWrapper.yoshikoAlgorithm;
+
+import org.cytoscape.model.CyNode;
+
+import java.util.HashSet;
+import java.util.Set;
+import java.util.TreeSet;
+
+public class YoshikoGraph {
+ Set<Long> nodeSet;
+ Set<YoshikoEdge> edgeSet;
+
+ public YoshikoGraph(){
+ this.nodeSet = new HashSet<>();
+ this.edgeSet = new TreeSet<>();
+ }
+
+ public void addNode(long node){
+ nodeSet.add(node);
+ }
+
+ public void addEdge(YoshikoEdge edge){
+ edgeSet.add(edge);
+ }
+
+ public void addEdge(Set<YoshikoEdge> edges){
+ for (YoshikoEdge e : edges){
+ edgeSet.add(e);
+ }
+ }
+
+ public void addEdge(long n1, long n2, double value, int id){
+ nodeSet.add(n1);
+ nodeSet.add(n2);
+
+ YoshikoEdge edge = new YoshikoEdge(n1, n2, value, id);
+ edgeSet.add(edge);
+ }
+
+ public boolean containsNode(CyNode node){
+ return nodeSet.contains(node);
+ }
+
+ public boolean containsEdge(YoshikoEdge edge){
+
+ return edgeSet.contains(edge);
+ }
+
+ public boolean containsEdge(long n1, long n2){
+ for(YoshikoEdge e : edgeSet){
+ if (n1 == (e.source)){
+ if (n2 == (e.target)){
+ return true;
+ }
+ }else if (n2 == (e.source)){
+ if (n1 == (e.target)){
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ public Set<Long> getNodeSet(){
+ return nodeSet;
+ }
+
+ public YoshikoEdge getEdge(long n1, long n2){
+ for(YoshikoEdge e : edgeSet){
+ if (n1 == (e.source)){
+ if (n2 == (e.target)){
+ return e;
+ }
+ }else if (n2 == (e.source)){
+ if (n1 == (e.target)){
+ return e;
+ }
+ }
+ }
+ return null;
+ }
+}