From e8d3a88ecde5b6ca0ff45f57bb21b0218220636f Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Sun, 13 Aug 2017 14:16:00 +0200
Subject: [PATCH] implemented very very basic functionality
---
.../de/hhu/ba/yoshikoWrapper/CyActivator.java | 4 +-
.../de/hhu/ba/yoshikoWrapper/core/Core.java | 63 +++++++++++++++++++
.../ba/yoshikoWrapper/core/GraphParser.java | 52 ---------------
.../ba/yoshikoWrapper/core/NetworkParser.java | 54 ++++++++++++++++
.../hhu/ba/yoshikoWrapper/core/NodeMap.java | 38 +++++++++++
.../hhu/ba/yoshikoWrapper/gui/MainPanel.java | 10 ++-
.../yoshikoWrapper/swig/LibraryInterface.java | 46 ++++++++++++++
.../swig/LibraryInterfaceJNI.java | 11 ++++
8 files changed, 221 insertions(+), 57 deletions(-)
create mode 100644 src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
delete mode 100644 src/main/java/de/hhu/ba/yoshikoWrapper/core/GraphParser.java
create mode 100644 src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
create mode 100644 src/main/java/de/hhu/ba/yoshikoWrapper/core/NodeMap.java
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index 1dd4db5..bcc6679 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -9,7 +9,7 @@ import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.service.util.AbstractCyActivator;
import org.osgi.framework.BundleContext;
-import de.hhu.ba.yoshikoWrapper.core.GraphParser;
+import de.hhu.ba.yoshikoWrapper.core.Core;
import de.hhu.ba.yoshikoWrapper.gui.MainPanel;
import de.hhu.ba.yoshikoWrapper.gui.MainPanelAction;
@@ -24,7 +24,7 @@ public class CyActivator extends AbstractCyActivator {
public void start(BundleContext context) throws Exception {
//TODO: Load shared library if installed on startup
CyApplicationManager cyApplicationManager = getService(context, CyApplicationManager.class);
- GraphParser.registerApplicationManager(cyApplicationManager);
+ Core.registerApplicationManager(cyApplicationManager);
CySwingApplication cytoscapeDesktopService = getService(context,CySwingApplication.class);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
new file mode 100644
index 0000000..04a3c68
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/Core.java
@@ -0,0 +1,63 @@
+package de.hhu.ba.yoshikoWrapper.core;
+
+import java.util.HashMap;
+
+//TODO: ADD LOGGER SYSTEM
+
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
+import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
+import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_std__vectorT_int_t;
+import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
+import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_ysk__ClusterEditingSolutions;
+
+public class Core {
+
+ private static CyApplicationManager cy;
+
+ public static void registerApplicationManager(CyApplicationManager cyApplicationManager) {
+ cy = cyApplicationManager;
+ }
+
+ public static void performYoshiko() {
+ CyNetwork currentNetwork = cy.getCurrentNetwork();
+ if (currentNetwork == null) {
+ //TODO
+ }
+
+ NodeMap nodeMap = new NodeMap(currentNetwork);
+
+ SWIGTYPE_p_yskInput__LibraryInput input = NetworkParser.parseNetwork(currentNetwork,nodeMap);
+ SWIGTYPE_p_ysk__ClusterEditingSolutions solutions = LibraryInterface.processLibraryInput(input);
+ long numberOfSolutions = LibraryInterface.ClusterEditingSolutions_getNumberOfSolutions(solutions);
+ System.out.println("Found: "+numberOfSolutions+" solutions!");
+ double modificationCost = LibraryInterface.ClusterEditingSolutions_getTotalCost(solutions);
+ System.out.println("Paid a total modification cost of: "+modificationCost);
+ for (long i=0;i<numberOfSolutions;i++) {
+ System.out.println("Processing solution "+(i+1)+" of "+numberOfSolutions);
+ String columnName = "YOSHIKO_SOLUTION_"+(i+1);
+ currentNetwork.getDefaultNodeTable().createColumn(columnName, String.class, false);
+ long numberOfClusters = LibraryInterface.ClusterEditingSolutions_getNumberOfClusters(solutions, i);
+ for (long k=0;k<numberOfClusters;k++) {
+ System.out.println("Processing cluster "+(k+1)+" of "+numberOfClusters);
+ SWIGTYPE_p_std__vectorT_int_t cluster = LibraryInterface.ClusterEditingSolutions_getCluster(solutions, i, k);
+ long sizeOfCluster = LibraryInterface.IntVector_size(cluster);
+ for (int l=0;l<sizeOfCluster;l++) { //Unsafe mismatch int long
+ System.out.println("Processing entry "+(l+1)+ " of "+sizeOfCluster);
+ int nodeID = LibraryInterface.IntVector_get(cluster, l);
+ CyNode node = nodeMap.indexOf(nodeID); //<<< Another int/long conversion
+ if (node == null) {
+ System.out.println("FATAL ERROR: Node was not previously mapped!");
+ return;
+ }
+ currentNetwork.getRow(node).set(columnName, ""+(k+1));
+ }
+ }
+ }
+
+ LibraryInterface.delete_LibraryInput(input);
+ }
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/GraphParser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/GraphParser.java
deleted file mode 100644
index 83a007c..0000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/GraphParser.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package de.hhu.ba.yoshikoWrapper.core;
-
-import java.util.List;
-
-import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableUtil;
-
-import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
-import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
-
-public class GraphParser {
-
- private static CyApplicationManager cy;
- //**TODO MAKE DYNAMIC
- private static String weightIndex = "weight";
-
- public static SWIGTYPE_p_yskInput__LibraryInput parseGraph() {
- if (cy == null) {
- //TODO:
- }
- SWIGTYPE_p_yskInput__LibraryInput generatedInput = LibraryInterface.new_LibraryInput();
- CyNetwork net = cy.getCurrentNetwork();
- if (net != null){
- LibraryInterface.LibraryInput_setSize(generatedInput, net.getNodeCount());
- List<CyEdge> edges = net.getEdgeList();
- CyTable edgeTable = net.getDefaultEdgeTable();
- for (CyEdge e : edges) {
- LibraryInterface.LibraryInput_addEdge(
- generatedInput,
- (e.getSource().getSUID()),
- (e.getTarget().getSUID()),
- 0.0
- );
-
- }
- }
- return generatedInput;
- }
-
- public static void registerApplicationManager(CyApplicationManager cyApplicationManager) {
- cy = cyApplicationManager;
- }
-
-
-
-
-
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
new file mode 100644
index 0000000..632f109
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
@@ -0,0 +1,54 @@
+package de.hhu.ba.yoshikoWrapper.core;
+
+import java.util.HashMap;
+import java.util.List;
+
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+
+import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
+import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
+
+public class NetworkParser {
+
+ //**TODO MAKE DYNAMIC
+ private static String weightIndex = "Weight";
+
+
+
+
+ public static SWIGTYPE_p_yskInput__LibraryInput parseNetwork(CyNetwork net,NodeMap nodeMap) {
+ SWIGTYPE_p_yskInput__LibraryInput generatedInput = LibraryInterface.new_LibraryInput();
+ if (net != null){
+ LibraryInterface.LibraryInput_setSize(generatedInput, net.getNodeCount());
+ List<CyEdge> edges = net.getEdgeList();
+ Class<?> weightType = net.getDefaultEdgeTable().getColumn(weightIndex).getType();
+ System.out.println("Column has type:"+weightType.getName());
+ for (CyEdge e : edges) {
+ CyRow edgeEntry = net.getRow(e);
+ double weight = 0.0;
+ if (weightType == Integer.class) {
+ weight = (double)edgeEntry.get(weightIndex, Integer.class);
+ }
+ System.out.println("Found Edge: "+edgeEntry.get("name", String.class)+ "with weight:"+weight);
+
+ LibraryInterface.LibraryInput_addEdge(generatedInput,
+ nodeMap.get(e.getSource()),
+ nodeMap.get(e.getTarget())
+ , weight);
+
+ }
+ }
+ return generatedInput;
+ }
+
+
+
+
+
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NodeMap.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NodeMap.java
new file mode 100644
index 0000000..821b51a
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NodeMap.java
@@ -0,0 +1,38 @@
+package de.hhu.ba.yoshikoWrapper.core;
+
+import java.util.HashMap;
+import java.util.Map.Entry;
+
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
+public class NodeMap {
+
+ private HashMap<CyNode,Long> nodeMap;
+
+
+ public NodeMap(CyNetwork net){
+ nodeMap = new HashMap<CyNode,Long> ();
+ long index = 0;
+ for (CyNode n :net.getNodeList()) {
+ nodeMap.put(n, index);
+ index++;
+ }
+
+ }
+
+
+ public long get(CyNode key) {
+ return nodeMap.get(key);
+ }
+
+
+ public CyNode indexOf(long nodeID) {
+ for (Entry<CyNode, Long> entry : nodeMap.entrySet()) {
+ if (nodeID == entry.getValue()) {
+ return entry.getKey();
+ }
+ }
+ return null;
+ }
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
index 71c6de5..5aa2e73 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
@@ -3,6 +3,7 @@ package de.hhu.ba.yoshikoWrapper.gui;
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.HashMap;
import javax.swing.Icon;
import javax.swing.JButton;
@@ -12,8 +13,11 @@ import javax.swing.JOptionPane;
import javax.swing.JPanel;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
+import org.cytoscape.model.CyNode;
-import de.hhu.ba.yoshikoWrapper.core.GraphParser;
+import de.hhu.ba.yoshikoWrapper.core.Core;
+import de.hhu.ba.yoshikoWrapper.core.NetworkParser;
+import de.hhu.ba.yoshikoWrapper.core.NodeMap;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
@@ -77,8 +81,8 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
@Override
public void actionPerformed(ActionEvent e) {
if (yoshikoLoader.isLibraryLoaded()){
- SWIGTYPE_p_yskInput__LibraryInput input = GraphParser.parseGraph();
- LibraryInterface.delete_LibraryInput(input);
+ Core.performYoshiko();
+
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
index b12ec2d..d06fa11 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
@@ -9,6 +9,52 @@
package de.hhu.ba.yoshikoWrapper.swig;
public class LibraryInterface {
+ public static SWIGTYPE_p_std__vectorT_int_t new_IntVector() {
+ long cPtr = LibraryInterfaceJNI.new_IntVector__SWIG_0();
+ return (cPtr == 0) ? null : new SWIGTYPE_p_std__vectorT_int_t(cPtr, true);
+ }
+
+ public static SWIGTYPE_p_std__vectorT_int_t new_IntVector(long n) {
+ long cPtr = LibraryInterfaceJNI.new_IntVector__SWIG_1(n);
+ return (cPtr == 0) ? null : new SWIGTYPE_p_std__vectorT_int_t(cPtr, true);
+ }
+
+ public static long IntVector_size(SWIGTYPE_p_std__vectorT_int_t self) {
+ return LibraryInterfaceJNI.IntVector_size(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self));
+ }
+
+ public static long IntVector_capacity(SWIGTYPE_p_std__vectorT_int_t self) {
+ return LibraryInterfaceJNI.IntVector_capacity(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self));
+ }
+
+ public static void IntVector_reserve(SWIGTYPE_p_std__vectorT_int_t self, long n) {
+ LibraryInterfaceJNI.IntVector_reserve(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self), n);
+ }
+
+ public static boolean IntVector_isEmpty(SWIGTYPE_p_std__vectorT_int_t self) {
+ return LibraryInterfaceJNI.IntVector_isEmpty(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self));
+ }
+
+ public static void IntVector_clear(SWIGTYPE_p_std__vectorT_int_t self) {
+ LibraryInterfaceJNI.IntVector_clear(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self));
+ }
+
+ public static void IntVector_add(SWIGTYPE_p_std__vectorT_int_t self, int x) {
+ LibraryInterfaceJNI.IntVector_add(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self), x);
+ }
+
+ public static int IntVector_get(SWIGTYPE_p_std__vectorT_int_t self, int i) {
+ return LibraryInterfaceJNI.IntVector_get(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self), i);
+ }
+
+ public static void IntVector_set(SWIGTYPE_p_std__vectorT_int_t self, int i, int val) {
+ LibraryInterfaceJNI.IntVector_set(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self), i, val);
+ }
+
+ public static void delete_IntVector(SWIGTYPE_p_std__vectorT_int_t self) {
+ LibraryInterfaceJNI.delete_IntVector(SWIGTYPE_p_std__vectorT_int_t.getCPtr(self));
+ }
+
public static SWIGTYPE_p_ysk__ClusterEditingSolutions new_ClusterEditingSolutions() {
long cPtr = LibraryInterfaceJNI.new_ClusterEditingSolutions();
return (cPtr == 0) ? null : new SWIGTYPE_p_ysk__ClusterEditingSolutions(cPtr, true);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
index f2e0d84..aa49472 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
@@ -9,6 +9,17 @@
package de.hhu.ba.yoshikoWrapper.swig;
public class LibraryInterfaceJNI {
+ 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);
+ public final static native long IntVector_capacity(long jarg1);
+ public final static native void IntVector_reserve(long jarg1, long jarg2);
+ public final static native boolean IntVector_isEmpty(long jarg1);
+ public final static native void IntVector_clear(long jarg1);
+ public final static native void IntVector_add(long jarg1, int jarg2);
+ public final static native int IntVector_get(long jarg1, int jarg2);
+ public final static native void IntVector_set(long jarg1, int jarg2, int jarg3);
+ public final static native void delete_IntVector(long jarg1);
public final static native long new_ClusterEditingSolutions();
public final static native long ClusterEditingSolutions_getNumberOfClusters(long jarg1, long jarg2);
public final static native long ClusterEditingSolutions_getCluster(long jarg1, long jarg2, long jarg3);
--
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