diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index b79892ee08f50af56220b59916d69d6ba2beb93d..f34df8026716566d65a387afae841db54cfa564b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -110,7 +110,7 @@ public class CyActivator extends AbstractCyActivator {
}
}
- //Register commands / CyRest
+ //Register commands / CyRest //TODO: Group shared calls for better code readability / less lines of code
TaskFactory commandTaskFactory_PERFORM_ALGORITHM = new CommandTaskFactory(YoshikoCommand.PERFORM_ALGORITHM);
Properties props_PERFORM_ALGORITHM = new Properties();
props_PERFORM_ALGORITHM.setProperty(COMMAND_NAMESPACE, "yoshiko");
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java
index 1fbcaac81d772d4823c42011b40a246ce02ff402..d564e2090eeb1390ff8ca2e4d79bab943c35bc3e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java
@@ -1,16 +1,16 @@
/*******************************************************************************
* Copyright (C) 2017 Philipp Spohr
- *
+ *
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
- *
+ *
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
- *
+ *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -25,9 +25,9 @@ import org.cytoscape.property.AbstractConfigDirPropsReader;
import org.cytoscape.property.CyProperty;
public class ConfigurationManager extends AbstractConfigDirPropsReader{
-
+
public ConfigurationManager(String appName, String fileName){
super(appName, fileName, CyProperty.SavePolicy.CONFIG_DIR);
- this.getProperties().list(System.out);
- }
+ //this.getProperties().list(System.out);
+ }
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
index 08ac18a7aa2ab569817cdbee9f7f90dcf7467331..ce7fbd136ec6bf41ee259a750c545b578216c6af 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -4,21 +4,25 @@ package de.hhu.ba.yoshikoWrapper.core;
import java.io.IOException;
import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
public class ParameterSet implements TunableValidator
{
+ @Tunable(description="Network to analyze for clusters", context="nogui")
+ public CyNetwork net = CyCore.cy.getCurrentNetwork();
+
@Tunable(description="Time Limit for the ILP mode", context="nogui")
public int timeLimit = -1;
@Tunable(description="A column in the edge table containing weights", context="nogui")
- public CyColumn weightColumn;
+ public String weightColumnName;
@Tunable(description="A column containing boolean entries for edges that are to be treated as permanent",context="nogui")
- public CyColumn permanentColumn;
+ public String permanentColumnName;
@Tunable(description="A column containing boolean entries for edges that are to be treated as forbidden",context="nogui")
- public CyColumn forbiddenColumn;
+ public String forbiddenColumnName;
@Tunable(description="The default insertion cost that is to be used for non-existing edges",context="nogui")
public double defaultInsertionCost = -1;
@@ -48,18 +52,36 @@ public class ParameterSet implements TunableValidator
/**Describes whether auto configuration of the reduction rules is to be used. Overrides the bit mask.**/
public boolean suggestReduction = true;
+ @Tunable(description="Determines the number of clusters that are to be generated. -1 generates the optimal amount of clusters in the sense of WCE",context="nogui")
+ public int clusterCount = -1;
+
@Override
public ValidationState getValidationState(Appendable errMsg) {
- if (!checkBitmask(reductionRulesBitMask)) {
- try {
- errMsg.append("The Bitmask provided is invalid! Needs to be six bit binary (example: 011001)");
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ System.out.println("DEBUG: Running VALIDATION of tunables"); //TODO: Move to logger (if it would work)
+ try {
+ if (net!= null) {
+ //Verify column validity
+ CyColumn weightColumn = net.getDefaultEdgeTable().getColumn(weightColumnName);
+ if (weightColumn == null) {
+ errMsg.append("Could not find a column named: "+weightColumnName+"\n");
+ return ValidationState.INVALID;
+ }
+ }
+ if (!checkBitmask(reductionRulesBitMask)) {
+ errMsg.append("The Bitmask provided is invalid! Needs to be six bit binary (example: 011001)\n");
+ return ValidationState.INVALID;
+ }
+ //Checks for cluster count number
+ if ((clusterCount < 0 && clusterCount != -1)||(clusterCount == 0)) {
+ errMsg.append("Invalid cluster count number!");
+ return ValidationState.INVALID;
}
- return ValidationState.INVALID;
+ return ValidationState.OK;
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
}
- return ValidationState.OK;
+ return ValidationState.INVALID;
}
/**
@@ -79,4 +101,12 @@ public class ParameterSet implements TunableValidator
return true;
}
+ @Override
+ public String toString(){
+ String ret = "";
+ ret += "Target Cluster Count: "+clusterCount+"\n";
+ //TODO
+ return ret;
+ }
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
index 1ef7cc8345a480edecdeadb8803c5e8634e838e4..24ca2d5df9c0002ac7ca3cf7b6d976184d6834bc 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
@@ -15,6 +15,11 @@ public class GraphAnalyzer {
//private static Logger logger = YoshikoLogger.getInstance().getLogger();
+ /**
+ * Simple helper function, checks if a network contains multiple edges between a pair of nodes
+ * @param net The CyNetwork that is to be analyzed
+ * @return <b>true</b> if a pair of nodes exists that is connected with more than one edge, <b>false</b> otherwise
+ */
public static boolean isMultiGraph(CyNetwork net) {
//TODO: Better algorithm?
@@ -43,7 +48,7 @@ public class GraphAnalyzer {
* This function is symmetric
* @param e1 An arbitrary CyEdge
* @param e2 An arbitrary CyEdge
- * @return true if the edges connect the same pair of nodes, false otherwise
+ * @return <b>true</b> if the edges connect the same pair of nodes, <b>false</b> otherwise
*/
private static boolean connectSameNodes(CyEdge e1, CyEdge e2) {
if (//Treating all edges as undirected here
@@ -98,12 +103,23 @@ public class GraphAnalyzer {
ret += (usePDRRule ? "1" : "0");
ret += (useSNRule ? "1" : "0");
+ //TODO: Spend some thoughts on logging, make a coherent design decision on logging
//logger.info("Suggesting the following reduction-rules bitmask: "+ret);
- System.out.println("Suggesting the following reduction-rules bitmask: "+ret);
+ //System.out.println("Suggesting the following reduction-rules bitmask: "+ret);
return ret;
}
+ /**
+ * Simple helper function that checks if a WCE instance contains real values (as opposed to only integers)
+ * @param net The network from which the WCE instance is to be derived
+ * @param weightColumn The CyColumn from which - if != null - the edge weights are taken
+ * @param permanentColumn The CyColumn from which - if != null - we derive if edges are permanent
+ * @param forbiddenColumn The CyColumn from which - if != null - we derive if edges are forbidden
+ * @param defaultInsertionCost The insertion cost used for non-existing edges or ones with no mapping associated
+ * @param defaultDeletionCost The deletion cost for edges with no mapping associated
+ * @return true if the WCE instance is real-valued, false otherwise
+ */
public static boolean containsRealValues(
CyNetwork net,
CyColumn weightColumn,
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java b/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
index 58fdf46211f98224e07e218effff8d87b35b6a45..edefa932dce4a11925351be112944e59ae126a01 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
@@ -27,7 +27,8 @@ public final class HelpLinks {
public static final HashMap<String,Object> mainInfo = new HashMap<String,Object>();
static {
- mainInfo.put("url", "https://spqrph.github.io/cytoscape-tutorials/presentations/yoshiko.html#/title");
+ mainInfo.put("url", "file:///home/philipp/workspace/cs/cytoscape-tutorials/presentations/yoshiko.html");
+ //mainInfo.put("url", "https://spqrph.github.io/cytoscape-tutorials/presentations/yoshiko.html#/title");
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/ClusterEditingSolutions.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/ClusterEditingSolutions.java
index 10eab6276ae28f1834ada45e49b549979c532555..ae586e770de1d3b690605f796256845df2c7054e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/ClusterEditingSolutions.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/ClusterEditingSolutions.java
@@ -59,6 +59,10 @@ public class ClusterEditingSolutions {
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/LibraryInterface.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
index 82e0dee42b697daf9b2669c8a35bea80c5070fe7..227ab8a923211019d5bf0f831f9055addfadd5f1 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java
@@ -25,8 +25,8 @@ public class LibraryInterface {
LibraryInterfaceJNI.setVerbosity(level);
}
- public static CoreAlgorithm getRun(LibraryInput input, int nrOptimalSolutions, String rulesBitMask, double multiplicativeFactor, boolean useHeuristic, boolean separatePartitionCuts, boolean separateTriangles) {
- long cPtr = LibraryInterfaceJNI.getRun(LibraryInput.getCPtr(input), input, nrOptimalSolutions, rulesBitMask, multiplicativeFactor, useHeuristic, separatePartitionCuts, separateTriangles);
+ 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
index 10744f7c6dc6ec23408e90eb9e0169dd6df0482c..49549a4b657af8b0dd0a8ef300f2319e92c77f75 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java
@@ -53,6 +53,7 @@ public class LibraryInterfaceJNI {
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();
@@ -79,7 +80,7 @@ public class LibraryInterfaceJNI {
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);
+ 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));
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterCountChooser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterCountChooser.java
new file mode 100644
index 0000000000000000000000000000000000000000..852cd5ec25c55dd2687d1dde4908aa871fe92302
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterCountChooser.java
@@ -0,0 +1,56 @@
+/*******************************************************************************
+ * 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 javax.swing.BoxLayout;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+
+@SuppressWarnings("serial")
+public class ClusterCountChooser extends JPanel {
+ private final IntegerInputField numSolutionsSetter;
+ private final JLabel label;
+
+ public ClusterCountChooser() {
+ //Swing Component init
+ numSolutionsSetter = new IntegerInputField(1,Integer.MAX_VALUE);
+ numSolutionsSetter.setValue(2);
+ label = new JLabel(LocalizationManager.get("nrClusters"));
+
+ SwingUtil.addAll(this,label, numSolutionsSetter);
+
+ BoxLayout layout = new BoxLayout(this, BoxLayout.LINE_AXIS);
+ this.setLayout(layout);
+ }
+
+ @Override
+ public void setEnabled(boolean enabled) {
+ numSolutionsSetter.setEnabled(enabled);
+ }
+
+ public int getClusterCount() {
+ return numSolutionsSetter.getValueAsInt();
+ }
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
index ada41217a66d5f9c8265426c933e1cbb47e5997e..1f1169b514f83956a7321d793f0608d3039890ef 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
@@ -60,7 +60,7 @@ SetCurrentNetworkListener
{
//Swing components
- private final JComboBox<CyColumn> editingCostMapper;
+ private final JComboBox<CyColumn> weightMapper;
private final JComboBox<CyColumn> permanentMapper;
private final JComboBox<CyColumn> forbiddenMapper;
@@ -79,12 +79,12 @@ SetCurrentNetworkListener
//SWING COMPONENTS
//Combo-Boxes that map to the CyColumns
- editingCostMapper = new JComboBox<CyColumn>();
+ weightMapper = new JComboBox<CyColumn>();
permanentMapper = new JComboBox<CyColumn>();
forbiddenMapper = new JComboBox<CyColumn>();
//Should only be enabled if the option is checked
- editingCostMapper.setEnabled(false);
+ weightMapper.setEnabled(false);
permanentMapper.setEnabled(false);
forbiddenMapper.setEnabled(false);
@@ -93,7 +93,7 @@ SetCurrentNetworkListener
useMappingForb = new JCheckBox("Map edges as forbidden");
useMappingCost.addActionListener(
- new EnableWhenSelectedListener(useMappingCost, editingCostMapper)
+ new EnableWhenSelectedListener(useMappingCost, weightMapper)
);
useMappingPerm.addActionListener(
new EnableWhenSelectedListener(useMappingPerm, permanentMapper)
@@ -103,7 +103,7 @@ SetCurrentNetworkListener
);
- SwingUtil.addAll(this,useMappingCost,editingCostMapper);
+ SwingUtil.addAll(this,useMappingCost,weightMapper);
SwingUtil.addAll(this,useMappingPerm,permanentMapper);
SwingUtil.addAll(this,useMappingForb,forbiddenMapper);
@@ -117,7 +117,7 @@ SetCurrentNetworkListener
.addComponent(useMappingForb)
)
.addGroup(layout.createParallelGroup(Alignment.LEADING)
- .addComponent(editingCostMapper)
+ .addComponent(weightMapper)
.addComponent(permanentMapper)
.addComponent(forbiddenMapper)
)
@@ -127,7 +127,7 @@ SetCurrentNetworkListener
layout.setVerticalGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup()
.addComponent(useMappingCost)
- .addComponent(editingCostMapper)
+ .addComponent(weightMapper)
)
.addGroup(layout.createParallelGroup()
.addComponent(useMappingPerm)
@@ -153,18 +153,18 @@ SetCurrentNetworkListener
if (net != null) { //Check if a network is loaded
//Clear entries
- editingCostMapper.removeAllItems();
+ weightMapper.removeAllItems();
for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
//Only add columns with numeric values
if (c.getType() == Integer.class || c.getType() == Double.class) {
- editingCostMapper.addItem(c);
+ weightMapper.addItem(c);
}
}
- boolean enable = (editingCostMapper.getItemCount() > 0) ? true : false;
+ boolean enable = (weightMapper.getItemCount() > 0) ? true : false;
useMappingCost.setEnabled(enable);
if (!useMappingCost.isEnabled()) {
useMappingCost.setSelected(false);
- editingCostMapper.setEnabled(false);
+ weightMapper.setEnabled(false);
}
forbiddenMapper.removeAllItems();
@@ -247,7 +247,7 @@ SetCurrentNetworkListener
public CyColumn getEditingCostColumn() {
if (useMappingCost.isSelected()) {
- return editingCostMapper.getItemAt(editingCostMapper.getSelectedIndex());
+ return weightMapper.getItemAt(weightMapper.getSelectedIndex());
}
return null;
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
index ccbc108a8db5bb79d4000ba07a0280b74c6a239d..b52e77685d866a4aa3c30643e17e4f4260ceae57 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/EditCostPanel.java
@@ -25,10 +25,9 @@ package de.hhu.ba.yoshikoWrapper.swing.components;
import javax.swing.GroupLayout;
import javax.swing.JLabel;
import javax.swing.JPanel;
+import javax.swing.JSeparator;
import javax.swing.GroupLayout.Alignment;
-import org.cytoscape.model.CyColumn;
-
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@@ -40,6 +39,8 @@ public class EditCostPanel extends JPanel {
private final DoubleInputField icField;
private final DoubleInputField dcField;
+
+ private final JSeparator separator;
private final JLabel icLabel;
private final JLabel dcLabel;
@@ -59,15 +60,16 @@ public class EditCostPanel extends JPanel {
icField.setText("-1.0");
icField.setToolTipText(LocalizationManager.get("icTooltip"));
dcField.setText("1.0");
+
+ separator = new JSeparator(JSeparator.HORIZONTAL);
icLabel = new JLabel(LocalizationManager.get("defaultInsertion"));
dcLabel = new JLabel(LocalizationManager.get("defaultDeletion"));
//Add components
- SwingUtil.addAll(this,icLabel,icField);
- SwingUtil.addAll(this,dcLabel,dcField);
+ SwingUtil.addAll(this,columnMapper,separator,icLabel,icField,dcLabel,dcField);
//SwingUtil.addAll(helpButton);
- SwingUtil.addAll(this,columnMapper);
+
//Layout
@@ -76,6 +78,7 @@ public class EditCostPanel extends JPanel {
layout.setHorizontalGroup(layout.createParallelGroup()
//.addComponent(helpButton,Alignment.TRAILING)
.addComponent(columnMapper)
+ .addComponent(separator)
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(Alignment.LEADING)
.addComponent(icLabel)
@@ -92,6 +95,7 @@ public class EditCostPanel extends JPanel {
layout.setVerticalGroup(layout.createSequentialGroup()
//.addComponent(helpButton)
.addComponent(columnMapper)
+ .addComponent(separator)
.addGroup(layout.createParallelGroup(Alignment.BASELINE)
.addComponent(icLabel)
.addGap(4)
@@ -109,17 +113,11 @@ public class EditCostPanel extends JPanel {
}
//SETTER / GETTER
- public CyColumn getWeightColumn() {
- return columnMapper.getEditingCostColumn();
- }
-
- public CyColumn getPermanentColumn() {
- return columnMapper.getPermanentColumn();
- }
+ public String getPermanentColumnName() {
+ return columnMapper.getPermanentColumn() != null ? columnMapper.getPermanentColumn().getName() : null; }
- public CyColumn getForbiddenColumn() {
- return columnMapper.getForbiddenColumn();
- }
+ public String getForbiddenColumnName() {
+ return columnMapper.getForbiddenColumn() != null ? columnMapper.getForbiddenColumn().getName() : null; }
public double getDefaultInsertionCost() {
return icField.getValueAsDouble();
@@ -133,4 +131,8 @@ public class EditCostPanel extends JPanel {
return columnMapper;
}
+ public String getWeightColumnName() {
+ return columnMapper.getEditingCostColumn() != null ? columnMapper.getEditingCostColumn().getName() : null;
+ }
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/IntegerInputField.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/IntegerInputField.java
index d7d337652ee5627a088f5eb4d714c69fcdc9e95a..7b39fd0bf2e1028120ba27092f8f167fc2712c3b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/IntegerInputField.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/IntegerInputField.java
@@ -34,12 +34,12 @@ public class IntegerInputField extends JFormattedTextField{
private final NumberFormatter formatter;
-// public IntegerInputField(int minValue, int maxValue) {
-// super();
-// formatter = FormatHelper.getIntegerFormatter(minValue,maxValue);
-// this.setFormatter(formatter);
-// this.setColumns(8);
-// }
+ public IntegerInputField(int minValue, int maxValue) {
+ super();
+ formatter = FormatHelper.getIntegerFormatter(minValue,maxValue);
+ this.setFormatter(formatter);
+ this.setColumns(8);
+ }
public IntegerInputField() {
super();
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 b0771da0950f3cb95c9a366a511cd6ddbd8095fb..5fc0e50b3554b91bb10f23563ba2c5eae93d1e68 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
@@ -209,7 +209,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(about,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
)
- .addGap(4)
+ .addGap(8)
.addComponent(showAdvancedOptions,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(scrollPane,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(runButton,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
@@ -228,7 +228,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
.addComponent(header,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(about,Alignment.TRAILING,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
)
- .addGap(4)
+ .addGap(8)
.addComponent(showAdvancedOptions,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(scrollPane,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(runButton,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
@@ -314,7 +314,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
if (YoshikoLoader.isLibraryLoaded()){
AbstractTask yoshiko = new AlgorithmTask(
popupLevel,
- networkToBeProcessed,
fetchParameters(networkToBeProcessed)
);
/**
@@ -345,10 +344,11 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
*/
private ParameterSet fetchParameters(CyNetwork net) {
ParameterSet ret = new ParameterSet();
+ ret.net = net;
ret.timeLimit = opModePanel.getTimeLimit();
- ret.weightColumn = ecPanel.getWeightColumn();
- ret.permanentColumn = ecPanel.getPermanentColumn();
- ret.forbiddenColumn = ecPanel.getForbiddenColumn();
+ ret.weightColumnName = ecPanel.getWeightColumnName();
+ ret.permanentColumnName = ecPanel.getPermanentColumnName();
+ ret.forbiddenColumnName = ecPanel.getForbiddenColumnName();
ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
ret.useHeuristic = opModePanel.useHeuristic();
@@ -359,6 +359,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
ret.usePartitionCuts = opModePanel.usePartitionCuts();
ret.solCount = opModePanel.getSolCount();
ret.disableMultiThreading = opModePanel.isMultiThreadingDisabled();
+ ret.clusterCount = opModePanel.getClusterCount();
return ret;
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
index bda3f6f4b5c69a8a640831aa076d23df28e04fef..e49f4aed07d885cf11cb6fc030efbe902c2cee1d 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/OperationModePanel.java
@@ -41,6 +41,8 @@ import javax.swing.GroupLayout.Alignment;
public class OperationModePanel extends JPanel{
//SWING COMPONENTS
+ private final JCheckBox useClusterCount;
+ private final ClusterCountChooser ccChooser;
private final JRadioButton useHeuristic;
private final JRadioButton useILP;
private final TimeLimitSetter timeLimitSetter;
@@ -53,6 +55,12 @@ public class OperationModePanel extends JPanel{
public OperationModePanel() {
+ useClusterCount = new JCheckBox(LocalizationManager.get("useClusterCount"));
+ ccChooser = new ClusterCountChooser();
+ ccChooser.setEnabled(false);
+
+ useClusterCount.addActionListener(ccSwitch);
+
heuristicGroup = new ButtonGroup();
useILP = new JRadioButton("Use Integer Linear Programming");
@@ -79,6 +87,8 @@ public class OperationModePanel extends JPanel{
useHeuristic.addActionListener(ilpHeuristicSwitch);
SwingUtil.addAll(this,
+ useClusterCount,
+ ccChooser,
useHeuristic,
useILP,
solutionNumberChooser,
@@ -97,6 +107,8 @@ public class OperationModePanel extends JPanel{
layout.setAutoCreateContainerGaps(true);
layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
+ .addComponent(useClusterCount, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+ .addComponent(ccChooser, DEFAULT_SIZE, DEFAULT_SIZE, DEFAULT_SIZE)
.addComponent(useHeuristic, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(useILP, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(solutionNumberChooser, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
@@ -107,6 +119,8 @@ public class OperationModePanel extends JPanel{
);
layout.setVerticalGroup(layout.createSequentialGroup()
+ .addComponent(useClusterCount)
+ .addComponent(ccChooser)
.addComponent(useHeuristic)
.addComponent(useILP)
.addComponent(solutionNumberChooser)
@@ -137,13 +151,21 @@ public class OperationModePanel extends JPanel{
}
}
- ActionListener ilpHeuristicSwitch = new ActionListener() {
+ private ActionListener ilpHeuristicSwitch = new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
ilpHeuristicSwitch();
}
};
+ private ActionListener ccSwitch = new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ ccChooser.setEnabled(useClusterCount.isSelected());
+ }
+
+ };
//SETTER GETTER
public int getTimeLimit() {
@@ -169,4 +191,8 @@ public class OperationModePanel extends JPanel{
public int getSolCount() {
return solutionNumberChooser.getSolCount();
}
+
+ public int getClusterCount() {
+ return useClusterCount.isSelected() ? ccChooser.getClusterCount() : -1;
+ }
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
index eab819be1f5b29b128c855e53f36b9b328fc19e9..d276d08c05343ca9a817a6aeeb697059abd0867f 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
@@ -43,7 +43,6 @@ import javax.swing.JPanel;
import javax.swing.JTabbedPane;
import javax.swing.LayoutStyle;
import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
@@ -185,7 +184,7 @@ NetworkAboutToBeDestroyedListener
verticalGroup
.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(invalidLabel,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
- .addComponent(tabbedPane,PREFERRED_SIZE, DEFAULT_SIZE,Short.MAX_VALUE)
+ .addComponent(tabbedPane,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(destroyButton,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
index 104d39ae14275af3f91d1aad40f72f308e7af8b1..83a7ef3ae76973f81b6a4bf2d751de1de2a89d9a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
@@ -203,27 +203,32 @@ public class SolutionTab extends JPanel {
layout = new GroupLayout(this);
layout.setHorizontalGroup(layout.createParallelGroup(Alignment.CENTER,true)
+ .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
+ .addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addGap(8)
.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
.addComponent(hideSingles,DEFAULT_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
.addGap(8)
.addComponent(scrollPane,PREFERRED_SIZE,PREFERRED_SIZE,Short.MAX_VALUE)
- .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
- .addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
+ .addGap(4)
);
layout.setVerticalGroup(layout.createSequentialGroup()
+ .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
+ .addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
.addGap(8)
.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(hideSingles,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
- .addGap(8)
- .addComponent(scrollPane,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
- .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
- .addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
+ .addGap(4)
+ .addComponent(scrollPane,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
+ .addGap(4)
);
this.setLayout(layout);
}
+ /**
+ * Simply disables the CCV and CMG graph to visually highlight the fact that those tasks are no longer possible
+ */
public void invalidateResult() {
createClusterView.setEnabled(false);
createMetaGraph.setEnabled(false);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
index dc9e5cc66d1be0ab208b55a210d73e4f931d7335..ebd95002c5446435990241db14abeee6ce3b0b02 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
@@ -45,7 +45,6 @@ public class CommandTaskFactory implements TaskFactory{
else if (command == YoshikoCommand.PERFORM_ALGORITHM) {
return new TaskIterator(
new AlgorithmTask(
- null,
null,
new ParameterSet()
)
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
index d764f9e387b34b9411110f0fd78a14efcfbc81f4..1f252f95c85a0038134f0717efd2e7816061b5ea 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -30,13 +30,13 @@ 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.CyNetwork;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNode;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.ContainsTunables;
import org.cytoscape.work.ObservableTask;
import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.Tunable;
+import org.cytoscape.work.TunableValidator;
import org.slf4j.Logger;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
@@ -58,7 +58,7 @@ import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
-public class AlgorithmTask extends AbstractTask implements ObservableTask {
+public class AlgorithmTask extends AbstractTask implements ObservableTask, TunableValidator {
//Constants
private static final String SOLUTION_COLUMN_PREFIX = "yoshikoSolution_"; //TODO: Make customizable?
@@ -77,8 +77,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
@ContainsTunables
public ParameterSet parameterSet = null;
- @Tunable(description="Network to analyze for clusters", context="nogui")
- public CyNetwork net = CyCore.cy.getCurrentNetwork();
+
//Temps, pointing to and need to be freed in C++
private LibraryInput c_input;
@@ -98,12 +97,10 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
*/
public AlgorithmTask(
Window statusWindow,
- CyNetwork net,
ParameterSet parameterSet
)
{
this.statusWindow = statusWindow;
- this.net = net;
this.parameterSet = parameterSet;
}
@@ -115,8 +112,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
taskMonitor.setTitle(LocalizationManager.get("yoshTask"));
taskMonitor.setProgress(0.0);
- //Get current network
- if (net == null) {
+ //Check current network
+ if (parameterSet.net == null) {
logger.warn("CoreAlgorithm called on a net that is NULL!");
throw new Exception("CoreAlgorithm called on a net that is NULL!"); //TODO: Localize
}
@@ -131,25 +128,30 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
}
//Create a node map to identify nodes and eges in the solution
- NodeMap nodeMap = new NodeMap(net);
+ NodeMap nodeMap = new NodeMap(parameterSet.net);
taskMonitor.setProgress(0.1);
+ //We identify the columns if they exist from their given names
+ CyColumn weightColumn = parameterSet.weightColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName) : null;
+ CyColumn permanentColumn = parameterSet.permanentColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.permanentColumnName) : null;
+ CyColumn forbiddenColumn = parameterSet.forbiddenColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.forbiddenColumnName) : null;
+
//Generate an c_input instance from the network
c_input = NetworkParser.parseNetwork(
- net,
+ parameterSet.net,
nodeMap,
- parameterSet.weightColumn,
- parameterSet.permanentColumn,
- parameterSet.forbiddenColumn,
+ weightColumn,
+ permanentColumn,
+ forbiddenColumn,
parameterSet.defaultDeletionCost
);
taskMonitor.setProgress(0.2);
boolean containsRealValues = GraphAnalyzer.containsRealValues(
- net,
- parameterSet.weightColumn,
- parameterSet.permanentColumn,
- parameterSet.forbiddenColumn,
+ parameterSet.net,
+ weightColumn,
+ permanentColumn,
+ forbiddenColumn,
parameterSet.defaultInsertionCost,
parameterSet.defaultDeletionCost);
@@ -161,6 +163,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
//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,
@@ -168,7 +172,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
parameterSet.snrMultFactor,
parameterSet.useHeuristic,
parameterSet.usePartitionCuts,
- parameterSet.useTriangleCuts
+ parameterSet.useTriangleCuts,
+ parameterSet.clusterCount
);
@@ -184,7 +189,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO: Localize
- result = new YoshikoResult(net,c_result.getFlags());
+ result = new YoshikoResult(parameterSet.net,c_result.getFlags());
//Loop over (multiple) solutions
for (long i=0;i<numberOfSolutions;i++) {
@@ -195,8 +200,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
- net.getDefaultNodeTable().deleteColumn(columnName);
- net.getDefaultNodeTable().createColumn(columnName, String.class, false);
+ parameterSet.net.getDefaultNodeTable().deleteColumn(columnName);
+ parameterSet.net.getDefaultNodeTable().createColumn(columnName, String.class, false);
//Fetch number of clusters in the solution
long numberOfClusters = c_result.getNumberOfClusters(i);
@@ -218,7 +223,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
CyNode node = nodeMap.indexOf(nodeID); //<<< Another int/long conversion
cluster.addNode(node);
- net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
+ parameterSet.net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
}
//Register clusters with solution for further reference
solution.addCluster(cluster);
@@ -259,7 +264,13 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
}
+ /**
+ * 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"));
@@ -308,4 +319,10 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
}
return null;
}
+
+ @Override
+ public ValidationState getValidationState(Appendable errMsg) {
+ //In order to validate the arguments for this task we simply check the ParameterSet
+ return parameterSet.getValidationState(errMsg);
+ }
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
index 72d6270300e9c7cb0f846599e7681cd24cc4245c..0531fa72a63ae661e5e6889ad1200edce2c8cc24 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
@@ -22,6 +22,10 @@ public class CreateClusterViewsTask implements Task {
@Tunable
public ArrayList<YoshikoCluster> clusters; //TODO: Make Tunable, reference by ID?
+ /**
+ * Killswitch, used to determine if the algorithm has been terminated.
+ * We can use this to cancel at a given point (so we don't need to finish the entire task)
+ */
private boolean isTerminated;
/**
@@ -77,11 +81,8 @@ public class CreateClusterViewsTask implements Task {
StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
CyCore.networkViewManager.addNetworkView(subnetView);
}
-
}
);
-
-
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
index 1f24dea291ab3a44cd99620a3e77873ec348e0d3..dd1c24e4b543ed1fa48a5b106ed32d1e00f0b748 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
@@ -20,6 +20,8 @@ import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+//TODO: Should also not be possible / throw an exception if the result was invalidated (might currently just be disabled via GUI)
+
public class CreateMetaGraphTask extends AbstractTask{
private final YoshikoSolution solution;
@@ -94,7 +96,7 @@ public class CreateMetaGraphTask extends AbstractTask{
//Link clusters node in meta graph and subnet graph to use Cytoscape Nested Network feature
clusterNode.setNetworkPointer(subnet);
//Set node attributes
- metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("clusters")+" "+c.getID());
+ metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("clusters")+" "+(c.getID()+1));
metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
map.put(c, clusterNode);
}
@@ -105,12 +107,13 @@ public class CreateMetaGraphTask extends AbstractTask{
taskMonitor.setStatusMessage(LocalizationManager.get("metaGraph_edges"));
Iterator<YoshikoCluster> it1 = solution.getClusters().iterator();
- Iterator<YoshikoCluster> it2 = solution.getClusters().iterator();
while (it1.hasNext()) {
YoshikoCluster c1 = it1.next();
+ Iterator<YoshikoCluster> it2 = solution.getClusters().iterator();
while(it2.hasNext()) {
YoshikoCluster c2 = it2.next();
+ System.out.println("Debug: Processing edges between cluster "+c1.getID()+" and "+c2.getID());
if(isTerminated) {
throw new Exception("Terminated by user!");
@@ -126,7 +129,9 @@ public class CreateMetaGraphTask extends AbstractTask{
for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
if (solution.getOriginalGraph().containsEdge(c1n, c2n) || solution.getOriginalGraph().containsEdge(c2n, c1n)) {
+ System.out.println("Debug: Found relevant edge from "+c1n.getSUID()+ " to "+c2n.getSUID());
if (!metaGraph.containsEdge(map.get(c1), map.get(c2))){
+ System.out.println("We create a new edge for it");
CyEdge edge = metaGraph.addEdge(map.get(c1), map.get(c2), false);
metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,1);
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
index 0afa05ee33f92ccef1c46a09cdcccb6cfd4ba1c5..6a49b1ec30360ba2c7587d1d3d934301bb991b51 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
@@ -9,16 +9,32 @@ import org.cytoscape.work.Tunable;
import de.hhu.ba.yoshikoWrapper.core.ResultList;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
-import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+/**
+ * A task that retrieves the clusters associated with a given solution in a given result. This is meant to be used via CyRest / command line functionality exclusively
+ *
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
public class GetClustersTask implements ObservableTask {
+
+ /**
+ * The ID of the result for which the clusters are to be retrieved
+ */
@Tunable(description="The result ID for which the solutions should be displayed", context="nogui")
public int resultID = -1;
+ /**
+ * The ID of the solution for which the clusters are to be retrieved
+ */
@Tunable(description="The solution ID for which the solutions should be displayed", context="nogui")
public long solutionID = -1;
+
+ /**
+ * The clusters as a collection when they are retrieved
+ */
private Collection<YoshikoCluster> clusters;
@Override
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
index b36ef963bb0ea5351638f4897718f6e571fa21f3..b4d60d6e441b55b250880ebb1c2d5eaf55444051 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
@@ -10,11 +10,23 @@ import de.hhu.ba.yoshikoWrapper.core.ResultList;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+/**
+ * Basic task that retrieves solutions associated with a run (result)
+ * This is meant to be invoked from cmd / CyRest exclusively to receive solution IDs
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
public class GetSolutionsTask implements ObservableTask {
+ /**
+ * The result ID for the result/run for which the solutions are to be retrieved
+ */
@Tunable(description="The result ID for which the solutions should be displayed", context="nogui")
public int resultID = -1;
+ /**
+ * The solutions as a collection in case the task was successful
+ */
private Collection<YoshikoSolution> solutions;
@Override
@@ -27,9 +39,7 @@ public class GetSolutionsTask implements ObservableTask {
}
@Override
- public void cancel() {
- // TODO Auto-generated method stub
- }
+ public void cancel() {} //There is nothing here that remains in an instable state as we are simply reading / retrieving data
@SuppressWarnings("unchecked")
@Override
@@ -44,4 +54,5 @@ public class GetSolutionsTask implements ObservableTask {
return null;
}
+
}
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index b20a177a70f2a91e877d6071906459d786118ec7..c123781d3c6361033c37b6a20c09f495d710fc8e 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -61,7 +61,7 @@ libraryPanel = Library
metaGraph = Meta Graph
metaGraph_edges = Fetching edges and calculating edge strengths
multFactor = Multiplicative Factor for SNR:
-multiGraphWarning = This graph is a multigraph. This algorithms behavior on multigraphs is not yet researched.
+multiGraphWarning = This graph is a multigraph. Running Yoshiko on the corresponding simple graph...
networkParsingException: An error occured while parsing the network:
noFeasible = No feasible solution found!
@@ -74,6 +74,8 @@ optionpane_title = Yoshiko Info
noClustersSelected = You have not selected any clusters
notOptimal = Optimality not guaranteed
nrSolutions = Number of Solutions:
+nrClusters = Number of Clusters:
+useClusterCount = Define cluster count
operationMode = Operation Mode
optimal = Optimal Solution
paidCost = Paid a total modification cost of: