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 1ae45b2815d7d6cb4327e50b3fff20423a0f0953..f050e37004277cd841ce03810ea04eb9c6bf0519 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -44,11 +44,11 @@ public class ParameterSet implements TunableValidator
//COLUMN-MAPPINGS
@Tunable(description="A column in the edge table containing weights", context="nogui")
- public ListSingleSelection<String> weightColumnName = null;
+ public ListSingleSelection<CyColumn> weightColumn = null;
@Tunable(description="A column containing boolean entries for edges that are to be treated as permanent",context="nogui")
- public ListSingleSelection<String> permanentColumnName = null;
+ public ListSingleSelection<CyColumn> permanentColumn = null;
@Tunable(description="A column containing boolean entries for edges that are to be treated as forbidden",context="nogui")
- public ListSingleSelection<String> forbiddenColumnName = null;
+ public ListSingleSelection<CyColumn> forbiddenColumn = null;
@Tunable(description="The default insertion cost that is to be used for non-existing edges",context="nogui")
public double defaultInsertionCost = -1;
@@ -86,40 +86,32 @@ public class ParameterSet implements TunableValidator
*/
public ParameterSet() {
- ArrayList<String> columnNames = new ArrayList<String>();
+ ArrayList<CyColumn> columns = new ArrayList<CyColumn>();
//Only numeric columns are relevant for weight mapping
for (CyColumn col : net.getDefaultEdgeTable().getColumns()) {
if (Number.class.isAssignableFrom(col.getType())) {
- columnNames.add(col.getName());
+ columns.add(col);
}
}
- weightColumnName = new ListSingleSelection<String>(columnNames);
+ weightColumn = new ListSingleSelection<CyColumn>(columns);
- columnNames = new ArrayList<String>();
+ columns.clear();
//Only boolean columns are relevant for forbidden/permanent mapping
for (CyColumn col : net.getDefaultEdgeTable().getColumns()) {
if (col.getType() == Boolean.class) {
- columnNames.add(col.getName());
+ columns.add(col);
}
}
- forbiddenColumnName = new ListSingleSelection<String>(columnNames);
- permanentColumnName = new ListSingleSelection<String>(columnNames);
+ forbiddenColumn = new ListSingleSelection<CyColumn>(columns);
+ permanentColumn = new ListSingleSelection<CyColumn>(columns);
}
@Override
public ValidationState getValidationState(Appendable errMsg) {
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.getSelectedValue());
- 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;
@@ -156,8 +148,11 @@ public class ParameterSet implements TunableValidator
@Override
public String toString(){
- String ret = "";
+ String ret = "[ParameterSet]:\n";
ret += "Target Cluster Count: "+clusterCount+"\n";
+ ret += "Weight mapped to column: "+(weightColumn.getSelectedValue() != null ? weightColumn.getSelectedValue().getName() : "[NONE]")+"\n";
+ ret += "Permanent edges mapped to column: "+(permanentColumn.getSelectedValue() != null ? permanentColumn.getSelectedValue().getName() : "[NONE]")+"\n";
+ ret += "Forbidden edges mapped to column: "+(forbiddenColumn.getSelectedValue() != null ? forbiddenColumn.getSelectedValue().getName() : "[NONE]")+"\n";
//TODO
return ret;
}
@@ -166,46 +161,28 @@ public class ParameterSet implements TunableValidator
//TODO: Code Redundancy, might be smart to insert the three columns into some sort of super structure and then remove the redundant setters/getters, pass column type as argument
- public void setWeightColumnName(String columnName) {
- if (weightColumnName.getPossibleValues().contains(columnName)) {
- weightColumnName.setSelectedValue(columnName);
- }
- else {
- //Attempting to set a column that is not part of the possible values
- //TODO: Output debug/warning if Cytoscape logger will eventually work
- }
+ public void setWeightColumn(CyColumn column) {
+ weightColumn.setSelectedValue(column);
}
- public void setPermanentColumnName(String columnName) {
- if (permanentColumnName.getPossibleValues().contains(columnName)) {
- permanentColumnName.setSelectedValue(columnName);
- }
- else {
- //Attempting to set a column that is not part of the possible values
- //TODO: Output debug/warning if Cytoscape logger will eventually work
- }
+ public void setPermanentColumn(CyColumn column) {
+ permanentColumn.setSelectedValue(column);
}
- public void setForbiddenColumnName(String columnName) {
- if (forbiddenColumnName.getPossibleValues().contains(columnName)) {
- forbiddenColumnName.setSelectedValue(columnName);
- }
- else {
- //Attempting to set a column that is not part of the possible values
- //TODO: Output debug/warning if Cytoscape logger will eventually work
- }
+ public void setForbiddenColumn(CyColumn column) {
+ forbiddenColumn.setSelectedValue(column);
}
- public String getWeightColumnName() {
- return weightColumnName.getSelectedValue();
+ public CyColumn getWeightColumn() {
+ return weightColumn.getSelectedValue();
}
- public String getPermanentColumnName() {
- return permanentColumnName.getSelectedValue();
+ public CyColumn getPermanentColumn() {
+ return permanentColumn.getSelectedValue();
}
- public String getForbiddenColumnName() {
- return forbiddenColumnName.getSelectedValue();
+ public CyColumn getForbiddenColumn() {
+ return forbiddenColumn.getSelectedValue();
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
index 6b8ebbbd3df0374f80f0c31cddc1197358aa1011..57c4563dfe84a7ce3428729fc04c6fd6a7f794e6 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
@@ -1,5 +1,5 @@
/*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 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
@@ -50,9 +50,14 @@ import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NETWOR
public class YoshikoCluster {
-
+ /**
+ * The internal id used to uniquely identify the cluster
+ */
private final long id;
+ /**
+ * All nodes associated with this cluster
+ */
private ArrayList<CyNode> nodes;
private Image img;
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 d6af2cf7e707541e5542495db92681d8a1eedca1..16bb1f782a56f19b1f2ec3584415e3e744614d71 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
@@ -1,5 +1,5 @@
/*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 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
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
index e86274532bc5875c091a2f3d8967c57d9a22ee71..d54fbe5149675fde7368f11e51f0f1fd2dcedec4 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -1,5 +1,5 @@
/*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 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
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 b52e77685d866a4aa3c30643e17e4f4260ceae57..257ff59c002f0f2948a03a9e38e60064ae1965db 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
@@ -26,6 +26,9 @@ import javax.swing.GroupLayout;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JSeparator;
+
+import org.cytoscape.model.CyColumn;
+
import javax.swing.GroupLayout.Alignment;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -113,12 +116,6 @@ public class EditCostPanel extends JPanel {
}
//SETTER / GETTER
- public String getPermanentColumnName() {
- return columnMapper.getPermanentColumn() != null ? columnMapper.getPermanentColumn().getName() : null; }
-
- public String getForbiddenColumnName() {
- return columnMapper.getForbiddenColumn() != null ? columnMapper.getForbiddenColumn().getName() : null; }
-
public double getDefaultInsertionCost() {
return icField.getValueAsDouble();
}
@@ -131,8 +128,14 @@ public class EditCostPanel extends JPanel {
return columnMapper;
}
- public String getWeightColumnName() {
- return columnMapper.getEditingCostColumn() != null ? columnMapper.getEditingCostColumn().getName() : null;
+ public CyColumn getWeightColumn() {
+ return columnMapper.getEditingCostColumn() != null ? columnMapper.getEditingCostColumn() : null;
}
+
+ public CyColumn getPermanentColumn() {
+ return columnMapper.getPermanentColumn() != null ? columnMapper.getPermanentColumn() : null; }
+
+ public CyColumn getForbiddenColumn() {
+ return columnMapper.getForbiddenColumn() != null ? columnMapper.getForbiddenColumn(): null; }
}
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 e48efbf388f40781884f32c96be856e28f1c31b2..b8277bc372c9f538336b697bbd04340ce1112096 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
@@ -346,9 +346,9 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
ParameterSet ret = new ParameterSet();
ret.net = net;
ret.timeLimit = opModePanel.getTimeLimit();
- ret.setWeightColumnName(ecPanel.getWeightColumnName());
- ret.setPermanentColumnName(ecPanel.getPermanentColumnName());
- ret.setForbiddenColumnName(ecPanel.getForbiddenColumnName());
+ ret.setWeightColumn(ecPanel.getWeightColumn());
+ ret.setPermanentColumn(ecPanel.getPermanentColumn());
+ ret.setForbiddenColumn(ecPanel.getForbiddenColumn());
ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
ret.useHeuristic = opModePanel.useHeuristic();
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 52d75a32a3f50dab1f7d49180be9509e29ad03e1..3d0d53fb7412c0e7905c422f419a78718ce20882 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -132,9 +132,9 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
taskMonitor.setProgress(0.1);
//We identify the columns if they exist from their given names
- CyColumn weightColumn = parameterSet.getWeightColumnName() != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.getWeightColumnName()) : null;
- CyColumn permanentColumn = parameterSet.permanentColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.getPermanentColumnName()) : null;
- CyColumn forbiddenColumn = parameterSet.forbiddenColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.getForbiddenColumnName()) : null;
+ CyColumn weightColumn = parameterSet.getWeightColumn();
+ CyColumn permanentColumn = parameterSet.getPermanentColumn();
+ CyColumn forbiddenColumn = parameterSet.getForbiddenColumn();
//Generate an c_input instance from the network
c_input = NetworkParser.parseNetwork(