From f1f3c7c6b329269a87bb3e57fdb95f896d7fe32d Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Mon, 5 Mar 2018 13:47:01 +0100
Subject: [PATCH] More elegant handling of CyColumn tunable, removed workaround
via String completely
Updated some headers, some Javadoc
---
.../ba/yoshikoWrapper/core/ParameterSet.java | 75 +++++++------------
.../graphModel/YoshikoCluster.java | 9 ++-
.../graphModel/YoshikoResult.java | 2 +-
.../graphModel/YoshikoSolution.java | 2 +-
.../swing/components/EditCostPanel.java | 19 +++--
.../swing/components/MainPanel.java | 6 +-
.../yoshikoWrapper/tasks/AlgorithmTask.java | 6 +-
7 files changed, 52 insertions(+), 67 deletions(-)
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 1ae45b2..f050e37 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 6b8ebbb..57c4563 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 d6af2cf..16bb1f7 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 e862745..d54fbe5 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 b52e776..257ff59 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 e48efbf..b8277bc 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 52d75a3..3d0d53f 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(
--
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