From 335c02422ae7519eabafbfef53ddf781b798a215 Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Mon, 5 Mar 2018 12:34:22 +0100
Subject: [PATCH] Changed column mapping parameters to Cytoscape
ListSingleSelection -> easier and more intuitive for automation users
Updated some license headers
---
.../ba/yoshikoWrapper/core/ParameterSet.java | 107 +++++++++++++++++-
.../yoshikoWrapper/cytoUtil/StyleManager.java | 2 +-
.../hhu/ba/yoshikoWrapper/help/HelpLinks.java | 2 +-
.../ba/yoshikoWrapper/swing/SwingUtil.java | 2 +-
.../swing/components/MainPanel.java | 6 +-
.../swing/components/SolutionTab.java | 2 +-
.../yoshikoWrapper/tasks/AlgorithmTask.java | 6 +-
7 files changed, 113 insertions(+), 14 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 ce7fbd1..1ae45b2 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -1,12 +1,36 @@
+/*******************************************************************************
+ * 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
+ * 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.IOException;
+import java.util.ArrayList;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
+import org.cytoscape.work.util.ListSingleSelection;
public class ParameterSet implements TunableValidator
{
@@ -16,13 +40,15 @@ public class ParameterSet implements TunableValidator
@Tunable(description="Time Limit for the ILP mode", context="nogui")
public int timeLimit = -1;
+
+ //COLUMN-MAPPINGS
@Tunable(description="A column in the edge table containing weights", context="nogui")
- public String weightColumnName;
+ public ListSingleSelection<String> weightColumnName = null;
@Tunable(description="A column containing boolean entries for edges that are to be treated as permanent",context="nogui")
- public String permanentColumnName;
+ public ListSingleSelection<String> permanentColumnName = null;
@Tunable(description="A column containing boolean entries for edges that are to be treated as forbidden",context="nogui")
- public String forbiddenColumnName;
+ public ListSingleSelection<String> forbiddenColumnName = null;
@Tunable(description="The default insertion cost that is to be used for non-existing edges",context="nogui")
public double defaultInsertionCost = -1;
@@ -54,6 +80,33 @@ public class ParameterSet implements TunableValidator
@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;
+
+ /**
+ * Default constructor, initializes the column mappings to provide a selection of fitting columns
+ */
+ public ParameterSet() {
+
+ ArrayList<String> columnNames = new ArrayList<String>();
+
+ //Only numeric columns are relevant for weight mapping
+ for (CyColumn col : net.getDefaultEdgeTable().getColumns()) {
+ if (Number.class.isAssignableFrom(col.getType())) {
+ columnNames.add(col.getName());
+ }
+ }
+ weightColumnName = new ListSingleSelection<String>(columnNames);
+
+ columnNames = new ArrayList<String>();
+
+ //Only boolean columns are relevant for forbidden/permanent mapping
+ for (CyColumn col : net.getDefaultEdgeTable().getColumns()) {
+ if (col.getType() == Boolean.class) {
+ columnNames.add(col.getName());
+ }
+ }
+ forbiddenColumnName = new ListSingleSelection<String>(columnNames);
+ permanentColumnName = new ListSingleSelection<String>(columnNames);
+ }
@Override
public ValidationState getValidationState(Appendable errMsg) {
@@ -61,7 +114,7 @@ public class ParameterSet implements TunableValidator
try {
if (net!= null) {
//Verify column validity
- CyColumn weightColumn = net.getDefaultEdgeTable().getColumn(weightColumnName);
+ CyColumn weightColumn = net.getDefaultEdgeTable().getColumn(weightColumnName.getSelectedValue());
if (weightColumn == null) {
errMsg.append("Could not find a column named: "+weightColumnName+"\n");
return ValidationState.INVALID;
@@ -108,5 +161,51 @@ public class ParameterSet implements TunableValidator
//TODO
return ret;
}
+
+ //SETTER & GETTER
+
+ //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 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 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 String getWeightColumnName() {
+ return weightColumnName.getSelectedValue();
+ }
+
+ public String getPermanentColumnName() {
+ return permanentColumnName.getSelectedValue();
+ }
+
+ public String getForbiddenColumnName() {
+ return forbiddenColumnName.getSelectedValue();
+ }
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java
index 48c8d13..65d7e79 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.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/help/HelpLinks.java b/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
index d96a9c8..04fde39 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.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/SwingUtil.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.java
index 003518e..7310c61 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.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/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
index 5fc0e50..e48efbf 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.weightColumnName = ecPanel.getWeightColumnName();
- ret.permanentColumnName = ecPanel.getPermanentColumnName();
- ret.forbiddenColumnName = ecPanel.getForbiddenColumnName();
+ ret.setWeightColumnName(ecPanel.getWeightColumnName());
+ ret.setPermanentColumnName(ecPanel.getPermanentColumnName());
+ ret.setForbiddenColumnName(ecPanel.getForbiddenColumnName());
ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
ret.useHeuristic = opModePanel.useHeuristic();
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 83a7ef3..e6fd5b2 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
@@ -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/tasks/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
index bf314c9..52d75a3 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.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;
+ 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;
//Generate an c_input instance from the network
c_input = NetworkParser.parseNetwork(
--
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