From e4462426011cb9341b40d652492a67729a4b98ce Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Tue, 12 Dec 2017 15:58:00 +0100
Subject: [PATCH] Some JavaDoc additions / CyRest, some cleanup
---
.../core/LocalizationManager.java | 3 +-
.../core/NetworkParsingException.java | 5 +++
.../ba/yoshikoWrapper/core/ParameterSet.java | 39 ++++++++++++++++++-
.../graphModel/YoshikoResult.java | 2 -
.../graphModel/YoshikoSolution.java | 12 ++++++
.../ba/yoshikoWrapper/swing/FormatHelper.java | 15 +++++++
.../yoshikoWrapper/swing/GraphicsLoader.java | 3 ++
.../ba/yoshikoWrapper/swing/SwingUtil.java | 6 +++
.../yoshikoWrapper/tasks/AlgorithmTask.java | 12 ++++++
.../tasks/GetSolutionsTask.java | 1 -
10 files changed, 91 insertions(+), 7 deletions(-)
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/LocalizationManager.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/LocalizationManager.java
index 7f55098..6a50738 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/LocalizationManager.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/LocalizationManager.java
@@ -53,7 +53,6 @@ public class LocalizationManager {
locales.put("deDE", german);
locales.put("hrHR", serbocroatianLatin);
locales.put("elEL", modernGreek);
-
}
@@ -104,7 +103,7 @@ public class LocalizationManager {
}
public static void switchLanguage(String key) {
- System.out.println("DEBUG: SWITCHING TO: "+key);
+ //System.out.println("DEBUG: SWITCHING TO: "+key);
currentLocale = locales.get(key);
updateBundle();
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java
index 65b9c43..c556b9d 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java
@@ -1,5 +1,10 @@
package de.hhu.ba.yoshikoWrapper.core;
+/**
+ * Simple Exception that should be thrown when the CyNetwork combined with the given parameters can not be parsed in a meaningful WCE instance
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
@SuppressWarnings("serial")
public class NetworkParsingException extends Exception {
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 79d7daa..08ac18a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/ParameterSet.java
@@ -1,10 +1,14 @@
package de.hhu.ba.yoshikoWrapper.core;
+import java.io.IOException;
+
import org.cytoscape.model.CyColumn;
import org.cytoscape.work.Tunable;
+import org.cytoscape.work.TunableValidator;
-public class ParameterSet {
+public class ParameterSet implements TunableValidator
+{
@Tunable(description="Time Limit for the ILP mode", context="nogui")
public int timeLimit = -1;
@@ -21,7 +25,7 @@ public class ParameterSet {
@Tunable(description="The default deletion cost that is to be used for edges without an associated weight",context="nogui")
public double defaultDeletionCost = 1;
- @Tunable(description="A bitmask representing which reduction rules should be used",context="nogui") //TODO: Filter bad bitmasks
+ @Tunable(description="A bitmask representing which reduction rules should be used",context="nogui")
public String reductionRulesBitMask = "000000";
@Tunable(description="A value controlling the resolution of the SNR reduction rule. Higher values mean a longer running time but possibly better reduction.",context="nogui")
public double snrMultFactor = 1.0;
@@ -44,4 +48,35 @@ public class ParameterSet {
/**Describes whether auto configuration of the reduction rules is to be used. Overrides the bit mask.**/
public boolean suggestReduction = true;
+ @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();
+ }
+ return ValidationState.INVALID;
+ }
+ return ValidationState.OK;
+ }
+
+ /**
+ * Helper function that verifies a String and checks if it represents a 6-bit bitmask
+ * @param mask
+ * @return
+ */
+ private boolean checkBitmask(String mask) {
+ if (mask.length() != 6) {
+ return false;
+ }
+ for (byte c : mask.getBytes()) {
+ if (((char)c)!='0'&&((char)c)!='0') {
+ return false;
+ }
+ }
+ return true;
+ }
+
}
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 0a4ea3b..d6af2cf 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
@@ -21,7 +21,6 @@
******************************************************************************/
package de.hhu.ba.yoshikoWrapper.graphModel;
-import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
@@ -67,7 +66,6 @@ public class YoshikoResult{
return flags;
}
-
public void addSolution(YoshikoSolution solution) {
solutions.put(solution.getId(),solution);
}
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 1a20245..e862745 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -34,11 +34,23 @@ import org.slf4j.Logger;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
+/**
+ * Represents a solution found by the Yoshiko algorithm.
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
public class YoshikoSolution {
+ /**A reference to the result (and thus the Yoshiko run) to which this solution belongs
+ * TODO: I hate this codestyle wise maybe replace in the long run
+ */
private final YoshikoResult result;
+ /**
+ * The CyNetwork representing the meta-graph for this solution if such a graph exists.
+ */
private CyNetwork metaGraph;
+
private HashMap<YoshikoCluster, CyNode> metaGraphMap;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/FormatHelper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/FormatHelper.java
index 284757e..2a7fbff 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/FormatHelper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/FormatHelper.java
@@ -26,12 +26,27 @@ import java.text.NumberFormat;
import javax.swing.text.NumberFormatter;
+/**
+ * Serves as a Factory for various formatters that might be helpful for restricted input fields.
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
public class FormatHelper {
+ /**Returns a basic integer input formatter accepting only positive integers
+ * Equivalent to getIntegerFormatter(0,Integer.MAX_VALUE)
+ * @return The NumberFormatter object
+ */
public static NumberFormatter getIntegerFormatter() {
return getIntegerFormatter(0, Integer.MAX_VALUE);
}
+ /**
+ * Returns a basic integer input formatter accepting only integers in the given range
+ * @param minValue The smallest, accepted integer
+ * @param maxValue The largest, accepted integer
+ * @return A NumberFormatter object accepting only integers in the given range
+ */
public static NumberFormatter getIntegerFormatter(int minValue, int maxValue) {
NumberFormat format = NumberFormat.getInstance();
NumberFormatter formatter = new NumberFormatter(format);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/GraphicsLoader.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/GraphicsLoader.java
index ee1ae4b..27a5272 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/GraphicsLoader.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/GraphicsLoader.java
@@ -43,6 +43,9 @@ public class GraphicsLoader {
private static BufferedImage infoIcon;
private static BufferedImage infoIcon_highlighted;
+ /**
+ * The fixed Yoshiko styled color, for quick reference
+ */
public final static Color yoshikoGreen = new Color(0,128,0);
private final static ClassLoader classLoader = GraphicsLoader.class.getClassLoader();
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 b190b5a..003518e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.java
@@ -26,7 +26,13 @@ import java.text.DecimalFormat;
import javax.swing.JComponent;
+/**
+ * Contains some basic convenience functions for working with Swing that have no other place (as of now)
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
public class SwingUtil {
+
public static void addAll(Container container, JComponent ... components) {
for (JComponent c: components) {
container.add(c);
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 8f7299e..d764f9e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -24,6 +24,8 @@ package de.hhu.ba.yoshikoWrapper.tasks;
import java.awt.Window;
import java.util.Properties;
+import javax.swing.SwingUtilities;
+
import org.cytoscape.application.swing.CytoPanel;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
@@ -243,6 +245,16 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
eastPanel.setSelectedIndex(eastPanel.indexOfComponent(resultPanel));
//Show (might be invisible)
eastPanel.setState(CytoPanelState.DOCK);
+ //Blackest magic, attempts to scale the result panel to a good size
+ SwingUtilities.invokeLater(
+ new Runnable() {
+ @Override
+ public void run() {
+ eastPanel.getThisComponent().setMinimumSize(eastPanel.getThisComponent().getPreferredSize());
+ eastPanel.getThisComponent().revalidate();
+ }
+ }
+ );
//eastPanel.getThisComponent().revalidate();
}
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 cac56b2..b36ef96 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
@@ -29,7 +29,6 @@ public class GetSolutionsTask implements ObservableTask {
@Override
public void cancel() {
// TODO Auto-generated method stub
-
}
@SuppressWarnings("unchecked")
--
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