gew 2.3 missing files

Jonathan Bell [2012-02-15 15:39:31]
gew 2.3 missing files
Filename
genspace-common/src/org/geworkbench/components/genspace/entity/IgnoredHost.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/AddCommentToWf.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/AddCommentToWfResponse.java
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-client-1.4.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-common-1.4.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-stubs-1.4.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-client-1.4.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-common-1.4.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-stubs-1.4.jar.svn-base
geworkbench-core/components/analysis/lib/caGrid-Transfer-client-1.4.jar
geworkbench-core/components/analysis/lib/caGrid-Transfer-common-1.4.jar
geworkbench-core/components/analysis/lib/caGrid-Transfer-stubs-1.4.jar
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/ExportFileFilter.java.svn-base
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/ExportFileFilter.java
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/prop-base/RetrievedSequenceTableModel.java.svn-base
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/text-base/RetrievedSequenceTableModel.java.svn-base
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/RetrievedSequenceTableModel.java
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/IgnoredHost.java b/genspace-common/src/org/geworkbench/components/genspace/entity/IgnoredHost.java
new file mode 100644
index 0000000..6d20017
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/IgnoredHost.java
@@ -0,0 +1,24 @@
+package org.geworkbench.components.genspace.entity;
+
+import javax.persistence.Entity;
+import javax.persistence.Id;
+
+@Entity
+public class IgnoredHost {
+	private int ip;
+	private String comment;
+
+	@Id
+	public int getIp() {
+		return ip;
+	}
+	public void setIp(int ip) {
+		this.ip = ip;
+	}
+	public String getComment() {
+		return comment;
+	}
+	public void setComment(String comment) {
+		this.comment = comment;
+	}
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/AddCommentToWf.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/AddCommentToWf.java
new file mode 100644
index 0000000..96cb074
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/AddCommentToWf.java
@@ -0,0 +1,87 @@
+
+package org.geworkbench.components.genspace.server.stubs;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for addCommentToWf complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType name="addCommentToWf">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="arg0" type="{http://server.genspace.components.geworkbench.org/}workflowComment" minOccurs="0"/>
+ *         &lt;element name="arg1" type="{http://server.genspace.components.geworkbench.org/}workflow" minOccurs="0"/>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "addCommentToWf", propOrder = {
+    "arg0",
+    "arg1"
+})
+public class AddCommentToWf {
+
+    protected WorkflowComment arg0;
+    protected Workflow arg1;
+
+    /**
+     * Gets the value of the arg0 property.
+     *
+     * @return
+     *     possible object is
+     *     {@link WorkflowComment }
+     *
+     */
+    public WorkflowComment getArg0() {
+        return arg0;
+    }
+
+    /**
+     * Sets the value of the arg0 property.
+     *
+     * @param value
+     *     allowed object is
+     *     {@link WorkflowComment }
+     *
+     */
+    public void setArg0(WorkflowComment value) {
+        this.arg0 = value;
+    }
+
+    /**
+     * Gets the value of the arg1 property.
+     *
+     * @return
+     *     possible object is
+     *     {@link Workflow }
+     *
+     */
+    public Workflow getArg1() {
+        return arg1;
+    }
+
+    /**
+     * Sets the value of the arg1 property.
+     *
+     * @param value
+     *     allowed object is
+     *     {@link Workflow }
+     *
+     */
+    public void setArg1(Workflow value) {
+        this.arg1 = value;
+    }
+
+}
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/AddCommentToWfResponse.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/AddCommentToWfResponse.java
new file mode 100644
index 0000000..199ec84
--- /dev/null
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/AddCommentToWfResponse.java
@@ -0,0 +1,62 @@
+
+package org.geworkbench.components.genspace.server.stubs;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for addCommentToWfResponse complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType name="addCommentToWfResponse">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="return" type="{http://server.genspace.components.geworkbench.org/}workflowComment" minOccurs="0"/>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "addCommentToWfResponse", propOrder = {
+    "_return"
+})
+public class AddCommentToWfResponse {
+
+    @XmlElement(name = "return")
+    protected WorkflowComment _return;
+
+    /**
+     * Gets the value of the return property.
+     *
+     * @return
+     *     possible object is
+     *     {@link WorkflowComment }
+     *
+     */
+    public WorkflowComment getReturn() {
+        return _return;
+    }
+
+    /**
+     * Sets the value of the return property.
+     *
+     * @param value
+     *     allowed object is
+     *     {@link WorkflowComment }
+     *
+     */
+    public void setReturn(WorkflowComment value) {
+        this._return = value;
+    }
+
+}
diff --git a/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-client-1.4.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-client-1.4.jar.svn-base
new file mode 100644
index 0000000..5e9587e
--- /dev/null
+++ b/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-client-1.4.jar.svn-base
@@ -0,0 +1,5 @@
+K 13
+svn:mime-type
+V 24
+application/octet-stream
+END
diff --git a/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-common-1.4.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-common-1.4.jar.svn-base
new file mode 100644
index 0000000..5e9587e
--- /dev/null
+++ b/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-common-1.4.jar.svn-base
@@ -0,0 +1,5 @@
+K 13
+svn:mime-type
+V 24
+application/octet-stream
+END
diff --git a/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-stubs-1.4.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-stubs-1.4.jar.svn-base
new file mode 100644
index 0000000..5e9587e
--- /dev/null
+++ b/geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-Transfer-stubs-1.4.jar.svn-base
@@ -0,0 +1,5 @@
+K 13
+svn:mime-type
+V 24
+application/octet-stream
+END
diff --git a/geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-client-1.4.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-client-1.4.jar.svn-base
new file mode 100644
index 0000000..a41a0ce
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diff --git a/geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-common-1.4.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-common-1.4.jar.svn-base
new file mode 100644
index 0000000..9c2466a
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diff --git a/geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-stubs-1.4.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-Transfer-stubs-1.4.jar.svn-base
new file mode 100644
index 0000000..5791685
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diff --git a/geworkbench-core/components/analysis/lib/caGrid-Transfer-client-1.4.jar b/geworkbench-core/components/analysis/lib/caGrid-Transfer-client-1.4.jar
new file mode 100644
index 0000000..a41a0ce
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diff --git a/geworkbench-core/components/analysis/lib/caGrid-Transfer-common-1.4.jar b/geworkbench-core/components/analysis/lib/caGrid-Transfer-common-1.4.jar
new file mode 100644
index 0000000..9c2466a
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diff --git a/geworkbench-core/components/analysis/lib/caGrid-Transfer-stubs-1.4.jar b/geworkbench-core/components/analysis/lib/caGrid-Transfer-stubs-1.4.jar
new file mode 100644
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diff --git a/geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/ExportFileFilter.java.svn-base b/geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/ExportFileFilter.java.svn-base
new file mode 100644
index 0000000..552d5d0
--- /dev/null
+++ b/geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/ExportFileFilter.java.svn-base
@@ -0,0 +1,39 @@
+package org.geworkbench.components.masterregulator;
+
+import java.io.File;
+
+import javax.swing.filechooser.FileFilter;
+
+public class ExportFileFilter extends FileFilter {
+	private final String extension;
+	private final String description;
+	private final String delimiter;
+
+	ExportFileFilter(String extension, String description,  String delimiter) {
+		this.extension = extension;
+		this.description = description;
+		this.delimiter = delimiter;
+	}
+
+	public String getDelimiter() {
+		return delimiter;
+	}
+
+	public String getExtension() {
+		return extension;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public boolean accept(File f) {
+		boolean returnVal = false;
+		if (f.isDirectory() || f.getName().endsWith(extension)) {
+			return true;
+		}
+
+		return returnVal;
+	}
+
+}
diff --git a/geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/ExportFileFilter.java b/geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/ExportFileFilter.java
new file mode 100644
index 0000000..552d5d0
--- /dev/null
+++ b/geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/ExportFileFilter.java
@@ -0,0 +1,39 @@
+package org.geworkbench.components.masterregulator;
+
+import java.io.File;
+
+import javax.swing.filechooser.FileFilter;
+
+public class ExportFileFilter extends FileFilter {
+	private final String extension;
+	private final String description;
+	private final String delimiter;
+
+	ExportFileFilter(String extension, String description,  String delimiter) {
+		this.extension = extension;
+		this.description = description;
+		this.delimiter = delimiter;
+	}
+
+	public String getDelimiter() {
+		return delimiter;
+	}
+
+	public String getExtension() {
+		return extension;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public boolean accept(File f) {
+		boolean returnVal = false;
+		if (f.isDirectory() || f.getName().endsWith(extension)) {
+			return true;
+		}
+
+		return returnVal;
+	}
+
+}
diff --git a/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/prop-base/RetrievedSequenceTableModel.java.svn-base b/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/prop-base/RetrievedSequenceTableModel.java.svn-base
new file mode 100644
index 0000000..1630e9c
--- /dev/null
+++ b/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/prop-base/RetrievedSequenceTableModel.java.svn-base
@@ -0,0 +1,5 @@
+K 12
+svn:keywords
+V 52
+LastChangedDate LastChangedRevision LastChangedBy Id
+END
diff --git a/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/text-base/RetrievedSequenceTableModel.java.svn-base b/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/text-base/RetrievedSequenceTableModel.java.svn-base
new file mode 100644
index 0000000..d856d29
--- /dev/null
+++ b/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/text-base/RetrievedSequenceTableModel.java.svn-base
@@ -0,0 +1,142 @@
+package org.geworkbench.components.sequenceretriever;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.table.AbstractTableModel;
+
+import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
+
+/*
+ * Table model for the 'line view' of retrieved sequences,
+ * which is implemented as RetrievedSequenceDisplayPanel.
+ */
+class RetrievedSequenceTableModel extends AbstractTableModel {
+	/**
+	 *
+	 */
+	private final RetrievedSequenceDisplayPanel retrievedSequenceDisplayPanel;
+
+	private static final long serialVersionUID = -6009654606398029902L;
+
+	private List<String> sequenceNames;
+
+	RetrievedSequenceTableModel(RetrievedSequenceDisplayPanel retrievedSequenceDisplayPanel) {
+		this.retrievedSequenceDisplayPanel = retrievedSequenceDisplayPanel;
+		resetNameList(false);
+	}
+
+	void resetNameList(boolean hideDuplicate) {
+		if(this.retrievedSequenceDisplayPanel.sequenceDB==null)return;
+
+		sequenceNames = new ArrayList<String>();
+		List<String> startingSites = new ArrayList<String>();
+
+		for(DSSequence sequence: this.retrievedSequenceDisplayPanel.sequenceDB) {
+			String n = sequence.toString();
+			int i = n.lastIndexOf("_");
+			i = n.lastIndexOf("_", i);
+			String startingSite = n.substring(i);
+			if(!hideDuplicate || !startingSites.contains(startingSite)) {
+				sequenceNames.add(n);
+				startingSites.add(startingSite);
+			}
+		}
+		fireTableDataChanged();
+	}
+
+	@Override
+	public String getColumnName(int column) {
+		switch (column) {
+		case 0:
+			return "Include";
+		case 1:
+			return "Name";
+		case 2:
+			return "Sequence Detail";
+		default:
+			return "Sequence Detail";
+		}
+	}
+
+	@Override
+	public int getRowCount() {
+		if (sequenceNames == null) {
+			return 0;
+		} else {
+			return sequenceNames.size();
+		}
+	}
+
+	@Override
+	public int getColumnCount() {
+		if (sequenceNames == null) {
+			return 0;
+		} else {
+			return 3;
+		}
+	}
+
+	@Override
+	public Object getValueAt(int rowIndex, int columnIndex) {
+		String sequenceName = sequenceNames.get(rowIndex);
+		RetrievedSequenceView retrievedSequenceView = this.retrievedSequenceDisplayPanel
+				.getRetrievedSequenceView(sequenceName);
+		if (retrievedSequenceView == null) {
+			return null;
+		}
+		switch (columnIndex) {
+		case 0:
+			return retrievedSequenceView.isIncluded();
+		case 1:
+			if (this.retrievedSequenceDisplayPanel.sequenceDB.isDNA()) {
+				return sequenceName;
+			} else {
+				return "<html><font  color=\"#0000FF\"><u>"
+						+ sequenceName + "</u></font>";
+			}
+		case 2:
+			return retrievedSequenceView;
+		default:
+			return sequenceName;
+		}
+	}
+
+	@Override
+	public Class<?> getColumnClass(int columnIndex) {
+		switch (columnIndex) {
+		case 0:
+			return Boolean.class;
+		case 2:
+			return RetrievedSequenceView.class;
+		default:
+			return String.class;
+		}
+	}
+
+	/*
+	 * returns if the cell is editable; returns false for all cells in
+	 * columns except the first column (check box)
+	 */
+	@Override
+	public boolean isCellEditable(int row, int col) {
+		return col == 0;
+	}
+
+	/*
+	 * detect change in cell at (row, col); set cell to value; update the
+	 * table
+	 */
+	@Override
+	public void setValueAt(Object value, int row, int col) {
+		String sequenceName = sequenceNames.get(row);
+		if (col==0 && sequenceName != null && value != null) {
+			RetrievedSequenceView retrievedSequenceView = this.retrievedSequenceDisplayPanel
+					.getRetrievedSequenceView(sequenceName);
+			retrievedSequenceView.setIncluded(((Boolean) value) // FIXME java.lang.NullPointerException
+					.booleanValue());
+//			fireTableCellUpdated(row, col);
+		}
+	}
+
+}
\ No newline at end of file
diff --git a/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/RetrievedSequenceTableModel.java b/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/RetrievedSequenceTableModel.java
new file mode 100644
index 0000000..d856d29
--- /dev/null
+++ b/geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/RetrievedSequenceTableModel.java
@@ -0,0 +1,142 @@
+package org.geworkbench.components.sequenceretriever;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.table.AbstractTableModel;
+
+import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
+
+/*
+ * Table model for the 'line view' of retrieved sequences,
+ * which is implemented as RetrievedSequenceDisplayPanel.
+ */
+class RetrievedSequenceTableModel extends AbstractTableModel {
+	/**
+	 *
+	 */
+	private final RetrievedSequenceDisplayPanel retrievedSequenceDisplayPanel;
+
+	private static final long serialVersionUID = -6009654606398029902L;
+
+	private List<String> sequenceNames;
+
+	RetrievedSequenceTableModel(RetrievedSequenceDisplayPanel retrievedSequenceDisplayPanel) {
+		this.retrievedSequenceDisplayPanel = retrievedSequenceDisplayPanel;
+		resetNameList(false);
+	}
+
+	void resetNameList(boolean hideDuplicate) {
+		if(this.retrievedSequenceDisplayPanel.sequenceDB==null)return;
+
+		sequenceNames = new ArrayList<String>();
+		List<String> startingSites = new ArrayList<String>();
+
+		for(DSSequence sequence: this.retrievedSequenceDisplayPanel.sequenceDB) {
+			String n = sequence.toString();
+			int i = n.lastIndexOf("_");
+			i = n.lastIndexOf("_", i);
+			String startingSite = n.substring(i);
+			if(!hideDuplicate || !startingSites.contains(startingSite)) {
+				sequenceNames.add(n);
+				startingSites.add(startingSite);
+			}
+		}
+		fireTableDataChanged();
+	}
+
+	@Override
+	public String getColumnName(int column) {
+		switch (column) {
+		case 0:
+			return "Include";
+		case 1:
+			return "Name";
+		case 2:
+			return "Sequence Detail";
+		default:
+			return "Sequence Detail";
+		}
+	}
+
+	@Override
+	public int getRowCount() {
+		if (sequenceNames == null) {
+			return 0;
+		} else {
+			return sequenceNames.size();
+		}
+	}
+
+	@Override
+	public int getColumnCount() {
+		if (sequenceNames == null) {
+			return 0;
+		} else {
+			return 3;
+		}
+	}
+
+	@Override
+	public Object getValueAt(int rowIndex, int columnIndex) {
+		String sequenceName = sequenceNames.get(rowIndex);
+		RetrievedSequenceView retrievedSequenceView = this.retrievedSequenceDisplayPanel
+				.getRetrievedSequenceView(sequenceName);
+		if (retrievedSequenceView == null) {
+			return null;
+		}
+		switch (columnIndex) {
+		case 0:
+			return retrievedSequenceView.isIncluded();
+		case 1:
+			if (this.retrievedSequenceDisplayPanel.sequenceDB.isDNA()) {
+				return sequenceName;
+			} else {
+				return "<html><font  color=\"#0000FF\"><u>"
+						+ sequenceName + "</u></font>";
+			}
+		case 2:
+			return retrievedSequenceView;
+		default:
+			return sequenceName;
+		}
+	}
+
+	@Override
+	public Class<?> getColumnClass(int columnIndex) {
+		switch (columnIndex) {
+		case 0:
+			return Boolean.class;
+		case 2:
+			return RetrievedSequenceView.class;
+		default:
+			return String.class;
+		}
+	}
+
+	/*
+	 * returns if the cell is editable; returns false for all cells in
+	 * columns except the first column (check box)
+	 */
+	@Override
+	public boolean isCellEditable(int row, int col) {
+		return col == 0;
+	}
+
+	/*
+	 * detect change in cell at (row, col); set cell to value; update the
+	 * table
+	 */
+	@Override
+	public void setValueAt(Object value, int row, int col) {
+		String sequenceName = sequenceNames.get(row);
+		if (col==0 && sequenceName != null && value != null) {
+			RetrievedSequenceView retrievedSequenceView = this.retrievedSequenceDisplayPanel
+					.getRetrievedSequenceView(sequenceName);
+			retrievedSequenceView.setIncluded(((Boolean) value) // FIXME java.lang.NullPointerException
+					.booleanValue());
+//			fireTableCellUpdated(row, col);
+		}
+	}
+
+}
\ No newline at end of file