Trying to fix synchronization problem in evidence panel

pgaudet · May 9, 2017 · f0bab3d · f0bab3d
1 parent c178735
commit f0bab3d
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Showing 24 changed files with 362 additions and 343 deletions.
diff --git a/config/preferences.yaml b/config/preferences.yaml
@@ -1,8 +1,8 @@
 !!org.paint.config.PaintConfig
 GOlrURL: http://golr.geneontology.org/solr
 collapse_no_exp: true
-full_msa: false
-gafdir: /Users/suzi/projects/go/gene-associations/submission/paint/PTHR10003/
+full_msa: true
+gafdir: /Users/suzi/projects/go/gene-associations/submission/paint/PTHR11348/
 msa_colors:
 - !color '51, 102, 77, 255'
 - !color '112, 153, 92, 255'

diff --git a/pom.xml b/pom.xml
@@ -28,8 +28,8 @@
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
-	  			<artifactId>maven-assembly-plugin</artifactId>
-	  			<version>2.5.3</version>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<version>2.5.3</version>
 				<configuration>
 					<finalName>paint-all</finalName>
 					<appendAssemblyId>false</appendAssemblyId>
@@ -82,45 +82,6 @@
 	</repositories>
 
 	<dependencies>
-		<dependency>
-			<groupId>org.bbop</groupId>
-			<artifactId>golr-client</artifactId>
-			<version>0.2.2-SNAPSHOT</version>
-		</dependency>
-		<dependency>
-			<groupId>commons-lang</groupId>
-			<artifactId>commons-lang</artifactId>
-			<version>2.4</version>
-		</dependency>
-		<dependency>
-			<groupId>dom4j</groupId>
-			<artifactId>dom4j</artifactId>
-			<version>1.6.1</version>
-		</dependency>
-		<dependency>
-		    <groupId>commons-io</groupId>
-    		<artifactId>commons-io</artifactId>
-    		<version>2.5</version>
-		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-			<version>1.2.15</version>
-			<exclusions>
-				<exclusion>
-					<artifactId>jmxtools</artifactId>
-					<groupId>com.sun.jdmk</groupId>
-				</exclusion>
-				<exclusion>
-					<artifactId>jmxri</artifactId>
-					<groupId>com.sun.jmx</groupId>
-				</exclusion>
-				<exclusion>
-					<artifactId>jms</artifactId>
-					<groupId>javax.jms</groupId>
-				</exclusion>
-			</exclusions>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.xmlgraphics</groupId>
 			<artifactId>batik-bridge</artifactId>
@@ -157,4 +118,4 @@
 			<version>0.0.1-SNAPSHOT</version>
 		</dependency>
 	</dependencies>
-</project>
+</project>
diff --git a/src/org/paint/dialog/ChallengeDialog.java b/src/org/paint/dialog/ChallengeDialog.java
@@ -46,7 +46,7 @@
 
 import org.bbop.phylo.model.Bioentity;
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.paint.gui.AspectSelector;
 import org.paint.util.RenderUtil;
 

diff --git a/src/org/paint/dialog/TaxonDialog.java b/src/org/paint/dialog/TaxonDialog.java
@@ -39,8 +39,8 @@
 import javax.swing.JPanel;
 import javax.swing.border.Border;
 
+import org.bbop.phylo.owl.OWLutil;
 import org.bbop.phylo.species.TaxonFinder;
-import org.bbop.phylo.util.OWLutil;
 import org.paint.util.RenderUtil;
 
 public class TaxonDialog extends JDialog {

diff --git a/src/org/paint/dialog/find/ResultRenderer.java b/src/org/paint/dialog/find/ResultRenderer.java
@@ -27,7 +27,7 @@
 import javax.swing.table.DefaultTableCellRenderer;
 
 import org.apache.log4j.Logger;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.paint.dialog.find.FindPanel.SEARCH_TYPE;
 import org.paint.gui.AspectSelector;
 import org.paint.util.GuiConstant;

diff --git a/src/org/paint/gui/AspectSelectorPanel.java b/src/org/paint/gui/AspectSelectorPanel.java
@@ -32,7 +32,7 @@
 import javax.swing.border.Border;
 import javax.swing.border.EtchedBorder;
 
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.paint.config.PaintConfig;
 import org.paint.gui.event.AspectChangeEvent;
 import org.paint.gui.event.AspectChangeListener;

diff --git a/src/org/paint/gui/association/AssociationsTableModel.java b/src/org/paint/gui/association/AssociationsTableModel.java
@@ -32,7 +32,7 @@
 import org.bbop.phylo.annotate.AnnotationUtil;
 import org.bbop.phylo.model.Bioentity;
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.bbop.swing.HyperlinkLabel;
 import org.paint.gui.association.AssociationsTable.PHYLO_ACTION;
 import org.paint.gui.event.TermHyperlinkListener;

diff --git a/src/org/paint/gui/association/ECOCellRenderer.java b/src/org/paint/gui/association/ECOCellRenderer.java
@@ -14,7 +14,7 @@
 import org.bbop.phylo.annotate.AnnotationUtil;
 import org.bbop.phylo.model.Bioentity;
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.bbop.swing.ScaledIcon;
 import org.paint.config.IconResource;
 import org.paint.gui.AspectSelector;

diff --git a/src/org/paint/gui/association/EvidenceComparator.java b/src/org/paint/gui/association/EvidenceComparator.java
@@ -3,7 +3,7 @@
 import java.util.Comparator;
 
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 
 public class EvidenceComparator implements Comparator<GeneAnnotation> {
 

diff --git a/src/org/paint/gui/association/GOTermRenderer.java b/src/org/paint/gui/association/GOTermRenderer.java
@@ -35,7 +35,7 @@
 
 import org.apache.log4j.Logger;
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.bbop.swing.ScaledIcon;
 import org.paint.config.IconResource;
 import org.paint.gui.AspectSelector;

diff --git a/src/org/paint/gui/association/HyperlinkCellRenderer.java b/src/org/paint/gui/association/HyperlinkCellRenderer.java
@@ -13,7 +13,7 @@
 
 import org.apache.log4j.Logger;
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.bbop.swing.ExtensibleLabelUI.Renderer;
 import org.bbop.swing.HyperlinkLabel;
 import org.paint.gui.AspectSelector;

diff --git a/src/org/paint/gui/association/TrashCellRenderer.java b/src/org/paint/gui/association/TrashCellRenderer.java
@@ -10,7 +10,7 @@
 import javax.swing.table.TableCellRenderer;
 
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.paint.gui.AspectSelector;
 import org.paint.util.RenderUtil;
 

diff --git a/src/org/paint/gui/event/EventManager.java b/src/org/paint/gui/event/EventManager.java
@@ -59,6 +59,8 @@ public class EventManager {
 	protected List<Bioentity> selectedNodes;
 	protected String term_selection;
 	protected Bioentity top_node;
+
+	private static final org.apache.log4j.Logger log = org.apache.log4j.Logger.getLogger(EventManager.class);
 
 	private List<FamilyChangeListener> family_listeners = new ArrayList<FamilyChangeListener>(6);
 
@@ -482,11 +484,12 @@ public void setCurrentSelectedNode(Bioentity node) {
 		top_node = node;
 	}
 
-	public void fireNewFamilyEvent(Object source, Family data_bag) {
-		FamilyChangeEvent e = new FamilyChangeEvent(source, data_bag);
-		if (data_bag != null) {
-			for (FamilyChangeListener l : family_listeners)
+	public void fireNewFamilyEvent(Object source, Family family) {
+		FamilyChangeEvent e = new FamilyChangeEvent(source, family);
+		if (family != null) {
+			for (FamilyChangeListener l : family_listeners) {
 				l.newFamilyData(e);
+			}
 		}
 		TreePanel tree = PaintManager.inst().getTree();
 		tree.scrollToTop();

diff --git a/src/org/paint/gui/matrix/AnnotMatrix.java b/src/org/paint/gui/matrix/AnnotMatrix.java
@@ -50,8 +50,8 @@
 import org.bbop.phylo.model.Bioentity;
 import org.bbop.phylo.model.GeneAnnotation;
 import org.bbop.phylo.model.Tree;
+import org.bbop.phylo.owl.OWLutil;
 import org.bbop.phylo.tracking.LogEntry;
-import org.bbop.phylo.util.OWLutil;
 import org.bbop.phylo.util.TaxonChecker;
 import org.paint.dialog.AnnotUtil;
 import org.paint.displaymodel.DisplayBioentity;

diff --git a/src/org/paint/gui/matrix/AnnotMatrixModel.java b/src/org/paint/gui/matrix/AnnotMatrixModel.java
@@ -33,7 +33,7 @@
 import org.bbop.phylo.annotate.AnnotationUtil;
 import org.bbop.phylo.model.Bioentity;
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.paint.config.CustomTermList;
 import org.paint.displaymodel.DisplayBioentity;
 import org.paint.gui.AspectSelector;

diff --git a/src/org/paint/gui/matrix/AnnotationTransferHandler.java b/src/org/paint/gui/matrix/AnnotationTransferHandler.java
@@ -56,9 +56,9 @@
 import org.bbop.framework.GUIManager;
 import org.bbop.phylo.annotate.PaintAction;
 import org.bbop.phylo.model.Tree;
+import org.bbop.phylo.owl.OWLutil;
 import org.bbop.phylo.tracking.LogEntry;
 import org.bbop.phylo.tracking.LogEntry.LOG_ENTRY_TYPE;
-import org.bbop.phylo.util.OWLutil;
 import org.bbop.phylo.util.TaxonChecker;
 import org.paint.dialog.AnnotUtil;
 import org.paint.dialog.TaxonDialog;

diff --git a/src/org/paint/gui/matrix/ColumnTermData.java b/src/org/paint/gui/matrix/ColumnTermData.java
@@ -14,7 +14,7 @@
 import javax.swing.JPopupMenu;
 import javax.swing.JRadioButtonMenuItem;
 
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.paint.config.CustomTermList;
 
 public class ColumnTermData extends JPopupMenu implements ActionListener {

diff --git a/src/org/paint/gui/matrix/MatrixCellRenderer.java b/src/org/paint/gui/matrix/MatrixCellRenderer.java
@@ -16,7 +16,7 @@
 import org.apache.log4j.Logger;
 import org.bbop.phylo.annotate.AnnotationUtil;
 import org.bbop.phylo.model.GeneAnnotation;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.bbop.swing.ScaledIcon;
 import org.paint.config.IconResource;
 import org.paint.displaymodel.DisplayBioentity;

diff --git a/src/org/paint/gui/matrix/MatrixHeaderRenderer.java b/src/org/paint/gui/matrix/MatrixHeaderRenderer.java
@@ -37,7 +37,7 @@
 import javax.swing.table.TableColumnModel;
 
 import org.apache.log4j.Logger;
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 import org.paint.config.IconResource;
 import org.paint.gui.AspectSelector;
 import org.paint.util.GuiConstant;

diff --git a/src/org/paint/gui/matrix/TermComparator.java b/src/org/paint/gui/matrix/TermComparator.java
@@ -2,7 +2,7 @@
 
 import java.util.Comparator;
 
-import org.bbop.phylo.util.OWLutil;
+import org.bbop.phylo.owl.OWLutil;
 
 
 public class TermComparator implements Comparator<String> {