make sure annotations from experiments are using non-obsolete terms

sped up sorting of matrix term-column headings

restored older macify

pom.xml

@@ -147,9 +147,9 @@
 			<version>1.5.0</version>
 		</dependency>
 		<dependency>
-			<groupId>org.simplericity.macify</groupId>
+			<groupId>macify</groupId>
 			<artifactId>macify</artifactId>
-			<version>1.6</version>
+			<version>1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.bbop</groupId>

resources/org/paint/resources/VERSION

@@ -1 +1 @@
-v2.23
+v2.24

src/org/paint/gui/matrix/AnnotMatrixModel.java

@@ -162,15 +162,36 @@ private void sortTerms(List<Bioentity> nodes, List<String> temp_list) {
 		 * Then sort by the number of genes annotated to each term
 		 * The more genes annotated the higher in the list the term will be
 		 */
-		Collections.sort(cellular_list, new TermCountComparator(nodes));
-		Collections.sort(temp_list, new TermCountComparator(nodes));
+		SortByCount(nodes, cellular_list);
+		SortByCount(nodes, temp_list);
+
 		/*
-		 * But then insert the related terms immediately after their child
+		 * But then insert the related terms immediately afterwards
 		 */
 		boolean odd_column = true;
 		odd_column = groupParentTerms(cellular_list, odd_column);
 		groupParentTerms(temp_list, odd_column);
 	}
+
+	private void SortByCount(List<Bioentity> nodes, List<String> terms) {
+		Map<String, List<Bioentity>> term2node = new HashMap<>();
+		for (Bioentity node : nodes) {
+			for (String term : terms) {
+				GeneAnnotation assoc = AnnotationUtil.isAnnotatedToTerm(node.getAnnotations(), term);
+				if (assoc != null && AnnotationUtil.isExpAnnotation(assoc)) {
+					List<Bioentity> annotated_nodes = term2node.get(term);
+					if (annotated_nodes == null) {
+						annotated_nodes = new ArrayList<Bioentity>();
+						term2node.put(term, annotated_nodes);
+					}
+					if (!annotated_nodes.contains(node)) {
+						annotated_nodes.add(node);
+					}
+				}
+			}
+		}
+		Collections.sort(terms, new TermCountComparator(term2node));
+	}
 
 	private boolean groupParentTerms(List<String> orig_termlist, boolean odd_column) {
 		while (orig_termlist.size() > 0) {

src/org/paint/gui/matrix/TermCountComparator.java

@@ -1,11 +1,11 @@
 package org.paint.gui.matrix;
 
 import java.util.Comparator;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.bbop.phylo.annotate.AnnotationUtil;
-import org.bbop.phylo.util.OWLutil;
-import org.paint.displaymodel.DisplayBioentity;
 
 import owltools.gaf.Bioentity;
 import owltools.gaf.GeneAnnotation;
@@ -17,24 +17,23 @@ public class TermCountComparator implements Comparator<String> {
 	private static final int GREATER_THAN = 1;
 	private static final int EQUAL_TO = 0;
 
-	private List<Bioentity> nodes;
-	
-	public TermCountComparator (List<Bioentity> nodes2) {
-		this.nodes = nodes2;
+	private Map<String, List<Bioentity>> term2nodes;
+
+	public TermCountComparator (Map<String, List<Bioentity>> term2nodes) {
+		this.term2nodes = term2nodes;
 	}
-	
+
 	public int compare(String term_a, String term_b) {
 		int count_a = 0;
 		int count_b = 0;
-
-		if (nodes != null) {
-			for (Bioentity node : nodes) {
-				GeneAnnotation assoc_a = AnnotationUtil.isAnnotatedToTerm(node.getAnnotations(), term_a);
-				GeneAnnotation assoc_b = AnnotationUtil.isAnnotatedToTerm(node.getAnnotations(), term_b);
-				count_a += assoc_a != null && AnnotationUtil.isExpAnnotation(assoc_a) ? 1 : 0;
-				count_b += assoc_b != null && AnnotationUtil.isExpAnnotation(assoc_b) ? 1 : 0;
-			}
-		}		
+
+		if (term2nodes.get(term_a) != null) {
+			count_a = term2nodes.get(term_a).size();
+		}
+		if (term2nodes.get(term_b) != null) {
+			count_b = term2nodes.get(term_b).size();
+		}
+
 		if (count_b > count_a)
 			return GREATER_THAN;
 		else if (count_b < count_a)

src/org/paint/gui/menu/TreeMenu.java

@@ -170,7 +170,7 @@ public void actionPerformed(ActionEvent e) {
 				case TREE_COLLAPSE_NONEXP_NODES:
 					PaintConfig.inst().collapse_no_exp = ((JCheckBoxMenuItem) e.getSource()).isSelected();
 					if (PaintConfig.inst().collapse_no_exp) {
-						tree.collapseNonExperimental(true);
+						tree.collapseNonExperimental();
 					} else {
 						tree.expandAllNodes();
 					}

src/org/paint/gui/tracking/EvidencePanel.java

@@ -296,37 +296,6 @@ public void run() {
 		}
 	}
 
-	//	private class CommentThread extends Thread {
-	//		private JTextArea text_area;
-	//		private String comment;
-	//
-	//		public CommentThread (JTextArea text_area) {
-	//			this.text_area = text_area;
-	//			comment = getLoggedComment();
-	//		}
-	//
-	//		public void run() {
-	//			if (SwingUtilities.isEventDispatchThread()) {
-	//				text_area.setText(comment);
-	//			} else {
-	//				try {
-	////					SwingUtilities.invokeAndWait(new Runnable() {
-	//					while (true) {
-	////						public void run() {
-	//							comment = text_area.getText();
-	//							Logger.updateNotes(comment);
-	//							Thread.sleep(1000);
-	////						};
-	//					}
-	//				} catch (InterruptedException ex) {
-	//					log.error(ex.toString());
-	////				} catch (InvocationTargetException ex) {
-	////					log.error(ex.toString());
-	//				}
-	//			}
-	//		}
-	//	}
-	//
 	@Override
 	public void newFamilyData(FamilyChangeEvent e) {
 		comment_set = false;