Fixed bug #45 (which wasn't replacing obsolete terms for negated anno…

…tations)

Added feature #46 so that the experimental evidence shows for descendent annotations

.classpath

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry excluding="org/paint/gui/PaintTable.java" kind="src" output="target/classes" path="src">
+	<classpathentry excluding="org/paint/gui/PaintTable.java|org/paint/dialog/CurationStatusColorPane.java|org/paint/dialog/CurationStatusColorDialog.java|org/paint/dialog/AspectColorPane.java" kind="src" output="target/classes" path="src">
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>

config/preferences.yaml

@@ -1,14 +1,8 @@
 !!org.paint.config.PaintConfig
 GOlrURL: http://golr.geneontology.org/solr
-bpPaintColor: !color '138, 190, 204, 255'
-ccPaintColor: !color '138, 204, 177, 255'
 collapse_no_exp: true
-curatedPaintColor: !color '255, 204, 0, 255'
-expPaintColor: !color '61, 153, 61, 255'
 full_msa: false
-gafdir: /Users/suzi/test2/PTHR10003/
-inferPaintColor: !color '61, 100, 153, 255'
-mfPaintColor: !color '177, 204, 138, 255'
+gafdir: /Users/suzi/projects/go/gene-associations/submission/paint/PTHR10003/
 msa_colors:
 - !color '51, 102, 77, 255'
 - !color '112, 153, 92, 255'
@@ -23,7 +17,7 @@ msa_weighted_colors:
 msa_weighted_threshold:
 - 90.0
 - 75.0
-tree_distance_scaling: 25.0
+tree_distance_scaling: 50.0
 treedir: /Users/suzi/projects/go/data/trees/panther/
 use_distances: true
 weighted: true

resources/org/paint/resources/VERSION

@@ -1 +1 @@
-v2.28.1
+v2.28.2

src/org/paint/config/PaintConfig.java

@@ -3,9 +3,8 @@
 import java.awt.Color;
 import java.io.StringWriter;
 
-import org.yaml.snakeyaml.Yaml;
 import org.bbop.phylo.config.TouchupConfig;
-import org.paint.util.GuiConstant;
+import org.yaml.snakeyaml.Yaml;
 
 public class PaintConfig extends TouchupConfig {
 
@@ -17,13 +16,14 @@ public class PaintConfig extends TouchupConfig {
 	public double tree_distance_scaling; 
 	public boolean collapse_no_exp;
 
-	public Color expPaintColor;
-	public Color curatedPaintColor;
-	public Color inferPaintColor;
+//	public Color expPaintColor;
+//	public Color curatedPaintColor;
+//	public Color inferPaintColor;
 
-	public Color mfPaintColor;
-	public Color ccPaintColor;
-	public Color bpPaintColor;
+//	public Color mfPaintColor;
+//	public Color ccPaintColor;
+//	public Color bpPaintColor;
+//	public Color allPaintColor;
 
 	public float[] msa_threshold;
 	public float[]  msa_weighted_threshold;
@@ -55,13 +55,14 @@ public PaintConfig() {
 		super();
 		use_distances = true;
 		tree_distance_scaling = 50; 
-		expPaintColor = new Color(142, 35, 35);
-		curatedPaintColor = new Color(255, 127, 0);
-		inferPaintColor = new Color(16, 64, 128);
+//		expPaintColor = new Color(142, 35, 35);
+//		curatedPaintColor = new Color(255, 127, 0);
+//		inferPaintColor = new Color(16, 64, 128);
 
-		mfPaintColor = new Color(232, 248, 232);
-		ccPaintColor = new Color(224, 248, 255);
-		bpPaintColor = new Color(255, 248, 220);
+//		mfPaintColor = new Color(232, 248, 232);
+//		ccPaintColor = new Color(224, 248, 255);
+//		bpPaintColor = new Color(255, 248, 220);
+//		allPaintColor = new Color(255, 248, 220);
 
 		msa_threshold = new float[3];
 		msa_threshold[0] = 80f;
@@ -99,40 +100,46 @@ public static void main(String[] args) {
 		blah.save(PREF_FILE);
 	}
 
-	public Color getAspectColor(int aspect) {
-		Color color = GuiConstant.BACKGROUND_COLOR;
-		if (aspect > 0) {
-			switch (aspect) {
-			case GuiConstant.HIGHLIGHT_MF:
-				color = mfPaintColor;
-				break;
-			case GuiConstant.HIGHLIGHT_CC:
-				color = ccPaintColor;
-				break;
-			case GuiConstant.HIGHLIGHT_BP:
-				color = bpPaintColor;
-				break;
-			}
-		}
-		return color;
-	}
-
-	public void setAspectColor(int aspect, Color color) {
-		if (aspect > 0) {
-			switch (aspect) {
-			case GuiConstant.HIGHLIGHT_MF:
-				mfPaintColor = color;
-				break;
-			case GuiConstant.HIGHLIGHT_CC:
-				ccPaintColor = color;
-				break;
-			case GuiConstant.HIGHLIGHT_BP:
-				bpPaintColor = color;
-				break;
-			}
-		}
-	}
-
+//	public Color getAspectColor(int aspect) {
+//		Color color = GuiConstant.BACKGROUND_COLOR;
+//		if (aspect > 0) {
+//			switch (aspect) {
+//			case GuiConstant.HIGHLIGHT_MF:
+//				color = mfPaintColor;
+//				break;
+//			case GuiConstant.HIGHLIGHT_CC:
+//				color = ccPaintColor;
+//				break;
+//			case GuiConstant.HIGHLIGHT_BP:
+//				color = bpPaintColor;
+//				break;
+//			case GuiConstant.HIGHLIGHT_ALLGO:
+//				color = allPaintColor;
+//				break;
+//			}
+//		}
+//		return color;
+//	}
+//
+//	public void setAspectColor(int aspect, Color color) {
+//		if (aspect > 0) {
+//			switch (aspect) {
+//			case GuiConstant.HIGHLIGHT_MF:
+//				mfPaintColor = color;
+//				break;
+//			case GuiConstant.HIGHLIGHT_CC:
+//				ccPaintColor = color;
+//				break;
+//			case GuiConstant.HIGHLIGHT_BP:
+//				bpPaintColor = color;
+//				break;
+//			case GuiConstant.HIGHLIGHT_ALLGO:
+//				allPaintColor = color;
+//				break;
+//			}
+//		}
+//	}
+//
 	public float[] getMSAThresholds(boolean weighted) {
 		if (weighted)
 			return msa_weighted_threshold;

src/org/paint/dialog/CurationStatusColorDialog.java

@@ -30,14 +30,14 @@ private void initLayout() {
 		JPanel everything = new JPanel();
 		everything.setLayout(new BoxLayout(everything, BoxLayout.Y_AXIS));
 
-		final CurationStatusColorPane annot_color;
+//		final CurationStatusColorPane annot_color;
 		final AspectColorPane aspect_color;
 		final JTabbedPane tab_pane;
 
-		annot_color = new CurationStatusColorPane();
+//		annot_color = new CurationStatusColorPane();
 		aspect_color = new AspectColorPane();
 		tab_pane = new JTabbedPane();
-		tab_pane.addTab("Annotation Colors", annot_color);
+//		tab_pane.addTab("Annotation Colors", annot_color);
 		tab_pane.addTab("Aspect Colors", aspect_color);
 		tab_pane.setOpaque(true);
 
@@ -52,7 +52,7 @@ public void actionPerformed(ActionEvent e) {
 		JButton cancel = new JButton("Cancel");
 		cancel.addActionListener(new ActionListener() {
 			public void actionPerformed(ActionEvent e) {
-				annot_color.cancelColorChange();
+//				annot_color.cancelColorChange();
 				aspect_color.cancelColorChange();
 				CurationStatusColorDialog.this.dispose();
 			}
@@ -63,8 +63,8 @@ public void actionPerformed(ActionEvent e) {
 			public void actionPerformed(ActionEvent e) {
 				int selIndex = tab_pane.getSelectedIndex();
 				if (selIndex == 0) 
-					annot_color.resetColorChange();
-				else
+//					annot_color.resetColorChange();
+//				else
 					aspect_color.resetColorChange();
 			}
 		});

src/org/paint/displaymodel/DisplayBioentity.java

@@ -99,6 +99,7 @@ public class DisplayBioentity extends Bioentity {
 	private Hashtable<String, String> attrLookup = new Hashtable<String, String>();
 
 	private Color dropColor;
+	private Color fillColor;
 
 	// Methods
 	public DisplayBioentity(boolean isExpanded) {
@@ -189,12 +190,9 @@ public void drawMarker(Bioentity currentRoot, Graphics g, boolean triangle, Rect
 
 		Rectangle r = new Rectangle(getScreenRectangle());
 		Point p = new Point(getScreenPosition());
-		Color       fillColor = dropColor != null ? dropColor :
+		fillColor = dropColor != null ? dropColor :
 			RenderUtil.annotationStatusColor(this, GuiConstant.BACKGROUND_COLOR, true);
-		if (isSelected()) {
-			fillColor = fillColor.brighter();
-		}
-		Color       drawColor = GuiConstant.FOREGROUND_COLOR;
+		Color lineColor = isSelected() ? GuiConstant.SELECTION_COLOR : GuiConstant.FOREGROUND_COLOR;
 
 		connectToParent(root, g);
 
@@ -212,7 +210,7 @@ public void drawMarker(Bioentity currentRoot, Graphics g, boolean triangle, Rect
 			};
 			g.setColor(fillColor);
 			g.fillPolygon(xCoords, yCoords, 4);
-			g.setColor(drawColor);
+			g.setColor(lineColor);
 			g.drawPolygon(xCoords, yCoords, 4);
 		}
 		else if (!isLeaf()) {
@@ -226,7 +224,7 @@ else if (!isLeaf()) {
 
 				g.setColor(fillColor);
 				g.fillPolygon(xCoords, yCoords, 3);
-				g.setColor(drawColor);
+				g.setColor(lineColor);
 				g.drawPolygon(xCoords, yCoords, 3);
 			} else if (isExpanded() && !isPruned()) {
 				if (isDuplication()) {
@@ -236,7 +234,7 @@ else if (!isLeaf()) {
 					 */
 					g.setColor(fillColor);
 					g.fillRect(p.x, p.y - GLYPH_RADIUS, GLYPH_DIAMETER, GLYPH_DIAMETER);
-					g.setColor(drawColor);
+					g.setColor(lineColor);
 					g.drawRect(p.x, p.y - GLYPH_RADIUS, GLYPH_DIAMETER, GLYPH_DIAMETER);
 				}
 				else if (isHorizontalTransfer()) {
@@ -251,7 +249,7 @@ else if (isHorizontalTransfer()) {
 					};
 					g.setColor(fillColor);
 					g.fillPolygon(xCoords, yCoords, 4);
-					g.setColor(drawColor);
+					g.setColor(lineColor);
 					g.drawPolygon(xCoords, yCoords, 4);
 				}
 				else {
@@ -262,7 +260,7 @@ else if (isHorizontalTransfer()) {
 					 */
 					g.setColor(fillColor);
 					g.fillOval(p.x, p.y - GLYPH_RADIUS, GLYPH_DIAMETER, GLYPH_DIAMETER);
-					g.setColor(drawColor);
+					g.setColor(lineColor);
 					g.drawOval(p.x, p.y - GLYPH_RADIUS, GLYPH_DIAMETER, GLYPH_DIAMETER);
 				}
 			}
@@ -274,7 +272,7 @@ else if (isPruned()) {
 				 */
 				g.setColor(Color.gray.brighter());
 				g.fillRect(p.x, p.y - GLYPH_RADIUS, GLYPH_DIAMETER, GLYPH_DIAMETER);
-				g.setColor(drawColor);
+				g.setColor(lineColor);
 				g.drawRect(p.x, p.y - GLYPH_RADIUS, GLYPH_DIAMETER, GLYPH_DIAMETER);
 				g.drawLine(p.x, p.y - GLYPH_RADIUS, p.x + GLYPH_DIAMETER, p.y + GLYPH_RADIUS);
 				g.drawLine(p.x, p.y + GLYPH_RADIUS, p.x + GLYPH_DIAMETER, p.y - GLYPH_RADIUS);
@@ -285,7 +283,7 @@ else if (isPruned()) {
 				 */
 				g.setColor(fillColor);
 				g.fillRect(p.x, p.y - GLYPH_RADIUS, GLYPH_RADIUS, GLYPH_DIAMETER);
-				g.setColor(drawColor);
+				g.setColor(lineColor);
 				g.drawRect(p.x, p.y - GLYPH_RADIUS, GLYPH_RADIUS, GLYPH_DIAMETER);
 			}
 		}
@@ -310,7 +308,11 @@ else if (isPruned()) {
 
 			AttributedString as = new AttributedString(s);
 			as.addAttribute(TextAttribute.FONT, f);
-			g.setColor(RenderUtil.annotationStatusColor(this, GuiConstant.FOREGROUND_COLOR, false));
+			if (isSelected()) {
+				as.addAttribute(TextAttribute.UNDERLINE, TextAttribute.UNDERLINE_ON);
+			}
+			Color text_color = RenderUtil.annotationFontColor(this);
+			g.setColor(text_color);
 			if (null != s) {
 				int text_x = p.x + NODE_TO_TEXT_OFFSET;
 				int text_y = p.y + (r.height / 2);
@@ -324,7 +326,7 @@ else if (isPruned()) {
 
 			x += TEXT_TO_LINE_OFFSET;
 
-			g.setColor(drawColor);
+			g.setColor(lineColor);
 			if (!(g instanceof Graphics2D)) {
 				g.drawLine(x, p.y, viewport.width, p.y);
 			}
@@ -586,4 +588,8 @@ public void setOriginalChildrenToCurrentChildren() {
 		originalChildrenOrder.clear();
 		originalChildrenOrder.addAll(children);
 	}
+
+	public Color getFillColor() {
+		return fillColor;
+	}
 }

src/org/paint/gui/AspectSelector.java

@@ -37,6 +37,7 @@ public enum Aspect {
 		BIOLOGICAL_PROCESS,
 		CELLULAR_COMPONENT,
 		MOLECULAR_FUNCTION;
+//		ALL_TERMS;
 
 		public String toString() {
 			return super.toString().toLowerCase();
@@ -48,9 +49,10 @@ public String toString() {
 		aspects.put(Aspect.BIOLOGICAL_PROCESS.toString(), "P");
 		aspects.put(Aspect.CELLULAR_COMPONENT.toString(), "C");
 		aspects.put(Aspect.MOLECULAR_FUNCTION.toString(), "F");
+//		aspects.put(Aspect.ALL_TERMS.toString(), "A");
 	}
-	
-	
+
+
 
 	private AspectSelector() {
 		aspect = Aspect.MOLECULAR_FUNCTION;
@@ -71,7 +73,7 @@ public void setAspect(Aspect new_aspect) {
 				EventManager.inst().fireAspectChangeEvent(new AspectChangeEvent(this));
 		}
 	}
-	
+
 	public void setAspect(String code) {
 		Set<String> names = aspects.keySet();
 		Aspect new_aspect = null;
@@ -84,26 +86,28 @@ public void setAspect(String code) {
 					new_aspect = Aspect.MOLECULAR_FUNCTION;
 				} else if (name.equals(Aspect.CELLULAR_COMPONENT.toString())) {
 					new_aspect = Aspect.CELLULAR_COMPONENT;
+//				} else if (name.equals(Aspect.ALL_TERMS.toString())) {
+//					new_aspect = Aspect.ALL_TERMS;
 				}
 			}
 		}
 		if (new_aspect != null) {
 			setAspect(new_aspect);
 		}
 	}
-	
+
 	public Aspect getAspect() {
 		return aspect;
 	}
-	
+
 	public String getAspectName() {
 		return aspect.toString();
 	}
-	
+
 	public String getAspectCode() {
 		return getAspectCode(aspect.toString());
 	}
-	
+
 	public String getAspectCode(String aspect_name) {
 		return aspects.get(aspect_name);
 	}