From d1268e6da85b48f10384a5838d692a8a7b3f3d4b Mon Sep 17 00:00:00 2001
From: lingutln <lingutln@localhost>
Date: Wed, 10 Apr 2013 23:14:31 +0000
Subject: [PATCH] svn path=/; revision=465

---
 .../src/ie/dcu/apps/ist/labelling/Labels.java | 18 ++++++-
 .../dcu/apps/ist/labelling/OntologyTerm.java  |  3 +-
 .../dcu/apps/ist/views/SegmentationView.java  | 50 +++++++++++++------
 .../ist/widgets/AnnotatedImageControl.java    | 32 +++---------
 4 files changed, 62 insertions(+), 41 deletions(-)

diff --git a/Annotation/src/ie/dcu/apps/ist/labelling/Labels.java b/Annotation/src/ie/dcu/apps/ist/labelling/Labels.java
index 0eafac8..db3cb68 100644
--- a/Annotation/src/ie/dcu/apps/ist/labelling/Labels.java
+++ b/Annotation/src/ie/dcu/apps/ist/labelling/Labels.java
@@ -9,6 +9,9 @@ import java.net.HttpURLConnection;
 import java.net.URL;
 import java.net.URLEncoder;
 import java.util.ArrayList;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
 import javax.xml.bind.DatatypeConverter;
 
 import javax.xml.parsers.*;
@@ -58,7 +61,7 @@ public class Labels
 		        {
 		        	OntologyTerm term = new OntologyTerm();
 		        	term.setAccessionId(array.getJSONObject(i).getString("accession_id"));
-		        	term.setName(array.getJSONObject(i).getString("match"));
+		        	term.setName(formatizeToUnescapeHTML(array.getJSONObject(i).getString("match")));
 		        	terms.add(term);
 		        }
 		        in.close();
@@ -74,6 +77,19 @@ public class Labels
 	    return terms;
 	}
 	
+	public static String formatizeToUnescapeHTML(String term)
+	{
+		Pattern pattern = Pattern.compile("&#[0-9]+");
+	    Matcher matcher = pattern.matcher(term);
+	    StringBuffer formattedTerm = new StringBuffer();
+	    while (matcher.find()) {
+	    	String matchedText = matcher.group();
+	    	matcher.appendReplacement(formattedTerm, matchedText + ";");
+	    }
+	    matcher.appendTail(formattedTerm);
+	    return formattedTerm.toString();
+	}
+	
 	
 	
 	
diff --git a/Annotation/src/ie/dcu/apps/ist/labelling/OntologyTerm.java b/Annotation/src/ie/dcu/apps/ist/labelling/OntologyTerm.java
index 76b22ab..39d30f7 100644
--- a/Annotation/src/ie/dcu/apps/ist/labelling/OntologyTerm.java
+++ b/Annotation/src/ie/dcu/apps/ist/labelling/OntologyTerm.java
@@ -4,6 +4,8 @@
 package ie.dcu.apps.ist.labelling;
 
 import java.util.ArrayList;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.StringEscapeUtils;
 
@@ -66,5 +68,4 @@ public class OntologyTerm {
 	public OntologyTerm() {
 		this.synonyms = new ArrayList<String>();
 	}
-	
 }
diff --git a/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java b/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
index 246f4b4..aee4863 100644
--- a/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
+++ b/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
@@ -21,10 +21,11 @@ import java.net.*;
 import java.util.ArrayList;
 import java.util.Properties;
 import java.util.logging.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.jface.action.*;
-import org.eclipse.jface.action.Action;
 import org.eclipse.jface.operation.*;
 import org.eclipse.jface.resource.ImageDescriptor;
 import org.eclipse.swt.SWT;
@@ -304,7 +305,7 @@ public class SegmentationView extends Composite {
         	if(view.getContext().isEnabled())
     		{
         		OntologyTerm term = new OntologyTerm();
-        		term.setName((String)comboLabel.getData(comboLabel.getText()));
+        		term.setName((String)comboLabel.getData(formatizeToUnescapeHTML(comboLabel.getText())));
         		term.setAccessionId(parseAccessionIdFromComboLabel(comboLabel));
         		view.getContext().getEnabledMask().ontologyTerm = term;
         	}
@@ -313,6 +314,19 @@ public class SegmentationView extends Composite {
 		});
 	}
 	
+	public static String formatizeToUnescapeHTML(String term)
+	{
+		Pattern pattern = Pattern.compile("&#[0-9]+");
+	    Matcher matcher = pattern.matcher(term);
+	    StringBuffer formattedTerm = new StringBuffer();
+	    while (matcher.find()) {
+	    	String matchedText = matcher.group();
+	    	matcher.appendReplacement(formattedTerm, matchedText + ";");
+	    }
+	    matcher.appendTail(formattedTerm);
+	    return formattedTerm.toString();
+	}
+	
 	/**
 	 * For dropping down the labels on pressing the down arrow key just like "Google suggests" functionality.
 	 * @param e
@@ -414,7 +428,7 @@ public class SegmentationView extends Composite {
 		        
 				for (int j=0; j<synArray.length(); j++) {
 			        TableItem item = new TableItem (termSynonymTable, SWT.NONE);
-					item.setText(0,synArray.getString(j));
+					item.setText(0,formatizeToUnescapeHTML(synArray.getString(j)));
 				}
     			termSynonymTable.getColumn(0).pack();
 				termSynonymTable.pack();
@@ -482,7 +496,7 @@ public class SegmentationView extends Composite {
 		termDetailTable.pack();
 	}
 
-	public void clearTermDetailTable() {
+	public static void clearTermDetailTable() {
 		TableItem[] items = termDetailTable.getItems();
         for(int i=0; i<items.length; i++)
         {
@@ -493,7 +507,7 @@ public class SegmentationView extends Composite {
         }
 	}
 
-	public void clearTermSynonymTable() {
+	public static void clearTermSynonymTable() {
 		TableItem[] items = termSynonymTable.getItems();
         for(TableItem item : items)
         {
@@ -787,6 +801,11 @@ public class SegmentationView extends Composite {
 			{
 				view.getTool().detach();
 			}
+			
+			String segmentName = view.getContext().getEnabledMask().ontologyTerm.getName();
+			if (segmentName.equals("")) {
+				clearCurrentSegmentAnnotation();
+			}
 		}
 		else
 		{
@@ -798,6 +817,16 @@ public class SegmentationView extends Composite {
 		updateToolStates();
 	}
 	
+	/**
+	 * Clears annotation details of currently highlighted segment
+	*/
+	
+	public static void clearCurrentSegmentAnnotation() {
+		SegmentationView.comboLabel.removeAll();
+		SegmentationView.clearTermDetailTable();
+		SegmentationView.clearTermSynonymTable();
+	}
+	
 	/**
 	 * Forms a segmentation object based on the current view skipping previous segmentation objects.
 	*/
@@ -807,16 +836,7 @@ public class SegmentationView extends Composite {
 		view.getContext().formSegmentationObject();
 		updateToolStates();
 	}
-	
-	/**
-	 * Predicts the segments in the image using active learning.
-	*/
-	/*public void predictSegments() {
-		SIFTDescriptor sift = new SIFTDescriptor();
-		sift.calculateDescriptors(view.getContext().getImage());
-		updateToolStates();
-	}*/	
-	
+
 	public boolean isAutoApply() {
 		return this.auto;
 	}
diff --git a/Annotation/src/ie/dcu/apps/ist/widgets/AnnotatedImageControl.java b/Annotation/src/ie/dcu/apps/ist/widgets/AnnotatedImageControl.java
index 8d28314..4880b63 100644
--- a/Annotation/src/ie/dcu/apps/ist/widgets/AnnotatedImageControl.java
+++ b/Annotation/src/ie/dcu/apps/ist/widgets/AnnotatedImageControl.java
@@ -411,28 +411,7 @@ public class AnnotatedImageControl extends Composite {
 
 		public void mouseUp(MouseEvent event) {
 			Point mouseClickedPoint = new Point(event.x,event.y);
-			// For the right click
-			if(event.button == 3)
-			{ /* // JP - don't want this functionality right now
-				PopUpLabelDialog dialog = new PopUpLabelDialog(getShell());
-				PopUpLabelDialog.Result result = dialog.open();
-				if (result != null) 
-				{
-					String lab = null;
-					if(result.comboText.indexOf('{') != -1)
-		        	{
-						lab = result.comboText.substring(0,result.comboText.indexOf('{')-1);
-		        	}
-		        	else
-		        	{
-		        		lab = result.comboText;
-		        	}
-		        	System.out.println("selected"+lab);
-					//comboLabel.setText(result.comboText);
-					//execute(Tool.AssignButton, null);
-				}*/
-			}
-			else if(event.button == 1)
+			if(event.button == 1)
 			{
 				if(view.imageContains(mouseClickedPoint))
 				{
@@ -440,8 +419,13 @@ public class AnnotatedImageControl extends Composite {
 					// For setting the comboLabel value and tooltip on clicking a segment
 					String segmentName = ctx.getEnabledMask().ontologyTerm.getName();
 					getCanvas().setToolTipText(segmentName);
-					SegmentationView.comboLabel.setText(segmentName);
-					SegmentationView.termDetailLookup(ctx.getEnabledMask().ontologyTerm.getAccessionId());
+					if (segmentName.equals("")) {
+						SegmentationView.clearCurrentSegmentAnnotation();
+					}
+					else {
+						SegmentationView.comboLabel.setText(segmentName);
+						SegmentationView.termDetailLookup(ctx.getEnabledMask().ontologyTerm.getAccessionId());
+					}
 				}
 				repaint();
 			}
-- 
2.34.1