From: preecej <preecej@localhost>
Date: Tue, 31 Jan 2012 23:25:19 +0000 (+0000)
Subject: Refactored web service response term data into Term object. Created Term class; now... 
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=1b6df056f718bced80a22077ed065a30e0d6caae;p=old-jaiswallab-svn%2F.git

Refactored web service response term data into Term object. Created Term class; now used by term lookup dropdown and "term edit" popup dialogue. Should also be added to term label, term detail web service response and file metadata export.

svn path=/; revision=291
---

diff --git a/Annotation/src/ie/dcu/apps/ist/dialogs/PopUpLabelDialog.java b/Annotation/src/ie/dcu/apps/ist/dialogs/PopUpLabelDialog.java
index 6b19e62..3ee09e5 100644
--- a/Annotation/src/ie/dcu/apps/ist/dialogs/PopUpLabelDialog.java
+++ b/Annotation/src/ie/dcu/apps/ist/dialogs/PopUpLabelDialog.java
@@ -6,6 +6,7 @@ import ie.dcu.swt.SwtUtils;
 import ie.dcu.apps.ist.labelling.*;
 import ie.dcu.swt.layout.LayoutFactory;
 
+import org.apache.commons.lang3.StringEscapeUtils;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.events.KeyEvent;
 import org.eclipse.swt.events.KeyListener;
@@ -104,22 +105,25 @@ public class PopUpLabelDialog extends Dialog {
 		labelCombo.addKeyListener(new KeyListener() {
 			@Override
 			public void keyReleased(KeyEvent e) {
-				ArrayList<String> listElements = new ArrayList<String>();
+				ArrayList<OntologyTerm> terms = new ArrayList<OntologyTerm>();
 				//For the down arrow functionality
 				if(e.keyCode == 16777218)
 				{
 					labelCombo.setListVisible(true);
 				}
-				// If key pressed is only a number of charecter or space.
+				// If key pressed is only a number of character or space.
 				else if ((e.keyCode >= 48 && e.keyCode <= 57) || (e.keyCode >= 97 && e.keyCode <= 122) || e.keyCode == 32)
 				{
 					//For removing all previously assigned labels
 					labelCombo.remove(0,labelCombo.getItemCount()-1);
-					listElements = labels.getLabels(labelCombo.getText());
+					terms = labels.getLabels(labelCombo.getText());
 				}
-				for (int i=0; i<listElements.size();i++)
+				int i = 0;
+				for (OntologyTerm term : terms)
 				{
-					labelCombo.add(listElements.get(i),i);
+		        	// set text for term label
+					labelCombo.add(term.getFormattedTerm(),i);
+					i++;
 				}
 			}
 
diff --git a/Annotation/src/ie/dcu/apps/ist/labelling/Labels.java b/Annotation/src/ie/dcu/apps/ist/labelling/Labels.java
index c85b7f6..f5235d3 100644
--- a/Annotation/src/ie/dcu/apps/ist/labelling/Labels.java
+++ b/Annotation/src/ie/dcu/apps/ist/labelling/Labels.java
@@ -2,6 +2,7 @@ package ie.dcu.apps.ist.labelling;
 
 import ie.dcu.apps.ist.AppWindow;
 
+import java.awt.List;
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
 import java.net.HttpURLConnection;
@@ -24,10 +25,9 @@ public class Labels
 	 * ArrayList<String> containing each Label item
 	 * 
 	 */
-	public ArrayList<String> getLabels(String content) {
-		ArrayList<String> labels = new ArrayList<String>();
+	public ArrayList<OntologyTerm> getLabels(String content) {
+        ArrayList<OntologyTerm> terms = new ArrayList<OntologyTerm>();
 		// temporary variable for storing each list element in the loop
-		String listElement;
 		try
 	    {
 			String encodedContent = URLEncoder.encode(content.toString(),"UTF-8");
@@ -45,11 +45,14 @@ public class Labels
 		        {
 		        	object = new JSONObject(inputLine);
 		      	}
+		        
 		        JSONArray array = new JSONArray(object.getString("PO_term_search_response"));
 		        for(int i=0; i<array.length();i++)
 		        {
-		        	listElement = (array.getJSONObject(i).getString("match")+" {"+array.getJSONObject(i).getString("accession_id")+"}");
-		        	labels.add(i,StringEscapeUtils.unescapeHtml4(listElement));
+		        	OntologyTerm term = new OntologyTerm();
+		        	term.setAccessionId(array.getJSONObject(i).getString("accession_id"));
+		        	term.setName(array.getJSONObject(i).getString("match"));
+		        	terms.add(term);
 		        }
 		        in.close();
 	        }
@@ -61,7 +64,7 @@ public class Labels
 	    catch(Exception ex)
 	    {
 	    }
-	    return labels;
+	    return terms;
 	}
 	
 }
\ No newline at end of file
diff --git a/Annotation/src/ie/dcu/apps/ist/labelling/OntologyTerm.java b/Annotation/src/ie/dcu/apps/ist/labelling/OntologyTerm.java
new file mode 100644
index 0000000..76b22ab
--- /dev/null
+++ b/Annotation/src/ie/dcu/apps/ist/labelling/OntologyTerm.java
@@ -0,0 +1,70 @@
+/**
+ * 
+ */
+package ie.dcu.apps.ist.labelling;
+
+import java.util.ArrayList;
+
+import org.apache.commons.lang3.StringEscapeUtils;
+
+/**
+ * @author preecej
+ * Contains attributes associated with terms received from ontologies.
+ */
+public class OntologyTerm {
+
+	private String accessionId;
+	private String name;
+	private String aspect;
+	private String definition;
+	private String comment;
+	private ArrayList<String> synonyms;
+
+	public String getAccessionId() {
+		return this.accessionId;
+	}
+	public String getName() {
+		return this.name;
+	}
+	public String getAspect() {
+		return this.aspect;
+	}
+	public String getDefinition() {
+		return this.definition;
+	}
+	public String getComment() {
+		return this.comment;
+	}
+	public ArrayList<String> getSynonyms() {
+		return this.synonyms;
+	}
+	// returns an HTML-safe label formatted to include both name and accession id
+	public String getFormattedTerm() {
+		return StringEscapeUtils.unescapeHtml4(this.name) + " {" + this.accessionId + "}";
+	}
+
+	public void setAccessionId(String accessionId) {
+		this.accessionId = accessionId;
+	}
+	public void setName(String name) {
+		this.name = name;
+	}
+	public void setAspect(String aspect) {
+		this.aspect = aspect;
+	}
+	public void setDefinition(String definition) {
+		this.definition = definition;
+	}
+	public void setComment(String comment) {
+		this.comment = comment;
+	}
+	public void setSynonyms(ArrayList<String> synonyms) {
+		this.synonyms = synonyms;
+	}
+
+	// constructor
+	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 c77c58e..d803e34 100644
--- a/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
+++ b/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
@@ -20,6 +20,7 @@ import java.util.ArrayList;
 import java.util.Properties;
 import java.util.logging.*;
 
+import org.apache.commons.lang3.StringEscapeUtils;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.jface.action.*;
 import org.eclipse.jface.operation.*;
@@ -239,11 +240,13 @@ public class SegmentationView extends Composite {
 				dropdownLabels(e);
 			}
 		});
+		/*
 		comboLabel.addFocusListener(new FocusAdapter() {
 			public void focusGained(FocusEvent e) {
 				termDetailLookup(e);
 			}
 		});
+		*/
 		assign = SwtUtils.addButton(termLookupBar, 52, "Assign");
 		assign.addSelectionListener(new SelectionAdapter() {
         public void widgetSelected(SelectionEvent arg0) {
@@ -271,7 +274,7 @@ public class SegmentationView extends Composite {
 	 */
 	public void dropdownLabels(KeyEvent e)
 	{
-		ArrayList<String> listElements = new ArrayList<String>();
+		ArrayList<OntologyTerm> terms = new ArrayList<OntologyTerm>();
 		//For the down arrow functionality
 		if(e.keyCode == 16777218)
 		{
@@ -282,17 +285,22 @@ public class SegmentationView extends Composite {
 		{
 			//For removing all previously assigned labels
 			comboLabel.remove(0,comboLabel.getItemCount()-1);
-			listElements = labels.getLabels(comboLabel.getText());
+			terms = labels.getLabels(comboLabel.getText());
 			assign.setEnabled(!(comboLabel.getText().isEmpty()));
-			
+			if (e.keyCode == 32) {
+				termDetailLookup();
+			}
 		}
-		for (int i=0; i<listElements.size();i++)
+		int i = 0;
+		for (OntologyTerm term : terms)
 		{
-			comboLabel.add(listElements.get(i),i);
+        	// set text for term label
+			comboLabel.add(term.getFormattedTerm(),i);
+			i++;
 		}
 	}
 
-	private void termDetailLookup(FocusEvent e) {
+	private void termDetailLookup() {
 		// call term detail web service method using accession id (from 1) segment obj or 2) label selection (before assign button is clicked))
 		termDetailTable.setEnabled(true);
 	}