Author: rodche
Date: 2012-05-28 15:35:17 -0700 (Mon, 28 May 2012)
New Revision: 29376
Added:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/NameValuePairListItem.java
Removed:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/JListWithToolTips.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/RecordList.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SelectEntity.java
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2Factory.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/DataSourceFilter.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/OrganismFilter.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/BioPaxUtil.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/ResultsModel.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchQueryPanel.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsFilterPanel.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsPanel.java
Log:
Worked out filtering features and bugs... (code is also much cleaner now)
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -77,7 +77,8 @@
return res;
}
- private static CPath2Client newClient() {
+
+ public static CPath2Client newClient() {
CPath2Client client = CPath2Client.newInstance();
// client.setEndPointURL("http://localhost:8080/cpath-web-service/";);
client.setEndPointURL("http://awabi.cbio.mskcc.org/cpath2/";);
@@ -94,9 +95,9 @@
*/
public static String getRecordsByIds(String[] ids, OutputFormat format)
{
- //TODO client must return other formats, if requested
- Model res = newClient().get(Arrays.asList(ids));
-
+ //TODO client to return other formats as well
+ CPath2Client cli = newClient();
+ Model res = cli.get(Arrays.asList(ids));
ByteArrayOutputStream baos = new ByteArrayOutputStream();
BioPaxUtil.getBiopaxIO().convertToOWL(res, baos);
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2Factory.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2Factory.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPath2Factory.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -2,6 +2,7 @@
import java.util.List;
+import javax.swing.JList;
import javax.swing.JPanel;
import org.cytoscape.application.CyApplicationManager;
@@ -113,8 +114,8 @@
return new DownloadDetails(passedRecordList);
}
- public static JPanel createSearchResultsFilterPanel(ResultsModel model)
{
- return new SearchResultsFilterPanel(model);
+ public static JPanel createSearchResultsFilterPanel(ResultsModel model,
JList hits) {
+ return new SearchResultsFilterPanel(model, hits);
}
public static DetailsPanel createDetailsPanel(SearchResultsPanel
searchHitsPanel) {
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/DataSourceFilter.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/DataSourceFilter.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/DataSourceFilter.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -19,7 +19,7 @@
public List<SearchHit> filter(List<SearchHit> recordList) {
ArrayList<SearchHit> passedList = new ArrayList<SearchHit>();
for (SearchHit record : recordList) {
- if (record.getDataSource() != null &&
!record.getDataSource().isEmpty())
+ if (!record.getDataSource().isEmpty())
{
//copy datasources to a new set
Set<String> ds = new
HashSet<String>(record.getDataSource());
@@ -27,6 +27,8 @@
if (!ds.isEmpty()) {
passedList.add(record);
}
+ } else {
+ passedList.add(record);
}
}
return passedList;
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/OrganismFilter.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/OrganismFilter.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/OrganismFilter.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -19,7 +19,7 @@
public List<SearchHit> filter(List<SearchHit> recordList) {
ArrayList<SearchHit> passedList = new ArrayList<SearchHit>();
for (SearchHit record : recordList) {
- if (record.getOrganism() != null &&
!record.getOrganism().isEmpty())
+ if (!record.getOrganism().isEmpty())
{
//copy organisms to a new set
Set<String> o = new
HashSet<String>(record.getOrganism());
@@ -27,6 +27,8 @@
if (!o.isEmpty()) {
passedList.add(record);
}
+ } else {
+ passedList.add(record);
}
}
return passedList;
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/BioPaxUtil.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/BioPaxUtil.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/BioPaxUtil.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -324,7 +324,7 @@
}
/**
- * Gets the FilterBoxItem Name.
+ * Gets the NameValuePairListItem Name.
*
* @param bpe BioPAX element
* @return organism field, or null if not available.
Deleted:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -1,33 +0,0 @@
-package org.cytoscape.cpathsquared.internal.view;
-
-
-public class FilterBoxItem implements Comparable<FilterBoxItem> {
- private String name;
- private String value;
-
-
- public FilterBoxItem (String name, String value) {
- this.name = name;
- this.value = value;
- }
-
-
- public String getName() {
- return name;
- }
-
- public String getValue() {
- return value;
- }
-
- public String toString() {
- return name;
- }
-
-
- //in order to order by name
- @Override
- public int compareTo(FilterBoxItem o) {
- return this.name.compareTo(o.getName());
- }
-}
Deleted:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/JListWithToolTips.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/JListWithToolTips.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/JListWithToolTips.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -1,48 +0,0 @@
-package org.cytoscape.cpathsquared.internal.view;
-
-import java.awt.event.MouseEvent;
-
-import javax.swing.JList;
-import javax.swing.ListModel;
-
-import cpath.service.jaxb.SearchHit;
-
-
-/**
- * Extension to JList to Support Tool Tips.
- * <p/>
- * Based on sample code from:
- * http://www.roseindia.net/java/example/java/swing/TooltipTextOfList.shtml
- *
- */
-public class JListWithToolTips extends JList {
-
- public JListWithToolTips(ListModel listModel) {
- super(listModel);
- }
-
- /**
- * Impelement Tool Tip Functionality.
- *
- * @param mouseEvent Mouse Event.
- * @return Tool Tip.
- */
- @Override
- public String getToolTipText(MouseEvent mouseEvent) {
- int index = locationToIndex(mouseEvent.getPoint());
- if (-1 < index) {
- SearchHit record = (SearchHit)
getModel().getElementAt(index);
- StringBuilder html = new StringBuilder();
- html.append("<html><table cellpadding=10><tr><td>");
- html.append("<B>").append(record.getBiopaxClass());
- if(record.getName() != null)
- html.append(" ").append(record.getName());
- html.append("</B> ");
- html.append("</td></tr></table></html>");
- return html.toString();
- } else {
- return null;
- }
- }
-
-}
Copied:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/NameValuePairListItem.java
(from rev 29345,
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/FilterBoxItem.java)
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/NameValuePairListItem.java
(rev 0)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/NameValuePairListItem.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -0,0 +1,33 @@
+package org.cytoscape.cpathsquared.internal.view;
+
+
+public class NameValuePairListItem implements
Comparable<NameValuePairListItem> {
+ private String name;
+ private String value;
+
+
+ public NameValuePairListItem (String name, String value) {
+ this.name = name;
+ this.value = value;
+ }
+
+
+ public String getName() {
+ return name;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public String toString() {
+ return name;
+ }
+
+
+ //in order to order by name
+ @Override
+ public int compareTo(NameValuePairListItem o) {
+ return this.name.compareTo(o.getName());
+ }
+}
Deleted:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/RecordList.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/RecordList.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/RecordList.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -1,101 +0,0 @@
-package org.cytoscape.cpathsquared.internal.view;
-
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import cpath.service.jaxb.SearchHit;
-import cpath.service.jaxb.SearchResponse;
-
-
-final class RecordList {
- private SearchResponse response;
- private Map<String, Integer> typeMap = new TreeMap<String, Integer>();
- private Map<String, Integer> organismMap = new TreeMap<String, Integer>();
- private Map<String, Integer> dataSourceMap = new TreeMap<String,
Integer>();
-
- /**
- * Constructor.
- * @param response
- */
- public RecordList (SearchResponse response) {
- this.response = response;
- catalog();
- }
-
- /**
- * Gets number of records.
- * @return number of records.
- */
- public int getNumRecords() {
- if (response != null && !response.isEmpty()) {
- return response.getSearchHit().size();
- } else {
- return -1;
- }
- }
-
- /**
- * Gets hits
- * @return
- */
- public List<SearchHit> getHits() {
- return response.getSearchHit();
- }
-
-
- /**
- * Gets catalog of entity types.
- * @return Map<Entity Type, # Records>
- */
- public Map<String, Integer> getTypeMap() {
- return typeMap;
- }
-
- public Map<String, Integer> getOrganismMap() {
- return organismMap;
- }
-
- public Map<String, Integer> getDataSourceMap() {
- return dataSourceMap;
- }
-
-
- private void catalog() {
- List<SearchHit> recordList = response.getSearchHit();
- if (recordList != null) {
- for (SearchHit record: recordList) {
- catalog(record);
- }
- }
- }
-
- private void catalog(SearchHit record) {
- String type = record.getBiopaxClass();
- Integer count = typeMap.get(type);
- if (count != null) {
- typeMap.put(type, count + 1);
- } else {
- typeMap.put(type, 1);
- }
-
-
- for(String org : record.getOrganism()) {
- Integer i = organismMap.get(org);
- if (i != null) {
- organismMap.put(org, i + 1);
- } else {
- organismMap.put(org, 1);
- }
- }
-
- for(String ds : record.getDataSource()) {
- Integer i = dataSourceMap.get(ds);
- if (i != null) {
- dataSourceMap.put(ds, i + 1);
- } else {
- dataSourceMap.put(ds, 1);
- }
- }
- }
-}
\ No newline at end of file
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/ResultsModel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/ResultsModel.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/ResultsModel.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -1,30 +1,100 @@
package org.cytoscape.cpathsquared.internal.view;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
import java.util.Observable;
+import java.util.TreeMap;
+import cpath.service.jaxb.SearchHit;
+import cpath.service.jaxb.SearchResponse;
+
/**
* Contains information regarding the currently selected set of interaction
bundles.
*
*/
-public class ResultsModel extends Observable {
- private RecordList recordList;
+public final class ResultsModel extends Observable {
+ private SearchResponse response;
+
+ Map<String, Integer> numHitsByTypeMap = new TreeMap<String, Integer>();
+ Map<String, Integer> numHitsByOrganismMap = new TreeMap<String, Integer>();
+ Map<String, Integer> numHitsByDatasourceMap = new TreeMap<String,
Integer>();
+
+ // URI-to-HTML summary text map
+ Map<String, String> summaryMap = new HashMap<String, String>();
+ Map<String, Collection<NameValuePairListItem>> pathwaysMap = new
HashMap<String, Collection<NameValuePairListItem>>();
+ Map<String, Collection<NameValuePairListItem>> moleculesMap = new
HashMap<String, Collection<NameValuePairListItem>>();
+
+ public int getNumRecords() {
+ if (response != null && !response.isEmpty()) {
+ return response.getSearchHit().size();
+ } else {
+ return -1;
+ }
+ }
+
+
/**
- * Sets the SummaryResponse Object.
- * @param recordList Record List.
+ * Re-builds hit-to-type, hit-to-organism, hit-to-datasource,
+ * etc. internal maps.
*/
- public void setRecordList (RecordList recordList) {
- this.recordList = recordList;
+ private void init() {
+ if (response != null && !response.isEmpty()) {
+ numHitsByTypeMap.clear();
+ numHitsByOrganismMap.clear();
+ numHitsByDatasourceMap.clear();
+ pathwaysMap.clear();
+ moleculesMap.clear();
+ summaryMap.clear();
+
+ for (SearchHit record : response.getSearchHit()) {
+ catalog(record);
+ }
+ }
+ }
+
+
+ private void catalog(SearchHit record) {
+ String type = record.getBiopaxClass();
+ Integer count = numHitsByTypeMap.get(type);
+ if (count != null) {
+ numHitsByTypeMap.put(type, count + 1);
+ } else {
+ numHitsByTypeMap.put(type, 1);
+ }
+
+ for(String org : record.getOrganism()) {
+ Integer i = numHitsByOrganismMap.get(org);
+ if (i != null) {
+ numHitsByOrganismMap.put(org, i + 1);
+ } else {
+ numHitsByOrganismMap.put(org, 1);
+ }
+ }
+
+ for(String ds : record.getDataSource()) {
+ Integer i = numHitsByDatasourceMap.get(ds);
+ if (i != null) {
+ numHitsByDatasourceMap.put(ds, i + 1);
+ } else {
+ numHitsByDatasourceMap.put(ds, 1);
+ }
+ }
+ }
+
+
+ public void setSearchResponse (SearchResponse response) {
+ this.response = response;
+ init();
+
this.setChanged();
this.notifyObservers();
}
- /**
- * Gets the Record List.
- * @return RecordList Object.
- */
- public RecordList getRecordList() {
- return recordList;
+
+ public SearchResponse getSearchResponse() {
+ return response;
}
}
\ No newline at end of file
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchQueryPanel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchQueryPanel.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchQueryPanel.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -40,12 +40,13 @@
* Search Box Panel.
*
*/
-public class SearchQueryPanel extends JPanel {
+public final class SearchQueryPanel extends JPanel {
private static final String ENTER_TEXT = "Enter Gene Name or ID";
private final CheckBoxJList organismList;
private final CheckBoxJList dataSourceList;
private final JTextField searchField;
-
+
+
/**
* Constructor.
*/
@@ -120,10 +121,10 @@
private final JComponent createOrganismFilterBox() {
- SortedJListModel<FilterBoxItem> model = new
SortedJListModel<FilterBoxItem>();
+ SortedJListModel<NameValuePairListItem> model = new
SortedJListModel<NameValuePairListItem>();
Map<String,String> map = CPath2.getAvailableOrganisms();
for(String o : map.keySet()) {
- model.addElement(new FilterBoxItem(map.get(o), o));
+ model.addElement(new NameValuePairListItem(map.get(o), o));
}
organismList.setModel(model);
organismList.setToolTipText("Select Organisms");
@@ -138,7 +139,7 @@
Map<String,String> map = CPath2.getLoadedDataSources();
for(String d : map.keySet()) {
- dataSourceBoxModel.addElement(new FilterBoxItem(map.get(d), d));
+ dataSourceBoxModel.addElement(new
NameValuePairListItem(map.get(d), d));
}
dataSourceList.setModel(dataSourceBoxModel);
@@ -185,11 +186,11 @@
Set<String> organisms = new HashSet<String>();
for(Object it : organism)
- organisms.add(((FilterBoxItem)it).getValue());
+ organisms.add(((NameValuePairListItem)it).getValue());
Set<String> datasources = new HashSet<String>();
for(Object it : datasource)
- datasources.add(((FilterBoxItem)it).getValue());
+ datasources.add(((NameValuePairListItem)it).getValue());
Window window = CPath2Factory.getCySwingApplication().getJFrame();
if (keyword == null || keyword.trim().length() == 0
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsFilterPanel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsFilterPanel.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsFilterPanel.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -1,21 +1,20 @@
package org.cytoscape.cpathsquared.internal.view;
-import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.HashSet;
import java.util.List;
-import java.util.Map;
import java.util.Observable;
import java.util.Observer;
import java.util.Set;
import javax.swing.BoxLayout;
+import javax.swing.DefaultListModel;
import javax.swing.JButton;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
+import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.border.EmptyBorder;
@@ -24,7 +23,6 @@
import javax.swing.tree.DefaultTreeModel;
import javax.swing.tree.TreePath;
-import org.cytoscape.cpathsquared.internal.CPath2Factory;
import org.cytoscape.cpathsquared.internal.filters.ChainedFilter;
import org.cytoscape.cpathsquared.internal.filters.DataSourceFilter;
import org.cytoscape.cpathsquared.internal.filters.EntityTypeFilter;
@@ -33,18 +31,21 @@
import cpath.service.jaxb.SearchHit;
-public class SearchResultsFilterPanel extends JPanel {
- private JLabel matchingItemsLabel;
- private ResultsModel model;
- private CheckNode typeFilter;
- private CheckNode dataSourceFilter;
- private CheckNode organismFilter;
- private JTreeWithCheckNodes tree;
- private CollapsablePanel filterTreePanel;
- private JButton applyButton;
+public class SearchResultsFilterPanel extends JPanel implements Observer {
+ private final JLabel matchingItemsLabel;
+ private final ResultsModel model;
+ private final JList hitsJList;
+ private final CheckNode rootNode;
+ private final CheckNode typeFilterNode;
+ private final CheckNode dataSourceFilterNode;
+ private final CheckNode organismFilterNode;
+ private final JTreeWithCheckNodes tree;
+ private final CollapsablePanel filterTreePanel;
+ private JButton downlodButton;
- public SearchResultsFilterPanel(ResultsModel resultsModel) {
+ public SearchResultsFilterPanel(ResultsModel resultsModel, JList
hitsJList) {
this.model = resultsModel;
+ this.hitsJList = hitsJList;
setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
@@ -56,10 +57,16 @@
matchingItemsLabel.setBorder(new EmptyBorder(5, 10, 5, 5));
add(matchingItemsLabel);
- final CheckNode rootNode = new CheckNode("All Filters");
+ // create an empty filter tree (barebone)
+ rootNode = new CheckNode("All Filters");
+ typeFilterNode = new CheckNode("BioPAX Type");
+ rootNode.add(typeFilterNode);
+ organismFilterNode = new CheckNode("and Organism");
+ rootNode.add(organismFilterNode);
+ dataSourceFilterNode = new CheckNode("and Datasource");
+ rootNode.add(dataSourceFilterNode);
tree = new JTreeWithCheckNodes(rootNode);
tree.setOpaque(false);
-
filterTreePanel = new CollapsablePanel("BioPAX Filters");
filterTreePanel.setAlignmentX(Component.LEFT_ALIGNMENT);
filterTreePanel.getContentPane().add(tree);
@@ -67,217 +74,163 @@
JScrollPane scrollPane = new JScrollPane(filterTreePanel);
add(scrollPane);
- addObserver(resultsModel, matchingItemsLabel, tree, rootNode);
+ model.addObserver(this);
- createApplyFiltersButton();
+// createDownloadButton();
}
/**
* Expands all Nodes.
*/
public void expandAllNodes() {
- filterTreePanel.setCollapsed(false);
+ TreePath path;
+ filterTreePanel.setCollapsed(false);
- typeFilter.setSelected(true);
- TreePath path = new TreePath(typeFilter.getPath());
- tree.expandPath(path);
+ typeFilterNode.setSelected(true);
+ path = new TreePath(typeFilterNode.getPath());
+ tree.expandPath(path);
- dataSourceFilter.setSelected(true);
- path = new TreePath(dataSourceFilter.getPath());
- tree.expandPath(path);
+ dataSourceFilterNode.setSelected(true);
+ path = new TreePath(dataSourceFilterNode.getPath());
+ tree.expandPath(path);
- organismFilter.setSelected(true);
- path = new TreePath(organismFilter.getPath());
- tree.expandPath(path);
+ organismFilterNode.setSelected(true);
+ path = new TreePath(organismFilterNode.getPath());
+ tree.expandPath(path);
}
- private void addObserver(final ResultsModel model,
- final JLabel matchingHitsLabel, final JTreeWithCheckNodes tree,
- final CheckNode rootNode) {
- model.addObserver(new Observer() {
- public void update(Observable observable, Object object) {
- RecordList recordList = model.getRecordList();
- matchingHitsLabel.setText("Matching entities: "
- + recordList.getNumRecords());
-
- if (recordList.getNumRecords() == 0) {
- filterTreePanel.setVisible(false);
- applyButton.setVisible(false);
- } else {
- filterTreePanel.setVisible(true);
- applyButton.setVisible(true);
- }
-
-
- Map<String, Integer> typeMap = recordList.getTypeMap();
- Map<String, Integer> organismMap = recordList.getOrganismMap();
- Map<String, Integer> dataSourceMap =
recordList.getDataSourceMap();
-
- // Store current expansion states
- boolean typeFilterExpanded = false;
- if (typeFilter != null) {
- TreePath path = new TreePath(typeFilter.getPath());
- typeFilterExpanded = tree.isExpanded(path);
- }
- boolean dataSourceFilterExpanded = false;
- if (dataSourceFilter != null) {
- TreePath path = new TreePath(dataSourceFilter.getPath());
- dataSourceFilterExpanded = tree.isExpanded(path);
- }
- boolean organismFilterExpanded = false;
- if (organismFilter != null) {
- TreePath path = new TreePath(organismFilter.getPath());
- organismFilterExpanded = tree.isExpanded(path);
- }
-
- // Remove all children
- rootNode.removeAllChildren();
-
- // Create Filters
- if (typeMap.size() > 0) {
- typeFilter = new CheckNode("by BioPAX Type");
- rootNode.add(typeFilter);
- for (String key : typeMap.keySet()) {
- CategoryCount categoryCount = new CategoryCount(key,
typeMap.get(key));
- CheckNode typeNode = new CheckNode(categoryCount,
false, true);
- typeFilter.add(typeNode);
- }
- }
- if (organismMap.size() > 0) {
- organismFilter = new CheckNode("by Organism");
- rootNode.add(organismFilter);
- for (String key : organismMap.keySet()) {
- CategoryCount categoryCount = new CategoryCount(key,
organismMap.get(key));
- CheckNode organismNode = new CheckNode(categoryCount,
false, true);
- organismFilter.add(organismNode);
- }
- }
- if (dataSourceMap.size() > 0) {
- dataSourceFilter = new CheckNode("by Datasource");
- rootNode.add(dataSourceFilter);
- for (String key : dataSourceMap.keySet()) {
- CategoryCount categoryCount = new CategoryCount(key,
dataSourceMap.get(key));
- CheckNode dataSourceNode = new
CheckNode(categoryCount, false, true);
- dataSourceFilter.add(dataSourceNode);
- }
- }
-
-
- DefaultTreeModel treeModel = new DefaultTreeModel(rootNode);
- tree.setModel(treeModel);
- treeModel.addTreeModelListener(new TreeModelListener() {
-
- /**
- * Respond to user check node selections.
- *
- * @param treeModelEvent Tree Model Event Object.
- */
- public void treeNodesChanged(TreeModelEvent
treeModelEvent) {
- java.util.List<SearchHit> passedRecordList =
executeFilter();
- if (passedRecordList != null) {
- matchingHitsLabel.setText("Matching entities: "
- + passedRecordList.size());
- }
- }
-
- public void treeNodesInserted(TreeModelEvent
treeModelEvent) {
- // no-op
- }
-
- public void treeNodesRemoved(TreeModelEvent
treeModelEvent) {
- // no-op
- }
-
- public void treeStructureChanged(TreeModelEvent
treeModelEvent) {
- // no-op
- }
- });
-
- // Restore expansion state.
- if (typeFilterExpanded) {
- TreePath path = new TreePath(typeFilter.getPath());
- tree.expandPath(path);
- }
- if (organismFilterExpanded) {
- TreePath path = new TreePath(organismFilter.getPath());
- tree.expandPath(path);
- }
- if (dataSourceFilterExpanded) {
- TreePath path = new TreePath(dataSourceFilter.getPath());
- tree.expandPath(path);
- }
- }
- });
- }
-
+
private List<SearchHit> executeFilter() {
- Set<String> entityTypeSet = new HashSet<String>();
- Set<String> entityOrganismSet = new HashSet<String>();
- Set<String> entityDataSourceSet = new HashSet<String>();
+ ChainedFilter chainedFilter = new ChainedFilter();
- if (typeFilter != null) {
- int childCount = typeFilter.getChildCount();
- for (int i = 0; i < childCount; i++) {
- CheckNode checkNode = (CheckNode)
typeFilter.getChildAt(i);
- CategoryCount categoryCount = (CategoryCount)
checkNode.getUserObject();
- String entityType =
categoryCount.getCategoryName();
- if (checkNode.isSelected()) {
- entityTypeSet.add(entityType);
- }
+ Set<String> entityTypeSet = new HashSet<String>();
+ for (int i = 0; i < typeFilterNode.getChildCount(); i++) {
+ CheckNode checkNode = (CheckNode)
typeFilterNode.getChildAt(i);
+ CategoryCount categoryCount = (CategoryCount)
checkNode.getUserObject();
+ String entityType = categoryCount.getCategoryName();
+ if (checkNode.isSelected()) {
+ entityTypeSet.add(entityType);
}
}
+ EntityTypeFilter entityTypeFilter = new
EntityTypeFilter(entityTypeSet);
+ chainedFilter.addFilter(entityTypeFilter);
- if (organismFilter != null) {
- int childCount = organismFilter.getChildCount();
- for (int i = 0; i < childCount; i++) {
- CheckNode checkNode = (CheckNode)
organismFilter.getChildAt(i);
- CategoryCount categoryCount = (CategoryCount)
checkNode.getUserObject();
- String entityType =
categoryCount.getCategoryName();
- if (checkNode.isSelected()) {
- entityOrganismSet.add(entityType);
- }
+ Set<String> entityOrganismSet = new HashSet<String>();
+ for (int i = 0; i < organismFilterNode.getChildCount(); i++) {
+ CheckNode checkNode = (CheckNode)
organismFilterNode.getChildAt(i);
+ CategoryCount categoryCount = (CategoryCount)
checkNode.getUserObject();
+ String entityType = categoryCount.getCategoryName();
+ if (checkNode.isSelected()) {
+ entityOrganismSet.add(entityType);
}
}
+ OrganismFilter organismFilter = new
OrganismFilter(entityOrganismSet);
+ chainedFilter.addFilter(organismFilter);
- if (dataSourceFilter != null) {
- int childCount = dataSourceFilter.getChildCount();
- for (int i = 0; i < childCount; i++) {
- CheckNode checkNode = (CheckNode)
dataSourceFilter.getChildAt(i);
- CategoryCount categoryCount = (CategoryCount)
checkNode.getUserObject();
- String entityType =
categoryCount.getCategoryName();
- if (checkNode.isSelected()) {
- entityDataSourceSet.add(entityType);
- }
+ Set<String> entityDataSourceSet = new HashSet<String>();
+ for (int i = 0; i < dataSourceFilterNode.getChildCount(); i++) {
+ CheckNode checkNode = (CheckNode)
dataSourceFilterNode.getChildAt(i);
+ CategoryCount categoryCount = (CategoryCount)
checkNode.getUserObject();
+ String entityType = categoryCount.getCategoryName();
+ if (checkNode.isSelected()) {
+ entityDataSourceSet.add(entityType);
}
}
+ DataSourceFilter dataSourceFilter = new
DataSourceFilter(entityDataSourceSet);
+ chainedFilter.addFilter(dataSourceFilter);
+ return chainedFilter.filter(model.getSearchResponse().getSearchHit());
+ }
+
+
+ private void applyFilter() {
+ List<SearchHit> passedRecordList = executeFilter();
+ matchingItemsLabel.setText("Matching entities: "
+ + passedRecordList.size());
- ChainedFilter chainedFilter = new ChainedFilter();
- EntityTypeFilter entityTypeFilter = new
EntityTypeFilter(entityTypeSet);
- chainedFilter.addFilter(entityTypeFilter);
- DataSourceFilter dataSourceFilter = new
DataSourceFilter(entityDataSourceSet);
- chainedFilter.addFilter(dataSourceFilter);
- OrganismFilter organismFilter = new OrganismFilter(entityOrganismSet);
- chainedFilter.addFilter(organismFilter);
+ DefaultListModel listModel = (DefaultListModel)
hitsJList.getModel();
+ listModel.clear();
+ listModel.setSize(passedRecordList.size());
+ int i = 0;
+ for (SearchHit searchHit : passedRecordList) {
+ listModel.setElementAt(searchHit, i++);
+ }
+ }
+
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void update(Observable o, Object arg) {
+ matchingItemsLabel.setText("Matching entities: "
+ + model.getNumRecords());
+
+ if (model.getNumRecords() == 0) {
+ filterTreePanel.setVisible(false);
+ } else {
+ filterTreePanel.setVisible(true);
+ }
- List<SearchHit> passedRecordList;
- passedRecordList =
chainedFilter.filter(model.getRecordList().getHits());
+ // Remove all children
+ typeFilterNode.removeAllChildren();
+ // Create Filter Nodes
+ for (String key : model.numHitsByTypeMap.keySet()) {
+ CategoryCount categoryCount = new CategoryCount(key,
model.numHitsByTypeMap.get(key));
+ CheckNode typeNode = new CheckNode(categoryCount, false, true);
+ typeFilterNode.add(typeNode);
+ }
- return passedRecordList;
- }
+ organismFilterNode.removeAllChildren();
+ for (String key : model.numHitsByOrganismMap.keySet()) {
+ CategoryCount categoryCount = new CategoryCount(key,
model.numHitsByOrganismMap.get(key));
+ CheckNode organismNode = new CheckNode(categoryCount, false, true);
+ organismFilterNode.add(organismNode);
+ }
+
+ dataSourceFilterNode.removeAllChildren();
+ for (String key : model.numHitsByDatasourceMap.keySet()) {
+ CategoryCount categoryCount = new CategoryCount(key,
model.numHitsByDatasourceMap.get(key));
+ CheckNode dataSourceNode = new CheckNode(categoryCount, false,
true);
+ dataSourceFilterNode.add(dataSourceNode);
+ }
+
+ DefaultTreeModel treeModel = new DefaultTreeModel(rootNode);
+ tree.setModel(treeModel);
+ treeModel.addTreeModelListener(new TreeModelListener() {
+ /**
+ * Respond to user check node selections.
+ *
+ * @param treeModelEvent Tree Model Event Object.
+ */
+ public void treeNodesChanged(TreeModelEvent treeModelEvent) {
+ applyFilter();
+ filterTreePanel.repaint();
+ }
+
+ public void treeNodesInserted(TreeModelEvent treeModelEvent) {
+ // no-op
+ }
+
+ public void treeNodesRemoved(TreeModelEvent treeModelEvent) {
+ // no-op
+ }
+
+ public void treeStructureChanged(TreeModelEvent treeModelEvent) {
+ // no-op
+ }
+ });
+
+ expandAllNodes();
+ }
+
+
- //TODO must apply to the hits list!
- private final void createApplyFiltersButton() {
- applyButton = new JButton("Apply Filter");
- applyButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent actionEvent) {
- List<SearchHit> passedRecordList = executeFilter();
- if (passedRecordList.size() == 0) {
-
JOptionPane.showMessageDialog(CPath2Factory.getCySwingApplication().getJFrame(),
- "Your current filter settings result in 0 matching
entities. "
- + "\nPlease check your filter settings and try
again.",
- "No matches.", JOptionPane.INFORMATION_MESSAGE);
- } else {
+ //TODO
+ private final void createDownloadButton() {
+ downlodButton = new JButton("Download");
+ downlodButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent actionEvent) {
// DownloadDetails detailsFrame =
factory.createDownloadDetails(passedRecordList);
// if (dialog != null) {
// SwingUtilities.invokeLater(new Runnable() {
@@ -287,11 +240,9 @@
// });
// }
// detailsFrame.setVisible(true);
-
- }
}
});
- add(applyButton);
+ add(downlodButton);
}
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsPanel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsPanel.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchResultsPanel.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -2,14 +2,13 @@
import java.awt.BorderLayout;
import java.awt.Component;
-import java.awt.Font;
import java.awt.Window;
+import java.awt.event.MouseEvent;
import java.util.List;
import java.util.Set;
import javax.swing.BoxLayout;
import javax.swing.DefaultListModel;
-import javax.swing.JFrame;
import javax.swing.JLayeredPane;
import javax.swing.JList;
import javax.swing.JOptionPane;
@@ -18,19 +17,15 @@
import javax.swing.JSplitPane;
import javax.swing.JTabbedPane;
import javax.swing.JTextPane;
+import javax.swing.ListModel;
import javax.swing.ListSelectionModel;
import javax.swing.SwingUtilities;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
import javax.swing.table.DefaultTableModel;
-import javax.swing.text.Document;
+import org.apache.commons.lang.StringUtils;
import org.cytoscape.application.swing.CySwingApplication;
-import org.cytoscape.application.swing.CytoPanel;
-import org.cytoscape.application.swing.CytoPanelName;
-import org.cytoscape.application.swing.CytoPanelState;
-import org.cytoscape.application.swing.events.CytoPanelStateChangedEvent;
-import org.cytoscape.application.swing.events.CytoPanelStateChangedListener;
import org.cytoscape.cpathsquared.internal.CPath2Factory;
import org.cytoscape.cpathsquared.internal.CPath2Properties;
import org.cytoscape.cpathsquared.internal.CPath2;
@@ -43,22 +38,22 @@
import cpath.service.jaxb.SearchResponse;
-public class SearchResultsPanel extends JPanel
-implements CPath2Listener, CytoPanelStateChangedListener
+public class SearchResultsPanel extends JPanel implements CPath2Listener
{
private JList resList;
private JList ppwList;
private JList molList;
+
// private HashMap <String, Map<String,String>> memberDetailsMap; //TODO
map: search hits - participant/component names, xrefs, entity ref's ids, etc.
- private Document summaryDocument;
private String currentKeyword;
- private ResultsModel resultsModel;
+
+ private final ResultsModel resultsModel;
+
private JTextPane summaryTextPane;
private DetailsPanel detailsPanel;
private JScrollPane ppwListScrollPane;
private JScrollPane molListScrollPane;
private JLayeredPane appLayeredPane;
-// private CytoPanelState cytoPanelState;
public SearchResultsPanel()
@@ -72,11 +67,10 @@
// Create Info Panel (the first tab)
detailsPanel = CPath2Factory.createDetailsPanel(this);
- summaryDocument = detailsPanel.getDocument();
summaryTextPane = detailsPanel.getTextPane();
//create parent pathways panel (the second tab)
- ppwList = new JListWithToolTips(new DefaultListModel());
+ ppwList = new ToolTipsSearchHitsJList(new DefaultListModel());
ppwList.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
ppwList.setPrototypeCellValue("12345678901234567890");
JPanel ppwListPane = new JPanel();
@@ -86,7 +80,7 @@
ppwListPane.add(ppwListScrollPane, BorderLayout.CENTER);
//create participants (the third tab is about Entity References,
Complexes, and Genes...)
- molList = new JListWithToolTips(new DefaultListModel());
+ molList = new ToolTipsSearchHitsJList(new DefaultListModel());
molList.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
molList.setPrototypeCellValue("12345678901234567890");
JPanel molListPane = new JPanel();
@@ -102,7 +96,7 @@
southPane.add("Molecules", molListPane);
// search hits list
- resList = new JListWithToolTips(new DefaultListModel());
+ resList = new ToolTipsSearchHitsJList(new DefaultListModel());
resList.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
resList.setPrototypeCellValue("12345678901234567890");
JPanel hitListPane = new JPanel();
@@ -118,7 +112,8 @@
hitListPane.add(vSplit, BorderLayout.CENTER);
// Create search results extra filtering panel
- JPanel filterPanel =
CPath2Factory.createSearchResultsFilterPanel(resultsModel);
+ SearchResultsFilterPanel filterPanel =
+ (SearchResultsFilterPanel)
CPath2Factory.createSearchResultsFilterPanel(resultsModel, resList);
// Create the Split Pane
JSplitPane hSplit = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,
filterPanel, hitListPane);
@@ -127,10 +122,6 @@
add(hSplit);
createSelectListener();
-
-// // listener for cytopanel events
-// CytoPanel cytoPanel =
application.getCytoPanel(CytoPanelName.EAST);
-// cytoPanelState = cytoPanel.getState();
}
/**
@@ -150,14 +141,9 @@
*
*/
public void searchCompleted(final SearchResponse searchResponse) {
-
if (!searchResponse.isEmpty()) {
-
- // set the all-results model - used for hits list filtering
- resultsModel.setRecordList(new RecordList(searchResponse));
-
- // init/reset the hits list
- updateHitsList(searchResponse);
+ resultsModel.setSearchResponse(searchResponse);
+ updateHitsList();
} else {
SwingUtilities.invokeLater(new Runnable(){
public void run() {
@@ -176,18 +162,16 @@
*
* @param searchResponse
*/
- public final void updateHitsList(final SearchResponse searchResponse) {
+ private final void updateHitsList() {
// init/reset the hits list
DefaultListModel listModel = (DefaultListModel)
resList.getModel();
listModel.clear();
-
- List<SearchHit> searchHits = searchResponse.getSearchHit();
+ List<SearchHit> searchHits =
resultsModel.getSearchResponse().getSearchHit();
listModel.setSize(searchHits.size());
int i = 0;
for (SearchHit searchHit : searchHits) {
listModel.setElementAt(searchHit, i++);
}
-
}
@@ -199,9 +183,7 @@
// Ignore the "unselect" event.
if (!listSelectionEvent.getValueIsAdjusting()) {
if (selectedIndex >=0) {
- (new SelectEntity()).selectItem(
-
(SearchHit)resList.getModel().getElementAt(selectedIndex),
- summaryDocument, summaryTextPane,
appLayeredPane);
+
selectHit((SearchHit)resList.getModel().getElementAt(selectedIndex));
}
}
}
@@ -209,9 +191,66 @@
}
- @Override
- public void handleEvent(CytoPanelStateChangedEvent e) {
-// cytoPanelState = e.getNewState();
+ private void selectHit(SearchHit item) {
+ if (item == null) {
+ return;
+ }
+
+ // get/create and show hit's summary
+ String summary = resultsModel.summaryMap.get(item.getUri());
+ if (summary == null) {
+ StringBuilder html = new StringBuilder();
+ html.append("<html>");
+
+ if (item.getName() != null)
+ html.append("<h2>" + item.getName() + "</h2>");
+ html.append("<h3>Class: " + item.getBiopaxClass() +
+ "</h3><h3>URI: " + item.getUri() + "</h3>");
+
+ List<String> items = item.getOrganism();
+ if (items != null && !items.isEmpty()) {
+ html.append("<H3>Organisms:<br/>"
+ + StringUtils.join(items, "<br/>") +
"</H3>");
+ }
+
+ items = item.getPathway();
+ if (items != null && !items.isEmpty()) {
+ html.append("<H3>Pathway URIs:<br/>"
+ + StringUtils.join(items,
"<br/>") + "</H3>");
+ }
+
+ items = item.getDataSource();
+ if (items != null && !items.isEmpty()) {
+ html.append("<H3>Data sources:<br/>"
+ + StringUtils.join(items,
"<br/>") + "</H3>");
+ }
+
+ String primeExcerpt = item.getExcerpt();
+ if (primeExcerpt != null) {
+ html.append("<H4>Matched in</H4>");
+ html.append("<span class='excerpt'>" +
primeExcerpt
+ + "</span><BR>");
+ }
+
+ // TODO add more details here
+
+ html.append("</html>");
+ summary = html.toString();
+ resultsModel.summaryMap.put(item.getUri(), summary);
+ }
+
+ summaryTextPane.setText(summary);
+ summaryTextPane.setCaretPosition(0);
+ appLayeredPane.repaint();
+
+
+
+ // TODO update pathways list
+
+
+
+ // TODO update mol. list
+
}
@@ -246,4 +285,55 @@
CPath2Factory.getTaskManager().execute(taskFactory.createTaskIterator());
}
+
+ static class ToolTipsSearchHitsJList extends JList {
+
+ public ToolTipsSearchHitsJList(ListModel listModel) {
+ super(listModel);
+ }
+
+ @Override
+ public String getToolTipText(MouseEvent mouseEvent) {
+ int index = locationToIndex(mouseEvent.getPoint());
+ if (-1 < index) {
+ SearchHit record = (SearchHit)
getModel().getElementAt(index);
+ StringBuilder html = new StringBuilder();
+ html.append("<html><table cellpadding=10><tr><td>");
+ html.append("<B>").append(record.getBiopaxClass());
+ if(!record.getDataSource().isEmpty())
+
html.append(" ").append(record.getDataSource().toString());
+ if(!record.getOrganism().isEmpty())
+
html.append(" ").append(record.getOrganism().toString());
+ html.append("</B> ");
+ html.append("</td></tr></table></html>");
+ return html.toString();
+ } else {
+ return null;
+ }
+ }
+
+ }
+
+ static class ToolTipsNameValuePairJList extends JList {
+
+ public ToolTipsNameValuePairJList(ListModel listModel) {
+ super(listModel);
+ }
+
+ @Override
+ public String getToolTipText(MouseEvent mouseEvent) {
+ int index = locationToIndex(mouseEvent.getPoint());
+ if (-1 < index) {
+ StringBuilder html = new StringBuilder();
+ html.append("<html><table cellpadding=10><tr><td>");
+ html.append("<B>").append("TODO");
+ html.append("</B> ");
+ html.append("</td></tr></table></html>");
+ return html.toString();
+ } else {
+ return null;
+ }
+ }
+
+ }
}
\ No newline at end of file
Deleted:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SelectEntity.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SelectEntity.java
2012-05-28 18:42:13 UTC (rev 29375)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SelectEntity.java
2012-05-28 22:35:17 UTC (rev 29376)
@@ -1,65 +0,0 @@
-package org.cytoscape.cpathsquared.internal.view;
-
-import java.util.List;
-
-import javax.swing.JComponent;
-import javax.swing.JTextPane;
-import javax.swing.text.Document;
-
-import cpath.service.jaxb.*;
-
-import org.apache.commons.lang.StringUtils;
-
-
-public final class SelectEntity {
-
- public final void selectItem(
- SearchHit item,
- Document summaryDocumentModel,
- JTextPane textPane,
- JComponent textPaneOwner)
- {
-
- if (item != null) {
- StringBuffer html = new StringBuffer();
- html.append("<html>");
-
- if(item.getName() != null)
- html.append ("<h2>" + item.getName() + "</h2>");
- html.append ("<h3>Class: " + item.getBiopaxClass() + "</h3>");
- html.append ("<h3>URI: " + item.getUri() + "</h3>");
-
- List<String> items = item.getOrganism();
- if (items != null && !items.isEmpty()) {
- html.append ("<H3>Organisms:<br/>" + StringUtils.join(items,
"<br/>") + "</H3>");
- }
-
- items = item.getPathway();
- if (items != null && !items.isEmpty()) {
- html.append ("<H3>Pathway URIs:<br/>" +
StringUtils.join(items, "<br/>") + "</H3>");
- }
-
- items = item.getDataSource();
- if (items != null && !items.isEmpty()) {
- html.append ("<H3>Data sources:<br/>" +
StringUtils.join(items, "<br/>") + "</H3>");
- }
-
- String primeExcerpt = item.getExcerpt();
- if (primeExcerpt != null) {
- html.append("<H4>Matched in</H4>");
- html.append("<span class='excerpt'>" + primeExcerpt +
"</span><BR>") ;
- }
-
-
- //TODO add more details here
-
- html.append ("</html>");
- textPane.setText(html.toString());
- textPane.setCaretPosition(0);
-
- textPaneOwner.repaint();
- }
- }
-
-
-}
\ No newline at end of file
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