Author: jm
Date: 2011-09-20 08:43:41 -0700 (Tue, 20 Sep 2011)
New Revision: 26874
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchPlugin.java
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/SearchTaskFactory.java
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/ui/EnhancedSearchPanel.java
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/util/AttributeFields.java
core3/impl/trunk/search-impl/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Removed unnecessary references to CyTableManager
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchPlugin.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchPlugin.java
2011-09-20 15:41:12 UTC (rev 26873)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchPlugin.java
2011-09-20 15:43:41 UTC (rev 26874)
@@ -36,7 +36,6 @@
import org.cytoscape.application.swing.AbstractToolBarComponent;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
import org.cytoscape.session.events.SessionLoadedEvent;
@@ -57,14 +56,13 @@
public EnhancedSearchPlugin(final CySwingApplication desktopApp,
final CyApplicationManager appManager,
- final CyTableManager tableMgr,
final GUITaskManager taskMgr,
final CyEventHelper eventHelper, final
CyNetworkViewManager viewManager)
{
searchMgr = new EnhancedSearchManager();
// Add a text-field and a search button on tool-bar
- searchPnl = new EnhancedSearchPanel(appManager, viewManager,
tableMgr, searchMgr, taskMgr);
+ searchPnl = new EnhancedSearchPanel(appManager, viewManager,
searchMgr, taskMgr);
this.setToolBarGravity(150.0f);
EnhancedSearchPlugin.eventHelper = eventHelper;
}
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
2011-09-20 15:41:12 UTC (rev 26873)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
2011-09-20 15:43:41 UTC (rev 26874)
@@ -45,7 +45,6 @@
import org.apache.lucene.util.Version;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.search.internal.util.AttributeFields;
import org.cytoscape.search.internal.util.CustomMultiFieldQueryParser;
import org.cytoscape.search.internal.util.EnhancedSearchUtils;
@@ -59,14 +58,12 @@
private final RAMDirectory idx;
private final CyNetwork network;
- private final CyTableManager tableMgr;
private IdentifiersCollector hitCollector = null;
private Searcher searcher = null;
- public EnhancedSearchQuery(CyNetwork network, RAMDirectory index,
CyTableManager tableMgr) {
+ public EnhancedSearchQuery(CyNetwork network, RAMDirectory index) {
this.network = network;
this.idx = index;
- this.tableMgr = tableMgr;
}
public void executeQuery(String queryString) {
@@ -74,7 +71,7 @@
logger.debug("Query start for: " + queryString);
// Define attribute fields in which the search is to be
carried on
- AttributeFields attFields = new
AttributeFields(network, tableMgr);
+ AttributeFields attFields = new
AttributeFields(network);
// Build an IndexSearcher using the in-memory index
searcher = new IndexSearcher(idx);
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
2011-09-20 15:41:12 UTC (rev 26873)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
2011-09-20 15:43:41 UTC (rev 26874)
@@ -37,7 +37,6 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.task.AbstractNetworkTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -53,7 +52,6 @@
private boolean interrupted = false;
private final EnhancedSearch enhancedSearch;
- private final CyTableManager tableMgr;
private final CyNetworkViewManager viewManager;
private final CyApplicationManager appManager;
@@ -64,13 +62,12 @@
* the user should be provided as arguments to the constructor.
*/
public IndexAndSearchTask(final CyNetwork network, final EnhancedSearch
enhancedSearch,
- final CyTableManager tableMgr, final String query,
final CyNetworkViewManager viewManager,
+ final String query, final CyNetworkViewManager
viewManager,
final CyApplicationManager appManager) {
// Will set a CyNetwork field called "net".
super(network);
this.enhancedSearch = enhancedSearch;
- this.tableMgr = tableMgr;
this.query = query;
this.viewManager = viewManager;
this.appManager = appManager;
@@ -104,7 +101,7 @@
// Execute query
taskMonitor.setStatusMessage("Executing query");
- EnhancedSearchQuery queryHandler = new
EnhancedSearchQuery(network, idx, tableMgr);
+ EnhancedSearchQuery queryHandler = new
EnhancedSearchQuery(network, idx);
queryHandler.executeQuery(query);
if (interrupted)
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/SearchTaskFactory.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/SearchTaskFactory.java
2011-09-20 15:41:12 UTC (rev 26873)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/SearchTaskFactory.java
2011-09-20 15:43:41 UTC (rev 26874)
@@ -2,7 +2,6 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.task.AbstractNetworkTaskFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.TaskFactory;
@@ -10,24 +9,22 @@
public class SearchTaskFactory extends AbstractNetworkTaskFactory implements
TaskFactory {
- private CyTableManager tableMgr;
private EnhancedSearch searchMgr;
private String query;
private final CyNetworkViewManager viewManager;
private final CyApplicationManager appManager;
- public SearchTaskFactory(final CyNetwork network, EnhancedSearch
searchMgr, CyTableManager tableMgr, String query,
+ public SearchTaskFactory(final CyNetwork network, EnhancedSearch
searchMgr, String query,
final CyNetworkViewManager viewManager, final
CyApplicationManager appManager) {
this.network = network;
this.searchMgr = searchMgr;
- this.tableMgr = tableMgr;
this.query = query;
this.viewManager = viewManager;
this.appManager = appManager;
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new IndexAndSearchTask(network,
searchMgr, tableMgr, query, viewManager, appManager));
+ return new TaskIterator(new IndexAndSearchTask(network,
searchMgr, query, viewManager, appManager));
}
}
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/ui/EnhancedSearchPanel.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/ui/EnhancedSearchPanel.java
2011-09-20 15:41:12 UTC (rev 26873)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/ui/EnhancedSearchPanel.java
2011-09-20 15:43:41 UTC (rev 26874)
@@ -2,13 +2,9 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.search.internal.EnhancedSearch;
import org.cytoscape.search.internal.SearchTaskFactory;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewManager;
-import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.swing.GUITaskManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -20,14 +16,13 @@
private static final Logger logger =
LoggerFactory.getLogger(EnhancedSearchPanel.class);
private CyApplicationManager appManager;
- private CyTableManager tableMgr;
private EnhancedSearch searchMgr;
private GUITaskManager taskMgr;
private final CyNetworkViewManager viewManager;
/** Creates new form NewJPanel */
- public EnhancedSearchPanel(CyApplicationManager appManager, final
CyNetworkViewManager viewManager, CyTableManager tableMgr, EnhancedSearch
searchMgr,
+ public EnhancedSearchPanel(CyApplicationManager appManager, final
CyNetworkViewManager viewManager, EnhancedSearch searchMgr,
GUITaskManager taskMgr) {
initComponents();
@@ -36,7 +31,6 @@
this.lbSearch.setVisible(true);
this.appManager = appManager;
- this.tableMgr = tableMgr;
this.searchMgr = searchMgr;
this.taskMgr = taskMgr;
this.viewManager = viewManager;
@@ -60,7 +54,7 @@
logger.debug("Target Network ID = " +
currentNetwork.getSUID());
final SearchTaskFactory factory = new
SearchTaskFactory(currentNetwork, searchMgr,
- tableMgr, queryStr, viewManager,
appManager);
+ queryStr, viewManager, appManager);
this.taskMgr.execute(factory);
} else
logger.error("Could not find network for search");
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/util/AttributeFields.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/util/AttributeFields.java
2011-09-20 15:41:12 UTC (rev 26873)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/util/AttributeFields.java
2011-09-20 15:43:41 UTC (rev 26874)
@@ -28,20 +28,12 @@
package org.cytoscape.search.internal.util;
-import java.util.ArrayList;
-import java.util.Collection;
import java.util.HashMap;
-import java.util.List;
import java.util.Map;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.CyTable;
/**
@@ -50,11 +42,9 @@
* This way CustomMultiFieldQueryParser can recognize numeric attribute fields.
*/
public class AttributeFields {
- private final CyTableManager tableMgr;
private final Map<String, Class<?>> columnTypeMap;
- public AttributeFields(final CyNetwork network, final CyTableManager
tableMgr) {
- this.tableMgr = tableMgr;
+ public AttributeFields(final CyNetwork network) {
this.columnTypeMap = new HashMap<String, Class<?>>();
initFields(network);
}
@@ -67,12 +57,12 @@
* There are probably better ways to do this, but there you go :)
*/
private void initFields(final CyNetwork network) {
- CyTable nodeCyDataTable = tableMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
+ CyTable nodeCyDataTable = network.getDefaultNodeTable();
for (final CyColumn column : nodeCyDataTable.getColumns())
columnTypeMap.put(EnhancedSearchUtils.replaceWhitespace(column.getName()),
column.getType());
- CyTable edgeCyDataTable = (CyTable)
tableMgr.getTableMap(CyEdge.class, network).get(CyNetwork.DEFAULT_ATTRS);
+ CyTable edgeCyDataTable = network.getDefaultEdgeTable();
for (final CyColumn column : edgeCyDataTable.getColumns())
columnTypeMap.put(EnhancedSearchUtils.replaceWhitespace(column.getName()),
column.getType());
Modified:
core3/impl/trunk/search-impl/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/impl/trunk/search-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-20 15:41:12 UTC (rev 26873)
+++
core3/impl/trunk/search-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-20 15:43:41 UTC (rev 26874)
@@ -18,7 +18,6 @@
class="org.cytoscape.search.internal.EnhancedSearchPlugin">
<constructor-arg ref="cytoscapeDesktopService" />
<constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="cyTableManagerServiceRef" />
<constructor-arg ref="guiTaskManagerServiceRef" />
<constructor-arg ref="cyEventHelperServiceRef" />
<constructor-arg ref="cyNetworkViewManagerServiceRef" />
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