Author: rodche
Date: 2012-02-21 08:09:56 -0800 (Tue, 21 Feb 2012)
New Revision: 28326
Removed:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/DataSourceFilter.java
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/InteractionBundlePanel.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/SearchHitsPanel.java
Log:
Removing the datasource filter stuff from the interactions panel (both organism
and datasource filters are now to be set before search results are returned -
TODO)
Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
===================================================================
--- csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2012-02-20
21:48:53 UTC (rev 28325)
+++ csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2012-02-21
16:09:56 UTC (rev 28326)
@@ -81,7 +81,7 @@
<dependency>
<groupId>pathwaycommons.cpath</groupId>
<artifactId>cpath-api</artifactId>
- <version>5.0.0-SNAPSHOT</version>
+ <version>5.1.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>pathwaycommons.cpath</groupId>
Deleted:
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
2012-02-20 21:48:53 UTC (rev 28325)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/filters/DataSourceFilter.java
2012-02-21 16:09:56 UTC (rev 28326)
@@ -1,46 +0,0 @@
-package org.cytoscape.cpathsquared.internal.filters;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-
-import cpath.service.jaxb.SearchHit;
-
-/**
- * Data Source Filter.
- *
- * @author Ethan Cerami, Igor Rodchenkov
- */
-public class DataSourceFilter implements Filter {
- private final Set<String> dataSourceSet;
-
- /**
- * Constructor.
- *
- * @param dataSourceSet Set of Data Sources we want to keep.
- */
- public DataSourceFilter(Set<String> dataSourceSet) {
- this.dataSourceSet = dataSourceSet;
- }
-
- /**
- * Filters the record list. Those items which pass the filter
- * are included in the returned list.
- *
- * @param recordList
- * @return
- */
- public List<SearchHit> filter(List<SearchHit> recordList) {
- ArrayList<SearchHit> passedList = new ArrayList<SearchHit>();
- for (SearchHit record : recordList) {
- List<String> dataSources = record.getDataSource();
- if (dataSources != null && !dataSources.isEmpty()) {
- dataSources.retainAll(dataSourceSet); // intersection
- if (!dataSources.isEmpty()) {
- passedList.add(record);
- }
- }
- }
- return passedList;
- }
-}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/InteractionBundlePanel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/InteractionBundlePanel.java
2012-02-20 21:48:53 UTC (rev 28325)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/InteractionBundlePanel.java
2012-02-21 16:09:56 UTC (rev 28326)
@@ -29,7 +29,6 @@
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;
import cpath.service.jaxb.SearchHit;
@@ -42,7 +41,6 @@
public class InteractionBundlePanel extends JPanel {
private JLabel matchingInteractionsLabel;
private InteractionBundleModel interactionBundleModel;
- private CheckNode dataSourceFilter;
private CheckNode interactionTypeFilter;
private JButton retrieveButton;
private JTreeWithCheckNodes tree;
@@ -98,12 +96,9 @@
*/
public void expandAllNodes() {
filterPanel.setCollapsed(false);
- dataSourceFilter.setSelected(true);
interactionTypeFilter.setSelected(true);
- TreePath path = new TreePath(dataSourceFilter.getPath());
+ TreePath path = new TreePath(interactionTypeFilter.getPath());
tree.expandPath(path);
- path = new TreePath(interactionTypeFilter.getPath());
- tree.expandPath(path);
}
private void addObserver(final InteractionBundleModel
interactionBundleModel,
@@ -123,15 +118,9 @@
retrieveButton.setVisible(true);
}
- TreeMap<String, Integer> dataSourceMap =
recordList.getDataSourceMap();
TreeMap<String, Integer> entityTypeMap =
recordList.getEntityTypeMap();
// Store current expansion states
- boolean dataSourceFilterExpanded = false;
- if (dataSourceFilter != null) {
- TreePath path = new TreePath(dataSourceFilter.getPath());
- dataSourceFilterExpanded = tree.isExpanded(path);
- }
boolean interactionTypeFilterExpanded = false;
if (interactionTypeFilter != null) {
TreePath path = new
TreePath(interactionTypeFilter.getPath());
@@ -141,20 +130,7 @@
// Remove all children
rootNode.removeAllChildren();
- // Create Data Source Filter
- if (dataSourceMap.size() > 0) {
- dataSourceFilter = new CheckNode("Filter by Data Source");
- 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);
- }
- dataSourceFilter.setSelected(true);
- }
-
- // Create Entity Type Filter
+ // Create Entity Type Filter
if (entityTypeMap.size() > 0) {
interactionTypeFilter = new CheckNode("Filter by
Interaction Type");
rootNode.add(interactionTypeFilter);
@@ -201,10 +177,6 @@
});
// Restore expansion state.
- if (dataSourceFilterExpanded) {
- TreePath path = new TreePath(dataSourceFilter.getPath());
- tree.expandPath(path);
- }
if (interactionTypeFilterExpanded) {
TreePath path = new
TreePath(interactionTypeFilter.getPath());
tree.expandPath(path);
@@ -241,30 +213,23 @@
}
private List<SearchHit> executeFilter() {
- Set<String> dataSourceSet = new HashSet<String>();
Set<String> entityTypeSet = new HashSet<String>();
- int childCount = dataSourceFilter.getChildCount();
- for (int i = 0; i < childCount; i++) {
- CheckNode checkNode = (CheckNode) dataSourceFilter.getChildAt(i);
- CategoryCount categoryCount = (CategoryCount)
checkNode.getUserObject();
- String dataSource = categoryCount.getCategoryName();
- if (checkNode.isSelected()) {
- dataSourceSet.add(dataSource);
- }
- }
- childCount = interactionTypeFilter.getChildCount();
- for (int i = 0; i < childCount; i++) {
- CheckNode checkNode = (CheckNode)
interactionTypeFilter.getChildAt(i);
- CategoryCount categoryCount = (CategoryCount)
checkNode.getUserObject();
- String entityType = categoryCount.getCategoryName();
- if (checkNode.isSelected()) {
- entityTypeSet.add(entityType);
- }
- }
+
+ if (interactionTypeFilter != null) {
+ int childCount = interactionTypeFilter.getChildCount();
+ for (int i = 0; i < childCount; i++) {
+ CheckNode checkNode = (CheckNode)
interactionTypeFilter
+ .getChildAt(i);
+ CategoryCount categoryCount = (CategoryCount)
checkNode
+ .getUserObject();
+ String entityType =
categoryCount.getCategoryName();
+ if (checkNode.isSelected()) {
+ entityTypeSet.add(entityType);
+ }
+ }
+ }
ChainedFilter chainedFilter = new ChainedFilter();
- DataSourceFilter dataSourceFilter = new
DataSourceFilter(dataSourceSet);
EntityTypeFilter entityTypeFilter = new
EntityTypeFilter(entityTypeSet);
- chainedFilter.addFilter(dataSourceFilter);
chainedFilter.addFilter(entityTypeFilter);
List<SearchHit> passedRecordList;
try {
Modified:
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
2012-02-20 21:48:53 UTC (rev 28325)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/JListWithToolTips.java
2012-02-21 16:09:56 UTC (rev 28326)
@@ -43,16 +43,6 @@
html.append(organisms.toString());
}
- // TODO Next, add synonyms
-// for (String synonym : synList) {
-// if (!synonym.equalsIgnoreCase(record.getName()))
-// synBuffer.append("- " + synonym +
"<BR>");
-// }
-// if (synBuffer.length() > 0) {
-// html.append("<BR><BR>");
-// html.append(synBuffer.toString());
-// }
-
html.append("</td></tr></table>");
html.append("</html>");
return html.toString();
Modified:
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
2012-02-20 21:48:53 UTC (rev 28325)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/RecordList.java
2012-02-21 16:09:56 UTC (rev 28326)
@@ -14,7 +14,6 @@
*/
public class RecordList {
private SearchResponse response;
- TreeMap<String, Integer> dataSourceMap = new TreeMap<String, Integer>();
TreeMap<String, Integer> interactionTypeMap = new TreeMap<String,
Integer>();
/**
@@ -46,13 +45,6 @@
return response;
}
- /**
- * Gets catalog of data sources.
- * @return Map<Data Source Name, # Records>
- */
- public TreeMap<String, Integer> getDataSourceMap() {
- return dataSourceMap;
- }
/**
* Gets catalog of entity sources.
@@ -66,25 +58,12 @@
List<SearchHit> recordList = response.getSearchHit();
if (recordList != null) {
for (SearchHit record: recordList) {
- catalogDataSource(record.getDataSource());
catalogInteractionType(record);
// TODO: additional catalogs, as needed.
}
}
}
- private void catalogDataSource(List<String> dataSources) {
- for (String name : dataSources) {
- Integer count = dataSourceMap.get(name);
- if (count != null) {
- count = count + 1;
- } else {
- count = 1;
- }
- dataSourceMap.put(name, count);
- }
- }
-
private void catalogInteractionType(SearchHit record) {
String type = record.getBiopaxClass();
Integer count = interactionTypeMap.get(type);
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchHitsPanel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchHitsPanel.java
2012-02-20 21:48:53 UTC (rev 28325)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchHitsPanel.java
2012-02-21 16:09:56 UTC (rev 28326)
@@ -147,7 +147,7 @@
peListModel.setSize(searchHits.size());
int i = 0;
for (SearchHit searchHit : searchHits) {
- peListModel.setElementAt(searchHit.toString(), i++);
+ peListModel.setElementAt(searchHit, i++);
}
} else {
SwingUtilities.invokeLater(new Runnable(){
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