Author: kono
Date: 2012-08-09 13:00:42 -0700 (Thu, 09 Aug 2012)
New Revision: 30142
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
Log:
fixes #1353 Go Slim ontology works.
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
2012-08-09 18:40:19 UTC (rev 30141)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReader.java
2012-08-09 20:00:42 UTC (rev 30142)
@@ -1,6 +1,5 @@
package org.cytoscape.tableimport.internal.reader.ontology;
-import static
org.cytoscape.tableimport.internal.reader.TextFileDelimiters.PIPE;
import static org.cytoscape.tableimport.internal.reader.TextFileDelimiters.TAB;
import java.io.BufferedReader;
@@ -13,8 +12,6 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
import org.cytoscape.io.read.CyTableReader;
import org.cytoscape.model.CyNetwork;
@@ -30,6 +27,7 @@
import org.slf4j.LoggerFactory;
public class GeneAssociationReader extends AbstractTask implements
CyTableReader {
+
private static final Logger logger =
LoggerFactory.getLogger(GeneAssociationReader.class);
private static final String COMPATIBLE_VERSION = "gaf-version: 2.0";
@@ -39,6 +37,7 @@
// The following columns should be handled as List in GA v2 spec.
private static final List<Integer> LIST_INDEX = new
ArrayList<Integer>();
private static final Map<String, String> NAMESPACE_MAP = new
HashMap<String, String>();
+
static {
LIST_INDEX.add(4);
LIST_INDEX.add(8);
@@ -60,26 +59,11 @@
private static final int EXPECTED_COL_COUNT = 15;
private static final int DB_OBJ_ID = 1;
- private static final int OBJ_NAME = 9;
private static final int ASPECT = 8;
- private static final int SYNONYM = 10;
- private static final int GOID = 4;
- private int key = 2;
-
private InputStream is;
- // private Aliases nodeAliases;
- private Map<String, List<String>> attr2id;
- private CyTable nodeAttributes;
- // private GeneOntology geneOntology;
private Map<String, String> speciesMap;
-
- private Map<String, String> uppercaseIDMap;
-
private CyNetwork ontologyDAG;
-
- private CyTable dagTable;
-
private final CyTableFactory tableFactory;
private final String tableName;
@@ -141,7 +125,6 @@
if (ontologyDAG == null)
logger.warn("Could not find associated Ontology DAG.");
else {
- this.dagTable = ontologyDAG.getDefaultNodeTable();
termIDList =
ontologyDAG.getDefaultNodeTable().getColumn(CyNetwork.NAME).getValues(String.class);
}
@@ -245,9 +228,6 @@
if (currentList.contains(goidString) == false)
currentList.add(goidString);
row.set(namespace, currentList);
-
- // TODO: create term name list here.
-
break;
case EVIDENCE:
@@ -321,7 +301,7 @@
private String convertToName(final String id) {
final Collection<CyRow> rows =
ontologyDAG.getDefaultNodeTable().getMatchingRows(CyNetwork.NAME, id);
- if (rows != null) {
+ if (!rows.isEmpty()) {
final CyRow row = rows.iterator().next();
final String termName = row.get(OBOReader.TERM_NAME,
String.class);
if (termName != null)
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
2012-08-09 18:40:19 UTC (rev 30141)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
2012-08-09 20:00:42 UTC (rev 30142)
@@ -82,7 +82,9 @@
private void buildMapping(final CyNetwork network, final CyTable
nodeTable, final CyTable globalTable) {
final List<String> globalKeys =
globalTable.getColumn(CyNetwork.NAME).getValues(String.class);
- nodeTable.createColumn(MAPPING_KEY, String.class, true);
+
+ if(nodeTable.getColumn(MAPPING_KEY) == null)
+ nodeTable.createColumn(MAPPING_KEY, String.class, true);
for (final CyNode node : network.getNodeList()) {
final String nodeName =
network.getRow(node).get(CyNetwork.NAME, String.class);
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
