Author: kono
Date: 2008-09-15 15:17:39 -0700 (Mon, 15 Sep 2008)
New Revision: 14910
Modified:
cytoscape/trunk/src/cytoscape/data/ontology/readers/OBOFlatFileReader.java
cytoscape/trunk/src/cytoscape/data/ontology/readers/OBOTags.java
Log:
Some of the attributes in OBO will be imported as List instead of String.
Modified:
cytoscape/trunk/src/cytoscape/data/ontology/readers/OBOFlatFileReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/ontology/readers/OBOFlatFileReader.java
2008-09-15 22:07:56 UTC (rev 14909)
+++ cytoscape/trunk/src/cytoscape/data/ontology/readers/OBOFlatFileReader.java
2008-09-15 22:17:39 UTC (rev 14910)
@@ -41,7 +41,7 @@
import cytoscape.data.Semantics;
import cytoscape.data.ontology.Ontology;
-import cytoscape.util.URLUtil;
+import static cytoscape.data.ontology.readers.OBOTags.*;
import static cytoscape.data.ontology.readers.OBOTags.BROAD_SYNONYM;
import static cytoscape.data.ontology.readers.OBOTags.DEF;
import static cytoscape.data.ontology.readers.OBOTags.EXACT_SYNONYM;
@@ -55,6 +55,8 @@
import static cytoscape.data.ontology.readers.OBOTags.XREF;
import static cytoscape.data.ontology.readers.OBOTags.XREF_ANALOG;
+import cytoscape.util.URLUtil;
+
import giny.model.Edge;
import giny.model.Node;
@@ -142,7 +144,7 @@
*/
public OBOFlatFileReader(URL dataSource, String name) throws
IOException {
// this(dataSource.openStream(), name);
- // Use URLUtil to get the InputStream since we might be using a proxy
server
+ // Use URLUtil to get the InputStream since we might be using a
proxy server
// and because pages may be cached:
this(URLUtil.getBasicInputStream(dataSource), name);
}
@@ -192,7 +194,7 @@
Cytoscape.setOntologyRootID(rootID);
}
}
-
+
ontologyDAG = Cytoscape.createNetwork(name,
Cytoscape.getNetwork(rootID), false);
}
@@ -206,6 +208,7 @@
String key;
String val;
int colonInx;
+
while ((line = bufRd.readLine()) != null) {
// Read header
if (line.startsWith(TERM_TAG)) {
@@ -214,7 +217,10 @@
break;
} else if (line.length() != 0) {
colonInx = line.indexOf(':');
- if(colonInx == -1) continue;
+
+ if (colonInx == -1)
+ continue;
+
key = line.substring(0, colonInx).trim();
val = line.substring(colonInx + 1).trim();
header.put(key, val);
@@ -250,10 +256,19 @@
private void readEntry(final BufferedReader rd) throws IOException {
String id = "";
String line = null;
-
+
String key;
String val;
+
int colonInx;
+
+ String[] definitionParts;
+ String[] synonymParts;
+ String[] entry;
+ String targetId;
+ List<String> listAttr;
+ Map<String, String> synoMap;
+
while (true) {
line = rd.readLine().trim();
@@ -263,6 +278,7 @@
colonInx = line.indexOf(':');
key = line.substring(0, colonInx).trim();
val = line.substring(colonInx + 1).trim();
+
Node source = null;
if (key.equals(ID.toString())) {
@@ -270,44 +286,40 @@
id = val;
} else if (key.equals(DEF.toString())) {
// CyLogger.getLogger().info("DEF: " + id + " =
" + val);
- String[] definitionParts = val.split("\"");
+ definitionParts = val.split("\"");
termAttributes.setAttribute(id, OBO_PREFIX +
"." + key, definitionParts[1]);
List<String> originList =
getReferences(val.substring(definitionParts[1].length()
+ 2));
- if (originList != null) {
+ if (originList != null)
termAttributes.setListAttribute(id,
OBO_PREFIX + "." + DEF_ORIGIN, originList);
- }
} else if (key.equals(EXACT_SYNONYM.toString())
|| key.equals(RELATED_SYNONYM.toString())
|| key.equals(BROAD_SYNONYM.toString())
|| key.equals(NARROW_SYNONYM.toString()) ||
key.equals(SYNONYM.toString())) {
- String[] synonymParts = val.split("\"");
- Map<String, String> synoMap =
termAttributes.getMapAttribute(id,
-
OBO_PREFIX + "."
-
+ OBOTags.SYNONYM
-
.toString());
+ synonymParts = val.split("\"");
- if (synoMap == null) {
+ synoMap = termAttributes.getMapAttribute(id,
+
OBO_PREFIX + "."
+ +
OBOTags.SYNONYM.toString());
+
+ if (synoMap == null)
synoMap = new HashMap<String, String>();
- }
if (key.equals(SYNONYM.toString())) {
synoMap.put(synonymParts[1],
synonymParts[2].trim());
- } else {
+ } else
synoMap.put(synonymParts[1], key);
- }
- termAttributes.setMapAttribute(id, OBO_PREFIX +
"." + OBOTags.SYNONYM.toString(),
- synoMap);
+ termAttributes.setMapAttribute(id, OBO_PREFIX +
"." + SYNONYM.toString(), synoMap);
} else if (key.equals(RELATIONSHIP.toString())) {
if (source == null) {
source = Cytoscape.getCyNode(id, true);
ontologyDAG.addNode(source);
}
- String[] entry = val.split(" ");
+ entry = val.split(" ");
final String[] itr = new String[3];
itr[0] = id;
@@ -328,14 +340,11 @@
}
int colonidx = val.indexOf('!');
- final String targetId;
- if (colonidx == -1) {
- // GO Slim.
+ if (colonidx == -1)
targetId = val.trim();
- } else {
+ else
targetId = val.substring(0,
colonidx).trim();
- }
target = Cytoscape.getCyNode(targetId, true);
ontologyDAG.addNode(target);
@@ -347,23 +356,24 @@
interactionList.add(itr);
} else if (key.equals(IS_OBSOLETE.toString())) {
termAttributes.setAttribute(id, OBO_PREFIX +
"." + key, Boolean.parseBoolean(val));
- } else if (key.equals(XREF.toString()) ||
key.equals(XREF_ANALOG.toString())) {
- List xrefAnalog =
termAttributes.getListAttribute(id,
-
OBO_PREFIX + "."
-
+ XREF.toString());
+ } else if (key.equals(XREF.toString()) ||
key.equals(XREF_ANALOG.toString())
+ || key.equals(ALT_ID.toString()) ||
key.equals(SUBSET.toString())
+ || key.equals(DISJOINT_FROM.toString())) {
+ listAttr = termAttributes.getListAttribute(id,
OBO_PREFIX + "." + key);
- if (xrefAnalog == null) {
- xrefAnalog = new ArrayList<String>();
- }
+ if (listAttr == null)
+ listAttr = new ArrayList<String>();
if (val != null) {
- xrefAnalog.add(val.toString());
+ if
(key.equals(DISJOINT_FROM.toString())) {
+
listAttr.add(val.split("!")[0].trim());
+ } else
+ listAttr.add(val);
}
- termAttributes.setListAttribute(id, OBO_PREFIX
+ "." + XREF.toString(), xrefAnalog);
- } else {
+ termAttributes.setListAttribute(id, OBO_PREFIX
+ "." + key, listAttr);
+ } else
termAttributes.setAttribute(id, OBO_PREFIX +
"." + key, val);
- }
}
}
Modified: cytoscape/trunk/src/cytoscape/data/ontology/readers/OBOTags.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/ontology/readers/OBOTags.java
2008-09-15 22:07:56 UTC (rev 14909)
+++ cytoscape/trunk/src/cytoscape/data/ontology/readers/OBOTags.java
2008-09-15 22:17:39 UTC (rev 14910)
@@ -105,6 +105,9 @@
IS_SYMMETRIC("This tag indicates that the relationship is marked as
symmetric (meaning that if the relationship holds from "
+ "the child to parent, it also holds from parent to
child). This information is very useful to reasoners and other "
+ "automatic traversals of the graph."),
+ DISJOINT_FROM("This tag indicates that a term is disjoint from another,
meaning that the two terms have no instances or " +
+ "subclasses in common. The value is the id of the term
from which the current term is disjoint. This tag may not be " +
+ "applied to relationship types."),
/*
* This is a local tag defined by Kei. This is a reference extracted
from "DEF" tag.
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