Author: pwang
Date: 2013-03-01 13:45:27 -0800 (Fri, 01 Mar 2013)
New Revision: 31145
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/AnnotationParser.java
Log:
Updated
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/AnnotationParser.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/AnnotationParser.java
2013-02-28 23:58:41 UTC (rev 31144)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/AnnotationParser.java
2013-03-01 21:45:27 UTC (rev 31145)
@@ -58,7 +58,7 @@
* *************************************************************
*/
-public class AnnotationParser {
+public class AnnotationParser {
/**
* constant string for the loadcorrect of the filechooser.
@@ -124,7 +124,7 @@
}
private String openResourceFile(String name) {
- return getClass().getResource("/" + name).toString();
+ return getClass().getResource("/data/" + name).toString();
}
/**
@@ -263,7 +263,7 @@
*
* @return string string with either loadcorrect or a parsing error.
*/
- public String setCustomAnnotation() {
+ private String setCustomAnnotation() {
String fileString = params.getAnnotationFile();
annotation = null;
@@ -325,7 +325,7 @@
*
* @return string string with either loadcorrect or a parsing error.
*/
- public String setDefaultAnnotation() {
+ private String setDefaultAnnotation() {
String fileString = params.getAnnotationFile();
annotation = null;
@@ -360,7 +360,7 @@
*
* @return string string with either loadcorrect or a parsing error.
*/
- public String setCustomOntology() {
+ private String setCustomOntology() {
String fileString = params.getOntologyFile();
String namespace = params.getNameSpace();
@@ -412,7 +412,7 @@
* @return string string with either loadcorrect or a parsing error.
*/
- public String setDefaultOntology(Map synonymHash) {
+ private String setDefaultOntology(Map synonymHash) {
String fileString = params.getOntologyFile().toString();
ontology = null;
@@ -440,11 +440,11 @@
*
* @return string string with either loadcorrect or a parsing error.
*/
- public String setFullOntology() {
+ private String setFullOntology() {
fullOntology = null;
synonymHash = null;
String resultString = "";
-
+
if (params.getOntologyFile().endsWith(".obo")) {
// read full ontology.
try {
@@ -489,7 +489,7 @@
}
- public void checkOntology(Ontology ontology) throws IOException {
+ private void checkOntology(Ontology ontology) throws IOException {
HashMap ontMap = ontology.getTerms();
Iterator it = ontMap.keySet().iterator();
while (it.hasNext()) {
@@ -506,7 +506,7 @@
* @throws InterruptedException
*/
- public Annotation remap(Annotation annotation, Ontology ontology,
Set<String> genes) throws InterruptedException {
+ private Annotation remap(Annotation annotation, Ontology ontology,
Set<String> genes) throws InterruptedException {
Annotation parsedAnnotation = new
Annotation(annotation.getSpecies(), annotation.getType(),
annotation.getCurator());
HashMap annMap = annotation.getMap();
@@ -570,7 +570,7 @@
* @throws InterruptedException
*/
- public Annotation customRemap(Annotation annotation, Ontology ontology,
Set<String> genes)
+ private Annotation customRemap(Annotation annotation, Ontology
ontology, Set<String> genes)
throws InterruptedException {
Annotation parsedAnnotation = new
Annotation(annotation.getSpecies(), annotation.getType(),
annotation.getCurator());
@@ -631,7 +631,7 @@
* method for recursing through tree to root
*/
- public void up(String node, int id, Annotation parsedAnnotation,
Ontology ontology, Ontology flOntology) {
+ private void up(String node, int id, Annotation parsedAnnotation,
Ontology ontology, Ontology flOntology) {
OntologyTerm child = flOntology.getTerm(id);
int[] parents = child.getParentsAndContainers();
for (int t = 0; t < parents.length; t++) {
@@ -653,7 +653,7 @@
* @throws IOException
*/
- public void up_go(int startID, int id, Ontology ontology) throws
IOException {
+ private void up_go(int startID, int id, Ontology ontology) throws
IOException {
OntologyTerm child = ontology.getTerm(id);
int[] parents = child.getParentsAndContainers();
for (int t = 0; t < parents.length; t++) {
@@ -685,7 +685,7 @@
return ontology;
}
- public Map getAlias() {
+ public Map getAlias() {
return alias;
}
@@ -696,7 +696,7 @@
public boolean getOrphans() {
return orphansFound;
}
-
+
/**
* @return the parser status : true if OK, false if something's wrong
*/
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