Author: mes
Date: 2012-01-27 18:06:09 -0800 (Fri, 27 Jan 2012)
New Revision: 28151
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
Log:
minor cleanup to better understand the code
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
2012-01-28 01:29:49 UTC (rev 28150)
+++
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
2012-01-28 02:06:09 UTC (rev 28151)
@@ -32,6 +32,7 @@
// Separator for multiple entries.
private static final String SEPARATOR = "\\|";
+ private static final String SUBSEPARATOR = ":";
private static final String ATTR_PREFIX = "PSI-MI-25.";
private static final int COLUMN_COUNT = 15;
@@ -132,6 +133,8 @@
continue;
try {
+
+ //aaa:bbb:ccc|aa:bb:cc|a:b:c<tab>
entry = line.split(TAB);
// Validate entry list.
@@ -140,8 +143,8 @@
sourceID = entry[0].split(SEPARATOR);
targetID = entry[1].split(SEPARATOR);
- final String sourceRawID =
sourceID[0].split(":")[1];
- final String targetRawID =
targetID[0].split(":")[1];
+ final String sourceRawID =
sourceID[0].split(SUBSEPARATOR)[1];
+ final String targetRawID =
targetID[0].split(SUBSEPARATOR)[1];
CyNode source = nodeMap.get(sourceRawID);
if (source == null) {
@@ -158,9 +161,8 @@
network.getRow(target).set(CyTableEntry.NAME,
targetRawID);
// Set type if not protein
- if (sourceID[0].contains(CHEBI)) {
+ if (sourceID[0].contains(CHEBI))
network.getRow(source).set(INTERACTOR_TYPE, COMPOUND);
- }
if (targetID[0].contains(CHEBI))
network.getRow(target).set(INTERACTOR_TYPE, COMPOUND);
@@ -216,7 +218,7 @@
}
private void setTaxID(CyRow row, String value) {
- String[] buf = value.split(":", 2);
+ String[] buf = value.split(SUBSEPARATOR, 2);
String attrName;
String taxonName;
if (buf != null && buf.length == 2) {
@@ -243,7 +245,7 @@
String[] temp;
for (String val : pubID) {
- temp = val.split(":", 2);
+ temp = val.split(SUBSEPARATOR, 2);
if (temp == null || temp.length < 2)
continue;
@@ -263,7 +265,7 @@
String value;
for (String val : entry) {
- temp = val.split(":", 2);
+ temp = val.split(SUBSEPARATOR, 2);
if (temp == null || temp.length < 2)
continue;
@@ -294,7 +296,7 @@
String scoreType;
for (String val : entry) {
- final String[] parts = val.split(":");
+ final String[] parts = val.split(SUBSEPARATOR);
if (parts == null || parts.length != 2)
continue;
--
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