Author: pwang
Date: 2013-02-27 15:40:00 -0800 (Wed, 27 Feb 2013)
New Revision: 31142
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOAnnotationDefaultReader.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOJarReader.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOOntologyDefaultReader.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOOntologyFlatFileReader.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/SettingsPanelActionListener.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/ui/SettingsPanel.java
Log:
Updated
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOAnnotationDefaultReader.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOAnnotationDefaultReader.java
2013-02-26 17:25:37 UTC (rev 31141)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOAnnotationDefaultReader.java
2013-02-27 23:40:00 UTC (rev 31142)
@@ -100,6 +100,11 @@
String annotationType, String curator) throws
IllegalArgumentException, IOException, Exception {
// System.out.println ("AnnotationFlatFileReader on " +
filename);
this.filename = filename;
+
+ if (filename.startsWith("bundle:")){
+ filename = filename.replaceFirst("bundle:", "jar:");
+ }
+
try {
if (filename.trim().startsWith("jar:")) {
BiNGOJarReader reader = new
BiNGOJarReader(filename);
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOJarReader.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOJarReader.java
2013-02-26 17:25:37 UTC (rev 31141)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOJarReader.java
2013-02-27 23:40:00 UTC (rev 31142)
@@ -66,12 +66,14 @@
// null
// reference then we'll fall back to the class loader that
loaded this
// class
- URL url = getClass().getResource("/" + filename);
- JarURLConnection juc = (JarURLConnection) url.openConnection();
- JarFile jarFile = juc.getJarFile();
- InputStream is =
jarFile.getInputStream(jarFile.getJarEntry(filename));
+// URL url = getClass().getResource("/" + filename);
+// JarURLConnection juc = (JarURLConnection) url.openConnection();
+// JarFile jarFile = juc.getJarFile();
+// InputStream is =
jarFile.getInputStream(jarFile.getJarEntry(filename));
+
+ InputStream is =
getClass().getResourceAsStream("/data/"+filename);
+
reader = new InputStreamReader(is);
-
}
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOOntologyDefaultReader.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOOntologyDefaultReader.java
2013-02-26 17:25:37 UTC (rev 31141)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOOntologyDefaultReader.java
2013-02-27 23:40:00 UTC (rev 31142)
@@ -76,6 +76,11 @@
IOException, Exception {
this.filename = filename;
this.synonymHash = synonymHash;
+
+ if (filename.startsWith("bundle:")){
+ filename = filename.replaceFirst("bundle:", "jar:");
+ }
+
try {
if (filename.trim().startsWith("jar:")) {
BiNGOJarReader reader = new
BiNGOJarReader(filename);
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOOntologyFlatFileReader.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOOntologyFlatFileReader.java
2013-02-26 17:25:37 UTC (rev 31141)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOOntologyFlatFileReader.java
2013-02-27 23:40:00 UTC (rev 31142)
@@ -74,6 +74,11 @@
public BiNGOOntologyFlatFileReader(String filename) throws
IllegalArgumentException, IOException, Exception {
this.filename = filename;
+
+ if (filename.startsWith("bundle:")){
+ filename = filename.replaceFirst("bundle:", "jar:");
+ }
+
try {
if (filename.trim().startsWith("jar:")) {
BiNGOJarReader reader = new
BiNGOJarReader(filename);
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/SettingsPanelActionListener.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/SettingsPanelActionListener.java
2013-02-26 17:25:37 UTC (rev 31141)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/SettingsPanelActionListener.java
2013-02-27 23:40:00 UTC (rev 31142)
@@ -315,8 +315,8 @@
}
}
- private String openResourceFile(String name) {
- return getClass().getResource("/" + name).toString();
+ private String openResourceFile(String name) {
+ return getClass().getResource("/data/"+name).toString();
}
public Set<String> conformize(Set<String> selection, Set<String>
allNodes) {
@@ -354,7 +354,7 @@
final Set<CyNetwork> networkSet =
adapter.getCyNetworkManager().getNetworkSet();
for (final CyNetwork network : networkSet) {
//final String title =
network.getCyRow().get(CyNetwork.NAME, String.class);
- final String title =
network.getDefaultNetworkTable().getRow(network).get(CyNetwork.NAME,
String.class);
+ final String title =
network.getDefaultNetworkTable().getRow(network.getSUID()).get(CyNetwork.NAME,
String.class);
if (params.getCluster_name().equals(title)) {
JOptionPane.showMessageDialog(settingsPanel,
@@ -383,7 +383,7 @@
final List<CyNode> nodes =
network.getNodeList();
for (CyNode node: nodes) {
//if
(node.getCyRow().get(CyNetwork.SELECTED, Boolean.class) == true) {
- if
(network.getDefaultNodeTable().getRow(node).get(CyNetwork.SELECTED,
Boolean.class) == true) {
+ if
(network.getDefaultNodeTable().getRow(node.getSUID()).get(CyNetwork.SELECTED,
Boolean.class) == true) {
selectedFound = true;
break;
}
@@ -595,9 +595,9 @@
// should be called again
if (params.getStatus() == false) {
AnnotationParser annParser =
params.initializeAnnotationParser();
- //TaskManager taskManager = adapter.getTaskManager();
- System.out.println("Calling annotation parser...");
- //taskManager.execute(new
GenericTaskFactory(annParser));
+// TaskManager taskManager = adapter.getTaskManager();
+ System.out.println("\nCalling annotation parser...");
+// taskManager.execute(new
GenericTaskFactory(annParser).createTaskIterator());
try {
annParser.calculate();
} catch (IOException e) {
@@ -643,12 +643,12 @@
final List<CyNode> nodes = network.getNodeList();
for (CyNode node: nodes) {
//if (node.getCyRow().get(CyNetwork.SELECTED,
Boolean.class) == false)
- if
(network.getDefaultNodeTable().getRow(node).get(CyNetwork.SELECTED,
Boolean.class) == false)
+ if
(network.getDefaultNodeTable().getRow(node.getSUID()).get(CyNetwork.SELECTED,
Boolean.class) == false)
continue;
// gets the canonical name of the given node from the
attributes object
//final String canonicalName =
node.getCyRow().get(CyNetwork.NAME, String.class);
- final String canonicalName =
network.getDefaultNodeTable().getRow(node).get(CyNetwork.NAME, String.class);
+ final String canonicalName =
network.getDefaultNodeTable().getRow(node.getSUID()).get(CyNetwork.NAME,
String.class);
// String canonicalName =
node.getIdentifier().toUpperCase();
if (canonicalName != null && canonicalName.length() !=
0 && !canonicalNameVector.contains(canonicalName)) {
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/ui/SettingsPanel.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/ui/SettingsPanel.java
2013-02-26 17:25:37 UTC (rev 31141)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/ui/SettingsPanel.java
2013-02-27 23:40:00 UTC (rev 31142)
@@ -228,6 +228,7 @@
String namespace_label = "Select namespace:";
String ec_label = "Discard the following evidence codes:";
+ private final CySwingAppAdapter adapter;
/**
* This constructor creates the panel with its swing-components.
@@ -235,6 +236,7 @@
public SettingsPanel(final String bingoDir, final CySwingAppAdapter
adapter) {
super();
this.bingoDir = bingoDir;
+ this.adapter= adapter;
// Create a new bingo parameter set
try {
@@ -419,7 +421,7 @@
// JTextField.
alphaField = new
JTextField(bingo_props.getProperty("signif_def"));
- nameField = new JTextField();
+ nameField = new JTextField("Test");
// OverUnderPanel
overUnderPanel = new OverUnderPanel();
@@ -468,7 +470,7 @@
// the bingo-button to start the calculations.
bingoButton = new JButton("Start bingo");
bingoButton.setMnemonic(KeyEvent.VK_B);
- //bingoButton.addActionListener(new
SettingsPanelActionListener(params, this, adapter));
+ bingoButton.addActionListener(new
SettingsPanelActionListener(params, this, adapter));
}
public TextOrGraphPanel getTextOrGraphPanel() {
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