Author: mes
Date: 2012-03-08 16:16:04 -0800 (Thu, 08 Mar 2012)
New Revision: 28460
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java
Log:
added adj conversion and support for gxp
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2012-03-08 22:58:38 UTC (rev 28459)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2012-03-09 00:16:04 UTC (rev 28460)
@@ -18,6 +18,7 @@
import org.genomespace.client.ui.GSLoginDialog;
import org.genomespace.datamanager.core.GSFileMetadata;
+import org.genomespace.datamanager.core.GSDataFormat;
final class GSUtils {
@@ -96,5 +97,16 @@
return nm;
}
+
+ public static GSDataFormat
findConversionFormat(Collection<GSDataFormat> availableFormats, String
targetExt) {
+ if ( targetExt == null || targetExt.equals("") ||
availableFormats == null )
+ return null;
+
+ for ( GSDataFormat format : availableFormats )
+ if ( targetExt.equalsIgnoreCase(
format.getFileExtension() ) )
+ return format;
+
+ return null;
+ }
}
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromGenomeSpace.java
2012-03-08 22:58:38 UTC (rev 28459)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromGenomeSpace.java
2012-03-09 00:16:04 UTC (rev 28460)
@@ -22,6 +22,7 @@
import org.genomespace.client.GsSession;
import org.genomespace.client.User;
import org.genomespace.datamanager.core.GSFileMetadata;
+import org.genomespace.datamanager.core.GSDataFormat;
public class LoadNetworkFromGenomeSpace extends CytoscapeAction {
@@ -49,6 +50,8 @@
acceptableExtensions.add("sif");
acceptableExtensions.add("xgmml");
acceptableExtensions.add("gml");
+ acceptableExtensions.add("adj");
+ acceptableExtensions.add("gxp");
final GSFileBrowserDialog dialog =
new GSFileBrowserDialog(Cytoscape.getDesktop(),
dataManagerClient,
acceptableExtensions,
@@ -56,10 +59,14 @@
final GSFileMetadata fileMetadata =
dialog.getSelectedFileMetadata();
if (fileMetadata == null)
return;
+
+ GSDataFormat dataFormat = fileMetadata.getDataFormat();
+ if (
fileMetadata.getDataFormat().getFileExtension().equalsIgnoreCase("adj") )
+ dataFormat =
GSUtils.findConversionFormat(fileMetadata.getAvailableDataFormats(), "xgmml");
// Download the GenomeSpace file:
tempFile = File.createTempFile("temp", "cynetwork");
- dataManagerClient.downloadFile(fileMetadata, tempFile,
true);
+ dataManagerClient.downloadFile(fileMetadata,
dataFormat, tempFile, true);
// Select the type of network reader:
final String origFileName = fileMetadata.getName();
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java
2012-03-08 22:58:38 UTC (rev 28459)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java
2012-03-09 00:16:04 UTC (rev 28460)
@@ -22,6 +22,7 @@
import org.genomespace.client.User;
import org.genomespace.client.ui.GSFileBrowserDialog;
import org.genomespace.datamanager.core.GSFileMetadata;
+import org.genomespace.datamanager.core.GSDataFormat;
public class LoadTableAttrsFromGenomeSpace extends CytoscapeAction {
@@ -54,9 +55,14 @@
if (fileMetadata == null)
return;
+ GSDataFormat dataFormat = fileMetadata.getDataFormat();
+ if (
fileMetadata.getDataFormat().getFileExtension().equalsIgnoreCase("gct") ||
+
fileMetadata.getDataFormat().getFileExtension().equalsIgnoreCase("odf") )
+ dataFormat =
GSUtils.findConversionFormat(fileMetadata.getAvailableDataFormats(), "attr");
+
// Download the GenomeSpace file:
tempFile = File.createTempFile("temp",
fileMetadata.getName());
- dataManagerClient.downloadFile(fileMetadata, tempFile,
true);
+ dataManagerClient.downloadFile(fileMetadata,
dataFormat, tempFile, true);
final ImportTextTableDialog dialog =
new
ImportTextTableDialog(Cytoscape.getDesktop(), tempFile,
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