Invoked the new KAlign WS at EBI. Solves #3231

* New WS stub generated * Invocation now in Job
bioclipse · Sep 11, 2012 · 9aab7f2 · 9aab7f2
1 parent d36ec3e
commit 9aab7f2
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Showing 20 changed files with 2,377 additions and 1,313 deletions.
diff --git a/....bioclipse.align.kalign.ws/src/net/bioclipse/align/kalign/ws/business/IKalignManager.java b/....bioclipse.align.kalign.ws/src/net/bioclipse/align/kalign/ws/business/IKalignManager.java
@@ -12,6 +12,8 @@
 
 import java.util.List;
 
+import org.eclipse.core.runtime.IProgressMonitor;
+
 import net.bioclipse.core.PublishedClass;
 import net.bioclipse.core.PublishedMethod;
 import net.bioclipse.core.Recorded;
@@ -43,6 +45,7 @@ public interface IKalignManager extends IBioclipseManager {
                      methodSummary="Align a list of DNA sequences using the " +
                              "KAlign Web service at EBI.")
     public List<IDNA> alignDNA(List<IDNA> dnaList) throws BioclipseException;
+    public List<IDNA> alignDNA(List<IDNA> dnaList, IProgressMonitor monitor) throws BioclipseException;
 
 
     /**
@@ -60,6 +63,7 @@ public interface IKalignManager extends IBioclipseManager {
                      methodSummary="Align a list of protein sequences using " +
                              "the KAlign Web service at EBI.")
     public List<IProtein> alignProteins(List<IProtein> proteinList) throws BioclipseException;
+    public List<IProtein> alignProteins(List<IProtein> proteinList, IProgressMonitor monitor) throws BioclipseException;
 
 
 }