JAL-3070 additional interfaces for web services (not yet used!)

[jalview.git] / src / jalview / ws / api / MsaWithGuideTreeI.java

diff --git a/src/jalview/ws/api/MsaWithGuideTreeI.java b/src/jalview/ws/api/MsaWithGuideTreeI.java
new file mode 100644 (file)
index 0000000..6c2ff53
--- /dev/null
+++ b/src/jalview/ws/api/MsaWithGuideTreeI.java
@@ -0,0 +1,24 @@
+package jalview.ws.api;
+
+import jalview.analysis.NJTree;
+import jalview.datamodel.SequenceI;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.WsParamSetI;
+
+import java.io.IOError;
+import java.rmi.ServerError;
+import java.util.List;
+
+public interface MsaWithGuideTreeI
+{
+  /**
+   * Given a set of sequences
+   * 
+   * @param toalign
+   * @param parameters
+   * @return JobId or exceptions are thrown.
+   */
+  public JobId align(List<SequenceI> toalign, NJTree guideTree,
+          WsParamSetI parameters)
+          throws InvalidArgumentException, ServerError, IOError;
+}
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