X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fapi%2FMsaWithGuideTreeI.java;fp=src%2Fjalview%2Fws%2Fapi%2FMsaWithGuideTreeI.java;h=6c2ff53f62f7679b8c96ad36a124d606b5f60768;hb=49c9aa7503bfa484359c1486c816052d472e703a;hp=0000000000000000000000000000000000000000;hpb=16a0550dea32fbc1c4ebaee88cb9ebd4d6e190b1;p=jalview.git

diff --git a/src/jalview/ws/api/MsaWithGuideTreeI.java b/src/jalview/ws/api/MsaWithGuideTreeI.java
new file mode 100644
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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