From 49c9aa7503bfa484359c1486c816052d472e703a Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 6 Aug 2018 10:18:45 +0100
Subject: [PATCH] JAL-3070 additional interfaces for web services (not yet
 used!)

---
 src/jalview/ws/api/DistanceMatrixResultI.java |   16 ++++++++++++++++
 src/jalview/ws/api/MsaWithGuideTreeI.java     |   24 ++++++++++++++++++++++++
 src/jalview/ws/api/TreeResultI.java           |   14 ++++++++++++++
 3 files changed, 54 insertions(+)
 create mode 100644 src/jalview/ws/api/DistanceMatrixResultI.java
 create mode 100644 src/jalview/ws/api/MsaWithGuideTreeI.java
 create mode 100644 src/jalview/ws/api/TreeResultI.java

diff --git a/src/jalview/ws/api/DistanceMatrixResultI.java b/src/jalview/ws/api/DistanceMatrixResultI.java
new file mode 100644
index 0000000..a40d256
--- /dev/null
+++ b/src/jalview/ws/api/DistanceMatrixResultI.java
@@ -0,0 +1,16 @@
+package jalview.ws.api;
+
+import jalview.math.MatrixI;
+import jalview.ws.params.InvalidArgumentException;
+
+import java.io.IOError;
+import java.rmi.ServerError;
+
+public interface DistanceMatrixResultI
+{
+
+  public MatrixI getDistanceMatrixFor(JobId jobId)
+          throws InvalidArgumentException, ServerError, IOError;
+
+
+}
\ No newline at end of file
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;
+}
\ No newline at end of file
diff --git a/src/jalview/ws/api/TreeResultI.java b/src/jalview/ws/api/TreeResultI.java
new file mode 100644
index 0000000..1a0c3bd
--- /dev/null
+++ b/src/jalview/ws/api/TreeResultI.java
@@ -0,0 +1,14 @@
+package jalview.ws.api;
+
+import jalview.analysis.NJTree;
+import jalview.ws.params.InvalidArgumentException;
+
+import java.io.IOError;
+import java.rmi.ServerError;
+
+public interface TreeResultI
+{
+
+  public NJTree getTreeFor(JobId jobId)
+          throws InvalidArgumentException, ServerError, IOError;
+}
\ No newline at end of file
-- 
1.7.10.2