JAL-3807 JPred can now successfully submit and track the job.

[jalview.git] / src / jalview / ws / JPredClient.java

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
new file mode 100644 (file)
index 0000000..f431a0c
--- /dev/null
+++ b/src/jalview/ws/JPredClient.java
@@ -0,0 +1,67 @@
+package jalview.ws;
+
+import javax.swing.JMenuItem;
+
+import jalview.analysis.SeqsetUtils;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.ws.api.JPredMutlipleAlignmentServiceI;
+import jalview.ws.api.ServiceWithParameters;
+
+public class JPredClient extends WSClient
+{
+  JPredMutlipleAlignmentServiceI server;
+
+  public JPredClient(ServiceWithParameters sh, String title,
+      AlignmentView alView, AlignFrame alFrame, boolean viewOnly)
+  {
+    server = (JPredMutlipleAlignmentServiceI) sh.getEndpoint();
+    wsInfo = setWebService(sh, false);
+    startClient(title, alView, alFrame, viewOnly);
+  }
+
+  private void startClient(String title, AlignmentView view,
+      AlignFrame frame, boolean viewOnly)
+  {
+    var msf = view.getSequences();
+    var seq = msf[0].getSeq('-');
+    if (msf.length <= 1)
+      throw new RuntimeException("You need more than one sequence.");
+    var aln = new SequenceI[msf.length];
+    for (int i = 0; i < msf.length; i++)
+    {
+      aln[i] = msf[i].getSeq('-');
+    }
+    int[] delMap = viewOnly ?
+      view.getVisibleContigMapFor(seq.gapMap()) : null;
+    var sequenceInfo = SeqsetUtils.uniquify(aln, true);
+    var thread = new JPredThread(wsInfo, title, server, sequenceInfo, aln,
+        delMap, view, frame, WsURL);
+    wsInfo.setthisService(thread);
+    wsInfo.setVisible(true);
+    thread.start();
+  }
+
+  // sh parameter should be moved to the WSMenuEntryProvider interface
+  public static WSMenuEntryProviderI getMenuEntryProvider(ServiceWithParameters sh)
+  {
+    return (menu, frame) -> {
+      final JMenuItem mi = new JMenuItem(sh.getName());
+      mi.setToolTipText(sh.getHostURL());
+      mi.addActionListener((event) -> {
+        var view = frame.gatherSeqOrMsaForSecStrPrediction();
+        if (view.getSequences().length > 1)
+        {
+          new JPredClient(sh, frame.getTitle(), view, frame, true);
+        }
+        else
+        {
+          Cache.log.error("Single sequence not supported");
+        }
+      });
+      menu.add(mi);
+    };
+  }
+}