moved visible sub-alignment extraction and update from MsaWSThread to

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

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 2ec8e1e..d7e75f4 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -27,24 +27,54 @@ import jalview.analysis.*;
 import jalview.bin.*;\r
 import jalview.datamodel.*;\r
 import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentView;\r
 import jalview.gui.*;\r
 import jalview.io.*;\r
+import jalview.util.*;\r
 import jalview.ws.WSThread.*;\r
 import vamsas.objects.simple.*;\r
-import jalview.util.Comparison;\r
 \r
 public class JPredClient\r
     extends WSClient\r
 {\r
-  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq)\r
+  AlignFrame parentFrame=null;\r
+    /**\r
+     * crate a new GUI JPred Job\r
+     * @param sh ServiceHandle\r
+     * @param title String\r
+     * @param msa boolean - true - submit alignment as a sequence profile\r
+     * @param alview AlignmentView\r
+     */\r
+    public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) {\r
+    wsInfo=setWebService(sh);\r
+    this.parentFrame=parentFrame;\r
+    startJPredClient(title, msa, alview);\r
+\r
+  }\r
+\r
+  /**\r
+   * startJPredClient\r
+   *\r
+   * @param title String\r
+   * @param msa boolean\r
+   * @param alview AlignmentView\r
+   */\r
+  private void startJPredClient(String title, boolean msa,\r
+                                jalview.datamodel.AlignmentView alview)\r
+  {\r
+  }\r
+\r
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame)\r
   {\r
     wsInfo = setWebService(sh);\r
+    this.parentFrame=parentFrame;\r
     startJPredClient(title, seq);\r
   }\r
 \r
-  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa)\r
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame)\r
   {\r
     wsInfo = setWebService(sh);\r
+    this.parentFrame=parentFrame;\r
     startJPredClient(title, msa);\r
   }\r
 \r
@@ -633,7 +663,6 @@ public class JPredClient
         }\r
       }\r
     }\r
-\r
     void pollJob(WSJob job)\r
         throws Exception\r
     {\r
@@ -649,6 +678,11 @@ public class JPredClient
       throw new Error("Implementation error!");\r
     }\r
 \r
+    public boolean canMergeResults()\r
+    {\r
+      return false;\r
+    }\r
+\r
   }\r
 }\r
 \r