set gap char modified

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b217e9c..1b9ee91 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1188,6 +1188,39 @@ public class AlignFrame extends GAlignFrame
 \r
     }\r
   }\r
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    // TODO:resolve which menu item was actually selected\r
+    // Now, check we have enough sequences\r
+      if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)\r
+      {\r
+        // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+        SequenceGroup seqs = viewport.getSelectionGroup();\r
+        int sz;\r
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
+        for (int i = 0; i < sz; i++)\r
+        {\r
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+        }\r
+\r
+        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);\r
+      }\r
+      else\r
+      {\r
+        Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+        if (seqs.size() > 1) {\r
+          SequenceI[] msa = new SequenceI[seqs.size()];\r
+          for (int i = 0; i < seqs.size(); i++)\r
+          {\r
+            msa[i] = (SequenceI) seqs.elementAt(i);\r
+          }\r
+\r
+          MsaWSClient ct = new MsaWSClient(msa);\r
+        }\r
+\r
+      }\r
+    }\r
 \r
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
     // Pick the tree file\r