SequenceFetcher new class

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 77396c9..cfbd186 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -61,6 +61,7 @@ public class AlignFrame
   Stack redoList = new Stack();\r
   private int treeCount = 0;\r
 \r
+\r
   /**\r
    * Creates a new AlignFrame object.\r
    *\r
@@ -161,6 +162,16 @@ public class AlignFrame
 \r
   }\r
 \r
+\r
+  /*\r
+   Added so Castor Mapping file can obtain Jalview Version\r
+  */\r
+  public String getVersion()\r
+  {\r
+    return  jalview.bin.Cache.getProperty("VERSION");\r
+  }\r
+\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -249,6 +260,12 @@ public class AlignFrame
     }\r
   }\r
 \r
+  public void fetchSequence_actionPerformed(ActionEvent e)\r
+  {\r
+    new SequenceFetcher(this);\r
+  }\r
+\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -1872,7 +1889,7 @@ public class AlignFrame
   {\r
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
                                    HistoryItem.SORT));\r
-    AlignmentSorter.sortByID(viewport.getAlignment());\r
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);\r
     alignPanel.repaint();\r
   }\r
 \r
@@ -2372,7 +2389,7 @@ public class AlignFrame
             {\r
               SequenceI[] msa = gatherSequencesForAlignment();\r
               new jalview.ws.MsaWSClient(sh, title, msa,\r
-                  false, true);\r
+                  false, true, viewport.getAlignment().getDataset());\r
 \r
             }\r
 \r
@@ -2389,7 +2406,7 @@ public class AlignFrame
               {\r
                 SequenceI[] msa = gatherSequencesForAlignment();\r
                 new jalview.ws.MsaWSClient(sh, title, msa,\r
-                    true, true);\r
+                    true, true, viewport.getAlignment().getDataset());\r
 \r
               }\r
 \r
@@ -2464,8 +2481,8 @@ public class AlignFrame
     if (value == JalviewFileChooser.APPROVE_OPTION)\r
     {\r
       jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
-      vs.store(chooser.getSelectedFile().getAbsolutePath()\r
-          );\r
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );\r
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);\r
     }\r
   }\r
 \r