Correct title for sequence parameter applets

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 5d48ea3..5c9c941 100755 (executable)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -40,7 +40,7 @@ import javax.swing.*;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer\r
 {\r
 \r
-  AlignmentI addToThisAlignment;\r
+  AlignViewport viewport;\r
 \r
   public CutAndPasteTransfer()\r
   {\r
@@ -57,9 +57,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     /**\r
      * DOCUMENT ME!\r
      */\r
-    public void setForInput(AlignmentI alignment)\r
+    public void setForInput(AlignViewport viewport)\r
     {\r
-      addToThisAlignment = alignment;\r
+      this.viewport = viewport;\r
       getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);\r
     }\r
 \r
@@ -88,6 +88,40 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       textarea.append(text);\r
     }\r
 \r
+\r
+    public void save_actionPerformed(ActionEvent e)\r
+    {\r
+      JalviewFileChooser chooser = new JalviewFileChooser(\r
+          jalview.bin.Cache.getProperty(\r
+              "LAST_DIRECTORY"));\r
+\r
+      chooser.setAcceptAllFileFilterUsed(false);\r
+      chooser.setFileView(new JalviewFileView());\r
+      chooser.setDialogTitle("Save Text to File");\r
+      chooser.setToolTipText("Save");\r
+\r
+      int value = chooser.showSaveDialog(this);\r
+\r
+      if (value == JalviewFileChooser.APPROVE_OPTION)\r
+      {\r
+        try\r
+        {\r
+          java.io.PrintWriter out = new java.io.PrintWriter(\r
+              new java.io.FileWriter(chooser.getSelectedFile()));\r
+\r
+          out.print(getText());\r
+          out.close();\r
+        }\r
+        catch (Exception ex)\r
+        {\r
+          ex.printStackTrace();\r
+        }\r
+\r
+      }\r
+    }\r
+\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -135,7 +169,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         String format = new IdentifyFile().Identify(getText(), "Paste");\r
         SequenceI[] sequences = null;\r
 \r
-        if (FormatAdapter.formats.contains(format))\r
+        if (FormatAdapter.isValidFormat(format))\r
         {\r
           try{\r
             sequences = new FormatAdapter().readFile(getText(), "Paste", format);\r
@@ -150,10 +184,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 \r
         if (sequences != null)\r
         {\r
-          if(addToThisAlignment!=null)\r
+          if(viewport!=null)\r
           {\r
             for(int i=0; i<sequences.length; i++)\r
-              addToThisAlignment.addSequence(sequences[i]);\r
+              viewport.getAlignment().addSequence(sequences[i]);\r
+\r
+            viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
           }\r
           else\r
           {\r
@@ -171,15 +207,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
             catch (Exception ex)\r
             {\r
             }\r
-\r
           }\r
-            try\r
-            {\r
-                this.setClosed(true);\r
-            }\r
-            catch (Exception ex)\r
-            {\r
-            }\r
         }\r
     }\r
 \r