Return accurate RGB for transparent residues

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

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index ed89001..6627e88 100755 (executable)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -29,9 +29,11 @@ import jalview.jbappletgui.*;
 public class CutAndPasteTransfer\r
     extends GCutAndPasteTransfer\r
 {\r
-  public CutAndPasteTransfer(boolean forImport)\r
+  jalview.bin.JalviewLite applet;\r
+  public CutAndPasteTransfer(boolean forImport, jalview.bin.JalviewLite mainApplet)\r
   {\r
     super();\r
+    applet = mainApplet;\r
 \r
     if (!forImport)\r
     {\r
@@ -52,17 +54,32 @@ public class CutAndPasteTransfer
   protected void ok_actionPerformed(ActionEvent e)\r
   {\r
     String text = getText();\r
+    int length = text.length();\r
+    textarea.append("\n");\r
+    if(textarea.getText().length()==length)\r
+    {\r
+      String warning = "\n\n#################################################\n"\r
+          +"WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"\r
+          +"\nCAN'T INPUT FULL ALIGNMENT"\r
+          +"\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"\r
+          +"\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"\r
+          +"\n#################################################\n";\r
+      textarea.setText(text.substring(0, text.length()-warning.length())\r
+          +warning);\r
+\r
+      textarea.setCaretPosition(text.length());\r
+      return;\r
+    }\r
+\r
     SequenceI[] sequences = null;\r
 \r
     String format = IdentifyFile.Identify(text, "Paste");\r
-    sequences = FormatAdapter.readFile(text, "Paste", format);\r
+    sequences = new AppletFormatAdapter().readFile(text, "Paste", format);\r
 \r
     if (sequences != null)\r
     {\r
-      AlignFrame af = new AlignFrame(new Alignment(sequences));\r
-      jalview.bin.JalviewLite.addFrame(af, "Cut & Paste input - " + format,\r
-                                       AlignFrame.NEW_WINDOW_WIDTH,\r
-                                       AlignFrame.NEW_WINDOW_HEIGHT);\r
+      AlignFrame af = new AlignFrame(new Alignment(sequences), applet,\r
+                                     "Cut & Paste input - " + format);\r
       af.statusBar.setText("Successfully pasted alignment file");\r
     }\r
 \r