+ else if (annotationImport)\r
+ {\r
+ if (new AnnotationFile().readAnnotationFile(\r
+ alignFrame.viewport.alignment, textarea.getText(),\r
+ jalview.io.AppletFormatAdapter.PASTE))\r
+ {\r
+ alignFrame.alignPanel.fontChanged();\r
+ alignFrame.alignPanel.setScrollValues(0, 0);\r
+\r
+ }\r
+ else\r
+ {\r
+ alignFrame.parseFeaturesFile(textarea.getText(),\r
+ jalview.io.AppletFormatAdapter.PASTE);\r
+ }\r
+ }\r
+ else if (alignFrame != null)\r
+ {\r
+ Alignment al = null;\r
+\r
+ String format = new IdentifyFile().Identify(text,\r
+ AppletFormatAdapter.PASTE);\r
+ try\r
+ {\r
+ al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE,\r
+ format);\r
+ }\r
+ catch (java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if (al != null)\r
+ {\r
+ if (newWindow)\r
+ {\r
+ AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,\r
+ "Cut & Paste input - " + format,\r
+ false);\r
+ af.statusBar.setText("Successfully pasted alignment file");\r
+ }\r
+ else\r
+ {\r
+ alignFrame.addSequences(al.getSequencesArray());\r
+ }\r
+ }\r
+ }\r
+\r
+ if (this.getParent() instanceof Frame)\r
+ {\r
+ ( (Frame)this.getParent()).setVisible(false);\r
+ }\r
+ else\r
+ {\r
+ ( (Dialog)this.getParent()).setVisible(false);\r
+ }\r
+ }\r
+\r
+ protected void cancel()\r
+ {\r
+ textarea.setText("");\r
+ if (this.getParent() instanceof Frame)\r
+ {\r
+ ( (Frame)this.getParent()).setVisible(false);\r
+ }\r
+ else\r
+ {\r
+ ( (Dialog)this.getParent()).setVisible(false);\r
+ }\r
+ }\r
+\r
+ protected TextArea textarea = new TextArea();\r
+ Button accept = new Button("New Window");\r
+ Button addSequences = new Button("Add to Current Alignment");\r
+ Button cancel = new Button("Close");\r