/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
+import jalview.appletgui.FeatureSettings;\r
\r
\r
/**\r
\r
//The currentAlignFrame is static, it will change\r
//if and when the user selects a new window\r
- static AlignFrame currentAlignFrame;\r
+ public static AlignFrame currentAlignFrame;\r
\r
//This is the first frame to be displayed, and does not change\r
AlignFrame initialAlignFrame;\r
\r
file = getParameter("file");\r
\r
+ if(file==null)\r
+ {\r
+ //Maybe the sequences are added as parameters\r
+ StringBuffer data = new StringBuffer("PASTE");\r
+ int i=1;\r
+ while( (file=getParameter("sequence"+i))!=null)\r
+ {\r
+ data.append(file.toString()+"\n");\r
+ i++;\r
+ }\r
+ if(data.length()>5)\r
+ file = data.toString();\r
+ }\r
+\r
final JalviewLite applet = this;\r
if(getParameter("embedded")!=null\r
&& getParameter("embedded").equalsIgnoreCase("true"))\r
{\r
public void windowClosing(WindowEvent e)\r
{\r
+ if(frame instanceof AlignFrame)\r
+ ((AlignFrame)frame).closeMenuItem_actionPerformed();\r
if(currentAlignFrame == frame)\r
{\r
currentAlignFrame = null;\r
JalviewLite _applet)\r
{\r
file = _file;\r
- if(inArchive(file))\r
+ if(file.startsWith("PASTE"))\r
+ {\r
+ file = file.substring(5);\r
+ protocol = AppletFormatAdapter.PASTE;\r
+ }\r
+ else if(inArchive(file))\r
protocol = AppletFormatAdapter.CLASSLOADER;\r
else\r
{\r
file,\r
embedded);\r
\r
+ if(protocol==jalview.io.AppletFormatAdapter.PASTE)\r
+ currentAlignFrame.setTitle("Sequences from "+getDocumentBase());\r
\r
initialAlignFrame = currentAlignFrame;\r
\r
currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
\r
\r
- String treeFile = applet.getParameter("treeFile");\r
+ String treeFile = applet.getParameter("tree");\r
+ if(treeFile==null)\r
+ treeFile = applet.getParameter("treeFile");\r
+\r
if (treeFile != null)\r
{\r
try\r
if( !inArchive(param) )\r
param = addProtocol( param );\r
\r
- currentAlignFrame.parseFeaturesFile(param);\r
+ currentAlignFrame.parseFeaturesFile(param, protocol);\r
+ }\r
+\r
+ param = getParameter("showFeatureSettings");\r
+ if(param !=null && param.equalsIgnoreCase("true"))\r
+ {\r
+ currentAlignFrame.viewport.showSequenceFeatures(true);\r
+ new FeatureSettings(currentAlignFrame.alignPanel);\r
}\r
\r
param = getParameter("annotations");\r
if( !inArchive(param) )\r
param = addProtocol( param );\r
\r
- new AnnotationReader().readAnnotationFile(\r
+ new AnnotationFile().readAnnotationFile(\r
currentAlignFrame.viewport.getAlignment(),\r
param);\r
\r