/*
*
* created: Wed Aug 3 2004
*
* This file is part of Artemis
*
* Copyright(C) 2000 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or(at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
package uk.ac.sanger.artemis.editor;
import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.border.*;
import javax.swing.event.*;
import javax.swing.text.html.*;
import javax.swing.text.Document;
import javax.swing.*;
import java.awt.*;
import java.awt.event.*;
import java.io.BufferedReader;
import java.io.StringReader;
import java.io.IOException;
import javax.swing.text.BadLocationException;
import java.net.URL;
public class Annotation extends JEditorPane
implements HyperlinkListener
{
/** */
private static final long serialVersionUID = 1L;
private int startRange;
//private int endRange;
/** busy cursor */
private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
/** done cursor */
private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
/** desktop pane */
private JDesktopPane desktop = null;
/** back option */
private Vector back = new Vector();
/** popup menu */
private JPopupMenu popup;
/** known qualifiers */
private Vector qualifier = new Vector();
public Annotation(JDesktopPane desktop)
{
super();
this.desktop = desktop;
setEditable(false);
setContentType("text/html");
setFont(BigPane.font);
addHyperlinkListener(this);
}
public Annotation(URL url) throws IOException
{
super(url);
setEditable(false);
addHyperlinkListener(this);
// popup
addMouseListener(new PopupListener());
popup = new JPopupMenu();
JMenuItem backMenu = new JMenuItem("Back");
popup.add(backMenu);
backMenu.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
goBack();
}
});
back.add(url);
}
protected void setAnnotation(String text)
{
// setText(""+text+"");
// reportHTML();
// startRange = getDocument().getLength();
String line = null;
// record qualifiers used
try
{
BufferedReader buffRead = new BufferedReader(new StringReader(text));
while((line = buffRead.readLine()) != null)
{
int ind = line.indexOf("=");
if(ind > -1)
qualifier.add(line.substring(0,ind+1).toLowerCase());
}
}
catch(IOException ioe){}
qualifier.add("/similarity=");
qualifier.add("/gene=");
qualifier.add("/GO_component=");
qualifier.add("/product=");
qualifier.add("/EC_number=");
qualifier.add("/note=");
text = getDatabaseHTML(text,"SWALL:");
text = getDatabaseHTML(text,"UniProt:");
text = getDatabaseHTML(text,"EMBL:");
setText(""+text+"");
startRange = getDocument().getLength();
}
protected void reportHTML()
{
try
{
String txt = ((HTMLDocument)getDocument()).getText(0,getDocument().getLength());
System.out.println("TXT:\n"+txt);
System.out.println("\nHTML:\n"+getText()+"\n\n");
}
catch(BadLocationException ble)
{
ble.printStackTrace();
}
}
protected String getFeatureText()
{
String txt = "";
try
{
txt = ((HTMLDocument)getDocument()).getText(0,getDocument().getLength()).trim();
StringBuffer buff = new StringBuffer();
StringTokenizer tok = new StringTokenizer(txt,"/");
int ntok = 0;
while(tok.hasMoreTokens())
{
String tokTxt = "/"+tok.nextToken().trim();
int ind = tokTxt.indexOf("=");
if(ntok != 0 && ind > -1 && qualifier.contains(tokTxt.substring(0,ind+1)))
buff.append("\n"+tokTxt);
else
buff.append(tokTxt);
ntok++;
}
txt = buff.toString();
}
catch(BadLocationException ble)
{
ble.printStackTrace();
}
return txt;
}
protected void insert(String s, boolean ortholog)
{
s = getDatabaseHTML(s,"SWALL:");
s = getDatabaseHTML(s,"UniProt:");
s = getDatabaseHTML(s,"EMBL:");
s = getGeneDBHTML(s);
// int ind = s.indexOf("/gene");
Document doc = getDocument();
int offset = doc.getLength();
if(ortholog)
offset = startRange;
insert(s,offset);
setCaretPosition(doc.getLength());
// reportHTML();
}
protected void insert(String s, int offset)
{
try
{
HTMLEditorKit edKit = (HTMLEditorKit)getEditorKit();
// ((HTMLDocument)getDocument()).insertString(offset,"\n",null);
edKit.insertHTML((HTMLDocument)getDocument(),offset,"
\n"+s,0,0,HTML.Tag.BR);
// HTMLEditorKit.InsertHTMLTextAction("similarity",s,HTML.Tag.BODY,HTML.Tag.P);
}
catch(BadLocationException ble)
{
System.out.println("Offset "+offset);
ble.printStackTrace();
}
catch(Exception exp)
{
exp.printStackTrace();
}
}
private String getGeneDBHTML(String s)
{
int ind = s.indexOf("GeneDB");
if(ind>-1)
{
String startStr = s.substring(0,ind);
int ind2 = s.indexOf(";",ind);
String midStr = s.substring(ind,ind2);
String endStr = s.substring(ind2);
ind2 = midStr.indexOf(":")+1;
String db = midStr.substring(7,8)+".+"+
midStr.substring(8,ind2-1);
String genedb = "http://www.genedb.org/genedb/Search?name="+
midStr.substring(ind2)+
"&organism="+db;
s = startStr + "" +
midStr + "" + endStr;
}
return s;
}
private String getDatabaseHTML(String s, String db)
{
// int ind = s.indexOf(db);
// if(ind == -1)
// ind = s.indexOf(db.toLowerCase());
// if(ind>-1)
// {
// s = setHyperLinks(s,ind);
// String startStr = s.substring(0,ind);
// int ind2 = s.indexOf(" ",ind);
// int ind3 = s.indexOf(")",ind);
// if(ind3>-1 && ind3-1 && ind3" +
// midStr + "" + endStr;
// }
int ind = 0;
while((ind = s.indexOf(db, ind)) > -1)
{
s = setHyperLinks(s,ind);
ind = s.lastIndexOf("");
}
db = db.toLowerCase();
ind = 0;
while((ind = s.indexOf(db+":", ind)) > -1)
{
s = setHyperLinks(s,ind);
ind = s.lastIndexOf("");
}
return s;
}
private String setHyperLinks(String s, int ind)
{
String startStr = s.substring(0,ind);
int ind2 = s.indexOf(" ",ind);
if(ind2 == -1)
ind2 = s.indexOf(";",ind);
int ind3 = s.indexOf(")",ind);
if(ind3>-1 && ind3-1 && ind3-1 && ind3 -1)
srscmd = srscmd.substring(0,ind2+7)+"-acc:"+
srscmd.substring(ind2+8);
if(srscmd.indexOf("ebi.ac.uk") > -1)
srscmd = srscmd + "+-vn+2";
return startStr + "" +
midStr + "" + endStr;
}
/*private void replaceRange(String newStr,int start,int end)
{
HTMLDocument doc = (HTMLDocument)getDocument();
try
{
doc.remove(start,(end-start));
insert(newStr,start);
}
catch(BadLocationException ble)
{
ble.printStackTrace();
}
setDocument(doc);
}*/
/**
*
* Deletes the annotation line that contains an ID.
*
*/
protected void deleteGo(String id, String go_id)
{
String txt = getText();
int ind1 = 0;
int ind2 = 0;
int indID = 0;
while((ind2 = txt.indexOf("
",ind1)) > -1 ||
(ind2 = txt.indexOf("",ind1)) > -1)
{
String line = txt.substring(ind1,ind2);
if( ((indID = line.indexOf(id)) > -1) &&
(line.indexOf(go_id) > -1) )
break;
else
ind1 = ind2+1;
}
// ind2 = txt.indexOf("