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/* QualifierTextArea.java
*
* created: Tue Oct 23 2001
*
* 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.
*
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/QualifierTextArea.java,v 1.7 2007-09-18 09:36:52 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.editor.BrowserControl;
import uk.ac.sanger.artemis.editor.DataCollectionPane;
import uk.ac.sanger.artemis.io.QualifierParseException;
import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.EmblStreamFeature;
import uk.ac.sanger.artemis.util.StringVector;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.FontMetrics;
import java.awt.Point;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.IOException;
import java.io.StringReader;
import javax.swing.JTextPane;
import javax.swing.text.BadLocationException;
import javax.swing.text.Style;
import javax.swing.text.StyleConstants;
import javax.swing.text.StyledDocument;
* This component is a JTextPane that understands qualifiers.
* It provides hyperlinks to databases using a StyledDocument
* (rather than using HyperlinkListener) so it can remain editable.
public class QualifierTextArea extends JTextPane
{
private static String[] DATABASES =
{ "SWALL", "EMBL", "UniProt", "PMID", "PubMed", "InterPro" };
private static Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
private static Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
private static Cursor chand = new Cursor(Cursor.HAND_CURSOR);
private static Style DEFAULT_STYLE =
StyleContext.getDefaultStyleContext().getStyle(StyleContext.DEFAULT_STYLE);
public QualifierTextArea ()
{
super();
initStyles();
int nrows = (Options.getOptions ().getPropertyTruthValue ("alicat_mode") ||
18);
int ncolumns = 81;
setPreferredSize(new Dimension( ncolumns*getColumnWidth(), nrows*getRowHeight() ));
try // no such method in java1.3
{
setDragEnabled(true);
}
catch(java.lang.NoSuchMethodError err){}
addMouseListener(new MouseAdapter()
{
public void mouseClicked(MouseEvent e)
{
if(e.getClickCount() == 1)
handleMouseSingleClick(e);
public void append(final String s)
{
StyledDocument doc = super.getStyledDocument();
try
{
doc.insertString(doc.getLength(), s, getLogicalStyle());
for(int i=0; i<DATABASES.length; i++)
setStyleForHyperLinks(s, DATABASES[i]);
}
catch(BadLocationException e)
{
e.printStackTrace();
}
}
private void initStyles()
{
// Makes text Blue
Style style = addStyle("Blue", null);
StyleConstants.setForeground(style, Color.blue);
// Inherits from "Blue"; makes text red and underlined
style = addStyle("Blue Underline", style);
StyleConstants.setUnderline(style, true);
}
public void setText(String text)
{
super.setText(text);
// ensure we have the default style set
getStyledDocument().setCharacterAttributes(0, text.length(),
DEFAULT_STYLE, true);
for(int i=0; i<DATABASES.length; i++)
setStyleForHyperLinks(text, DATABASES[i]);
}
/**
* Parse and return the qualifiers in this TextArea in a QualifierVector.
**/
public QualifierVector
getParsedQualifiers (final EntryInformation entry_information)
throws QualifierParseException
{
final String qualifier_string = getText ();
return getQualifiersFromString (qualifier_string,
entry_information);
}
/**
* Return a QualifierVector containing the qualifiers from a String.
* @param qual_string contains the qualifiers to parse
*/
private static QualifierVector
getQualifiersFromString (final String qual_string,
final EntryInformation entry_information)
throws QualifierParseException
{
final StringReader string_reader = new StringReader (qual_string);
final QualifierVector embl_qualifiers =
EmblStreamFeature.readQualifiers (string_reader,
entry_information);
}
catch (IOException exception)
{
throw (new QualifierParseException (exception.getMessage ()));
}
}
private int getColumnWidth()
{
FontMetrics metrics = getFontMetrics(getFont());
return metrics.charWidth('m');
}
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private int getRowHeight()
{
FontMetrics metrics = getFontMetrics(getFont());
return metrics.getHeight();
}
/**
* This routine sets the hyerlink style for a given database
* @param s
* @param db
*/
private void setStyleForHyperLinks(final String s,
final String db)
{
int ind = 0;
while((ind = s.indexOf(db, ind)) > -1)
{
int ind2 = getEndOfLink(s,ind);
getStyledDocument().setCharacterAttributes(ind, ind2-ind,
getStyle("Blue Underline"), true);
ind = ind+1;
}
}
private int getEndOfLink(String s, int ind)
{
int ind2 = s.indexOf(" ",ind);
if(ind2 == -1)
ind2 = s.indexOf(";",ind);
int ind3 = s.indexOf(")",ind);
if(ind3>-1 && (ind3<ind2 || ind2 == -1))
ind2 = ind3;
ind3 = s.indexOf(";",ind);
if(ind3>-1 && (ind3<ind2 || ind2 == -1))
ind2 = ind3;
ind3 = s.indexOf("\"",ind);
if(ind3>-1 && (ind3<ind2 || ind2 == -1))
ind2 = ind3;
ind3 = s.indexOf("\n",ind);
if(ind3>-1 && (ind3<ind2 || ind2 == -1))
ind2 = ind3;
return ind2;
}
private int getStartOfLink(final String s)
{
int lastIndexLink = -1;
for(int i=0; i<DATABASES.length; i++)
{
int index = s.lastIndexOf(DATABASES[i]);
if(index > lastIndexLink)
lastIndexLink = index;
}
return lastIndexLink;
}
public static String getPubMedSite()
{
StringVector pubmed = Options.getOptions().getOptionValues("pubmed_url");
if(pubmed != null)
return (String)pubmed.elementAt(0);
return "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=";
}
public static String getInterProSite()
{
return "http://www.ebi.ac.uk/interpro/ISearch?query=";
}
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private void handleMouseSingleClick(final MouseEvent e)
{
final String hyperlinkText = getHyperlinkTextAtMouseEvent(e);
if(hyperlinkText == null)
return;
final String cmd;
if(hyperlinkText.indexOf("PMID") > -1 ||
hyperlinkText.indexOf("PubMed") > -1)
{
String id[] = hyperlinkText.split(":");
if(id.length < 2)
return;
cmd = getPubMedSite()+id[1];
}
else if(hyperlinkText.indexOf("InterPro") > -1)
{
String id[] = hyperlinkText.split(":");
if(id.length < 2)
return;
cmd = getInterProSite()+id[1];
}
else
{
String cmd2 = DataCollectionPane.getSrsSite()+"/wgetz?-e+["+hyperlinkText+"]";
int ind = cmd2.indexOf("UniProt:");
// link to uniprot accession
if(ind > -1)
cmd2 = cmd2.substring(0,ind+7)+"-acc:"+
cmd2.substring(ind+8);
if(cmd2.indexOf("ebi.ac.uk") > -1)
cmd2 = cmd2 + "+-vn+2";
cmd = cmd2;
}
SwingWorker browserLaunch = new SwingWorker()
{
public Object construct()
{
setCursor(cbusy);
BrowserControl.displayURL(cmd);
setCursor(cdone);
return null;
}
};
browserLaunch.start();
}
public void mouseDragged(MouseEvent e){}
public void mouseMoved(MouseEvent e)
{
String hyperlinkText = getHyperlinkTextAtMouseEvent(e);
if(hyperlinkText == null)
setCursor(cdone);
else
setCursor(chand);
}
/**
* Get hyperlink text from a MouseEvent position. Return null if
* no hyperlink found.
* @param e
* @return
*/
private String getHyperlinkTextAtMouseEvent(final MouseEvent e)
final Point pt = new Point(e.getX(), e.getY());
final int pos = viewToModel(pt);
final int start;
if(pos < 15)
start = 0;
else
start = pos - 15;
int length = 30;
if( (start+30) > getStyledDocument().getLength() )
length = getStyledDocument().getLength()-start;
try
{
String textAtPosition = getStyledDocument().getText(start, length);
int indEnd = getEndOfLink(textAtPosition, (pos-start));
textAtPosition = textAtPosition.substring(0, indEnd);
int indStart = getStartOfLink(textAtPosition);
if(indStart < 0)
return null;
return textAtPosition.substring(indStart);
}
catch(BadLocationException e1)
{