diff --git a/uk/ac/sanger/artemis/editor/Annotation.java b/uk/ac/sanger/artemis/editor/Annotation.java
new file mode 100644
index 0000000000000000000000000000000000000000..6d7978d25583ac59b5c536dd10ab79cacf1fcf23
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/Annotation.java
@@ -0,0 +1,328 @@
+/*
+ *
+ * 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 javax.swing.event.*;
+import javax.swing.text.html.*;
+import javax.swing.text.DefaultStyledDocument;
+import javax.swing.text.StyledDocument;
+import javax.swing.text.Document;
+import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Cursor;
+import java.awt.Dimension;
+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 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;
+
+ public Annotation(JDesktopPane desktop)
+ {
+ super();
+
+ this.desktop = desktop;
+ setEditable(false);
+ setContentType("text/html");
+ Font font = new Font("Monospaced",Font.PLAIN,12);
+ setFont(font);
+ addHyperlinkListener(this);
+ }
+
+
+ public Annotation(URL url) throws IOException
+ {
+ super(url);
+
+ setEditable(false);
+ addHyperlinkListener(this);
+ }
+
+
+ protected void setAnnotation(String text)
+ {
+ setText("<html><body>"+text+"</html></body>");
+ reportHTML();
+ 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 void insert(String s, boolean ortholog)
+ {
+ s = getDatabaseHTML(s,"SWALL:");
+ s = getDatabaseHTML(s,"UNIPROT:");
+ s = getDatabaseHTML(s,"EMBL:");
+
+ int ind = s.indexOf("/gene");
+
+ Document doc = getDocument();
+ int offset = doc.getLength();
+ if(ortholog)
+ offset = startRange;
+
+ insert(s,offset);
+ reportHTML();
+ }
+
+
+ protected void insert(String s, int offset)
+ {
+ try
+ {
+ HTMLEditorKit edKit = (HTMLEditorKit)getEditorKit();
+// ((HTMLDocument)getDocument()).insertString(offset,"\n",null);
+ edKit.insertHTML((HTMLDocument)getDocument(),offset,"<BR>\n"+s,0,0,HTML.Tag.BR);
+// HTMLEditorKit.InsertHTMLTextAction("similarity",s,HTML.Tag.BODY,HTML.Tag.P);
+ }
+ catch(BadLocationException ble)
+ {
+ ble.printStackTrace();
+ }
+ catch(Exception exp)
+ {
+ exp.printStackTrace();
+ }
+ }
+
+
+ private String getDatabaseHTML(String s, String db)
+ {
+ int ind = s.indexOf(db);
+ if(ind>-1)
+ {
+ String startStr = s.substring(0,ind);
+ int ind2 = s.indexOf(" ",ind);
+ int ind3 = s.indexOf(")",ind);
+ if(ind3>-1 && ind3<ind2)
+ ind2 = ind3;
+ ind3 = s.indexOf(";",ind);
+ if(ind3>-1 && ind3<ind2)
+ ind2 = ind3;
+
+ String midStr = s.substring(ind,ind2);
+ String endStr = s.substring(ind2);
+
+ String srscmd = "http://srs.sanger.ac.uk/srsbin/cgi-bin/wgetz?-e+" +
+ "["+midStr+"]";
+
+ s = startStr + "<a href=\""+srscmd+"\">" +
+ midStr + "</a>" + endStr;
+ }
+ return s;
+ }
+
+ 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 delete(String id, boolean ortholog)
+ {
+// try
+// {
+// reportHTML();
+
+// String txt = ((HTMLDocument)getDocument()).getText(0,getDocument().getLength());
+// String line = null;
+// int eol = 0;
+// int len = 0;
+// BufferedReader buffRead = new BufferedReader(new StringReader(txt));
+// while((line = buffRead.readLine()) != null)
+// {
+// len = line.length()+1;
+// if(line.indexOf("SWALL:"+id) > -1)
+// {
+// len += eol;
+//
+// if(ortholog)
+// {
+// line = buffRead.readLine();
+// if(line != null && line.startsWith("/gene="))
+// len += line.length();
+// }
+
+// if(len > txt.length())
+// len = txt.length();
+
+// replaceRange("",eol-1,len);
+// reportHTML();
+// return;
+// }
+// eol += len;
+// }
+ String txt = getText();
+ int indID = txt.indexOf("SWALL:"+id);
+ if(indID == -1)
+ indID = txt.indexOf("UNIPROT:"+id);
+
+ int ind1 = 0;
+ int ind2 = 0;
+
+ while((ind2 = txt.indexOf("<br>",ind1)) > -1)
+ {
+ if(ind2 < indID)
+ ind1 = ind2+1;
+ else
+ break;
+ }
+
+ ind2 = txt.indexOf("<br>",indID);
+
+ // if ortholog then delete gene line as well
+ if(ortholog)
+ ind2 = txt.indexOf("<br>",ind2+4);
+
+ if(ind2 == -1)
+ ind2 = txt.length();
+
+ setText(txt.substring(0,ind1-1)+txt.substring(ind2));
+// }
+// catch(BadLocationException ble) { ble.printStackTrace(); }
+// catch(IOException ioe) { ioe.printStackTrace(); }
+
+ }
+
+
+ /**
+ *
+ * Method to handle hyper link events.
+ * @param event hyper link event
+ *
+ */
+ public void hyperlinkUpdate(HyperlinkEvent event)
+ {
+ if (event.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
+ {
+ setCursor(cbusy);
+ try
+ {
+ URL url = event.getURL();
+
+ int ind1 = event.getDescription().indexOf("[");
+ int ind2 = event.getDescription().lastIndexOf("]");
+
+ String search = "";
+ if(ind1 > -1 && ind2 > -1)
+ search = event.getDescription().substring(ind1+1,ind2);
+
+ if(desktop != null)
+ {
+ if(BigPane.srsTabPane.isSelected())
+ {
+ if(BigPane.srsFrame == null)
+ BigPane.setUpSRSFrame((2*desktop.getHeight())/3,desktop);
+ Annotation edPane = new Annotation(url);
+ JScrollPane jsp = new JScrollPane(edPane);
+ JTabbedPane jtab = (JTabbedPane)BigPane.srsFrame.getContentPane().getComponent(0);
+ jtab.insertTab(search, null,jsp,null,0);
+ BigPane.srsFrame.setVisible(true);
+ }
+
+ if(BigPane.srsWin.isSelected())
+ {
+ int hgt = (2*desktop.getHeight())/3;
+ Annotation edPane = new Annotation(url);
+ JScrollPane jsp = new JScrollPane(edPane);
+ JInternalFrame jif = new JInternalFrame("SRS "+search,
+ true, //resizable
+ true, //closable
+ true, //maximizable
+ true);//iconifiable);
+ JMenuBar menuBar = new JMenuBar();
+ menuBar.add(new CommonMenu(jif));
+ jif.setJMenuBar(menuBar);
+ jif.getContentPane().add(jsp);
+ jif.setLocation(0,0);
+ jif.setSize(800,hgt);
+ jif.setVisible(true);
+ desktop.add(jif);
+ }
+
+ if(BigPane.srsBrowser.isSelected())
+ BrowserControl.displayURL(event.getDescription());
+ }
+ else
+ {
+ setPage(url);
+ }
+ }
+ catch(IOException ioe)
+ {
+ setCursor(cdone);
+ ioe.printStackTrace();
+// ("Can't follow link to " +
+// event.getURL().toExternalForm() );
+ }
+
+ setCursor(cdone);
+ }
+ }
+
+
+}
+
diff --git a/uk/ac/sanger/artemis/editor/BigPane.java b/uk/ac/sanger/artemis/editor/BigPane.java
new file mode 100644
index 0000000000000000000000000000000000000000..4928ae8949ae8dc56238920c2bfabbea82c5a6c0
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/BigPane.java
@@ -0,0 +1,199 @@
+/*
+ *
+ * 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.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.Dimension;
+import java.awt.Toolkit;
+import java.awt.Font;
+import java.util.Vector;
+
+import javax.swing.*;
+
+public class BigPane extends JFrame
+{
+
+ Font font = new Font("Monospaced",Font.PLAIN,12);
+ protected static JCheckBoxMenuItem srsBrowser;
+ protected static JCheckBoxMenuItem srsTabPane;
+ protected static JCheckBoxMenuItem srsWin;
+ protected static JInternalFrame srsFrame;
+
+ public BigPane(String dataFile[])
+ {
+ super();
+
+ setFont(font);
+ JDesktopPane desktop = new JDesktopPane();
+ desktop.setDragMode(JDesktopPane.LIVE_DRAG_MODE);
+ getContentPane().add(desktop);
+
+ //Make the big window be indented 100 pixels from each edge
+ //of the screen.
+ int inset = 100;
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ setBounds(inset, inset,
+ screenSize.width - inset*2,
+ screenSize.height - inset*2);
+
+ addWindowListener(new winExit());
+
+ JMenuBar menuBar = createMenuBar(desktop);
+ setJMenuBar(menuBar);
+
+ // data set
+ int hgt = getHeight()-60;
+ int wid = (getWidth()/2)-400;
+ DataViewInternalFrame dataView = new DataViewInternalFrame(dataFile,desktop);
+ dataView.setLocation(wid,0);
+ dataView.setSize(800,hgt);
+ dataView.setVisible(true);
+ desktop.add(dataView);
+
+ setVisible(true);
+ }
+
+ private JMenuBar createMenuBar(final JDesktopPane desktop)
+ {
+ JMenuBar menuBar = new JMenuBar();
+ JMenu fileMenu = new JMenu("File");
+ menuBar.add(fileMenu);
+
+ JMenuItem exitMenu = new JMenuItem("Exit");
+ exitMenu.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ System.exit(0);
+ }
+ });
+
+ fileMenu.add(exitMenu);
+
+ //srs menu items
+ JMenu optionMenu = new JMenu("Options");
+ menuBar.add(optionMenu);
+
+ JMenu srsMenu = new JMenu("Show SRS in");
+ optionMenu.add(srsMenu);
+
+ srsBrowser = new JCheckBoxMenuItem("External Broser",false);
+ srsTabPane = new JCheckBoxMenuItem("Tabbed Pane",true);
+ srsWin = new JCheckBoxMenuItem("New Window",false);
+
+ srsMenu.add(srsBrowser);
+ srsMenu.add(srsTabPane);
+ srsMenu.add(srsWin);
+
+ //drag mode
+ JMenu dragMenu = new JMenu("Drag Mode");
+ optionMenu.add(dragMenu);
+
+ JRadioButtonMenuItem liveDrag = new JRadioButtonMenuItem("Live",true);
+ liveDrag.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ desktop.setDragMode(JDesktopPane.LIVE_DRAG_MODE);
+ }
+ });
+
+ dragMenu.add(liveDrag);
+
+ JRadioButtonMenuItem outlineDrag = new JRadioButtonMenuItem("Outline",false);
+ outlineDrag.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+ }
+ });
+ dragMenu.add(outlineDrag);
+ ButtonGroup buttGroup = new ButtonGroup();
+ buttGroup.add(liveDrag);
+ buttGroup.add(outlineDrag);
+
+
+ return menuBar;
+ }
+
+
+ protected static void setUpSRSFrame(int hgt, JDesktopPane desktop)
+ {
+ BigPane.srsFrame = new JInternalFrame("SRS",
+ true, //resizable
+ true, //closable
+ true, //maximizable
+ true);//iconifiable
+ BigPane.srsFrame.setLocation(0,0);
+ BigPane.srsFrame.setSize(500,hgt);
+ final JTabbedPane jtab = new JTabbedPane();
+ BigPane.srsFrame.getContentPane().add(jtab);
+
+ JMenuBar menuBar = new JMenuBar();
+ CommonMenu cmen = new CommonMenu(BigPane.srsFrame);
+ menuBar.add(cmen);
+ JMenuItem closeTabMenu = new JMenuItem("Close tab");
+ cmen.add(closeTabMenu);
+ closeTabMenu.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ int select = jtab.getSelectedIndex();
+ jtab.removeTabAt(select);
+ }
+ });
+
+ BigPane.srsFrame.setJMenuBar(menuBar);
+ desktop.add(BigPane.srsFrame);
+ }
+
+ /**
+ *
+ * Extends WindowAdapter to close window.
+ *
+ */
+ class winExit extends WindowAdapter
+ {
+ public void windowClosing(WindowEvent we)
+ {
+ System.exit(0);
+ }
+ }
+
+
+ public static void main(String args[])
+ {
+ if(args.length < 1)
+ {
+ System.out.println("Usage:: java BigPane data_file");
+ System.exit(0);
+ }
+ new BigPane(args);
+ }
+}
diff --git a/uk/ac/sanger/artemis/editor/BrowserControl.java b/uk/ac/sanger/artemis/editor/BrowserControl.java
new file mode 100644
index 0000000000000000000000000000000000000000..7bdaf78a816e1fb5481676dfdd37aae3c82e5fe6
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/BrowserControl.java
@@ -0,0 +1,127 @@
+/*
+ *
+ * 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.
+ *
+ *
+ * A simple, static class to display a URL in the system browser.
+ *
+ * Under Unix, the system browser is hard-coded to be 'netscape'.
+ * Netscape must be in your PATH for this to work.
+ *
+ * Under Windows, this will bring up the default browser under windows,
+ * usually either Netscape or Microsoft IE. The default browser is
+ * determined by the OS.
+ *
+ * Taken from: http://www.javaworld.com/javaworld/javatips/jw-javatip66_p.html
+ *
+ */
+
+package uk.ac.sanger.artemis.editor;
+
+import java.io.IOException;
+
+public class BrowserControl
+{
+
+ // The default system browser under windows.
+ private static final String WIN_PATH = "rundll32";
+ // The flag to display a url.
+ private static final String WIN_FLAG = "url.dll,FileProtocolHandler";
+ // The default browser under unix.
+ private static final String UNIX_PATH = "netscape";
+ // The flag to display a url.
+ private static final String UNIX_FLAG = "-remote openURL";
+
+ /**
+ * Display a file in the system browser. If you want to display a
+ * file, you must include the absolute path name.
+ *
+ * @param url the file's url (the url must start with either "http://"
+ * or "file://").
+ */
+ public static void displayURL(String url)
+ {
+ boolean windows = isWindowsPlatform();
+ String cmd = null;
+ try
+ {
+ if(windows)
+ {
+ // cmd = 'rundll32 url.dll,FileProtocolHandler http://...'
+ cmd = WIN_PATH + " " + WIN_FLAG + " " + url;
+ Process p = Runtime.getRuntime().exec(cmd);
+ }
+ else
+ {
+ // Netscape has to be running for the "-remote" command to work
+ cmd = UNIX_PATH + " " + UNIX_FLAG + "(" + url + ")";
+ Process p = Runtime.getRuntime().exec(cmd);
+ try
+ {
+ // wait for exit code -- if it's 0, command worked,
+ // otherwise we need to start the browser up.
+ int exitCode = p.waitFor();
+ if(exitCode != 0)
+ {
+ // Command failed, start up the browser
+ cmd = UNIX_PATH + " " + url;
+ p = Runtime.getRuntime().exec(cmd);
+ }
+ }
+ catch(InterruptedException x)
+ {
+ System.err.println("Error bringing up browser, cmd='" +
+ cmd + "'");
+ System.err.println("Caught: " + x);
+ }
+ }
+ }
+ catch(IOException x)
+ {
+ // couldn't exec browser
+ System.err.println("Could not invoke browser, command=" + cmd);
+ System.err.println("Caught: " + x);
+ }
+ }
+
+ /**
+ * Try to determine whether this application is running under Windows
+ * or some other platform by examing the "os.name" property.
+ *
+ * @return true if this application is running under a Windows OS
+ */
+ public static boolean isWindowsPlatform()
+ {
+ String os = System.getProperty("os.name");
+ if ( os != null && os.startsWith("Windows"))
+ return true;
+ else
+ return false;
+
+ }
+ /**
+ * Simple example.
+ */
+ public static void main(String[] args)
+ {
+ displayURL("http://www.sanger.ac.uk");
+ }
+}
diff --git a/uk/ac/sanger/artemis/editor/CommonMenu.java b/uk/ac/sanger/artemis/editor/CommonMenu.java
new file mode 100644
index 0000000000000000000000000000000000000000..00be52c04e91b497351777ea778d33bffd5ab672
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/CommonMenu.java
@@ -0,0 +1,57 @@
+/*
+ *
+ * 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 javax.swing.*;
+import java.awt.event.*;
+
+public class CommonMenu extends JMenu
+{
+
+ public CommonMenu(final JInternalFrame f)
+ {
+ super("File");
+
+ JMenuItem closeMenu = new JMenuItem("Close");
+ closeMenu.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ f.setVisible(false);
+ try
+ {
+ JTabbedPane jtab = (JTabbedPane)f.getContentPane().getComponent(0);
+ jtab.removeAll();
+ }
+ catch(ClassCastException cce)
+ {
+ f.dispose();
+ }
+ }
+ });
+ add(closeMenu);
+ }
+
+}
diff --git a/uk/ac/sanger/artemis/editor/DataCollectionPane.java b/uk/ac/sanger/artemis/editor/DataCollectionPane.java
new file mode 100644
index 0000000000000000000000000000000000000000..f91b942c192b56b5ff2c044b1040ea931165b971
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/DataCollectionPane.java
@@ -0,0 +1,452 @@
+/*
+ *
+ * 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 javax.swing.*;
+import java.util.StringTokenizer;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Dimension;
+import java.awt.Color;
+import java.awt.Insets;
+import java.net.URL;
+
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+import java.util.Enumeration;
+import java.util.Hashtable;
+
+public class DataCollectionPane extends JScrollPane
+{
+
+ public DataCollectionPane(Vector hitInfoCollection, String dataFile,
+ final FastaTextPane fastaTextPane,
+ final Annotation ann, final JDesktopPane desktop)
+ {
+ super();
+
+ Font font = new Font("Monospaced",Font.PLAIN,12);
+
+ Box bdown = Box.createVerticalBox();
+ ScrollPanel scrollPanel = new ScrollPanel();
+ scrollPanel.add(bdown);
+
+ Hashtable goHash = new Hashtable();
+ Enumeration hitEnum = hitInfoCollection.elements();
+ while(hitEnum.hasMoreElements())
+ {
+ HitInfo hit = (HitInfo)hitEnum.nextElement();
+ Vector gov = hit.getGO();
+ if(gov != null)
+ {
+ Enumeration gov_enum = gov.elements();
+ while(gov_enum.hasMoreElements())
+ {
+ String id = ((String)gov_enum.nextElement()).trim();
+ goHash.put(id,"");
+ }
+ }
+ }
+
+ getGoHash("/nfs/disk222/yeastpub/analysis/pathogen/GO/go.flat",goHash);
+
+ final Vector orthoCheckBox = new Vector();
+ hitEnum = hitInfoCollection.elements();
+
+ while(hitEnum.hasMoreElements())
+ {
+ Box bacross = Box.createHorizontalBox();
+ final HitInfo hit = (HitInfo)hitEnum.nextElement();
+
+// ortholog / paralog
+ final JCheckBox orthoBox = new JCheckBox("ORTH");
+ final JCheckBox paraBox = new JCheckBox("PARA");
+
+ orthoBox.setMargin(new Insets(2,1,1,1));
+ paraBox.setMargin(new Insets(2,1,1,1));
+
+ orthoBox.setActionCommand(hit.getID());
+ orthoCheckBox.add(orthoBox);
+
+ bacross.add(orthoBox);
+ orthoBox.setFont(font);
+ orthoBox.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ Enumeration checkEnum = orthoCheckBox.elements();
+ while(checkEnum.hasMoreElements())
+ {
+ JCheckBox cb = (JCheckBox)checkEnum.nextElement();
+ if( cb.isSelected() &&
+ !cb.getActionCommand().equals(orthoBox.getActionCommand()))
+ {
+ cb.setSelected(false);
+ ann.delete(cb.getActionCommand(),true);
+ }
+ }
+
+ if(orthoBox.isSelected())
+ {
+ if(paraBox.isSelected())
+ {
+ paraBox.setSelected(false);
+ ann.delete(hit.getID(),false);
+ }
+
+ setAnnotation(hit,ann,fastaTextPane.getFormat(),true);
+ }
+ else
+ ann.delete(hit.getID(),true);
+ }
+ });
+
+ bacross.add(paraBox);
+ paraBox.setFont(font);
+ paraBox.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if(paraBox.isSelected())
+ {
+ if(orthoBox.isSelected())
+ {
+ orthoBox.setSelected(false);
+ ann.delete(hit.getID(),true);
+ }
+
+ setAnnotation(hit,ann,fastaTextPane.getFormat(),false);
+ }
+ else
+ ann.delete(hit.getID(),false);
+ }
+ });
+
+
+// heading
+ JLabel hiLabel = new JLabel(hit.getHeader());
+ hiLabel.setFont(font);
+ hiLabel.setForeground(Color.RED);
+
+// align button
+ final JButton selectButt = new JButton("ALIGN");
+ selectButt.setMargin(new Insets(1,1,1,1));
+ selectButt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ fastaTextPane.show(hit);
+ }
+ });
+ selectButt.setFont(font);
+
+// retrieve srs entry
+ JButton srsButt = new JButton("->SRS");
+ srsButt.setMargin(new Insets(1,1,1,1));
+
+ srsButt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String srscmd = "srs.sanger.ac.uk/srsbin/cgi-bin/wgetz?-e+";
+ if(hit.getID() != null)
+ {
+ String search = hit.getID();
+ srscmd = srscmd.concat("[{swall}-ID:"+search+"*]");
+ if(hit.getAcc() != null)
+ srscmd = srscmd.concat("|[{swall}-AccNumber:"+hit.getAcc()+"*]");
+
+ if(BigPane.srsBrowser.isSelected())
+ BrowserControl.displayURL(srscmd);
+
+ try
+ {
+ URL url = new URL("http://"+srscmd);
+ if(BigPane.srsTabPane.isSelected())
+ {
+ if(BigPane.srsFrame == null)
+ {
+ BigPane.setUpSRSFrame((2*desktop.getHeight())/3,desktop);
+// int hgt = (2*desktop.getHeight())/3;
+// BigPane.srsFrame = new JInternalFrame("SRS",
+// true, //resizable
+// true, //closable
+// true, //maximizable
+// true);//iconifiable
+// JTabbedPane jtab = new JTabbedPane();
+// BigPane.srsFrame.getContentPane().add(jtab);
+// BigPane.srsFrame.setLocation(0,0);
+// BigPane.srsFrame.setSize(800,hgt);
+
+// JMenuBar menuBar = new JMenuBar();
+// menuBar.add(new CommonMenu(BigPane.srsFrame));
+// BigPane.srsFrame.setJMenuBar(menuBar);
+
+// desktop.add(BigPane.srsFrame);
+ }
+ Annotation edPane = new Annotation(url);
+ JScrollPane jsp = new JScrollPane(edPane);
+ JTabbedPane jtab = (JTabbedPane)BigPane.srsFrame.getContentPane().getComponent(0);
+ jtab.insertTab(search,null,jsp,null,0);
+ BigPane.srsFrame.setVisible(true);
+ }
+
+ if(BigPane.srsWin.isSelected())
+ {
+ int hgt = (2*desktop.getHeight())/3;
+ Annotation edPane = new Annotation(url);
+ JScrollPane jsp = new JScrollPane(edPane);
+ JInternalFrame jif = new JInternalFrame("SRS "+search,
+ true, //resizable
+ true, //closable
+ true, //maximizable
+ true);//iconifiable);
+ JMenuBar menuBar = new JMenuBar();
+ menuBar.add(new CommonMenu(jif));
+ jif.setJMenuBar(menuBar);
+ jif.getContentPane().add(jsp);
+ jif.setLocation(0,0);
+ jif.setSize(800,hgt);
+ jif.setVisible(true);
+ desktop.add(jif);
+ }
+ }
+ catch(Exception exp)
+ {
+ exp.printStackTrace();
+ }
+ }
+ else
+ JOptionPane.showMessageDialog(DataCollectionPane.this,
+ "No ID to retrieve SRS entry!", "Missing ID",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+ });
+ srsButt.setFont(font);
+
+ bacross.add(hiLabel);
+ bacross.add(selectButt);
+ bacross.add(srsButt);
+
+ bacross.add(Box.createHorizontalGlue());
+ bdown.add(bacross);
+
+ Vector gov = hit.getGO();
+ if(gov != null)
+ {
+ Enumeration gov_enum = gov.elements();
+ while(gov_enum.hasMoreElements())
+ {
+ final String go_id = ((String)gov_enum.nextElement()).trim();
+ bacross = Box.createHorizontalBox();
+ JButton goButton = new JButton("GO:"+go_id);
+ goButton.setFont(font);
+ goButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String go_cmd = "http://www.godatabase.org/cgi-bin/amigo/go.cgi?query=GO%3A"+go_id;
+ BrowserControl.displayURL(go_cmd);
+ }
+ });
+ bacross.add(Box.createHorizontalStrut(10));
+ bacross.add(goButton);
+ goButton.setMargin(new Insets(0,1,0,1));
+
+ JLabel goLabel = new JLabel((String)goHash.get(go_id));
+ goLabel.setFont(font);
+ bacross.add(goLabel);
+ bdown.add(bacross);
+ bacross.add(Box.createHorizontalGlue());
+ }
+ }
+ }
+
+ setViewportView(scrollPanel);
+ setPreferredSize(new Dimension(500,300));
+ }
+
+
+ protected static void getzCall(HitInfo hit, boolean ortholog)
+ {
+ String env[] = { "PATH=/usr/local/pubseq/bin/" };
+ if(hit.getOrganism() == null ||
+ hit.getDescription()== null)
+ {
+
+ String cmd[] = { "getz", "-f", "org description",
+ "[libs={swall}-acc:"+
+ hit.getAcc()+"]|[libs={swall}-id:"+hit.getID()+"]" };
+ ExternalApplication app = new ExternalApplication(cmd,
+ env,null);
+ String res = app.getProcessStdout();
+
+ int ind1 = res.indexOf("OS ");
+ int ind2 = res.indexOf("\n");
+
+ if(ind1 > -1)
+ hit.setOrganism(res.substring(ind1+3,ind2).trim());
+
+ ind1 = res.indexOf("DE ");
+ if(ind1 > -1)
+ hit.setDescription(res.substring(ind1+3).trim());
+ }
+
+ if(hit.getEMBL() == null)
+ {
+ String cmd2[] = { "getz", "-f", "id",
+ "[libs={swall}-id:"+hit.getID()+"]>EMBL" };
+ ExternalApplication app = new ExternalApplication(cmd2,env,null);
+ String res = app.getProcessStdout();
+
+ int ind1 = res.indexOf("ID ");
+ if(ind1 > -1)
+ {
+ StringTokenizer tok = new StringTokenizer(res);
+ tok.nextToken();
+ hit.setEMBL(tok.nextToken());
+ }
+ }
+
+ if(ortholog)
+ {
+ String geneName = hit.getGeneName();
+ if(geneName == null)
+ {
+ String cmd3[] = { "getz", "-f", "gen",
+ "[libs={swall}-acc:"+
+ hit.getAcc()+"]|[libs={swall}-id:"+hit.getID()+"]" };
+ ExternalApplication app = new ExternalApplication(cmd3,
+ env,null);
+ geneName = app.getProcessStdout();
+ }
+
+ int ind1 = geneName.indexOf("GN ");
+ if(ind1 > -1)
+ {
+ geneName = geneName.substring(ind1+3).trim();
+ if(geneName.startsWith("Name="))
+ {
+ geneName = geneName.substring(5);
+ ind1 = geneName.indexOf(";");
+ if(ind1 > -1)
+ geneName = geneName.substring(0,ind1);
+ }
+
+ if(!geneName.toLowerCase().startsWith("orderedlocusnames="))
+ hit.setGeneName(geneName);
+ }
+ }
+ }
+
+ private void setAnnotation(HitInfo hit, Annotation ann,
+ String resultFormat, boolean ortholog)
+ {
+ getzCall(hit,ortholog);
+
+// gene name for orthologs
+ String orthoText = "";
+ if(ortholog)
+ {
+ String geneName = hit.getGeneName();
+ if(hit.getGeneName() != null)
+ orthoText = "<br>\n/gene=\""+hit.getGeneName()+"\"";
+ }
+
+ StringBuffer buff = new StringBuffer();
+
+ if(hit.getDB() != null)
+ buff.append(hit.getDB()+":"+hit.getID());
+ else
+ buff.append(" UNIPROT:"+hit.getID());
+
+ if(hit.getEMBL() != null)
+ buff.append(" (EMBL:"+hit.getEMBL()+")");
+ buff.append(";");
+
+ if(hit.getOrganism() != null)
+ buff.append(" "+hit.getOrganism()+";");
+ if(hit.getLength() != null)
+ buff.append(" length=" + hit.getLength()+";");
+ if(hit.getUngapped() != null)
+ buff.append("ungapped id=" + hit.getUngapped()+";");
+ if(hit.getEValue() != null)
+ buff.append(" E()=" + hit.getEValue()+";");
+ if(hit.getOverlap() != null)
+ buff.append(" "+hit.getOverlap()+";");
+ if(hit.getQueryRange() != null)
+ buff.append("query " + hit.getQueryRange()+";");
+ if(hit.getSubjectRange() != null)
+ buff.append("subject " + hit.getSubjectRange());
+ buff.append("\"");
+
+ ann.insert("\n/similarity=\""+resultFormat+";"+
+ buff.toString()+orthoText, ortholog);
+
+// ann.insert("\n/similarity=\""+resultFormat+"; SWALL:"+hit.getID()+
+// " (EMBL:"+hit.getEMBL()+"); "+
+// hit.getOrganism()+"; "+
+// hit.getDescription()+"; "+
+// "length=" + hit.getLength()+"; "+
+// "id=" + hit.getIdentity()+"; "+
+// "ungapped id=" + hit.getUngapped()+"; "+
+// "E()=" + hit.getEValue()+"; "+
+// hit.getOverlap()+"; "+
+// "query " + hit.getQueryRange()+"; "+
+// "subject " + hit.getSubjectRange()+"\""+
+// orthoText, ortholog);
+ }
+
+ public void getGoHash(String filename, Hashtable goHash)
+ {
+ try
+ {
+ String line = null;
+ BufferedReader buffRead = new BufferedReader(new FileReader(filename));
+ while((line = buffRead.readLine()) != null)
+ {
+ StringTokenizer tok = new StringTokenizer(line,"\t");
+ String ID = tok.nextToken().substring(3);
+ String desc = tok.nextToken();
+
+ if(tok.hasMoreTokens())
+ desc = desc.concat("; "+tok.nextToken());
+
+ if(goHash.containsKey(ID))
+ goHash.put(ID,desc);
+ }
+ }
+ catch(IOException ioe) { ioe.printStackTrace(); }
+ }
+
+
+}
+
diff --git a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
new file mode 100644
index 0000000000000000000000000000000000000000..90a8b5a85651f7afb3bf28a0e9fa25abb88fb78f
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
@@ -0,0 +1,84 @@
+/*
+ *
+ * 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 javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.util.Vector;
+
+public class DataViewInternalFrame extends JInternalFrame
+{
+ private JTabbedPane tabPane = new JTabbedPane();
+
+ public DataViewInternalFrame(String dataFile[],
+ JDesktopPane desktop)
+ {
+ super("Document " + dataFile[0],
+ true, //resizable
+ true, //closable
+ true, //maximizable
+ true);//iconifiable
+
+ Annotation ann = new Annotation(desktop);
+ JPanel dataPanel = (JPanel)getContentPane();
+ dataPanel.setLayout(new BorderLayout());
+
+ StringBuffer annFormat = new StringBuffer();
+
+ for(int i=0; i<dataFile.length; i++)
+ {
+ // add fasta results internal frame
+ FastaTextPane fastaPane = new FastaTextPane(dataFile[i]);
+
+ annFormat.append("/"+fastaPane.getFormat()+"_file=\""+
+ dataFile[i]+"\"\n");
+ // add data pane
+ Vector hits = fastaPane.getHitCollection();
+ DataCollectionPane dataPane =
+ new DataCollectionPane(hits, dataFile[i], fastaPane, ann, desktop);
+
+ JSplitPane split = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
+ fastaPane,dataPane);
+ split.setDividerLocation(150);
+
+ tabPane.add(fastaPane.getFormat(),split);
+ }
+
+ // add annotator text pane
+ ann.setAnnotation(annFormat.toString().trim());
+ JScrollPane annotationScroll = new JScrollPane(ann);
+ annotationScroll.setPreferredSize(new Dimension(500,300));
+
+ JSplitPane split = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
+ annotationScroll,tabPane);
+ split.setDividerLocation(250);
+ dataPanel.add(split);
+
+ setVisible(true);
+ }
+
+}
+
diff --git a/uk/ac/sanger/artemis/editor/ExternalApplication.java b/uk/ac/sanger/artemis/editor/ExternalApplication.java
new file mode 100644
index 0000000000000000000000000000000000000000..ce3ca9bfbcd28f8472b77fb435d66fd4cab13939
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/ExternalApplication.java
@@ -0,0 +1,313 @@
+/*
+ *
+ * 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.io.*;
+
+/**
+*
+* Used to run an external command and get the stdout
+* and stderr.
+*
+*/
+public class ExternalApplication
+{
+
+ /** running process */
+ private Process p;
+ /** standard out */
+ private StringBuffer stdout = new StringBuffer();
+ /** standard error */
+ private StringBuffer stderr = new StringBuffer();
+ /** running directory */
+ private File project;
+ /** process status */
+ private String status;
+ private StdoutHandler stdouth;
+ private StderrHandler stderrh;
+
+ /**
+ *
+ * @param cmd command to run
+ * @param envp environment
+ * @param project running directory
+ *
+ */
+ public ExternalApplication(String[] cmd,
+ String[] envp, File project)
+ {
+ this.project = project;
+ status = "0";
+
+ Runtime cmdRun = Runtime.getRuntime();
+ try
+ {
+ p = cmdRun.exec(cmd,envp,project);
+
+ // 2 threads to read in stdout & stderr buffers
+ // to prevent blocking
+ stdouth = new StdoutHandler(this);
+ stderrh = new StderrHandler(this);
+ stdouth.start();
+ stderrh.start();
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ System.out.println("ExternalApplication Error executing: "+
+ cmd);
+ status = "1";
+ }
+ }
+
+
+ /**
+ *
+ * Read in the process stderr.
+ *
+ */
+ private void readProcessStderr()
+ {
+
+ BufferedInputStream stderrStream = null;
+ BufferedReader stderrRead = null;
+ try
+ {
+ String line;
+ stderrStream =
+ new BufferedInputStream(p.getErrorStream());
+ stderrRead =
+ new BufferedReader(new InputStreamReader(stderrStream));
+ char c[] = new char[100];
+ int nc = 0;
+
+ while((nc = stderrRead.read(c,0,100)) != -1)
+ stderr = stderr.append(new String(c,0,nc));
+ }
+ catch (IOException io)
+ {
+ System.err.println("ExternalApplication: Error in "+
+ "collecting standard out");
+ }
+ finally
+ {
+ try
+ {
+ if(stderrStream!=null)
+ stderrStream.close();
+ }
+ catch(IOException ioe)
+ {
+ System.err.println("ExternalApplication: Error closing stream");
+ }
+ try
+ {
+ if(stderrRead!=null)
+ stderrRead.close();
+ }
+ catch(IOException ioe)
+ {
+ System.err.println("ExternalApplication: Error closing reader");
+ }
+ }
+
+ return;
+ }
+
+ /**
+ *
+ * Read in the process stdout.
+ *
+ */
+ private void readProcessStdout()
+ {
+
+ BufferedInputStream stdoutStream = null;
+ BufferedReader stdoutRead = null;
+ try
+ {
+ String line;
+ stdoutStream =
+ new BufferedInputStream(p.getInputStream());
+ stdoutRead =
+ new BufferedReader(new InputStreamReader(stdoutStream));
+
+
+ char c[] = new char[100];
+ int nc = 0;
+ String chunk;
+
+ while((nc = stdoutRead.read(c,0,100)) != -1)
+ {
+ chunk = new String(c,0,nc);
+ stdout = stdout.append(chunk);
+ }
+
+ }
+ catch (IOException io)
+ {
+ System.err.println("ExternalApplication: Error in "+
+ "collecting standard out");
+ }
+ finally
+ {
+ try
+ {
+ if(stdoutStream!=null)
+ stdoutStream.close();
+ }
+ catch(IOException ioe)
+ {
+ System.err.println("ExternalApplication: Error closing stream");
+ }
+ try
+ {
+ if(stdoutRead!=null)
+ stdoutRead.close();
+ }
+ catch(IOException ioe)
+ {
+ System.err.println("ExternalApplication: Error closing reader");
+ }
+ }
+
+ return;
+ }
+
+ /**
+ *
+ * Get the stdout for the process.
+ * @return standard out.
+ *
+ */
+ public String getProcessStdout()
+ {
+ try
+ {
+ // make sure we hang around for stdout
+ while(stdouth.isAlive())
+ Thread.currentThread().sleep(10);
+ }
+ catch(InterruptedException ie)
+ {
+ ie.printStackTrace();
+ }
+
+ return new String(stdout.toString().trim());
+ }
+
+
+ /**
+ *
+ * Get the stderr for the process.
+ * @return standard error.
+ *
+ */
+ public String getProcessStderr()
+ {
+ try
+ {
+ // make sure we hang around for stderr
+ while(stderrh.isAlive())
+ Thread.currentThread().sleep(10);
+ }
+ catch(InterruptedException ie)
+ {
+ ie.printStackTrace();
+ }
+
+ return new String(stderr.toString().trim());
+ }
+
+ /**
+ *
+ * Wait for the process to end
+ *
+ */
+ public int waitFor()
+ {
+ try
+ {
+ return p.waitFor();
+ }
+ catch(InterruptedException ie)
+ {
+ ie.printStackTrace();
+ }
+ return -1;
+ }
+
+ /**
+ *
+ * @return process
+ *
+ */
+ public Process getProcess()
+ {
+ return p;
+ }
+
+ /**
+ *
+ * @return status
+ *
+ */
+ public String getStatus()
+ {
+ return status;
+ }
+
+ class StdoutHandler extends Thread
+ {
+ ExternalApplication rea;
+
+ protected StdoutHandler(ExternalApplication rea)
+ {
+ this.rea = rea;
+ }
+
+ public void run()
+ {
+ rea.readProcessStdout();
+ }
+ }
+
+ class StderrHandler extends Thread
+ {
+ ExternalApplication rea;
+
+ protected StderrHandler(ExternalApplication rea)
+ {
+ this.rea = rea;
+ }
+
+ public void run()
+ {
+ rea.readProcessStderr();
+ }
+ }
+
+}
+
diff --git a/uk/ac/sanger/artemis/editor/FastaTextPane.java b/uk/ac/sanger/artemis/editor/FastaTextPane.java
new file mode 100644
index 0000000000000000000000000000000000000000..ef0e9a0d812185da32a0d7fb3712f46f4dee6643
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/FastaTextPane.java
@@ -0,0 +1,420 @@
+/*
+ *
+ * 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.awt.Point;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+import javax.swing.JScrollPane;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Dimension;
+import java.io.InputStream;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.File;
+import java.io.InputStreamReader;
+import java.io.BufferedReader;
+import java.util.Vector;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+
+import uk.ac.sanger.artemis.util.WorkingGZIPInputStream;
+
+public class FastaTextPane extends JScrollPane
+{
+ private JTextArea textArea;
+ private Vector hitInfoCollection = null;
+ private String format = null;
+
+ public FastaTextPane(String dataFile)
+ {
+ super();
+ //read fasta file
+
+ format = getResultsFormat(dataFile);
+ StringBuffer contents = null;
+
+ if(format.equals("fasta"))
+ contents = readFASTAFile(dataFile,format);
+ else if(format.equals("blastp"))
+ contents = readBLASTPFile(dataFile,format);
+
+ Font font = new Font("Monospaced",Font.PLAIN,12);
+
+ textArea = new JTextArea(contents.toString());
+ setTextAreaFont(font);
+ textArea.setEditable(false);
+
+ setViewportView(textArea);
+ setPreferredSize(new Dimension(500,300));
+ }
+
+ /**
+ *
+ * Get the format of the results (e.g. FASTA or BLASTP).
+ * @return format
+ *
+ */
+ protected String getFormat()
+ {
+ return format;
+ }
+
+ protected void setTextAreaFont(Font f)
+ {
+ textArea.setFont(f);
+ }
+
+ protected InputStream getInputStream(String dataFile)
+ throws IOException
+ {
+ FileInputStream inStream = new FileInputStream(dataFile);
+ if(dataFile.endsWith(".gz"))
+ return new WorkingGZIPInputStream(inStream);
+ else
+ return inStream;
+ }
+
+ /**
+ *
+ * Get the format of the results in a file. FASTA and
+ * BLASTP are supported.
+ *
+ */
+ protected String getResultsFormat(String dataFile)
+ {
+ File fn = new File(dataFile);
+ InputStreamReader streamReader = null;
+ BufferedReader buffReader = null;
+ String line = null;
+ String format = null;
+
+ try
+ {
+ streamReader = new InputStreamReader(getInputStream(dataFile));
+ buffReader = new BufferedReader(streamReader);
+ while( (line = buffReader.readLine()) != null)
+ {
+ if(line.startsWith("BLASTP"))
+ {
+ format = "blastp";
+ break;
+ }
+ else if(line.indexOf("FASTA") > -1)
+ {
+ format = "fasta";
+ break;
+ }
+ }
+ streamReader.close();
+ buffReader.close();
+ }
+ catch (IOException ioe)
+ {
+ System.out.println("Cannot read file: " + dataFile);
+ }
+
+ return format;
+ }
+
+
+ protected StringBuffer readBLASTPFile(String dataFile, String format)
+ {
+ File fn = new File(dataFile);
+ StringBuffer sbuff = new StringBuffer();
+
+ InputStreamReader streamReader = null;
+ BufferedReader buffReader = null;
+
+ hitInfoCollection = new Vector();
+ try
+ {
+ streamReader = new InputStreamReader(getInputStream(dataFile));
+ buffReader = new BufferedReader(streamReader);
+
+ String line = null;
+ int textPosition = 0;
+ int len = 0;
+ HitInfo hit = null;
+ int ind1 = 0;
+
+ while( (line = buffReader.readLine()) != null)
+ {
+ len = line.length()+1;
+ sbuff.append(line+"\n");
+ if(line.startsWith("Sequences producing significant alignments:"))
+ {
+ buffReader.readLine();
+ while( !(line = buffReader.readLine()).equals("") )
+ {
+ textPosition += line.length()+1;
+ sbuff.append(line+"\n");
+
+ hit = new HitInfo(line,format);
+ hitInfoCollection.add(hit);
+ }
+
+ }
+ else if(line.startsWith(">")) // start of alignment
+ {
+ String currentID = line;
+
+ int ind = line.indexOf(" ");
+ if(ind > -1)
+ currentID = line.substring(1,ind);
+
+ int ind2 = currentID.indexOf(":");
+ if(ind2 > -1)
+ {
+ currentID = currentID.substring(ind2+1);
+ }
+
+ if(hit != null)
+ hit.setEndPosition(textPosition);
+
+ hit = getHitInfo(currentID,hitInfoCollection);
+ hit.setStartPosition(textPosition);
+
+
+ String going = "";
+ ind = line.indexOf("GO:");
+ if(ind > -1)
+ going = line.substring(ind+3);
+
+ String nextLine = null;
+ buffReader.mark(210);
+ while((nextLine = buffReader.readLine()).indexOf("Length") == -1)
+ {
+ if(going.equals("") && ((ind = nextLine.indexOf("GO:")) > -1))
+ going = nextLine.substring(ind+3);
+ else if(!going.equals(""))
+ going = going.concat(nextLine);
+ }
+
+ buffReader.reset();
+ if(!going.equals(""))
+ hit.setGO(going);
+ }
+ else if( (ind1 = line.indexOf("Identities = ")) > -1)
+ {
+ ind1 = line.indexOf("(",ind1)+1;
+ if(ind1 > -1)
+ hit.setIdentity(line.substring(ind1,line.indexOf(")",ind1)).trim());
+ }
+ else if( (ind1 = line.indexOf(" Length = ")) > -1)
+ hit.setLength(line.substring(ind1+11));
+
+ textPosition += len;
+ }
+
+ if(hit != null)
+ hit.setEndPosition(textPosition);
+
+ streamReader.close();
+ buffReader.close();
+
+ GetzThread getz = new GetzThread(hitInfoCollection);
+ getz.start();
+ }
+ catch (IOException ioe)
+ {
+ System.out.println("Cannot read file: " + dataFile);
+ }
+ return sbuff;
+ }
+
+
+ protected StringBuffer readFASTAFile(String dataFile, String format)
+ {
+ File fn = new File(dataFile);
+ StringBuffer sbuff = new StringBuffer();
+
+ InputStreamReader streamReader = null;
+ BufferedReader buffReader = null;
+
+ hitInfoCollection = new Vector();
+ try
+ {
+ streamReader = new InputStreamReader(getInputStream(dataFile));
+ buffReader = new BufferedReader(streamReader);
+
+ String line = null;
+ int textPosition = 0;
+ int len = 0;
+ HitInfo hi = null;
+
+ while( (line = buffReader.readLine()) != null)
+ {
+ len = line.length()+1;
+ sbuff.append(line+"\n");
+
+ int ind1;
+
+ if(line.startsWith("The best scores are:"))
+ {
+ while( !(line = buffReader.readLine()).equals("") )
+ {
+ textPosition += line.length()+1;
+ sbuff.append(line+"\n");
+ hitInfoCollection.add(new HitInfo(line,format));
+ }
+ }
+ else if(line.startsWith(">>")) // start of alignment
+ {
+ int ind = line.indexOf(" ");
+ String currentID = line.substring(2,ind);
+
+ if(hi != null)
+ hi.setEndPosition(textPosition);
+
+ hi = getHitInfo(currentID,hitInfoCollection);
+ hi.setStartPosition(textPosition);
+ }
+ else if(line.startsWith("Smith-Waterman")) // Smith-Waterman
+ {
+ ind1 = line.indexOf("score:");
+ int ind2;
+ if(ind1 > -1)
+ {
+ ind2 = line.indexOf(";",ind1);
+ hi.setScore(line.substring(ind1+6,ind2));
+
+ ind1 = ind2+1;
+ ind2 = line.indexOf("identity");
+ if(ind2 > -1)
+ hi.setIdentity(line.substring(ind1,ind2).trim());
+
+ ind1 = line.indexOf("(",ind2);
+ if(ind1 > -1)
+ {
+ ind2 = line.indexOf("ungapped)",ind1);
+ hi.setUngapped(line.substring(ind1+1,ind2).trim());
+ }
+
+ ind1 = line.indexOf(" in ",ind2);
+ ind2 = line.indexOf("(",ind1);
+ if(ind1 > -1 && ind2 > -1)
+ hi.setOverlap(line.substring(ind1+4,ind2).trim());
+
+ ind1 = ind2+1;
+ ind2 = line.indexOf(":",ind1);
+ if(ind2 > -1)
+ hi.setQueryRange(line.substring(ind1,ind2));
+
+ ind1 = ind2+1;
+ ind2 = line.indexOf(")",ind1);
+ if(ind2 > -1)
+ hi.setSubjectRange(line.substring(ind1,ind2));
+ }
+ }
+ else if( (ind1 = line.indexOf(" E():")) > -1)
+ {
+ StringTokenizer tok = new StringTokenizer(line.substring(ind1+5));
+ hi.setEValue(tok.nextToken().trim());
+ }
+
+ textPosition += len;
+ }
+
+ if(hi != null)
+ hi.setEndPosition(textPosition);
+
+ streamReader.close();
+ buffReader.close();
+
+ GetzThread getz = new GetzThread(hitInfoCollection);
+ getz.start();
+ }
+ catch (IOException ioe)
+ {
+ System.out.println("Cannot read file: " + dataFile);
+ }
+ return sbuff;
+ }
+
+ protected Vector getHitCollection()
+ {
+ return hitInfoCollection;
+ }
+
+ protected HitInfo getHitInfo(String ID, Vector hitInfoCollection)
+ {
+ Enumeration hitInfo = hitInfoCollection.elements();
+
+ while(hitInfo.hasMoreElements())
+ {
+ HitInfo hi = (HitInfo)hitInfo.nextElement();
+ if(hi.getID().equals(ID))
+ return hi;
+ }
+
+ return null;
+ }
+
+ class GetzThread extends Thread
+ {
+ private Vector hitInfoCollection;
+
+ protected GetzThread(Vector hitInfoCollection)
+ {
+ this.hitInfoCollection = hitInfoCollection;
+ }
+
+ public void run()
+ {
+ int max = hitInfoCollection.size();
+ if(max > 10)
+ max = 10;
+
+ for(int i=0; i<max; i++)
+ DataCollectionPane.getzCall((HitInfo)hitInfoCollection.get(i),false);
+ }
+
+ }
+
+
+ public void show(Object obj)
+ {
+ if(obj instanceof HitInfo)
+ {
+ HitInfo hit = (HitInfo)obj;
+
+ int start = hit.getStartPosition();
+ int end = hit.getEndPosition();
+// textArea.moveCaretPosition(end);
+ textArea.moveCaretPosition(start);
+
+ Point pos = getViewport().getViewPosition();
+ Dimension rect = getViewport().getViewSize();
+ double hgt = rect.getHeight()+pos.getY();
+ pos.setLocation(pos.getX(),hgt);
+ getViewport().setViewPosition(pos);
+ }
+ }
+
+
+}
+
diff --git a/uk/ac/sanger/artemis/editor/HitInfo.java b/uk/ac/sanger/artemis/editor/HitInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..f1c3959e168b8e3b5949ae5773d58f3624df455f
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/HitInfo.java
@@ -0,0 +1,547 @@
+/*
+ *
+ * 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.NoSuchElementException;
+import java.util.Vector;
+
+/**
+*
+* Hit information is contained in this object.
+*
+*/
+public class HitInfo
+{
+ /** Hit in database */
+ private String db = null;
+ /** Hit ID */
+ private String id = null;
+ /** Hit accession number */
+ private String acc = null;
+ /** Organism source */
+ private String org = null;
+ /** Gene name */
+ private String geneName = null;
+ /** Description */
+ private String desc = null;
+ /** Sequence length */
+ private String length = null;
+ /** */
+ private String opt = null;
+ private String zscore = null;
+ private String evalue = null;
+ private String header = null;
+ /** EMBL ID from linking to EMBL in SRS */
+ private String emblID = null;
+ private String score = null;
+ /** percentage identity */
+ private String identity = null;
+ /** ungapped identity */
+ private String ungapped = null;
+ /** amino acid overlap */
+ private String aaOverlap = null;
+ /** query range in the alignment */
+ private String queryRange = null;
+ /** subject range in the alignment */
+ private String subjectRange = null;
+ /** start position of this hit in the results output */
+ private int startPosition = 0;
+ /** end position of this hit in the results output */
+ private int endPosition = 0;
+
+ /** collection of GO terms */
+ private Vector go;
+
+ public HitInfo(String header, String format)
+ {
+ header = header.trim();
+ this.header = header;
+ if(format.equals("fasta"))
+ setFastaHitInfo(header);
+ else if(format.equals("blastp"))
+ setBLASTPInfo(header);
+ }
+
+
+ /**
+ *
+ * Extract id, accession numbers etc. from the
+ * header of BLASTP results.
+ * @param header results header line from BLASTP.
+ *
+ */
+ protected void setBLASTPInfo(String header)
+ {
+ int ind1 = header.indexOf(" ");
+ if(ind1 > -1)
+ id = header.substring(0,ind1);
+ else
+ return;
+
+ int ind1a = id.indexOf(":");
+ if(ind1a > -1)
+ {
+ db = id.substring(0,ind1a);
+ id = id.substring(ind1a+1);
+ }
+
+ int ind2 = header.indexOf(" ",ind1+1);
+ if(ind2 > -1)
+ acc = header.substring(ind1+1,ind2);
+ else
+ return;
+
+ ind1 = header.lastIndexOf(" ");
+ evalue = header.substring(ind1).trim();
+
+ ind2 = header.substring(0,ind1).trim().lastIndexOf(" ");
+ if(ind2>-1)
+ score = header.substring(ind2,ind1).trim();
+ }
+
+ /**
+ *
+ * Extract id, accession numbers etc. from the
+ * header of FASTA results.
+ * @param header results header line from FASTA.
+ *
+ */
+ protected void setFastaHitInfo(String header)
+ {
+ int ind1 = header.indexOf(" ");
+ if(ind1 > -1)
+ id = header.substring(0,ind1);
+ else
+ return;
+
+ int ind2 = header.indexOf(" ",ind1+1);
+ if(ind2 > -1)
+ acc = header.substring(ind1+1,ind2);
+ else
+ return;
+
+ ind1 = ind2;
+ ind2 = header.indexOf("(",ind1);
+ if(ind2 > -1)
+ org = header.substring(ind1,ind2).trim();
+ else
+ return;
+
+ ind1 = ind2+1;
+ ind2 = header.indexOf(")",ind1);
+ if(ind2 > -1)
+ length = header.substring(ind1,ind2).trim();
+ else
+ return;
+
+ StringTokenizer tok = new StringTokenizer(header.substring(ind2+1));
+ try
+ {
+ opt = tok.nextToken();
+ zscore = tok.nextToken();
+ evalue = tok.nextToken();
+ }
+ catch(NoSuchElementException exp){}
+
+ }
+
+ /**
+ *
+ * Set the start position of the alignment in the
+ * results.
+ * @param startPosition start position.
+ *
+ */
+ protected void setStartPosition(int startPosition)
+ {
+ this.startPosition = startPosition;
+ }
+
+ /**
+ *
+ * Set the end position of the alignment in the
+ * results.
+ * @param endPosition end position.
+ *
+ */
+ protected void setEndPosition(int endPosition)
+ {
+ this.endPosition = endPosition;
+ }
+
+ /**
+ *
+ * Set the sequence length.
+ * @param length sequence length.
+ *
+ */
+ protected void setLength(String length)
+ {
+ this.length = length;
+ }
+
+ /**
+ *
+ * Get the sequence length.
+ * @return sequence length.
+ *
+ */
+ protected String getLength()
+ {
+ return length;
+ }
+
+ /**
+ *
+ * Get the results header.
+ * @return results header.
+ *
+ */
+ protected String getHeader()
+ {
+ return header;
+ }
+
+ /**
+ *
+ * Get the alignment start position.
+ * @return start position.
+ *
+ */
+ protected int getStartPosition()
+ {
+ return startPosition;
+ }
+
+ /**
+ *
+ * Get the alignment end position.
+ * @return end position.
+ *
+ */
+ protected int getEndPosition()
+ {
+ return endPosition;
+ }
+
+ /**
+ *
+ * Get the database.
+ * @return database.
+ *
+ */
+ protected String getDB()
+ {
+ return db;
+ }
+
+
+ /**
+ *
+ * Get the sequence ID.
+ * @return sequence ID.
+ *
+ */
+ protected String getID()
+ {
+ return id;
+ }
+
+ /**
+ *
+ * Get the sequence accession number.
+ * @return sequence accession number.
+ *
+ */
+ protected String getAcc()
+ {
+ return acc;
+ }
+
+ /**
+ *
+ * Get the organism source (OS).
+ * @return organism source.
+ *
+ */
+ protected String getOrganism()
+ {
+ return org;
+ }
+
+ /**
+ *
+ * Set the organism source (OS).
+ * @param org organism source.
+ *
+ */
+ protected void setOrganism(String org)
+ {
+ this.org = org;
+ }
+
+ /**
+ *
+ * Set the description (DE).
+ * @param desc sequence description.
+ *
+ */
+ protected void setDescription(String desc)
+ {
+ this.desc = desc;
+ }
+
+ /**
+ *
+ * Get the description (DE).
+ * @return sequence description.
+ *
+ */
+ protected String getDescription()
+ {
+ return desc;
+ }
+
+ /**
+ *
+ * Set the EMBL linked entry (obtained from database
+ * linking in SRS).
+ * @param emblID EMBL ID.
+ *
+ */
+ protected void setEMBL(String emblID)
+ {
+ this.emblID = emblID;
+ }
+
+ /**
+ *
+ * Get the EMBL linked entry (obtained from database
+ * linking in SRS).
+ * @return EMBL ID.
+ *
+ */
+ protected String getEMBL()
+ {
+ return emblID;
+ }
+
+ /**
+ *
+ * Set the sequence alignment score.
+ * @param score alignment score.
+ *
+ */
+ protected void setScore(String score)
+ {
+ this.score = score;
+ }
+
+ /**
+ *
+ * Get the sequence alignment score.
+ * @return alignment score.
+ *
+ */
+ protected String getScore()
+ {
+ return score;
+ }
+
+ /**
+ *
+ * Set the percentage identity found in the alignment.
+ * @param identity percentage identity.
+ *
+ */
+ protected void setIdentity(String identity)
+ {
+ this.identity = identity;
+ }
+
+ /**
+ *
+ * Get the percentage identity found in the alignment.
+ * @return percentage identity.
+ *
+ */
+ protected String getIdentity()
+ {
+ return identity;
+ }
+
+ /**
+ *
+ * Set the percentage ungapped identity found in the alignment.
+ * @param ungapped percentage ungapped identity.
+ *
+ */
+ protected void setUngapped(String ungapped)
+ {
+ this.ungapped = ungapped;
+ }
+
+ /**
+ *
+ * Get the percentage ungapped identity found in the alignment.
+ * @return percentage ungapped identity.
+ *
+ */
+ protected String getUngapped()
+ {
+ return ungapped;
+ }
+
+ /**
+ *
+ * Set the e-value for this hit.
+ * @param evalue e-value.
+ *
+ */
+ protected void setEValue(String evalue)
+ {
+ this.evalue = evalue;
+ }
+
+ /**
+ *
+ * Get the e-value for this hit.
+ * @return e-value.
+ *
+ */
+ protected String getEValue()
+ {
+ return evalue;
+ }
+
+ /**
+ *
+ * Set the number of amino acids that overlap in this
+ * alignment.
+ * @param aaOverlap number of aa-overlaps.
+ *
+ */
+ protected void setOverlap(String aaOverlap)
+ {
+ this.aaOverlap = aaOverlap;
+ }
+
+ /**
+ *
+ * Get the number of amino acids that overlap in this
+ * alignment.
+ * @return number of aa-overlaps.
+ *
+ */
+ protected String getOverlap()
+ {
+ return aaOverlap;
+ }
+
+ /**
+ *
+ * Set the query range in this alignment.
+ * @param queryRange query range.
+ *
+ */
+ protected void setQueryRange(String queryRange)
+ {
+ this.queryRange = queryRange;
+ }
+
+ /**
+ *
+ * Get the query range in this alignment.
+ * @return query range.
+ *
+ */
+ protected String getQueryRange()
+ {
+ return queryRange;
+ }
+
+ /**
+ *
+ * Set the subject range in this alignment.
+ * @param subjectRange subject range.
+ *
+ */
+ protected void setSubjectRange(String subjectRange)
+ {
+ this.subjectRange = subjectRange;
+ }
+
+ /**
+ *
+ * Get the subject range in this alignment.
+ * @return subject range.
+ *
+ */
+ protected String getSubjectRange()
+ {
+ return subjectRange;
+ }
+
+ /**
+ *
+ * Set the gene name (for ortholog).
+ * @param geneName gene name.
+ *
+ */
+ protected void setGeneName(String geneName)
+ {
+ this.geneName = geneName;
+ }
+
+ /**
+ *
+ * Get the gene name (for ortholog).
+ * @return gene name.
+ *
+ */
+ protected String getGeneName()
+ {
+ return geneName;
+ }
+
+ protected void setGO(String go_terms)
+ {
+ go_terms = go_terms.trim();
+ StringTokenizer tok = new StringTokenizer(go_terms);
+ while(tok.hasMoreElements())
+ {
+ if(go == null)
+ go = new Vector();
+ go.add(tok.nextToken());
+ }
+ }
+
+ protected Vector getGO()
+ {
+ return go;
+ }
+}
+
diff --git a/uk/ac/sanger/artemis/editor/ScrollPanel.java b/uk/ac/sanger/artemis/editor/ScrollPanel.java
new file mode 100644
index 0000000000000000000000000000000000000000..cb78b0e05d0766704e6bcf809dbe2c568e1bf2c6
--- /dev/null
+++ b/uk/ac/sanger/artemis/editor/ScrollPanel.java
@@ -0,0 +1,81 @@
+/*
+ *
+ * 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 javax.swing.*;
+import java.awt.LayoutManager;
+import java.awt.Rectangle;
+import java.awt.Dimension;
+import java.awt.Color;
+
+/**
+*
+* Extends JPanel to implement Scrollable to speed scroll pane
+* scrolling
+*
+*/
+public class ScrollPanel extends JPanel implements Scrollable
+{
+
+ public ScrollPanel()
+ {
+ super();
+ }
+
+ public ScrollPanel(LayoutManager l)
+ {
+ super(l);
+ }
+
+ public Dimension getPreferredScrollableViewportSize()
+ {
+ return getPreferredSize();
+ }
+
+ public boolean getScrollableTracksViewportHeight()
+ {
+ return false;
+ }
+
+ public boolean getScrollableTracksViewportWidth()
+ {
+ return false;
+ }
+
+ public int getScrollableBlockIncrement(Rectangle r,
+ int orientation, int direction)
+ {
+ return 60;
+ }
+
+ public int getScrollableUnitIncrement(Rectangle r,
+ int orientation, int direction)
+ {
+ return 10;
+ }
+
+
+}
+