/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* 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., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
package jalview.bin;
import java.applet.*;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import jalview.appletgui.*;
import jalview.datamodel.*;
import jalview.io.*;
/**
* Jalview Applet. Runs in Java 1.18 runtime
*
* @author $author$
* @version $Revision$
*/
public class JalviewLite
extends Applet
{
///////////////////////////////////////////
//The following public methods maybe called
//externally, eg via javascript in HTML page
/**
* @return String list of selected sequence IDs, each terminated by "¬" (¬)
*/
public String getSelectedSequences()
{
return getSelectedSequencesFrom(getDefaultTargetFrame());
}
/**
* @param sep separator string or null for default
* @return String list of selected sequence IDs, each terminated by sep or ("¬" as default)
*/
public String getSelectedSequences(String sep)
{
return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
}
/**
* @param alf alignframe containing selection
* @return String list of selected sequence IDs, each terminated by "¬"
*
*/
public String getSelectedSequencesFrom(AlignFrame alf)
{
return getSelectedSequencesFrom(alf, "¬");
}
/**
* get list of selected sequence IDs separated by given separator
* @param alf window containing selection
* @param sep separator string to use - default is "¬"
* @return String list of selected sequence IDs, each terminated by the given separator
*/
public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep==null || sep.length()==0)
{
sep = "¬";
}
if (alf.viewport.getSelectionGroup() != null)
{
SequenceI[] seqs = alf.viewport.getSelectionGroup().
getSequencesInOrder(
alf.viewport.getAlignment());
for (int i = 0; i < seqs.length; i++)
{
result.append(seqs[i].getName());
result.append(sep);
}
}
return result.toString();
}
/**
* get sequences selected in current alignFrame and return their alignment in format 'format' either with or without suffix
* @param alf - where selection is
* @param format - format of alignment file
* @param suffix - "true" to append /start-end string to each sequence ID
* @return selected sequences as flat file or empty string if there was no current selection
*/
public String getSelectedSequencesAsAlignment(String format, String suffix) {
return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format, suffix);
}
/**
* get sequences selected in alf and return their alignment in format 'format' either with or without suffix
* @param alf - where selection is
* @param format - format of alignment file
* @param suffix - "true" to append /start-end string to each sequence ID
* @return selected sequences as flat file or empty string if there was no current selection
*/
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix)
{
try
{
boolean seqlimits = suffix.equalsIgnoreCase("true");
if (alf.viewport.getSelectionGroup()!=null)
{
String reply = new AppletFormatAdapter().formatSequences(format,
new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits);
return reply;
}
}
catch (Exception ex)
{
ex.printStackTrace();
return "Error retrieving alignment in " + format + " format. ";
}
return "";
}
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
}
public String getAlignmentFrom(AlignFrame alf, String format)
{
return getAlignmentFrom(alf, format, "true");
}
public String getAlignment(String format, String suffix)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
}
public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
{
try
{
boolean seqlimits = suffix.equalsIgnoreCase("true");
String reply = new AppletFormatAdapter().formatSequences(format,
alf.viewport.getAlignment(), seqlimits);
return reply;
}
catch (Exception ex)
{
ex.printStackTrace();
return "Error retrieving alignment in " + format + " format. ";
}
}
public void loadAnnotation(String annotation)
{
loadAnnotationFrom(getDefaultTargetFrame(), annotation);
}
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (new AnnotationFile().readAnnotationFile(
alf.getAlignViewport().getAlignment(), annotation,
AppletFormatAdapter.PASTE))
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
}
else
{
alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
}
}
public String getFeatures(String format)
{
return getFeaturesFrom(getDefaultTargetFrame(), format);
}
public String getFeaturesFrom(AlignFrame alf, String format)
{
return alf.outputFeatures(false, format);
}
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
}
public String getAnnotationFrom(AlignFrame alf)
{
return alf.outputAnnotations(false);
}
public AlignFrame newView()
{
return newViewFrom(getDefaultTargetFrame());
}
public AlignFrame newView(String name)
{
return newViewFrom(getDefaultTargetFrame(), name);
}
public AlignFrame newViewFrom(AlignFrame alf)
{
return alf.newView(null);
}
public AlignFrame newViewFrom(AlignFrame alf, String name)
{
return alf.newView(name);
}
/**
*
* @param text alignment file as a string
* @param title window title
* @return null or new alignment frame
*/
public AlignFrame loadAlignment(String text, String title)
{
Alignment al = null;
String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
try
{
al = new AppletFormatAdapter().readFile(text,
AppletFormatAdapter.PASTE,
format);
if (al.getHeight() > 0)
{
return new AlignFrame(al, this, title, false);
}
}
catch (java.io.IOException ex)
{
ex.printStackTrace();
}
return null;
}
////////////////////////////////////////////////
////////////////////////////////////////////////
static int lastFrameX = 200;
static int lastFrameY = 200;
boolean fileFound = true;
String file = "No file";
Button launcher = new Button("Start Jalview");
/**
* The currentAlignFrame is static, it will change
* if and when the user selects a new window.
* Note that it will *never* point back to the embedded AlignFrame
* if the applet is started as embedded on the page and then afterwards a new view is created.
*/
public static AlignFrame currentAlignFrame;
/**
* This is the first frame to be displayed, and does not change.
* API calls will default to this instance if currentAlignFrame is null.
*/
AlignFrame initialAlignFrame;
boolean embedded = false;
public boolean jmolAvailable = false;
public static boolean debug;
/**
* init method for Jalview Applet
*/
public void init()
{
String dbg = getParameter("debug");
if (dbg!=null)
{
debug = dbg.toLowerCase().equals("true");
}
/**
* get the separator parameter if present
*/
String sep = getParameter("separator");
if (sep!=null)
{
if (sep.length()>0)
{ separator = sep;
if (debug)
{
System.err.println("Separator set to '"+separator+"'");
}
} else {
throw new Error("Invalid separator parameter - must be non-zero length");
}
}
int r = 255;
int g = 255;
int b = 255;
String param = getParameter("RGB");
if (param != null)
{
try
{
r = Integer.parseInt(param.substring(0, 2), 16);
g = Integer.parseInt(param.substring(2, 4), 16);
b = Integer.parseInt(param.substring(4, 6), 16);
}
catch (Exception ex)
{
r = 255;
g = 255;
b = 255;
}
}
param = getParameter("label");
if (param != null)
{
launcher.setLabel(param);
}
this.setBackground(new Color(r, g, b));
file = getParameter("file");
if (file == null)
{
//Maybe the sequences are added as parameters
StringBuffer data = new StringBuffer("PASTE");
int i = 1;
while ( (file = getParameter("sequence" + i)) != null)
{
data.append(file.toString() + "\n");
i++;
}
if (data.length() > 5)
{
file = data.toString();
}
}
LoadJmolThread jmolAvailable = new LoadJmolThread();
jmolAvailable.start();
final JalviewLite applet = this;
if (getParameter("embedded") != null
&& getParameter("embedded").equalsIgnoreCase("true"))
{
embedded = true;
LoadingThread loader = new LoadingThread(file, applet);
loader.start();
}
else if (file != null)
{
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
LoadingThread loader = new LoadingThread(file,
applet);
loader.start();
}
});
}
else
{
file = "NO FILE";
fileFound = false;
}
}
/**
* Initialises and displays a new java.awt.Frame
*
* @param frame java.awt.Frame to be displayed
* @param title title of new frame
* @param width width if new frame
* @param height height of new frame
*/
public static void addFrame(final Frame frame, String title, int width,
int height)
{
frame.setLocation(lastFrameX, lastFrameY);
lastFrameX += 40;
lastFrameY += 40;
frame.setSize(width, height);
frame.setTitle(title);
frame.addWindowListener(new WindowAdapter()
{
public void windowClosing(WindowEvent e)
{
if (frame instanceof AlignFrame)
{
( (AlignFrame) frame).closeMenuItem_actionPerformed();
}
if (currentAlignFrame == frame)
{
currentAlignFrame = null;
}
lastFrameX -= 40;
lastFrameY -= 40;
if (frame instanceof EmbmenuFrame)
{
((EmbmenuFrame) frame).destroyMenus();
}
frame.setMenuBar(null);
frame.dispose();
}
public void windowActivated(WindowEvent e)
{
if (frame instanceof AlignFrame)
{
currentAlignFrame = (AlignFrame) frame;
if (debug)
{
System.err.println("Activated window "+frame);
}
}
// be good.
super.windowActivated(e);
}
/* Probably not necessary to do this - see TODO above.
* (non-Javadoc)
* @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
*
public void windowDeactivated(WindowEvent e)
{
if (currentAlignFrame == frame)
{
currentAlignFrame = null;
if (debug)
{
System.err.println("Deactivated window "+frame);
}
}
super.windowDeactivated(e);
}
*/
});
frame.setVisible(true);
}
/**
* This paints the background surrounding the "Launch Jalview button"
*
*
If file given in parameter not found, displays error message
*
* @param g graphics context
*/
public void paint(Graphics g)
{
if (!fileFound)
{
g.setColor(new Color(200, 200, 200));
g.setColor(Color.cyan);
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.red);
g.drawString("Jalview can't open file", 5, 15);
g.drawString("\"" + file + "\"", 5, 30);
}
else if (embedded)
{
g.setColor(Color.black);
g.setFont(new Font("Arial", Font.BOLD, 24));
g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
g.drawString("Loading Data...", 50, this.getSize().height / 2);
}
}
class LoadJmolThread extends Thread
{
public void run()
{
try
{
if (!System.getProperty("java.version").startsWith("1.1"))
{
Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
jmolAvailable = true;
}
}
catch (java.lang.ClassNotFoundException ex)
{
System.out.println("Jmol not available - Using MCview for structures");
}
}
}
class LoadingThread
extends Thread
{
/**
* State variable: File source
*/
String file;
/**
* State variable: protocol for access to file source
*/
String protocol;
/**
* State variable: format of file source
*/
String format;
JalviewLite applet;
private void dbgMsg(String msg)
{
if (applet.debug)
{
System.err.println(msg);
}
}
/**
* update the protocol state variable for accessing the datasource
* located by file.
* @param file
* @return possibly updated datasource string
*/
public String setProtocolState(String file)
{
if (file.startsWith("PASTE"))
{
file = file.substring(5);
protocol = AppletFormatAdapter.PASTE;
}
else if (inArchive(file))
{
protocol = AppletFormatAdapter.CLASSLOADER;
}
else
{
file = addProtocol(file);
protocol = AppletFormatAdapter.URL;
}
dbgMsg("Protocol identified as '"+protocol+"'");
return file;
}
public LoadingThread(String _file,
JalviewLite _applet)
{
dbgMsg("Loading thread started with:\n>>file\n"+_file+">>endfile");
file = setProtocolState(_file);
format = new jalview.io.IdentifyFile().Identify(file, protocol);
dbgMsg("File identified as '"+format+"'");
applet = _applet;
}
public void run()
{
startLoading();
}
private void startLoading()
{
dbgMsg("Loading started.");
Alignment al = null;
try
{
al = new AppletFormatAdapter().readFile(file, protocol,
format);
}
catch (java.io.IOException ex)
{
dbgMsg("File load exception.");
ex.printStackTrace();
}
if ( (al != null) && (al.getHeight() > 0))
{
dbgMsg("Successfully loaded file.");
initialAlignFrame = new AlignFrame(al,
applet,
file,
embedded);
// update the focus.
currentAlignFrame = initialAlignFrame;
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
}
currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
String treeFile = applet.getParameter("tree");
if (treeFile == null)
{
treeFile = applet.getParameter("treeFile");
}
if (treeFile != null)
{
try
{
treeFile = setProtocolState(treeFile);
/*if (inArchive(treeFile))
{
protocol = AppletFormatAdapter.CLASSLOADER;
}
else
{
protocol = AppletFormatAdapter.URL;
treeFile = addProtocol(treeFile);
}
*/
jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
protocol);
fin.parse();
if (fin.getTree() != null)
{
currentAlignFrame.loadTree(fin, treeFile);
dbgMsg("Successfuly imported tree.");
} else {
dbgMsg("Tree parameter did not resolve to a valid tree.");
}
}
catch (Exception ex)
{
ex.printStackTrace();
}
}
String param = getParameter("features");
if (param != null)
{
param = setProtocolState(param);
currentAlignFrame.parseFeaturesFile(param, protocol);
}
param = getParameter("showFeatureSettings");
if (param != null && param.equalsIgnoreCase("true"))
{
currentAlignFrame.viewport.showSequenceFeatures(true);
new FeatureSettings(currentAlignFrame.alignPanel);
}
param = getParameter("annotations");
if (param != null)
{
param = setProtocolState(param);
if (new AnnotationFile().readAnnotationFile(
currentAlignFrame.viewport.getAlignment(),
param,
protocol))
{
currentAlignFrame.alignPanel.fontChanged();
currentAlignFrame.alignPanel.setScrollValues(0, 0);
} else {
System.err.println("Annotations were not added from annotation file '"+param+"'");
}
}
param = getParameter("jnetfile");
if (param != null)
{
try
{
param = setProtocolState(param);
jalview.io.JPredFile predictions = new jalview.io.JPredFile(
param, protocol);
JnetAnnotationMaker.add_annotation(predictions,
currentAlignFrame.viewport.getAlignment(),
0, false); // false==do not add sequence profile from concise output
currentAlignFrame.alignPanel.fontChanged();
currentAlignFrame.alignPanel.setScrollValues(0, 0);
}
catch (Exception ex)
{
ex.printStackTrace();
}
}
/*
*/
int pdbFileCount = 0;
do{
if (pdbFileCount > 0)
param = getParameter("PDBFILE" + pdbFileCount);
else
param = getParameter("PDBFILE");
if (param != null)
{
PDBEntry pdb = new PDBEntry();
String seqstring;
SequenceI[] seqs = null;
String [] chains = null;
StringTokenizer st = new StringTokenizer(param, " ");
if (st.countTokens() < 2)
{
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
seqs = new SequenceI[]
{
(Sequence) currentAlignFrame.
getAlignViewport().getAlignment().
findName(sequence)};
}
else
{
param = st.nextToken();
Vector tmp = new Vector();
Vector tmp2 = new Vector();
while (st.hasMoreTokens())
{
seqstring = st.nextToken();
StringTokenizer st2 = new StringTokenizer(seqstring,"=");
if(st2.countTokens()>1)
{
//This is the chain
tmp2.addElement(st2.nextToken());
seqstring = st2.nextToken();
}
tmp.addElement( (Sequence) currentAlignFrame.
getAlignViewport().getAlignment().
findName(seqstring));
}
seqs = new SequenceI[tmp.size()];
tmp.copyInto(seqs);
if(tmp2.size()==tmp.size())
{
chains = new String[tmp2.size()];
tmp2.copyInto(chains);
}
}
param = setProtocolState(param);
if (!jmolAvailable && protocol==AppletFormatAdapter.CLASSLOADER)
{
// TODO: pass PDB file in classloader on to Jmol
// This exception preserves the current behaviour where, even if the local pdb file was identified in the class loader
protocol = AppletFormatAdapter.URL; // this is probably NOT CORRECT!
param = addProtocol(param); //
}
pdb.setFile(param);
if(seqs!=null)
{
for (int i = 0; i < seqs.length; i++)
{
if (seqs[i]!=null)
{
( (Sequence) seqs[i]).addPDBId(pdb);
} else {
if (JalviewLite.debug)
{
// this may not really be a problem but we give a warning anyway
System.err.println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "+i+")");
}
}
}
if (jmolAvailable)
{
new jalview.appletgui.AppletJmol(pdb,
seqs,
chains,
currentAlignFrame.alignPanel,
protocol);
lastFrameX += 40;
lastFrameY+=40;
}
else
new MCview.AppletPDBViewer(pdb,
seqs,
chains,
currentAlignFrame.alignPanel,
protocol);
}
}
pdbFileCount++;
}
while(pdbFileCount < 10);
/////////////////////////////
// modify display of features
//
// hide specific groups
param = getParameter("hidefeaturegroups");
if (param != null)
{
applet.setFeatureGroupState(param, false);
}
// show specific groups
param = getParameter("showfeaturegroups");
if (param != null)
{
applet.setFeatureGroupState(param, true);
}
}
else
{
fileFound = false;
remove(launcher);
repaint();
}
}
/**
* Discovers whether the given file is in the Applet Archive
* @param file String
* @return boolean
*/
boolean inArchive(String file)
{
//This might throw a security exception in certain browsers
//Netscape Communicator for instance.
try
{
boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
if (debug)
{ System.err.println("Resource '"+file+"' was "+(rtn ? "" : "not") +" located by classloader.");
}
return rtn;
}
catch (Exception ex)
{
System.out.println("Exception checking resources: " + file + " " + ex);
return false;
}
}
String addProtocol(String file)
{
if (file.indexOf("://") == -1)
{
file = getCodeBase() + file;
if (debug)
{
System.err.println("Prepended codebase for resource: '"+file+"'");
}
}
return file;
}
}
/**
* @return the default alignFrame acted on by the public applet methods.
* May return null with an error message on System.err indicating the fact.
*/
protected AlignFrame getDefaultTargetFrame()
{
if (currentAlignFrame!=null)
{
return currentAlignFrame;
}
if (initialAlignFrame!=null)
{
return initialAlignFrame;
}
System.err.println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
return null;
}
/**
* separator used for separatorList
*/
protected String separator = "|"; // this is a safe(ish) separator - tabs don't work for firefox
/**
* parse the string into a list
* @param list
* @return elements separated by separator
*/
public String[] separatorListToArray(String list)
{
int seplen = separator.length();
if (list==null || list.equals(""))
return null;
java.util.Vector jv = new Vector();
int cp=0,pos;
while ((pos=list.indexOf(separator,cp))>cp)
{
jv.addElement(list.substring(cp,pos));
cp = pos+seplen;
}
if (cp0)
{ String[] v = new String[jv.size()];
for (int i=0; i