/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview 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 3 of the License, or (at your option) any later version.
*
* Jalview 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 Jalview. If not, see .
*/
package jalview.bin;
import jalview.api.SequenceStructureBinding;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AppletJmol;
import jalview.appletgui.EmbmenuFrame;
import jalview.appletgui.FeatureSettings;
import jalview.datamodel.Alignment;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JnetAnnotationMaker;
import java.applet.Applet;
import java.awt.Button;
import java.awt.Color;
import java.awt.Component;
import java.awt.Font;
import java.awt.Frame;
import java.awt.Graphics;
import java.awt.event.ActionEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.lang.reflect.Method;
import java.util.Enumeration;
import java.util.StringTokenizer;
import java.util.Vector;
/**
* 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;
}
// //////////////////////////////////////////////
// //////////////////////////////////////////////
public static int lastFrameX = 200;
public 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 = null;
/**
* 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 = null;
boolean embedded = false;
private boolean checkForJmol = true;
private boolean checkedForJmol = false; // ensure we don't check for jmol
// every time the app is re-inited
public boolean jmolAvailable = false;
private boolean alignPdbStructures = false;
public static boolean debug = false;
static String builddate = null, version = null;
private static void initBuildDetails()
{
if (builddate == null)
{
builddate = "unknown";
version = "test";
java.net.URL url = JalviewLite.class
.getResource("/.build_properties");
if (url != null)
{
try
{
BufferedReader reader = new BufferedReader(new InputStreamReader(
url.openStream()));
String line;
while ((line = reader.readLine()) != null)
{
if (line.indexOf("VERSION") > -1)
{
version = line.substring(line.indexOf("=") + 1);
}
if (line.indexOf("BUILD_DATE") > -1)
{
builddate = line.substring(line.indexOf("=") + 1);
}
}
} catch (Exception ex)
{
ex.printStackTrace();
}
}
}
}
public static String getBuildDate()
{
initBuildDetails();
return builddate;
}
public static String getVersion()
{
initBuildDetails();
return version;
}
/**
* init method for Jalview Applet
*/
public void init()
{
/**
* turn on extra applet debugging
*/
String dbg = getParameter("debug");
if (dbg != null)
{
debug = dbg.toLowerCase().equals("true");
}
if (debug)
{
System.err.println("JalviewLite Version " + getVersion());
System.err.println("Build Date : " + getBuildDate());
}
/**
* if true disable the check for jmol
*/
String chkforJmol = getParameter("nojmol");
if (chkforJmol != null)
{
checkForJmol = !chkforJmol.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();
}
}
final JalviewLite applet = this;
if (getParameter("embedded") != null
&& getParameter("embedded").equalsIgnoreCase("true"))
{
// Launch as embedded applet in page
embedded = true;
LoadingThread loader = new LoadingThread(file, applet);
loader.start();
}
else if (file != null)
{
if (getParameter("showbutton") == null
|| !getParameter("showbutton").equalsIgnoreCase("false"))
{
// Add the JalviewLite 'Button' to the page
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
LoadingThread loader = new LoadingThread(file, applet);
loader.start();
}
});
}
else
{
// Open jalviewLite immediately.
LoadingThread loader = new LoadingThread(file, applet);
loader.start();
}
}
else
{
// jalview initialisation with no alignment. loadAlignment() method can
// still be called to open new alignments.
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
{
private boolean running = false;
public void run()
{
if (running || checkedForJmol)
{
return;
}
running = true;
if (checkForJmol)
{
try
{
if (!System.getProperty("java.version").startsWith("1.1"))
{
Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
jmolAvailable = true;
}
if (!jmolAvailable)
{
System.out
.println("Jmol not available - Using MCview for structures");
}
} catch (java.lang.ClassNotFoundException ex)
{
}
}
else
{
jmolAvailable = false;
if (debug)
{
System.err
.println("Skipping Jmol check. Will use MCView (probably)");
}
}
checkedForJmol = true;
running = false;
}
public boolean notFinished()
{
return running || !checkedForJmol;
}
}
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;
String _file;
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)
{
this._file = _file;
applet = _applet;
}
public void run()
{
LoadJmolThread jmolchecker = new LoadJmolThread();
jmolchecker.start();
while (jmolchecker.notFinished())
{
// wait around until the Jmol check is complete.
try
{
Thread.sleep(2);
} catch (Exception e)
{
}
;
}
startLoading();
}
private void startLoading()
{
AlignFrame newAlignFrame;
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 + "'");
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 (debug)
{
try
{
FileParse fp = new FileParse(file, protocol);
String ln = null;
dbgMsg(">>>Dumping contents of '" + file + "' " + "("
+ protocol + ")");
while ((ln = fp.nextLine()) != null)
{
dbgMsg(ln);
}
dbgMsg(">>>Dump finished.");
} catch (Exception e)
{
System.err
.println("Exception when trying to dump the content of the file parameter.");
e.printStackTrace();
}
}
}
if ((al != null) && (al.getHeight() > 0))
{
dbgMsg("Successfully loaded file.");
newAlignFrame = new AlignFrame(al, applet, file, embedded);
if (initialAlignFrame == null)
{
initialAlignFrame = newAlignFrame;
}
// update the focus.
currentAlignFrame = newAlignFrame;
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
newAlignFrame.setTitle("Sequences from " + getDocumentBase());
}
newAlignFrame.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)
{
newAlignFrame.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);
newAlignFrame.parseFeaturesFile(param, protocol);
}
param = getParameter("showFeatureSettings");
if (param != null && param.equalsIgnoreCase("true"))
{
newAlignFrame.viewport.showSequenceFeatures(true);
new FeatureSettings(newAlignFrame.alignPanel);
}
param = getParameter("annotations");
if (param != null)
{
param = setProtocolState(param);
if (new AnnotationFile().readAnnotationFile(
newAlignFrame.viewport.getAlignment(), param, protocol))
{
newAlignFrame.alignPanel.fontChanged();
newAlignFrame.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,
newAlignFrame.viewport.getAlignment(), 0, false); // false==do
// not
// add
// sequence
// profile
// from
// concise
// output
newAlignFrame.alignPanel.fontChanged();
newAlignFrame.alignPanel.setScrollValues(0, 0);
} catch (Exception ex)
{
ex.printStackTrace();
}
}
/*
* Undocumented for 2.6
* - related to JAL-434
*/
applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
false));
/*
*
*
*
*
*
*/
int pdbFileCount = 0;
// Accumulate pdbs here if they are heading for the same view (if
// alignPdbStructures is true)
Vector pdbs = new Vector();
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) newAlignFrame.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) newAlignFrame.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: verify this Re:
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
// 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 (!alignPdbStructures)
{
newAlignFrame.newStructureView(applet, pdb, seqs, chains,
protocol);
}
else
{
pdbs.addElement(new Object[]
{ pdb, seqs, chains, new String(protocol) });
}
}
}
pdbFileCount++;
} while (pdbFileCount < 10);
if (pdbs.size() > 0)
{
SequenceI[][] seqs = new SequenceI[pdbs.size()][];
PDBEntry[] pdb = new PDBEntry[pdbs.size()];
String[][] chains = new String[pdbs.size()][];
String[] protocols = new String[pdbs.size()];
for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
{
Object[] o = (Object[]) pdbs.elementAt(pdbsi);
pdb[pdbsi] = (PDBEntry) o[0];
seqs[pdbsi] = (SequenceI[]) o[1];
chains[pdbsi] = (String[]) o[2];
protocols[pdbsi] = (String) o[3];
}
newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
protocols);
}
// ///////////////////////////
// modify display of features
//
// hide specific groups
param = getParameter("hidefeaturegroups");
if (param != null)
{
applet.setFeatureGroupStateOn(newAlignFrame, param, false);
}
// show specific groups
param = getParameter("showfeaturegroups");
if (param != null)
{
applet.setFeatureGroupStateOn(newAlignFrame, 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 (cp < list.length())
{
jv.addElement(list.substring(cp));
}
if (jv.size() > 0)
{
String[] v = new String[jv.size()];
for (int i = 0; i < v.length; i++)
{
v[i] = (String) jv.elementAt(i);
}
jv.removeAllElements();
if (debug)
{
System.err.println("Array from '" + separator
+ "' separated List:\n" + v.length);
for (int i = 0; i < v.length; i++)
{
System.err.println("item " + i + " '" + v[i] + "'");
}
}
return v;
}
if (debug)
{
System.err.println("Empty Array from '" + separator
+ "' separated List");
}
return null;
}
/**
* concatenate the list with separator
*
* @param list
* @return concatenated string
*/
public String arrayToSeparatorList(String[] list)
{
StringBuffer v = new StringBuffer();
if (list != null && list.length > 0)
{
for (int i = 0, iSize = list.length - 1; i < iSize; i++)
{
if (list[i] != null)
{
v.append(list[i]);
}
v.append(separator);
}
if (list[list.length - 1] != null)
{
v.append(list[list.length - 1]);
}
if (debug)
{
System.err.println("Returning '" + separator
+ "' separated List:\n");
System.err.println(v);
}
return v.toString();
}
if (debug)
{
System.err.println("Returning empty '" + separator
+ "' separated List\n");
}
return "";
}
/**
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroups()
*/
public String getFeatureGroups()
{
String lst = arrayToSeparatorList(getDefaultTargetFrame()
.getFeatureGroups());
return lst;
}
/**
* @param alf
* alignframe to get feature groups on
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroups()
*/
public String getFeatureGroupsOn(AlignFrame alf)
{
String lst = arrayToSeparatorList(alf.getFeatureGroups());
return lst;
}
/**
* @param visible
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
*/
public String getFeatureGroupsOfState(boolean visible)
{
return arrayToSeparatorList(getDefaultTargetFrame()
.getFeatureGroupsOfState(visible));
}
/**
* @param alf
* align frame to get groups of state visible
* @param visible
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
*/
public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
}
/**
* @param groups
* tab separated list of group names
* @param state
* true or false
* @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
* boolean)
*/
public void setFeatureGroupStateOn(AlignFrame alf, String groups,
boolean state)
{
boolean st = state;// !(state==null || state.equals("") ||
// state.toLowerCase().equals("false"));
alf.setFeatureGroupState(separatorListToArray(groups), st);
}
public void setFeatureGroupState(String groups, boolean state)
{
setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
}
/**
* List separator string
*
* @return the separator
*/
public String getSeparator()
{
return separator;
}
/**
* List separator string
*
* @param separator
* the separator to set
*/
public void setSeparator(String separator)
{
this.separator = separator;
}
/**
* get boolean value of applet parameter 'name' and return default if
* parameter is not set
*
* @param name
* name of paremeter
* @param def
* the value to return otherwise
* @return true or false
*/
public boolean getDefaultParameter(String name, boolean def)
{
String stn;
if ((stn = getParameter(name)) == null)
{
return def;
}
if (stn.toLowerCase().equals("true"))
{
return true;
}
return false;
}
/**
* bind a pdb file to a sequence in the given alignFrame.
*
* @param alFrame
* - null or specific alignFrame. This specifies the dataset that
* will be searched for a seuqence called sequenceId
* @param sequenceId
* - sequenceId within the dataset.
* @param pdbEntryString
* - the short name for the PDB file
* @param pdbFile
* - pdb file - either a URL or a valid PDB file.
* @return true if binding was as success TODO: consider making an exception
* structure for indicating when PDB parsing or seqeunceId location
* fails.
*/
public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
}
protected void setAlignPdbStructures(boolean alignPdbStructures)
{
this.alignPdbStructures = alignPdbStructures;
}
public boolean isAlignPdbStructures()
{
return alignPdbStructures;
}
/**
* get all components associated with the applet of the given type
*
* @param class1
* @return
*/
public Vector getAppletWindow(Class class1)
{
Vector wnds = new Vector();
Component[] cmp = getComponents();
if (cmp != null)
{
for (int i = 0; i < cmp.length; i++)
{
if (class1.isAssignableFrom(cmp[i].getClass()))
{
wnds.addElement(cmp);
}
}
}
return wnds;
}
/**
* bind structures in a viewer to any matching sequences in an alignFrame (use
* sequenceIds to limit scope of search to specific sequences)
*
* @param alFrame
* @param viewer
* @param sequenceIds
* @return TODO: consider making an exception structure for indicating when
* binding fails public SequenceStructureBinding
* addStructureViewInstance( AlignFrame alFrame, Object viewer, String
* sequenceIds) {
*
* if (sequenceIds != null && sequenceIds.length() > 0) { return
* alFrame.addStructureViewInstance(viewer,
* separatorListToArray(sequenceIds)); } else { return
* alFrame.addStructureViewInstance(viewer, null); } // return null; }
*/
}