/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
import java.util.Locale;
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AlignViewport;
import jalview.appletgui.EmbmenuFrame;
import jalview.appletgui.FeatureSettings;
import jalview.appletgui.SplitFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
import jalview.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import java.applet.Applet;
import java.awt.Button;
import java.awt.Color;
import java.awt.Component;
import java.awt.EventQueue;
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.IOException;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
import netscape.javascript.JSObject;
/**
* Jalview Applet. Runs in Java 1.18 runtime
*
* @author $author$
* @version $Revision: 1.92 $
*/
public class JalviewLite extends Applet
implements StructureSelectionManagerProvider, JalviewLiteJsApi
{
private static final String TRUE = "true";
private static final String FALSE = "false";
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager.getStructureSelectionManager(this);
}
// /////////////////////////////////////////
// The following public methods may be called
// externally, eg via javascript in HTML page
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
*/
@Override
public String getSelectedSequences()
{
return getSelectedSequencesFrom(getDefaultTargetFrame());
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
*/
@Override
public String getSelectedSequences(String sep)
{
return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame)
*/
@Override
public String getSelectedSequencesFrom(AlignFrame alf)
{
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
@Override
public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
sep = separator; // "+0x00AC;
}
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();
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
* java.lang.String, java.lang.String)
*/
@Override
public void highlight(String sequenceId, String position,
String alignedPosition)
{
highlightIn(getDefaultTargetFrame(), sequenceId, position,
alignedPosition);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public void highlightIn(final AlignFrame alf, final String sequenceId,
final String position, final String alignedPosition)
{
// TODO: could try to highlight in all alignments if alf==null
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
alf.viewport.getAlignment().getSequencesArray());
final SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
{
int apos = -1;
try
{
apos = Integer.valueOf(position).intValue();
apos--;
} catch (NumberFormatException ex)
{
return;
}
final StructureSelectionManagerProvider me = this;
final int pos = apos;
// use vamsas listener to broadcast to all listeners in scope
if (alignedPosition != null
&& (alignedPosition.trim().length() == 0 || alignedPosition
.toLowerCase(Locale.ROOT).indexOf("false") > -1))
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
StructureSelectionManager.getStructureSelectionManager(me)
.mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
}
});
}
else
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
StructureSelectionManager.getStructureSelectionManager(me)
.mouseOverVamsasSequence(sq, pos, null);
}
});
}
}
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
* java.lang.String)
*/
@Override
public void select(String sequenceIds, String columns)
{
selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
* java.lang.String, java.lang.String)
*/
@Override
public void select(String sequenceIds, String columns, String sep)
{
selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
@Override
public void selectIn(AlignFrame alf, String sequenceIds, String columns)
{
selectIn(alf, sequenceIds, columns, separator);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public void selectIn(final AlignFrame alf, String sequenceIds,
String columns, String sep)
{
if (sep == null || sep.length() == 0)
{
sep = separator;
}
else
{
if (debug)
{
System.err.println("Selecting region using separator string '"
+ separator + "'");
}
}
// deparse fields
String[] ids = separatorListToArray(sequenceIds, sep);
String[] cols = separatorListToArray(columns, sep);
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
AlignmentI al = alf.viewport.getAlignment();
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
alf.viewport.getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
boolean seqsfound = true;
if (ids != null && ids.length > 0)
{
seqsfound = false;
for (int i = 0; i < ids.length; i++)
{
if (ids[i].trim().length() == 0)
{
continue;
}
SequenceI sq = matcher.findIdMatch(ids[i]);
if (sq != null)
{
seqsfound = true;
sel.addSequence(sq, false);
}
}
}
boolean inseqpos = false;
if (cols != null && cols.length > 0)
{
boolean seset = false;
for (int i = 0; i < cols.length; i++)
{
String cl = cols[i].trim();
if (cl.length() == 0)
{
continue;
}
int p;
if ((p = cl.indexOf("-")) > -1)
{
int from = -1, to = -1;
try
{
from = Integer.valueOf(cl.substring(0, p)).intValue();
from--;
} catch (NumberFormatException ex)
{
System.err.println(
"ERROR: Couldn't parse first integer in range element column selection string '"
+ cl + "' - format is 'from-to'");
return;
}
try
{
to = Integer.valueOf(cl.substring(p + 1)).intValue();
to--;
} catch (NumberFormatException ex)
{
System.err.println(
"ERROR: Couldn't parse second integer in range element column selection string '"
+ cl + "' - format is 'from-to'");
return;
}
if (from >= 0 && to >= 0)
{
// valid range
if (from < to)
{
int t = to;
to = from;
to = t;
}
if (!seset)
{
start = from;
end = to;
seset = true;
}
else
{
// comment to prevent range extension
if (start > from)
{
start = from;
}
if (end < to)
{
end = to;
}
}
for (int r = from; r <= to; r++)
{
if (r >= 0 && r < alw)
{
csel.addElement(r);
}
}
if (debug)
{
System.err.println("Range '" + cl + "' deparsed as [" + from
+ "," + to + "]");
}
}
else
{
System.err.println("ERROR: Invalid Range '" + cl
+ "' deparsed as [" + from + "," + to + "]");
}
}
else
{
int r = -1;
try
{
r = Integer.valueOf(cl).intValue();
r--;
} catch (NumberFormatException ex)
{
if (cl.toLowerCase(Locale.ROOT).equals("sequence"))
{
// we are in the dataset sequence's coordinate frame.
inseqpos = true;
}
else
{
System.err.println(
"ERROR: Couldn't parse integer from point selection element of column selection string '"
+ cl + "'");
return;
}
}
if (r >= 0 && r <= alw)
{
if (!seset)
{
start = r;
end = r;
seset = true;
}
else
{
// comment to prevent range extension
if (start > r)
{
start = r;
}
if (end < r)
{
end = r;
}
}
csel.addElement(r);
if (debug)
{
System.err.println("Point selection '" + cl
+ "' deparsed as [" + r + "]");
}
}
else
{
System.err.println("ERROR: Invalid Point selection '" + cl
+ "' deparsed as [" + r + "]");
}
}
}
}
if (seqsfound)
{
// we only propagate the selection when it was the null selection, or the
// given sequences were found in the alignment.
if (inseqpos && sel.getSize() > 0)
{
// assume first sequence provides reference frame ?
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
List cs = new ArrayList<>(csel.getSelected());
csel.clear();
for (Integer selectedCol : cs)
{
csel.addElement(rs.findIndex(selectedCol));
}
}
sel.setStartRes(start);
sel.setEndRes(end);
EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
alf.select(sel, csel,
alf.getAlignViewport().getAlignment().getHiddenColumns());
}
});
}
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
* String, java.lang.String)
*/
@Override
public String getSelectedSequencesAsAlignment(String format,
String suffix)
{
return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
format, suffix);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
* .appletgui.AlignFrame, java.lang.String, java.lang.String)
*/
@Override
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix)
{
try
{
FileFormatI theFormat = FileFormats.getInstance().forName(format);
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
if (alf.viewport.getSelectionGroup() != null)
{
// JBPNote: getSelectionAsNewSequence behaviour has changed - this
// method now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
String reply = new AppletFormatAdapter().formatSequences(theFormat,
new Alignment(alf.viewport.getSelectionAsNewSequence()),
seqlimits);
return reply;
}
} catch (IllegalArgumentException ex)
{
ex.printStackTrace();
return "Error retrieving alignment, possibly invalid format specifier: "
+ format;
}
return "";
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
*/
@Override
public String getAlignmentOrder()
{
return getAlignmentOrderFrom(getDefaultTargetFrame());
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* )
*/
@Override
public String getAlignmentOrderFrom(AlignFrame alf)
{
return getAlignmentOrderFrom(alf, separator);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
@Override
public String getAlignmentOrderFrom(AlignFrame alf, String sep)
{
AlignmentI alorder = alf.getAlignViewport().getAlignment();
String[] order = new String[alorder.getHeight()];
for (int i = 0; i < order.length; i++)
{
order[i] = alorder.getSequenceAt(i).getName();
}
return arrayToSeparatorList(order);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
* java.lang.String)
*/
@Override
public String orderBy(String order, String undoName)
{
return orderBy(order, undoName, separator);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
* java.lang.String, java.lang.String)
*/
@Override
public String orderBy(String order, String undoName, String sep)
{
return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep)
{
String[] ids = separatorListToArray(order, sep);
SequenceI[] sqs = null;
if (ids != null && ids.length > 0)
{
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
alf.viewport.getAlignment().getSequencesArray());
int s = 0;
sqs = new SequenceI[ids.length];
for (int i = 0; i < ids.length; i++)
{
if (ids[i].trim().length() == 0)
{
continue;
}
SequenceI sq = matcher.findIdMatch(ids[i]);
if (sq != null)
{
sqs[s++] = sq;
}
}
if (s > 0)
{
SequenceI[] sqq = new SequenceI[s];
System.arraycopy(sqs, 0, sqq, 0, s);
sqs = sqq;
}
else
{
sqs = null;
}
}
if (sqs == null)
{
return "";
}
;
final AlignmentOrder aorder = new AlignmentOrder(sqs);
if (undoName != null && undoName.trim().length() == 0)
{
undoName = null;
}
final String _undoName = undoName;
// TODO: deal with synchronization here: cannot raise any events until after
// this has returned.
return alf.sortBy(aorder, _undoName) ? TRUE : "";
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
*/
@Override
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
@Override
public String getAlignmentFrom(AlignFrame alf, String format)
{
return getAlignmentFrom(alf, format, TRUE);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
* java.lang.String)
*/
@Override
public String getAlignment(String format, String suffix)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
@Override
public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
try
{
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
FileFormatI theFormat = FileFormats.getInstance().forName(format);
String reply = new AppletFormatAdapter().formatSequences(theFormat,
alf.viewport.getAlignment(), seqlimits);
return reply;
} catch (IllegalArgumentException ex)
{
ex.printStackTrace();
return "Error retrieving alignment, possibly invalid format specifier: "
+ format;
}
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
*/
@Override
public void loadAnnotation(String annotation)
{
loadAnnotationFrom(getDefaultTargetFrame(), annotation);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
@Override
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
annotation, DataSourceType.PASTE))
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
}
else
{
alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
}
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
*/
@Override
public void loadFeatures(String features, boolean autoenabledisplay)
{
loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
@Override
public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay)
{
return alf.parseFeaturesFile(features, DataSourceType.PASTE,
autoenabledisplay);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
*/
@Override
public String getFeatures(String format)
{
return getFeaturesFrom(getDefaultTargetFrame(), format);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
@Override
public String getFeaturesFrom(AlignFrame alf, String format)
{
return alf.outputFeatures(false, format);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getAnnotation()
*/
@Override
public String getAnnotation()
{
return getAnnotationFrom(getDefaultTargetFrame());
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
* )
*/
@Override
public String getAnnotationFrom(AlignFrame alf)
{
return alf.outputAnnotations(false);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#newView()
*/
@Override
public AlignFrame newView()
{
return newViewFrom(getDefaultTargetFrame());
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
*/
@Override
public AlignFrame newView(String name)
{
return newViewFrom(getDefaultTargetFrame(), name);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
*/
@Override
public AlignFrame newViewFrom(AlignFrame alf)
{
return alf.newView(null);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
* java.lang.String)
*/
@Override
public AlignFrame newViewFrom(AlignFrame alf, String name)
{
return alf.newView(name);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
* java.lang.String)
*/
@Override
public AlignFrame loadAlignment(String text, String title)
{
AlignmentI al = null;
try
{
FileFormatI format = new IdentifyFile().identify(text,
DataSourceType.PASTE);
al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
format);
if (al.getHeight() > 0)
{
return new AlignFrame(al, this, title, false);
}
} catch (IOException ex)
{
ex.printStackTrace();
}
return null;
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
*/
@Override
public void setMouseoverListener(String listener)
{
setMouseoverListener(currentAlignFrame, listener);
}
private Vector javascriptListeners = new Vector<>();
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
@Override
public void setMouseoverListener(AlignFrame af, String listener)
{
if (listener != null)
{
listener = listener.trim();
if (listener.length() == 0)
{
System.err.println(
"jalview Javascript error: Ignoring empty function for mouseover listener.");
return;
}
}
jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
this, af, listener);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
if (debug)
{
System.err.println("Added a mouseover listener for "
+ ((af == null) ? "All frames"
: "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
*/
@Override
public void setSelectionListener(String listener)
{
setSelectionListener(null, listener);
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
* , java.lang.String)
*/
@Override
public void setSelectionListener(AlignFrame af, String listener)
{
if (listener != null)
{
listener = listener.trim();
if (listener.length() == 0)
{
System.err.println(
"jalview Javascript error: Ignoring empty function for selection listener.");
return;
}
}
jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
this, af, listener);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addSelectionListener(mol);
if (debug)
{
System.err.println("Added a selection listener for "
+ ((af == null) ? "All frames"
: "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
/**
* Callable from javascript to register a javascript function to pass events
* to a structure viewer.
*
* @param listener
* the name of a javascript function
* @param modelSet
* a token separated list of PDB file names listened for
* @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
* java.lang.String)
*/
@Override
public void setStructureListener(String listener, String modelSet)
{
if (listener != null)
{
listener = listener.trim();
if (listener.length() == 0)
{
System.err.println(
"jalview Javascript error: Ignoring empty function for selection listener.");
return;
}
}
MouseOverStructureListener mol = new MouseOverStructureListener(this,
listener, separatorListToArray(modelSet));
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
if (debug)
{
System.err.println("Added a javascript structure viewer listener '"
+ listener + "'");
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
@Override
public void removeJavascriptListener(AlignFrame af, String listener)
{
if (listener != null)
{
listener = listener.trim();
if (listener.length() == 0)
{
listener = null;
}
}
boolean rprt = false;
for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
{
Object lstn = javascriptListeners.elementAt(ms);
JsCallBack lstner = (JsCallBack) lstn;
if ((af == null || lstner.getAlignFrame() == af) && (listener == null
|| lstner.getListenerFunction().equals(listener)))
{
javascriptListeners.removeElement(lstner);
msSize--;
if (lstner instanceof SelectionListener)
{
StructureSelectionManager.getStructureSelectionManager(this)
.removeSelectionListener((SelectionListener) lstner);
}
else
{
StructureSelectionManager.getStructureSelectionManager(this)
.removeStructureViewerListener(lstner, null);
}
rprt = debug;
if (debug)
{
System.err.println("Removed listener '" + listener + "'");
}
}
else
{
ms++;
}
}
if (rprt)
{
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
@Override
public void stop()
{
System.err.println("Applet " + getName() + " stop().");
tidyUp();
}
@Override
public void destroy()
{
System.err.println("Applet " + getName() + " destroy().");
tidyUp();
}
private void tidyUp()
{
removeAll();
if (currentAlignFrame != null && currentAlignFrame.viewport != null
&& currentAlignFrame.viewport.applet != null)
{
AlignViewport av = currentAlignFrame.viewport;
currentAlignFrame.closeMenuItem_actionPerformed();
av.applet = null;
currentAlignFrame = null;
}
if (javascriptListeners != null)
{
while (javascriptListeners.size() > 0)
{
jalview.javascript.JSFunctionExec mol = javascriptListeners
.elementAt(0);
javascriptListeners.removeElement(mol);
if (mol instanceof SelectionListener)
{
StructureSelectionManager.getStructureSelectionManager(this)
.removeSelectionListener((SelectionListener) mol);
}
else
{
StructureSelectionManager.getStructureSelectionManager(this)
.removeStructureViewerListener(mol, null);
}
mol.jvlite = null;
}
}
if (jsFunctionExec != null)
{
jsFunctionExec.stopQueue();
jsFunctionExec.jvlite = null;
}
initialAlignFrame = null;
jsFunctionExec = null;
javascriptListeners = null;
StructureSelectionManager.release(this);
}
private jalview.javascript.JSFunctionExec jsFunctionExec;
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
* java.lang.String, java.lang.String)
*/
@Override
public void mouseOverStructure(final String pdbResNum, final String chain,
final String pdbfile)
{
final StructureSelectionManagerProvider me = this;
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
try
{
StructureSelectionManager.getStructureSelectionManager(me)
.mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
chain, pdbfile);
if (debug)
{
System.err
.println("mouseOver for '" + pdbResNum + "' in chain '"
+ chain + "' in structure '" + pdbfile + "'");
}
} catch (NumberFormatException e)
{
System.err.println("Ignoring invalid residue number string '"
+ pdbResNum + "'");
}
}
});
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String)
*/
@Override
public void scrollViewToIn(final AlignFrame alf, final String topRow,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
try
{
alf.scrollTo(Integer.valueOf(topRow).intValue(),
Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
System.err.println("Couldn't parse integer arguments (topRow='"
+ topRow + "' and leftHandColumn='" + leftHandColumn
+ "')");
ex.printStackTrace();
}
}
});
}
/*
* (non-Javadoc)
*
* @see
* jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
@Override
public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
try
{
alf.scrollToRow(Integer.valueOf(topRow).intValue());
} catch (Exception ex)
{
System.err.println("Couldn't parse integer arguments (topRow='"
+ topRow + "')");
ex.printStackTrace();
}
}
});
}
/*
* (non-Javadoc)
*
* @see
* jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
@Override
public void scrollViewToColumnIn(final AlignFrame alf,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
try
{
alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
System.err.println(
"Couldn't parse integer arguments (leftHandColumn='"
+ leftHandColumn + "')");
ex.printStackTrace();
}
}
});
}
// //////////////////////////////////////////////
// //////////////////////////////////////////////
public static int lastFrameX = 200;
public static int lastFrameY = 200;
boolean fileFound = true;
String file = "No file";
String file2 = null;
Button launcher = new Button(
MessageManager.getString("label.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 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;
/**
* use an external structure viewer exclusively (no jmols or mc_views will be
* opened by JalviewLite itself)
*/
public boolean useXtrnalSviewer = false;
public static boolean debug = false;
static String builddate = null, version = null, installation = null;
private static void initBuildDetails()
{
if (builddate == null)
{
builddate = "unknown";
version = "test";
installation = "applet";
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);
}
if (line.indexOf("INSTALLATION") > -1)
{
installation = line.substring(line.indexOf("=") + 1);
}
}
} catch (Exception ex)
{
ex.printStackTrace();
}
}
}
}
public static String getBuildDate()
{
initBuildDetails();
return builddate;
}
public static String getInstallation()
{
initBuildDetails();
return installation;
}
public static String getVersion()
{
initBuildDetails();
return version;
}
// public JSObject scriptObject = null;
/**
* init method for Jalview Applet
*/
@Override
public void init()
{
debug = TRUE.equalsIgnoreCase(getParameter("debug"));
try
{
if (debug)
{
System.err.println("Applet context is '"
+ getAppletContext().getClass().toString() + "'");
}
JSObject scriptObject = JSObject.getWindow(this);
if (debug && scriptObject != null)
{
System.err.println("Applet has Javascript callback support.");
}
} catch (Exception ex)
{
System.err.println(
"Warning: No JalviewLite javascript callbacks available.");
if (debug)
{
ex.printStackTrace();
}
}
if (debug)
{
System.err.println("JalviewLite Version " + getVersion());
System.err.println("Build Date : " + getBuildDate());
System.err.println("Installation : " + getInstallation());
}
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT)
.equals(TRUE);
}
/**
* 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(MessageManager
.getString("error.invalid_separator_parameter"));
}
}
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);
}
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();
}
}
if (getDefaultParameter("enableSplitFrame", true))
{
file2 = getParameter("file2");
}
embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
if (embedded)
{
LoadingThread loader = new LoadingThread(file, file2, this);
loader.start();
}
else if (file != null)
{
/*
* Start the applet immediately or show a button to start it
*/
if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
{
LoadingThread loader = new LoadingThread(file, file2, this);
loader.start();
}
else
{
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
LoadingThread loader = new LoadingThread(file, file2,
JalviewLite.this);
loader.start();
}
});
}
}
else
{
// jalview initialisation with no alignment. loadAlignment() method can
// still be called to open new alignments.
file = "NO FILE";
fileFound = false;
callInitCallback();
}
}
private void initLiveConnect()
{
// try really hard to get the liveConnect thing working
boolean notFailed = false;
int tries = 0;
while (!notFailed && tries < 10)
{
if (tries > 0)
{
System.err.println("LiveConnect request thread going to sleep.");
}
try
{
Thread.sleep(700 * (1 + tries));
} catch (InterruptedException q)
{
}
;
if (tries++ > 0)
{
System.err.println("LiveConnect request thread woken up.");
}
try
{
JSObject scriptObject = JSObject.getWindow(this);
if (scriptObject.eval("navigator") != null)
{
notFailed = true;
}
} catch (Exception jsex)
{
System.err.println("Attempt " + tries
+ " to access LiveConnect javascript failed.");
}
}
}
private void callInitCallback()
{
String initjscallback = getParameter("oninit");
if (initjscallback == null)
{
return;
}
initjscallback = initjscallback.trim();
if (initjscallback.length() > 0)
{
JSObject scriptObject = null;
try
{
scriptObject = JSObject.getWindow(this);
} catch (Exception ex)
{
}
;
// try really hard to let the browser plugin know we want liveconnect
initLiveConnect();
if (scriptObject != null)
{
try
{
// do onInit with the JS executor thread
new JSFunctionExec(this).executeJavascriptFunction(true,
initjscallback, null,
"Calling oninit callback '" + initjscallback + "'.");
} catch (Exception e)
{
System.err.println("Exception when executing _oninit callback '"
+ initjscallback + "'.");
e.printStackTrace();
}
}
else
{
System.err.println("Not executing _oninit callback '"
+ initjscallback + "' - no scripting allowed.");
}
}
}
/**
* 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()
{
@Override
public void windowClosing(WindowEvent e)
{
if (frame instanceof AlignFrame)
{
AlignViewport vp = ((AlignFrame) frame).viewport;
((AlignFrame) frame).closeMenuItem_actionPerformed();
if (vp.applet.currentAlignFrame == frame)
{
vp.applet.currentAlignFrame = null;
}
vp.applet = null;
vp = null;
}
lastFrameX -= 40;
lastFrameY -= 40;
if (frame instanceof EmbmenuFrame)
{
((EmbmenuFrame) frame).destroyMenus();
}
frame.setMenuBar(null);
frame.dispose();
}
@Override
public void windowActivated(WindowEvent e)
{
if (frame instanceof AlignFrame)
{
((AlignFrame) frame).viewport.applet.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
*/
@Override
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(
MessageManager.getString("label.jalview_cannot_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(MessageManager.getString("label.jalview_applet"), 50,
getSize().height / 2 - 30);
g.drawString(MessageManager.getString("label.loading_data") + "...",
50, getSize().height / 2);
}
}
/**
* 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;
}
class LoadJmolThread extends Thread
{
private boolean running = false;
@Override
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 mc_view for structures");
}
} catch (java.lang.ClassNotFoundException ex)
{
}
}
else
{
jmolAvailable = false;
if (debug)
{
System.err.println(
"Skipping Jmol check. Will use mc_view (probably)");
}
}
checkedForJmol = true;
running = false;
}
public boolean notFinished()
{
return running || !checkedForJmol;
}
}
class LoadingThread extends Thread
{
/**
* State variable: protocol for access to file source
*/
DataSourceType protocol;
String _file; // alignment file or URL spec
String _file2; // second alignment file or URL spec
JalviewLite applet;
private void dbgMsg(String msg)
{
if (JalviewLite.debug)
{
System.err.println(msg);
}
}
/**
* update the protocol state variable for accessing the datasource located
* by file.
*
* @param path
* @return possibly updated datasource string
*/
public String resolveFileProtocol(String path)
{
/*
* is it paste data?
*/
if (path.startsWith("PASTE"))
{
protocol = DataSourceType.PASTE;
return path.substring(5);
}
/*
* is it a URL?
*/
if (path.indexOf("://") != -1)
{
protocol = DataSourceType.URL;
return path;
}
/*
* try relative to document root
*/
URL documentBase = getDocumentBase();
String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
if (HttpUtils.isValidUrl(withDocBase))
{
if (debug)
{
System.err.println("Prepended document base '" + documentBase
+ "' to make: '" + withDocBase + "'");
}
protocol = DataSourceType.URL;
return withDocBase;
}
/*
* try relative to codebase (if different to document base)
*/
URL codeBase = getCodeBase();
String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
codeBase);
if (!withCodeBase.equals(withDocBase)
&& HttpUtils.isValidUrl(withCodeBase))
{
protocol = DataSourceType.URL;
if (debug)
{
System.err.println("Prepended codebase '" + codeBase
+ "' to make: '" + withCodeBase + "'");
}
return withCodeBase;
}
/*
* try locating by classloader; try this last so files in the directory
* are resolved using document base
*/
if (inArchive(path))
{
protocol = DataSourceType.CLASSLOADER;
}
return path;
}
public LoadingThread(String file, String file2, JalviewLite _applet)
{
this._file = file;
this._file2 = file2;
applet = _applet;
}
@Override
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();
// applet.callInitCallback();
}
/**
* Load the alignment and any related files as specified by applet
* parameters
*/
private void startLoading()
{
dbgMsg("Loading thread started with:\n>>file\n" + _file
+ ">>endfile");
dbgMsg("Loading started.");
AlignFrame newAlignFrame = readAlignment(_file);
AlignFrame newAlignFrame2 = readAlignment(_file2);
if (newAlignFrame != null)
{
addToDisplay(newAlignFrame, newAlignFrame2);
loadTree(newAlignFrame);
loadScoreFile(newAlignFrame);
loadFeatures(newAlignFrame);
loadAnnotations(newAlignFrame);
loadJnetFile(newAlignFrame);
loadPdbFiles(newAlignFrame);
}
else
{
fileFound = false;
applet.remove(launcher);
applet.repaint();
}
callInitCallback();
}
/**
* Add an AlignFrame to the display; or if two are provided, a SplitFrame.
*
* @param af
* @param af2
*/
public void addToDisplay(AlignFrame af, AlignFrame af2)
{
if (af2 != null)
{
AlignmentI al1 = af.viewport.getAlignment();
AlignmentI al2 = af2.viewport.getAlignment();
AlignmentI cdna = al1.isNucleotide() ? al1 : al2;
AlignmentI prot = al1.isNucleotide() ? al2 : al1;
if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna))
{
al2.alignAs(al1);
SplitFrame sf = new SplitFrame(af, af2);
sf.addToDisplay(embedded, JalviewLite.this);
return;
}
else
{
String msg = "Could not map any sequence in " + af2.getTitle()
+ " as "
+ (al1.isNucleotide() ? "protein product" : "cDNA")
+ " for " + af.getTitle();
System.err.println(msg);
}
}
af.addToDisplay(embedded);
}
/**
* Read the alignment file (from URL, text 'paste', or archive by
* classloader).
*
* @return
*/
protected AlignFrame readAlignment(String fileParam)
{
if (fileParam == null)
{
return null;
}
String resolvedFile = resolveFileProtocol(fileParam);
AlignmentI al = null;
try
{
FileFormatI format = new IdentifyFile().identify(resolvedFile,
protocol);
dbgMsg("File identified as '" + format + "'");
al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
format);
if ((al != null) && (al.getHeight() > 0))
{
dbgMsg("Successfully loaded file.");
al.setDataset(null);
AlignFrame newAlignFrame = new AlignFrame(al, applet,
resolvedFile, embedded, false);
newAlignFrame.setTitle(resolvedFile);
if (initialAlignFrame == null)
{
initialAlignFrame = newAlignFrame;
}
// update the focus.
currentAlignFrame = newAlignFrame;
if (protocol == DataSourceType.PASTE)
{
newAlignFrame.setTitle(MessageManager
.formatMessage("label.sequences_from", new Object[]
{ applet.getDocumentBase().toString() }));
}
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
"label.successfully_loaded_file", new Object[]
{ resolvedFile }));
return newAlignFrame;
}
} catch (java.io.IOException ex)
{
dbgMsg("File load exception.");
ex.printStackTrace();
if (debug)
{
try
{
FileParse fp = new FileParse(resolvedFile, protocol);
String ln = null;
dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
+ 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();
}
}
}
return null;
}
/**
* Load PDBFiles if any specified by parameter(s). Returns true if loaded,
* else false.
*
* @param alignFrame
* @return
*/
protected boolean loadPdbFiles(AlignFrame alignFrame)
{
boolean result = false;
/*
* 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();
// create a lazy matcher if we're asked to
jalview.analysis.SequenceIdMatcher matcher = (applet
.getDefaultParameter("relaxedidmatch", false))
? new jalview.analysis.SequenceIdMatcher(
alignFrame.getAlignViewport().getAlignment()
.getSequencesArray())
: null;
String param;
do
{
if (pdbFileCount > 0)
{
param = applet.getParameter("PDBFILE" + pdbFileCount);
}
else
{
param = applet.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[] { matcher == null
? (Sequence) alignFrame.getAlignViewport()
.getAlignment().findName(sequence)
: matcher.findIdMatch(sequence) };
}
}
else
{
param = st.nextToken();
List tmp = new ArrayList<>();
List tmp2 = new ArrayList<>();
while (st.hasMoreTokens())
{
seqstring = st.nextToken();
StringTokenizer st2 = new StringTokenizer(seqstring, "=");
if (st2.countTokens() > 1)
{
// This is the chain
tmp2.add(st2.nextToken());
seqstring = st2.nextToken();
}
tmp.add(matcher == null
? (Sequence) alignFrame.getAlignViewport()
.getAlignment().findName(seqstring)
: matcher.findIdMatch(seqstring));
}
seqs = tmp.toArray(new SequenceI[tmp.size()]);
if (tmp2.size() == tmp.size())
{
chains = tmp2.toArray(new String[tmp2.size()]);
}
}
param = resolveFileProtocol(param);
// TODO check JAL-357 for files in a jar (CLASSLOADER)
pdb.setFile(param);
if (seqs != null)
{
for (int i = 0; i < seqs.length; i++)
{
if (seqs[i] != null)
{
((Sequence) seqs[i]).addPDBId(pdb);
StructureSelectionManager
.getStructureSelectionManager(applet)
.registerPDBEntry(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)
{
alignFrame.newStructureView(applet, pdb, seqs, chains,
protocol);
}
else
{
pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
}
}
}
pdbFileCount++;
} while (param != null || 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];
}
alignFrame.alignedStructureView(applet, pdb, seqs, chains,
protocols);
result = true;
}
return result;
}
/**
* Load in a Jnetfile if specified by parameter. Returns true if loaded,
* else false.
*
* @param alignFrame
* @return
*/
protected boolean loadJnetFile(AlignFrame alignFrame)
{
boolean result = false;
String param = applet.getParameter("jnetfile");
if (param == null)
{
// jnet became jpred around 2016
param = applet.getParameter("jpredfile");
}
if (param != null)
{
try
{
param = resolveFileProtocol(param);
JPredFile predictions = new JPredFile(param, protocol);
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
// false == do not add sequence profile from concise output
alignFrame.viewport.getAlignment().setupJPredAlignment();
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
} catch (Exception ex)
{
ex.printStackTrace();
}
}
return result;
}
/**
* Load annotations if specified by parameter. Returns true if loaded, else
* false.
*
* @param alignFrame
* @return
*/
protected boolean loadAnnotations(AlignFrame alignFrame)
{
boolean result = false;
String param = applet.getParameter("annotations");
if (param != null)
{
param = resolveFileProtocol(param);
if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
param, protocol))
{
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
}
else
{
System.err.println(
"Annotations were not added from annotation file '"
+ param + "'");
}
}
return result;
}
/**
* Load features file and view settings as specified by parameters. Returns
* true if features were loaded, else false.
*
* @param alignFrame
* @return
*/
protected boolean loadFeatures(AlignFrame alignFrame)
{
boolean result = false;
// ///////////////////////////
// modify display of features
// we do this before any features have been loaded, ensuring any hidden
// groups are hidden when features first displayed
//
// hide specific groups
//
String param = applet.getParameter("hidefeaturegroups");
if (param != null)
{
alignFrame.setFeatureGroupState(separatorListToArray(param), false);
// applet.setFeatureGroupStateOn(newAlignFrame, param, false);
}
// show specific groups
param = applet.getParameter("showfeaturegroups");
if (param != null)
{
alignFrame.setFeatureGroupState(separatorListToArray(param), true);
// applet.setFeatureGroupStateOn(newAlignFrame, param, true);
}
// and now load features
param = applet.getParameter("features");
if (param != null)
{
param = resolveFileProtocol(param);
result = alignFrame.parseFeaturesFile(param, protocol);
}
param = applet.getParameter("showFeatureSettings");
if (param != null && param.equalsIgnoreCase(TRUE))
{
alignFrame.viewport.setShowSequenceFeatures(true);
new FeatureSettings(alignFrame.alignPanel);
}
return result;
}
/**
* Load a score file if specified by parameter. Returns true if file was
* loaded, else false.
*
* @param alignFrame
*/
protected boolean loadScoreFile(AlignFrame alignFrame)
{
boolean result = false;
String sScoreFile = applet.getParameter("scoreFile");
if (sScoreFile != null && !"".equals(sScoreFile))
{
try
{
if (debug)
{
System.err.println(
"Attempting to load T-COFFEE score file from the scoreFile parameter");
}
result = alignFrame.loadScoreFile(sScoreFile);
if (!result)
{
System.err.println(
"Failed to parse T-COFFEE parameter as a valid score file ('"
+ sScoreFile + "')");
}
} catch (Exception e)
{
System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
sScoreFile, e.getMessage());
}
}
return result;
}
/**
* Load a tree for the alignment if specified by parameter. Returns true if
* a tree was loaded, else false.
*
* @param alignFrame
* @return
*/
protected boolean loadTree(AlignFrame alignFrame)
{
boolean result = false;
String treeFile = applet.getParameter("tree");
if (treeFile == null)
{
treeFile = applet.getParameter("treeFile");
}
if (treeFile != null)
{
try
{
treeFile = resolveFileProtocol(treeFile);
NewickFile fin = new NewickFile(treeFile, protocol);
fin.parse();
if (fin.getTree() != null)
{
alignFrame.loadTree(fin, treeFile);
result = true;
dbgMsg("Successfully imported tree.");
}
else
{
dbgMsg("Tree parameter did not resolve to a valid tree.");
}
} catch (Exception ex)
{
ex.printStackTrace();
}
}
return result;
}
/**
* Discovers whether the given file is in the Applet Archive
*
* @param f
* String
* @return boolean
*/
boolean inArchive(String f)
{
// This might throw a security exception in certain browsers
// Netscape Communicator for instance.
try
{
boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
if (debug)
{
System.err.println("Resource '" + f + "' was "
+ (rtn ? "" : "not ") + "located by classloader.");
}
return rtn;
} catch (Exception ex)
{
System.out.println("Exception checking resources: " + f + " " + ex);
return false;
}
}
}
/**
* @return the default alignFrame acted on by the public applet methods. May
* return null with an error message on System.err indicating the
* fact.
*/
public 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 = "" + ((char) 0x00AC); // the default used to be
// '|' but many sequence
// IDS include pipes.
/**
* set to enable the URL based javascript execution mechanism
*/
public boolean jsfallbackEnabled = false;
/**
* parse the string into a list
*
* @param list
* @return elements separated by separator
*/
public String[] separatorListToArray(String list)
{
return separatorListToArray(list, separator);
}
/**
* parse the string into a list
*
* @param list
* @param separator
* @return elements separated by separator
*/
public static String[] separatorListToArray(String list, String separator)
{
// TODO use StringUtils version (slightly different...)
int seplen = separator.length();
if (list == null || list.equals("") || list.equals(separator))
{
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())
{
String c = list.substring(cp);
if (!c.equals(separator))
{
jv.addElement(c);
}
}
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)
{
return arrayToSeparatorList(list, separator);
}
/**
* concatenate the list with separator
*
* @param list
* @param separator
* @return concatenated string
*/
public static String arrayToSeparatorList(String[] list, String separator)
{
// TODO use StringUtils version
StringBuffer v = new StringBuffer();
if (list != null && list.length > 0)
{
for (int i = 0, iSize = list.length; i < iSize; i++)
{
if (list[i] != null)
{
if (i > 0)
{
v.append(separator);
}
v.append(list[i]);
}
}
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 "" + separator;
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
*/
@Override
public String getFeatureGroups()
{
String lst = arrayToSeparatorList(
getDefaultTargetFrame().getFeatureGroups());
return lst;
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
* )
*/
@Override
public String getFeatureGroupsOn(AlignFrame alf)
{
String lst = arrayToSeparatorList(alf.getFeatureGroups());
return lst;
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
*/
@Override
public String getFeatureGroupsOfState(boolean visible)
{
return arrayToSeparatorList(
getDefaultTargetFrame().getFeatureGroupsOfState(visible));
}
/*
* (non-Javadoc)
*
* @see
* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
* .AlignFrame, boolean)
*/
@Override
public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
* AlignFrame, java.lang.String, boolean)
*/
@Override
public void setFeatureGroupStateOn(final AlignFrame alf,
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
// state.toLowerCase(Locale.ROOT).equals("false"));
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
alf.setFeatureGroupState(separatorListToArray(groups), st);
}
});
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
* boolean)
*/
@Override
public void setFeatureGroupState(String groups, boolean state)
{
setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getSeparator()
*/
@Override
public String getSeparator()
{
return separator;
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
*/
@Override
public void setSeparator(String separator)
{
if (separator == null || separator.length() < 1)
{
// reset to default
separator = "" + ((char) 0x00AC);
}
this.separator = separator;
if (debug)
{
System.err.println("Default Separator now: '" + 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 (TRUE.equalsIgnoreCase(stn))
{
return true;
}
return false;
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
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;
}
@Override
public void start()
{
// callInitCallback();
}
private Hashtable jshashes = new Hashtable<>();
private Hashtable> jsmessages = new Hashtable<>();
public void setJsMessageSet(String messageclass, String viewId,
String[] colcommands)
{
Hashtable msgset = jsmessages.get(messageclass);
if (msgset == null)
{
msgset = new Hashtable<>();
jsmessages.put(messageclass, msgset);
}
msgset.put(viewId, colcommands);
long[] l = new long[colcommands.length];
for (int i = 0; i < colcommands.length; i++)
{
l[i] = colcommands[i].hashCode();
}
jshashes.put(messageclass + "|" + viewId, l);
}
/*
* (non-Javadoc)
*
* @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
* java.lang.String)
*/
@Override
public String getJsMessage(String messageclass, String viewId)
{
Hashtable msgset = jsmessages.get(messageclass);
if (msgset != null)
{
String[] msgs = msgset.get(viewId);
if (msgs != null)
{
for (int i = 0; i < msgs.length; i++)
{
if (msgs[i] != null)
{
String m = msgs[i];
msgs[i] = null;
return m;
}
}
}
}
return "";
}
public boolean isJsMessageSetChanged(String string, String string2,
String[] colcommands)
{
long[] l = jshashes.get(string + "|" + string2);
if (l == null && colcommands != null)
{
return true;
}
for (int i = 0; i < colcommands.length; i++)
{
if (l[i] != colcommands[i].hashCode())
{
return true;
}
}
return false;
}
private Vector jsExecQueue = new Vector();
public Vector getJsExecQueue()
{
return jsExecQueue;
}
public void setExecutor(JSFunctionExec jsFunctionExec2)
{
jsFunctionExec = jsFunctionExec2;
}
/**
* return the given colour value parameter or the given default if parameter
* not given
*
* @param colparam
* @param defcolour
* @return
*/
public Color getDefaultColourParameter(String colparam, Color defcolour)
{
String colprop = getParameter(colparam);
if (colprop == null || colprop.trim().length() == 0)
{
return defcolour;
}
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
System.err.println("Couldn't parse '" + colprop + "' as a colour for "
+ colparam);
}
return (col == null) ? defcolour : col;
}
public void openJalviewHelpUrl()
{
String helpUrl = getParameter("jalviewhelpurl");
if (helpUrl == null || helpUrl.trim().length() < 5)
{
helpUrl = "http://www.jalview.org/help.html";
}
showURL(helpUrl, "HELP");
}
/**
* form a complete URL given a path to a resource and a reference location on
* the same server
*
* @param targetPath
* - an absolute path on the same server as localref or a document
* located relative to localref
* @param localref
* - a URL on the same server as url
* @return a complete URL for the resource located by url
*/
private String resolveUrlForLocalOrAbsolute(String targetPath,
URL localref)
{
String resolvedPath = "";
if (targetPath.startsWith("/"))
{
String codebase = localref.toString();
String localfile = localref.getFile();
resolvedPath = codebase.substring(0,
codebase.length() - localfile.length()) + targetPath;
return resolvedPath;
}
/*
* get URL path and strip off any trailing file e.g.
* www.jalview.org/examples/index.html#applets?a=b is trimmed to
* www.jalview.org/examples/
*/
String urlPath = localref.toString();
String directoryPath = urlPath;
int lastSeparator = directoryPath.lastIndexOf("/");
if (lastSeparator > 0)
{
directoryPath = directoryPath.substring(0, lastSeparator + 1);
}
if (targetPath.startsWith("/"))
{
/*
* construct absolute URL to a file on the server - this is not allowed?
*/
// String localfile = localref.getFile();
// resolvedPath = urlPath.substring(0,
// urlPath.length() - localfile.length())
// + targetPath;
resolvedPath = directoryPath + targetPath.substring(1);
}
else
{
resolvedPath = directoryPath + targetPath;
}
if (debug)
{
System.err.println(
"resolveUrlForLocalOrAbsolute returning " + resolvedPath);
}
return resolvedPath;
}
/**
* open a URL in the browser - resolving it according to relative refs and
* coping with javascript: protocol if necessary.
*
* @param url
* @param target
*/
public void showURL(String url, String target)
{
try
{
if (url.indexOf(":") == -1)
{
// TODO: verify (Bas Vroling bug) prepend codebase or server URL to
// form valid URL
// Should really use docbase, not codebase.
URL prepend;
url = resolveUrlForLocalOrAbsolute(url,
prepend = getDefaultParameter("resolvetocodebase", false)
? getCodeBase()
: getDocumentBase());
if (debug)
{
System.err.println("Show url (prepended " + prepend
+ " - toggle resolvetocodebase if code/docbase resolution is wrong): "
+ url);
}
}
else
{
if (debug)
{
System.err.println("Show url: " + url);
}
}
if (url.indexOf("javascript:") == 0)
{
// no target for the javascript context
getAppletContext().showDocument(new java.net.URL(url));
}
else
{
getAppletContext().showDocument(new java.net.URL(url), target);
}
} catch (Exception ex)
{
ex.printStackTrace();
}
}
/**
* 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; }
*/
}